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Molybdenum in PDB 6vxt: Activated Nitrogenase Mofe-Protein From Azotobacter Vinelandii

Enzymatic activity of Activated Nitrogenase Mofe-Protein From Azotobacter Vinelandii

All present enzymatic activity of Activated Nitrogenase Mofe-Protein From Azotobacter Vinelandii:
1.18.6.1;

Protein crystallography data

The structure of Activated Nitrogenase Mofe-Protein From Azotobacter Vinelandii, PDB code: 6vxt was solved by W.Kang, Y.Hu, M.W.Ribbe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.71 / 1.74
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 163.535, 203.435, 83.857, 90.00, 103.95, 90.00
R / Rfree (%) 17.2 / 20.3

Other elements in 6vxt:

The structure of Activated Nitrogenase Mofe-Protein From Azotobacter Vinelandii also contains other interesting chemical elements:

Iron (Fe) 32 atoms

Molybdenum Binding Sites:

The binding sites of Molybdenum atom in the Activated Nitrogenase Mofe-Protein From Azotobacter Vinelandii (pdb code 6vxt). This binding sites where shown within 5.0 Angstroms radius around Molybdenum atom.
In total 10 binding sites of Molybdenum where determined in the Activated Nitrogenase Mofe-Protein From Azotobacter Vinelandii, PDB code: 6vxt:
Jump to Molybdenum binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Molybdenum binding site 1 out of 10 in 6vxt

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Molybdenum binding site 1 out of 10 in the Activated Nitrogenase Mofe-Protein From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 1 of Activated Nitrogenase Mofe-Protein From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo602

b:32.2
occ:1.00
 MO1 A:ICS602 0.0 32.2 1.0
O6 A:HCA601 2.2 24.4 1.0
S3B A:ICS602 2.3 31.0 1.0
S4B A:ICS602 2.3 29.4 1.0
S1B A:ICS602 2.4 27.2 1.0
O7 A:HCA601 2.4 35.8 1.0
ND1 A:HIS442 2.4 28.2 1.0
FE7 A:ICS602 2.6 31.6 1.0
FE6 A:ICS602 2.6 30.5 1.0
FE5 A:ICS602 2.7 30.8 1.0
C7 A:HCA601 3.0 31.8 1.0
C3 A:HCA601 3.2 36.5 1.0
CE1 A:HIS442 3.3 33.4 1.0
CG A:HIS442 3.5 31.8 1.0
CX A:ICS602 3.5 27.1 1.0
CB A:HIS442 3.8 36.8 1.0
C2 A:HCA601 4.1 32.7 1.0
O5 A:HCA601 4.2 30.1 1.0
O A:HOH876 4.3 32.6 1.0
C5 A:HCA601 4.3 33.8 1.0
C4 A:HCA601 4.3 34.7 1.0
O2 A:HCA601 4.4 31.1 1.0
NE2 A:HIS442 4.5 30.8 1.0
CD2 A:HIS442 4.6 31.1 1.0
CA A:HIS442 4.6 33.6 1.0
S5A A:ICS602 4.7 28.7 1.0
S2B A:ICS602 4.7 31.9 1.0
C1 A:HCA601 4.8 36.1 1.0
S3A A:ICS602 4.9 30.8 1.0

Molybdenum binding site 2 out of 10 in 6vxt

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Molybdenum binding site 2 out of 10 in the Activated Nitrogenase Mofe-Protein From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 2 of Activated Nitrogenase Mofe-Protein From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo603

b:46.0
occ:0.68
 O A:CYS45 3.0 50.3 1.0
O A:LEU32 3.1 43.6 1.0
O A:ASN29 3.2 44.6 1.0
O A:HOH908 3.2 49.4 1.0
O A:HOH862 3.7 52.5 1.0
O A:LYS30 3.9 42.7 1.0
CA A:LYS30 4.1 44.5 1.0
C A:LYS30 4.1 40.5 1.0
C A:CYS45 4.1 48.6 1.0
C A:LEU32 4.2 40.2 1.0
C A:ASN29 4.3 42.3 1.0
CB A:ALA33 4.5 41.7 1.0
N A:LYS30 4.7 43.9 1.0
N A:LEU32 4.7 45.5 1.0
CA A:ILE46 4.8 38.9 1.0
CA A:ALA33 4.8 38.4 1.0
N A:ILE46 4.9 41.3 1.0
N A:HIS31 4.9 34.5 1.0
O A:HOH878 5.0 52.8 1.0
N A:ALA33 5.0 40.3 1.0

