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Molybdenum in PDB 4ndp: Crystal Structure Molybdenum Storage Protein with Fully Mo-Loaded Cavity

Protein crystallography data

The structure of Crystal Structure Molybdenum Storage Protein with Fully Mo-Loaded Cavity, PDB code: 4ndp was solved by J.Poppe, E.Warkentin, U.Demmer, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 9.99 / 1.60
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 115.585, 115.585, 234.174, 90.00, 90.00, 120.00
R / Rfree (%) 16.2 / 17.8

Other elements in 4ndp:

The structure of Crystal Structure Molybdenum Storage Protein with Fully Mo-Loaded Cavity also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Molybdenum Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 39;

Binding sites:

The binding sites of Molybdenum atom in the Crystal Structure Molybdenum Storage Protein with Fully Mo-Loaded Cavity (pdb code 4ndp). This binding sites where shown within 5.0 Angstroms radius around Molybdenum atom.
In total 39 binding sites of Molybdenum where determined in the Crystal Structure Molybdenum Storage Protein with Fully Mo-Loaded Cavity, PDB code: 4ndp:
Jump to Molybdenum binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Molybdenum binding site 1 out of 39 in 4ndp

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Molybdenum binding site 1 out of 39 in the Crystal Structure Molybdenum Storage Protein with Fully Mo-Loaded Cavity


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 1 of Crystal Structure Molybdenum Storage Protein with Fully Mo-Loaded Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mo302

b:17.5
occ:0.51
 MO1 B:8M0302 0.0 17.5 0.5
O2 B:8M0302 1.9 18.6 0.5
O1 B:8M0302 1.9 17.6 0.5
O3 B:8M0302 2.0 19.5 0.5
O24 B:8M0302 2.0 13.3 0.5
O5 B:8M0302 2.1 19.1 0.5
O4 B:8M0302 2.2 14.7 0.5
MO3 B:8M0302 3.3 19.3 0.5
MO2 B:8M0302 3.3 16.9 0.5
ND1 A:HIS156 3.5 30.2 1.0
MO4 B:8M0302 3.6 17.7 0.5
O10 B:8M0302 3.6 19.9 0.5
O26 B:8M0302 3.7 13.1 0.5
O7 B:8M0302 3.8 17.4 0.5
O B:HOH572 3.8 54.3 1.0
O6 B:8M0302 3.9 15.3 0.5
CE1 A:HIS156 4.0 27.2 1.0
MO8 B:8M0302 4.0 17.7 0.5
CB B:PRO151 4.1 20.5 1.0
O23 A:8M0302 4.1 21.4 0.8
O B:HOH500 4.3 29.6 1.0
O9 B:8M0302 4.3 22.0 0.5
O B:HOH592 4.3 48.1 1.0
O22 B:8M0302 4.4 14.4 0.5
O20 B:8M0302 4.4 19.4 0.5
O25 B:8M0302 4.5 11.5 0.5
O B:HOH655 4.6 38.8 1.0
CG A:HIS156 4.6 28.0 1.0
O11 B:8M0302 4.7 15.4 0.5
O8 B:8M0302 4.8 13.2 0.5
CG B:PRO151 4.9 22.7 1.0
O27 B:8M0302 4.9 26.0 0.6

Molybdenum binding site 2 out of 39 in 4ndp

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Molybdenum binding site 2 out of 39 in the Crystal Structure Molybdenum Storage Protein with Fully Mo-Loaded Cavity


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 2 of Crystal Structure Molybdenum Storage Protein with Fully Mo-Loaded Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mo302

