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Molybdenum in PDB 4brf: Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp

Enzymatic activity of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp

All present enzymatic activity of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp:
3.6.1.5;

Protein crystallography data

The structure of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp, PDB code: 4brf was solved by M.Zebisch, P.Schaefer, P.Lauble, N.Straeter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.87 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.144, 85.970, 71.888, 90.00, 106.14, 90.00
R / Rfree (%) 12.546 / 18.43

Other elements in 4brf:

The structure of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms
Chlorine (Cl) 2 atoms
Sodium (Na) 1 atom

Molybdenum Binding Sites:

The binding sites of Molybdenum atom in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp (pdb code 4brf). This binding sites where shown within 5.0 Angstroms radius around Molybdenum atom.
In total 4 binding sites of Molybdenum where determined in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp, PDB code: 4brf:
Jump to Molybdenum binding site number: 1; 2; 3; 4;

Molybdenum binding site 1 out of 4 in 4brf

Go back to Molybdenum Binding Sites List in 4brf
Molybdenum binding site 1 out of 4 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 1 of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo1395

b:13.8
occ:1.00
 MO A:MOO1395 0.0 13.8 1.0
O1 A:MOO1395 1.7 11.9 1.0
O2 A:MOO1395 1.7 12.7 1.0
O4 A:MOO1395 1.8 13.9 1.0
O3 A:MOO1395 1.8 12.9 1.0
O A:HOH2074 2.6 14.1 1.0
MG A:MG1396 3.6 13.7 1.0
OG1 A:THR118 3.7 12.8 1.0
O A:HOH2122 3.8 11.8 1.0
O A:HOH2298 3.8 14.3 1.0
N A:GLY189 3.8 11.1 1.0
N A:SER52 3.9 13.2 1.0
OG A:SER52 3.9 15.7 1.0
O A:HOH2011 4.1 12.9 1.0
CA A:GLY188 4.1 12.8 1.0
N A:ALA190 4.1 10.3 1.0
CB A:SER52 4.2 12.0 1.0
CB A:ALA119 4.3 11.9 1.0
N A:ALA119 4.3 11.9 1.0
C A:GLY188 4.4 11.1 1.0
OE2 A:GLU159 4.4 14.3 1.0
N A:SER191 4.5 11.1 1.0
OG A:SER191 4.5 11.3 1.0
CA A:GLY51 4.6 13.3 1.0
O A:HOH2134 4.6 12.3 1.0
O A:HOH2123 4.6 12.3 1.0
CB A:THR118 4.7 11.2 1.0
CA A:GLY189 4.7 9.9 1.0
CA A:SER52 4.7 13.9 1.0
C A:GLY51 4.8 14.0 1.0
CA A:ALA119 4.8 11.9 1.0
O A:SER191 4.8 11.6 1.0
CB A:ALA190 4.9 13.6 1.0
N A:GLY120 4.9 12.2 1.0
CA A:ALA190 4.9 9.7 1.0
C A:GLY189 5.0 11.1 1.0

Molybdenum binding site 2 out of 4 in 4brf

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Molybdenum binding site 2 out of 4 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 2 of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo1401

b:22.5
occ:0.70
 MO1 A:M271401 0.0 22.5 0.7
O1 A:M271401 1.7 26.3 0.7
O7 A:M271401 1.7 23.4 0.7
O2 A:EDO1402 2.0 21.3 0.7
O2 A:M271401 2.0 21.2 0.7
O1 A:EDO1402 2.2 24.0 0.7
OE1 A:GLN143 2.8 30.0 1.0
C2 A:EDO1402 3.2 22.0 0.7
MO2 A:M271401 3.2 23.3 0.7
C1 A:EDO1402 3.3 27.0 0.7
CD A:GLN143 3.8 27.4 1.0
CB A:GLN145 4.0 26.3 1.0
N A:GLN145 4.0 21.5 1.0
CB A:GLN143 4.1 24.4 1.0
N A:SER144 4.1 25.7 1.0
ND1 A:HIS109 4.1 25.7 1.0
O3 A:M271401 4.1 26.2 0.7
CG A:GLN145 4.3 34.6 1.0
CD1 A:TRP146 4.3 20.2 1.0
CA A:GLN143 4.3 29.7 1.0
O4 A:M271401 4.4 18.5 0.7
O8 A:M271401 4.5 28.3 0.7
OG A:SER144 4.5 30.0 1.0
CG A:GLN143 4.5 24.9 1.0
CA A:GLN145 4.6 23.7 1.0
C A:GLN143 4.7 27.1 1.0
NE2 A:GLN143 4.7 30.6 1.0
NE1 A:TRP146 4.7 21.0 1.0
N A:TRP146 4.7 18.8 1.0
CB A:HIS109 4.8 18.0 1.0
CG A:HIS109 4.9 19.8 1.0
C A:SER144 4.9 23.1 1.0