Molybdenum binding site 3 out of 10 in 6vxt

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Molybdenum binding site 3 out of 10 in the Activated Nitrogenase Mofe-Protein From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 3 of Activated Nitrogenase Mofe-Protein From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo604

b:53.9
occ:0.65
 O A:TRP294 3.1 46.4 1.0
CE2 A:TRP294 3.5 48.5 1.0
O A:HOH724 3.6 40.2 1.0
CD2 A:TRP294 3.6 49.7 1.0
CZ2 A:TRP294 3.6 56.9 1.0
CH2 A:TRP294 3.9 57.5 1.0
CE3 A:TRP294 3.9 54.0 1.0
CZ3 A:TRP294 4.0 55.0 1.0
NE1 A:TRP294 4.0 45.1 1.0
C A:TRP294 4.1 47.6 1.0
O A:HOH838 4.2 60.9 1.0
CG A:TRP294 4.2 48.2 1.0
CD1 A:TRP294 4.4 46.3 1.0
O A:HOH797 4.5 52.3 1.0
CA A:MET295 4.9 43.5 1.0
N A:MET295 4.9 38.5 1.0
N A:TRP294 5.0 42.8 1.0
CA A:TRP294 5.0 41.6 1.0

Molybdenum binding site 4 out of 10 in 6vxt

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Molybdenum binding site 4 out of 10 in the Activated Nitrogenase Mofe-Protein From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 4 of Activated Nitrogenase Mofe-Protein From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo606

b:53.2
occ:0.47
 O A:PRO37 2.8 60.2 1.0
O A:VAL39 3.0 50.4 1.0
C A:VAL39 3.9 51.9 1.0
C A:PRO37 4.0 45.1 1.0
C A:ALA38 4.3 55.5 1.0
CA A:THR40 4.3 51.2 1.0
O A:ALA38 4.3 51.8 1.0
N A:VAL39 4.5 53.8 1.0
N A:THR40 4.6 52.5 1.0
CA A:ALA38 4.6 49.6 1.0
N A:ALA38 4.8 53.8 1.0
O A:THR40 4.8 54.4 1.0
CA A:VAL39 4.9 52.3 1.0
C A:THR40 4.9 50.8 1.0
CA A:PRO37 5.0 51.1 1.0

Molybdenum binding site 5 out of 10 in 6vxt

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Molybdenum binding site 5 out of 10 in the Activated Nitrogenase Mofe-Protein From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 5 of Activated Nitrogenase Mofe-Protein From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo607

b:71.9
occ:0.44
 O A:ASP204 3.3 47.2 1.0
CE3 A:TRP205 3.9 50.9 1.0
CZ3 A:TRP205 3.9 58.2 1.0
CD2 A:TRP205 3.9 43.9 1.0
CH2 A:TRP205 4.0 60.1 1.0
CE2 A:TRP205 4.0 47.4 1.0
CZ2 A:TRP205 4.0 54.4 1.0
C A:ASP204 4.2 45.7 1.0
CG A:TRP205 4.6 37.6 1.0
NE1 A:TRP205 4.7 41.8 1.0
CB A:ASP204 4.7 48.5 1.0
CA A:TRP205 4.9 42.7 1.0
N A:TRP205 5.0 40.4 1.0
CA A:ASP204 5.0 45.4 1.0
CD1 A:TRP205 5.0 40.5 1.0

Molybdenum binding site 6 out of 10 in 6vxt

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Molybdenum binding site 6 out of 10 in the Activated Nitrogenase Mofe-Protein From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 6 of Activated Nitrogenase Mofe-Protein From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mo602

b:32.1
occ:1.00
 MO1 C:ICS602 0.0 32.1 1.0
O5 C:HCA601 2.3 27.1 1.0
S4B C:ICS602 2.3 30.0 1.0
O7 C:HCA601 2.3 33.9 1.0
S1B C:ICS602 2.3 30.8 1.0
S3B C:ICS602 2.4 30.7 1.0
ND1 C:HIS442 2.4 32.8 1.0
FE7 C:ICS602 2.6 31.8 1.0
FE6 C:ICS602 2.6 31.4 1.0
FE5 C:ICS602 2.7 32.1 1.0
C7 C:HCA601 3.1 39.0 1.0
C3 C:HCA601 3.2 29.9 1.0
CE1 C:HIS442 3.3 32.6 1.0
CG C:HIS442 3.5 32.8 1.0
CX C:ICS602 3.5 24.8 1.0
CB C:HIS442 3.8 35.1 1.0
C2 C:HCA601 4.2 27.6 1.0
O C:HOH840 4.2 34.8 1.0
O1 C:HCA601 4.2 30.9 1.0
O6 C:HCA601 4.3 30.5 1.0
C5 C:HCA601 4.3 30.9 1.0
C4 C:HCA601 4.3 33.4 1.0
NE2 C:HIS442 4.5 33.6 1.0
CD2 C:HIS442 4.6 33.4 1.0
CA C:HIS442 4.6 30.7 1.0
C1 C:HCA601 4.7 36.1 1.0
S5A C:ICS602 4.7 29.6 1.0
S2B C:ICS602 4.7 33.1 1.0
S3A C:ICS602 4.9 31.5 1.0