b:16.9
occ:0.51
 MO2 B:8M0302 0.0 16.9 0.5
O8 B:8M0302 1.8 13.2 0.5
O6 B:8M0302 1.9 15.3 0.5
O5 B:8M0302 1.9 19.1 0.5
O24 B:8M0302 2.0 13.3 0.5
O25 B:8M0302 2.0 11.5 0.5
O7 B:8M0302 2.1 17.4 0.5
MO8 B:8M0302 3.2 17.7 0.5
MO1 B:8M0302 3.3 17.5 0.5
MO4 B:8M0302 3.5 17.7 0.5
O22 B:8M0302 3.7 14.4 0.5
CB A:HIS156 3.8 20.3 1.0
O2 B:8M0302 3.8 18.6 0.5
O4 B:8M0302 3.8 14.7 0.5
ND1 A:HIS158 3.8 20.4 1.0
O11 B:8M0302 3.9 15.4 0.5
MO5 B:8M0302 4.0 18.1 0.5
N A:HIS157 4.0 18.1 1.0
O15 B:8M0302 4.1 18.5 0.5
ND1 A:HIS156 4.1 30.2 1.0
O13 B:8M0302 4.2 17.9 0.5
CG B:PRO151 4.2 22.7 1.0
CE1 A:HIS158 4.2 21.6 1.0
O16 B:8M0302 4.3 14.6 0.5
CB A:HIS157 4.3 21.4 1.0
O14 B:8M0302 4.4 17.6 0.5
CB B:PRO151 4.4 20.5 1.0
CG A:HIS156 4.4 28.0 1.0
ND1 A:HIS157 4.5 29.8 1.0
O B:HOH418 4.6 27.8 1.0
O1 B:8M0302 4.7 17.6 0.5
CG A:HIS157 4.7 27.9 1.0
CA A:HIS157 4.7 18.4 1.0
O3 B:8M0302 4.8 19.5 0.5
CD B:PRO151 4.8 18.1 1.0
N A:HIS158 4.9 16.4 1.0
O20 B:8M0302 4.9 19.4 0.5
O26 B:8M0302 4.9 13.1 0.5
C A:HIS156 4.9 16.4 1.0
O A:TYR155 4.9 19.9 1.0
CA A:HIS156 5.0 23.0 1.0

Molybdenum binding site 3 out of 39 in 4ndp

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Molybdenum binding site 3 out of 39 in the Crystal Structure Molybdenum Storage Protein with Fully Mo-Loaded Cavity


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 3 of Crystal Structure Molybdenum Storage Protein with Fully Mo-Loaded Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mo302

b:19.3
occ:0.51
 MO3 B:8M0302 0.0 19.3 0.5
O9 B:8M0302 1.9 22.0 0.5
O10 B:8M0302 1.9 19.9 0.5
O27 B:8M0302 1.9 26.0 0.6
O3 B:8M0302 2.0 19.5 0.5
O26 B:8M0302 2.0 13.1 0.5
O4 B:8M0302 2.1 14.7 0.5
MO4 B:8M0302 3.3 17.7 0.5
MO1 B:8M0302 3.3 17.5 0.5
MO B:MO307 3.4 49.1 0.5
O1 B:8M0302 3.8 17.6 0.5
O5 B:8M0302 3.9 19.1 0.5
O B:HOH572 3.9 54.3 1.0
O12 B:8M0302 4.0 16.6 0.5
MO6 B:8M0302 4.0 19.2 0.5
NZ B:LYS153 4.1 29.3 0.7
O B:HOH592 4.1 48.1 1.0
CE B:LYS153 4.2 37.7 0.7
O18 B:8M0302 4.4 16.2 0.5
O B:HOH500 4.4 29.6 1.0
O19 B:8M0302 4.5 19.1 0.5
O20 B:8M0302 4.5 19.4 0.5
O B:HOH563 4.5 32.7 1.0
O11 B:8M0302 4.6 15.4 0.5
O B:HOH505 4.6 41.7 1.0
CB B:PRO151 4.6 20.5 1.0
O24 B:8M0302 4.7 13.3 0.5
CA B:PRO151 4.8 19.3 1.0
O2 B:8M0302 4.8 18.6 0.5
O7 B:8M0302 4.9 17.4 0.5

Molybdenum binding site 4 out of 39 in 4ndp

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Molybdenum binding site 4 out of 39 in the Crystal Structure Molybdenum Storage Protein with Fully Mo-Loaded Cavity