Molybdenum binding site 3 out of 4 in 4brf

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Molybdenum binding site 3 out of 4 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 3 of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo1401

b:23.3
occ:0.70
 MO2 A:M271401 0.0 23.3 0.7
O3 A:M271401 1.7 26.2 0.7
O8 A:M271401 1.7 28.3 0.7
O4 A:M271401 1.7 18.5 0.7
O2 A:M271401 2.1 21.2 0.7
O1 A:EDO1402 2.4 24.0 0.7
OE1 A:GLN143 2.4 30.0 1.0
MO1 A:M271401 3.2 22.5 0.7
CD A:GLN143 3.4 27.4 1.0
C1 A:EDO1402 3.6 27.0 0.7
NE2 A:GLN143 3.6 30.6 1.0
ND1 A:HIS109 3.9 25.7 1.0
NE1 A:TRP146 4.0 21.0 1.0
CE1 A:HIS109 4.0 29.0 1.0
O A:HOH2067 4.2 37.4 1.0
CD1 A:TRP146 4.3 20.2 1.0
O1 A:M271401 4.3 26.3 0.7
O7 A:M271401 4.3 23.4 0.7
O2 A:EDO1402 4.4 21.3 0.7
CA A:ALA104 4.4 22.6 1.0
CH2 A:TRP139 4.5 19.9 1.0
CB A:ALA104 4.6 25.9 1.0
C2 A:EDO1402 4.7 22.0 0.7
CG A:GLN143 4.8 24.9 1.0
CZ2 A:TRP139 4.8 22.2 1.0

Molybdenum binding site 4 out of 4 in 4brf

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Molybdenum binding site 4 out of 4 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 4 of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mo1396

b:13.4
occ:1.00
 MO B:MOO1396 0.0 13.4 1.0
O2 B:MOO1396 1.8 13.2 1.0
O1 B:MOO1396 1.8 12.7 1.0
O4 B:MOO1396 1.8 14.2 1.0
O3 B:MOO1396 1.9 16.4 1.0
O B:HOH2069 2.6 11.8 1.0
MG B:MG1397 3.7 14.1 1.0
OG1 B:THR118 3.7 11.9 1.0
O B:HOH2112 3.7 13.4 1.0
N B:GLY189 3.8 11.9 1.0
O B:HOH2241 3.8 14.5 1.0
N B:SER52 3.9 13.2 1.0
OG B:SER52 3.9 15.6 1.0
O B:HOH2007 4.1 13.1 1.0
N B:ALA190 4.1 10.2 1.0
CA B:GLY188 4.1 12.5 1.0
CB B:ALA119 4.2 10.2 1.0
O B:HOH2016 4.2 27.2 1.0
CB B:SER52 4.2 14.6 1.0
N B:ALA119 4.3 10.4 1.0
C B:GLY188 4.4 9.4 1.0
OE2 B:GLU159 4.4 14.0 1.0
N B:SER191 4.5 10.5 1.0
CA B:GLY51 4.5 12.4 1.0
OG B:SER191 4.6 10.8 1.0
O B:HOH2113 4.6 11.8 1.0
CB B:THR118 4.6 9.0 1.0
O B:HOH2120 4.7 13.5 1.0
CA B:SER52 4.7 12.8 1.0
C B:GLY51 4.7 11.1 1.0
CA B:GLY189 4.7 12.2 1.0
CA B:ALA119 4.8 10.2 1.0
O B:SER191 4.8 11.1 1.0
CB B:ALA190 4.9 14.3 1.0
N B:GLY120 4.9 11.8 1.0
CA B:ALA190 4.9 10.9 1.0
C B:GLY189 5.0 10.2 1.0

Reference:

M.Zebisch, M.Krauss, P.Schaefer, P.Lauble, N.Straeter. Crystallographic Snapshots Along the Reaction Pathway of Nucleoside Triphosphate Diphosphohydrolases Structure V. 21 1460 2013.
ISSN: ISSN 0969-2126
PubMed: 23830739
DOI: 10.1016/J.STR.2013.05.016
Page generated: Sun Oct 6 15:59:18 2024

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