Molybdenum binding site 7 out of 10 in 6vxt

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Molybdenum binding site 7 out of 10 in the Activated Nitrogenase Mofe-Protein From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 7 of Activated Nitrogenase Mofe-Protein From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mo603

b:44.0
occ:0.67
 O C:LEU32 3.0 45.4 1.0
O C:CYS45 3.2 45.5 1.0
O C:ASN29 3.2 44.3 1.0
O C:HOH815 3.3 49.1 1.0
O C:LYS30 3.9 42.5 1.0
CA C:LYS30 4.1 43.3 1.0
C C:LYS30 4.1 44.2 1.0
C C:LEU32 4.2 43.8 1.0
C C:ASN29 4.2 42.6 1.0
C C:CYS45 4.2 42.6 1.0
CB C:ALA33 4.5 40.7 1.0
N C:LYS30 4.7 42.5 1.0
N C:LEU32 4.7 45.6 1.0
CA C:ILE46 4.8 38.9 1.0
CA C:ALA33 4.8 42.9 1.0
N C:HIS31 5.0 39.8 1.0
N C:ILE46 5.0 38.5 1.0
O C:HOH866 5.0 44.1 1.0
N C:ALA33 5.0 40.1 1.0

Molybdenum binding site 8 out of 10 in 6vxt

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Molybdenum binding site 8 out of 10 in the Activated Nitrogenase Mofe-Protein From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 8 of Activated Nitrogenase Mofe-Protein From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mo604

b:58.2
occ:0.64
 O C:TRP294 3.1 45.8 1.0
O C:HOH776 3.2 53.2 1.0
CE2 C:TRP294 3.5 49.1 1.0
CZ2 C:TRP294 3.6 54.5 1.0
CD2 C:TRP294 3.6 44.8 1.0
O C:HOH832 3.6 46.6 1.0
CH2 C:TRP294 3.7 51.8 1.0
CE3 C:TRP294 3.8 49.4 1.0
CZ3 C:TRP294 3.9 51.5 1.0
NE1 C:TRP294 4.1 43.3 1.0
C C:TRP294 4.1 46.5 1.0
O C:HOH893 4.2 51.5 1.0
CG C:TRP294 4.3 44.0 1.0
O C:HOH909 4.3 69.7 1.0
CD1 C:TRP294 4.5 45.4 1.0
CA C:MET295 4.8 50.2 1.0
N C:MET295 4.9 44.6 1.0
O C:HOH923 4.9 70.2 1.0

Molybdenum binding site 9 out of 10 in 6vxt

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Molybdenum binding site 9 out of 10 in the Activated Nitrogenase Mofe-Protein From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 9 of Activated Nitrogenase Mofe-Protein From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mo605

b:44.0
occ:0.41
 O C:PRO37 2.8 49.4 1.0
O C:HOH913 3.1 56.7 1.0
O C:VAL39 3.3 48.4 1.0
C C:PRO37 4.0 45.6 1.0
O C:HOH934 4.0 62.1 1.0
C C:VAL39 4.1 44.6 1.0
O C:ALA38 4.2 50.9 1.0
C C:ALA38 4.2 50.4 1.0
CA C:THR40 4.3 47.8 1.0
CA C:ALA38 4.6 46.4 1.0
N C:THR40 4.6 46.2 1.0
N C:VAL39 4.6 42.4 1.0
N C:ALA38 4.8 45.0 1.0
O C:THR40 4.9 47.7 1.0
C C:THR40 5.0 48.3 1.0
CA C:PRO37 5.0 47.9 1.0

Molybdenum binding site 10 out of 10 in 6vxt

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Molybdenum binding site 10 out of 10 in the Activated Nitrogenase Mofe-Protein From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 10 of Activated Nitrogenase Mofe-Protein From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mo606

b:76.9
occ:0.47
 O C:HOH940 3.1 61.2 1.0
O C:ASP204 3.4 48.4 1.0
CZ3 C:TRP205 3.7 63.0 1.0
CE3 C:TRP205 3.7 56.4 1.0
CH2 C:TRP205 3.7 61.2 1.0
CD2 C:TRP205 3.8 51.4 1.0
O C:HOH825 3.8 60.3 1.0
CE2 C:TRP205 3.8 51.7 1.0
CZ2 C:TRP205 3.8 55.8 1.0
C C:ASP204 4.3 49.2 1.0
CG C:TRP205 4.5 49.4 1.0
NE1 C:TRP205 4.5 47.6 1.0
CB C:ASP204 4.8 53.6 1.0
CD1 C:TRP205 4.9 46.5 1.0
CA C:TRP205 4.9 44.3 1.0

Reference:

W.Kang, C.C.Lee, A.J.Jasniewski, M.W.Ribbe, Y.Hu. Structural Evidence For A Dynamic Metallocofactor During N Reduction By Mo-Nitrogenase Science 2020.
ISSN: ESSN 1095-9203
DOI: 10.1126/SCIENCE.AAZ6748
Page generated: Sun Oct 6 16:54:30 2024

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