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 4 of Crystal Structure Molybdenum Storage Protein with Fully Mo-Loaded Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mo302

b:17.7
occ:0.51
 MO4 B:8M0302 0.0 17.7 0.5
O12 B:8M0302 1.9 16.6 0.5
O4 B:8M0302 2.0 14.7 0.5
O7 B:8M0302 2.0 17.4 0.5
O11 B:8M0302 2.1 15.4 0.5
O26 B:8M0302 2.1 13.1 0.5
O5 B:8M0302 2.3 19.1 0.5
MO6 B:8M0302 3.2 19.2 0.5
MO3 B:8M0302 3.3 19.3 0.5
MO8 B:8M0302 3.4 17.7 0.5
MO2 B:8M0302 3.5 16.9 0.5
O24 B:8M0302 3.5 13.3 0.5
MO1 B:8M0302 3.6 17.5 0.5
O25 B:8M0302 3.6 11.5 0.5
O27 B:8M0302 3.6 26.0 0.6
O3 B:8M0302 3.6 19.5 0.5
O19 B:8M0302 3.7 19.1 0.5
O B:HOH645 3.8 25.5 1.0
CB B:PRO151 3.8 20.5 1.0
O20 B:8M0302 3.8 19.4 0.5
O21 B:8M0302 4.0 15.7 0.5
MO7 B:8M0302 4.1 18.5 0.5
CD B:PRO151 4.1 18.1 1.0
O14 B:8M0302 4.1 17.6 0.5
CG B:PRO151 4.3 22.7 1.0
CA B:PRO151 4.3 19.3 1.0
N B:PRO151 4.3 16.4 1.0
CE1 A:HIS158 4.3 21.6 1.0
O17 B:8M0302 4.4 15.2 0.5
O16 B:8M0302 4.4 14.6 0.5
O8 B:8M0302 4.4 13.2 0.5
O9 B:8M0302 4.5 22.0 0.5
ND1 A:HIS158 4.6 20.4 1.0
O B:MET149 4.6 25.9 1.0
O B:HOH642 4.7 49.0 1.0
O10 B:8M0302 4.8 19.9 0.5
O1 B:8M0302 4.8 17.6 0.5
O B:HOH563 4.8 32.7 1.0
O18 B:8M0302 4.8 16.2 0.5
C B:PRO150 4.9 16.1 1.0

Molybdenum binding site 5 out of 39 in 4ndp

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Molybdenum binding site 5 out of 39 in the Crystal Structure Molybdenum Storage Protein with Fully Mo-Loaded Cavity


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 5 of Crystal Structure Molybdenum Storage Protein with Fully Mo-Loaded Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mo302

b:18.1
occ:0.51
 MO5 B:8M0302 0.0 18.1 0.5
O13 B:8M0302 1.9 17.9 0.5
O28 B:8M0302 1.9 24.5 0.6
O15 B:8M0302 1.9 18.5 0.5
O14 B:8M0302 2.0 17.6 0.5
O25 B:8M0302 2.1 11.5 0.5
O16 B:8M0302 2.2 14.6 0.5
MO7 B:8M0302 3.3 18.5 0.5
MO8 B:8M0302 3.3 17.7 0.5
O23 B:8M0302 3.8 19.7 0.5
O11 B:8M0302 3.8 15.4 0.5
O22 B:8M0302 3.9 14.4 0.5
MO2 B:8M0302 4.0 16.9 0.5
CD1 B:LEU176 4.0 27.0 1.0
CE1 A:HIS158 4.0 21.6 1.0
O B:HOH522 4.0 49.1 1.0
CE1 B:PHE180 4.1 25.3 1.0
ND1 A:HIS157 4.2 29.8 1.0
O8 B:8M0302 4.3 13.2 0.5
O7 B:8M0302 4.3 17.4 0.5
CB A:HIS157 4.4 21.4 1.0
CA B:GLY128 4.4 35.6 1.0
CG B:LEU176 4.4 28.7 1.0
CZ B:PHE180 4.4 26.1 1.0
N B:ALA129 4.5 35.2 1.0
ND1 A:HIS158 4.5 20.4 1.0
O6 B:8M0302 4.5 15.3 0.5
O5 B:8M0302 4.6 19.1 0.5
O21 B:8M0302 4.6 15.7 0.5
O17 B:8M0302 4.7 15.2 0.5
CG A:HIS157 4.8 27.9 1.0
N B:GLY130 4.8 35.3 1.0
N B:GLY128 4.8 35.6 1.0
C B:GLY128 4.8 39.5 1.0
O20 B:8M0302 5.0 19.4 0.5

Molybdenum binding site 6 out of 39 in 4ndp

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Molybdenum binding site 6 out of 39 in the Crystal Structure Molybdenum Storage Protein with Fully Mo-Loaded Cavity


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 6 of Crystal Structure Molybdenum Storage Protein with Fully Mo-Loaded Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mo302

b:19.2
occ:0.51
 MO6 B:8M0302 0.0 19.2 0.5
O19 B:8M0302 1.9 19.1 0.5
O18 B:8M0302 1.9 16.2 0.5
O17 B:8M0302 2.0 15.2 0.5
O26 B:8M0302 2.0 13.1 0.5
O20 B:8M0302 2.2 19.4 0.5
O11 B:8M0302 2.2 15.4 0.5
MO4 B:8M0302 3.2 17.7 0.5
MO7 B:8M0302 3.3 18.5 0.5
MO8 B:8M0302 3.4 17.7 0.5
O B:HOH453 3.6 29.3 1.0
O21 B:8M0302 3.6 15.7 0.5
O B:HOH645 3.8 25.5 1.0
O9 B:8M0302 3.8 22.0 0.5
O12 B:8M0302 3.8 16.6 0.5
O16 B:8M0302 3.8 14.6 0.5
O B:HOH592 3.9 48.1 1.0
MO3 B:8M0302 4.0 19.3 0.5
O B:HOH505 4.0 41.7 1.0
CA B:GLY127 4.1 35.4 1.0
O3 B:8M0302 4.1 19.5 0.5
O5 B:8M0302 4.2 19.1 0.5
O4 B:8M0302 4.3 14.7 0.5
O27 B:8M0302 4.3 26.0 0.6
N B:GLY128 4.4 35.6 1.0
O B:HOH613 4.5 59.8 1.0
O B:HOH642 4.6 49.0 1.0
O23 B:8M0302 4.7 19.7 0.5
O14 B:8M0302 4.8 17.6 0.5
C B:GLY127 4.8 44.1 1.0
O25 B:8M0302 4.9 11.5 0.5
O7 B:8M0302 4.9 17.4 0.5

Molybdenum binding site 7 out of 39 in 4ndp

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Molybdenum binding site 7 out of 39 in the Crystal Structure Molybdenum Storage Protein with Fully Mo-Loaded Cavity


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 7 of Crystal Structure Molybdenum Storage Protein with Fully Mo-Loaded Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mo302

b:18.5
occ:0.51
 MO7 B:8M0302 0.0 18.5 0.5
O21 B:8M0302 1.8 15.7 0.5
O23 B:8M0302 1.9 19.7 0.5
O14 B:8M0302 2.0 17.6 0.5
O17 B:8M0302 2.0 15.2 0.5
O11 B:8M0302 2.1 15.4 0.5
O16 B:8M0302 2.2 14.6 0.5
MO5 B:8M0302 3.3 18.1 0.5
MO6 B:8M0302 3.3 19.2 0.5
MO8 B:8M0302 3.5 17.7 0.5
O25 B:8M0302 3.7 11.5 0.5
O28 B:8M0302 3.8 24.5 0.6
O19 B:8M0302 3.8 19.1 0.5
O20 B:8M0302 3.8 19.4 0.5
O B:HOH645 4.0 25.5 1.0
N B:GLY128 4.0 35.6 1.0
CD1 B:LEU176 4.0 27.0 1.0
MO4 B:8M0302 4.1 17.7 0.5
O B:HOH453 4.2 29.3 1.0
CD1 B:PHE146 4.2 19.0 1.0
N B:ALA129 4.3 35.2 1.0
O A:HOH455 4.4 26.2 1.0
CB B:PHE146 4.5 17.9 1.0
O12 B:8M0302 4.5 16.6 0.5
CE1 A:HIS158 4.5 21.6 1.0
O26 B:8M0302 4.6 13.1 0.5
O7 B:8M0302 4.6 17.4 0.5
CA B:GLY128 4.6 35.6 1.0
CG B:PHE146 4.6 16.7 1.0
O13 B:8M0302 4.7 17.9 0.5
O B:SER147 4.7 17.1 1.0
O15 B:8M0302 4.8 18.5 0.5
O5 B:8M0302 4.8 19.1 0.5
O18 B:8M0302 4.9 16.2 0.5
CB B:ALA129 5.0 29.6 1.0
C B:GLY127 5.0 44.1 1.0

Molybdenum binding site 8 out of 39 in 4ndp

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Molybdenum binding site 8 out of 39 in the Crystal Structure Molybdenum Storage Protein with Fully Mo-Loaded Cavity


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 8 of Crystal Structure Molybdenum Storage Protein with Fully Mo-Loaded Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mo302

b:17.7
occ:0.51
 MO8 B:8M0302 0.0 17.7 0.5
O22 B:8M0302 1.8 14.4 0.5
O16 B:8M0302 2.0 14.6 0.5
O20 B:8M0302 2.0 19.4 0.5
O25 B:8M0302 2.1 11.5 0.5
O5 B:8M0302 2.3 19.1 0.5
O11 B:8M0302 2.3 15.4 0.5
MO2 B:8M0302 3.2 16.9 0.5
MO5 B:8M0302 3.3 18.1 0.5
MO4 B:8M0302 3.4 17.7 0.5
MO6 B:8M0302 3.4 19.2 0.5
O15 B:8M0302 3.5 18.5 0.5
MO7 B:8M0302 3.5 18.5 0.5
O17 B:8M0302 3.5 15.2 0.5
O26 B:8M0302 3.6 13.1 0.5
O7 B:8M0302 3.7 17.4 0.5
O14 B:8M0302 3.7 17.6 0.5
N B:GLY128 3.7 35.6 1.0
O6 B:8M0302 3.8 15.3 0.5
MO1 B:8M0302 4.0 17.5 0.5
CA B:GLY128 4.0 35.6 1.0
O B:HOH655 4.0 38.8 1.0
O3 B:8M0302 4.1 19.5 0.5
O B:HOH592 4.1 48.1 1.0
O2 B:8M0302 4.1 18.6 0.5
O24 B:8M0302 4.2 13.3 0.5
O4 B:8M0302 4.3 14.7 0.5
O18 B:8M0302 4.5 16.2 0.5
O B:HOH647 4.6 44.2 1.0
O28 B:8M0302 4.7 24.5 0.6
O8 B:8M0302 4.7 13.2 0.5
C B:GLY127 4.7 44.1 1.0
O23 B:8M0302 4.8 19.7 0.5
O21 B:8M0302 4.8 15.7 0.5
O13 B:8M0302 4.8 17.9 0.5
MO B:MO316 5.0 23.6 0.2

Molybdenum binding site 9 out of 39 in 4ndp

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Molybdenum binding site 9 out of 39 in the Crystal Structure Molybdenum Storage Protein with Fully Mo-Loaded Cavity


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 9 of Crystal Structure Molybdenum Storage Protein with Fully Mo-Loaded Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mo303

b:30.7
occ:0.54
 MO B:MO307 3.3 49.1 0.5
MO B:MO306 3.3 32.6 0.4
MO B:MO308 3.3 58.7 0.4
MO B:MO304 3.4 29.9 0.5
O B:HOH488 4.0 44.4 1.0
OD1 B:ASP108 4.3 26.2 1.0
O B:HOH505 4.4 41.7 1.0
O B:HOH614 4.7 53.1 1.0
O9 B:8M0302 4.8 22.0 0.5

Molybdenum binding site 10 out of 39 in 4ndp

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Molybdenum binding site 10 out of 39 in the Crystal Structure Molybdenum Storage Protein with Fully Mo-Loaded Cavity


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 10 of Crystal Structure Molybdenum Storage Protein with Fully Mo-Loaded Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mo304

b:29.9
occ:0.47
 MO B:MO303 3.4 30.7 0.5
MO B:MO308 3.4 58.7 0.4
MO B:MO307 3.5 49.1 0.5
MO A:MO305 3.6 25.2 0.4
O B:HOH488 3.7 44.4 1.0
NZ B:LYS153 4.7 29.3 0.7
CE B:LYS153 4.8 37.7 0.7

Reference:

J.Poppe, E.Warkentin, U.Demmer, B.Kowalewski, T.Dierks, K.Schneider, U.Ermler. Structural Diversity of Polyoxomolybdate Clusters Along the Three-Fold Axis of the Molybdenum Storage Protein. J.Inorg.Biochem. V. 138 122 2014.
ISSN: ISSN 0162-0134
PubMed: 24945101
DOI: 10.1016/J.JINORGBIO.2014.05.009
Page generated: Sun Oct 6 16:08:34 2024

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