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Iron in PDB 5n6y: Azotobacter Vinelandii Vanadium Nitrogenase

Enzymatic activity of Azotobacter Vinelandii Vanadium Nitrogenase

All present enzymatic activity of Azotobacter Vinelandii Vanadium Nitrogenase:
1.18.6.1;

Protein crystallography data

The structure of Azotobacter Vinelandii Vanadium Nitrogenase, PDB code: 5n6y was solved by D.Sippel, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 102.04 / 1.35
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 75.250, 79.790, 106.970, 84.06, 72.62, 75.15
R / Rfree (%) 10.9 / 14.6

Other elements in 5n6y:

The structure of Azotobacter Vinelandii Vanadium Nitrogenase also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Vanadium (V) 2 atoms

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the Azotobacter Vinelandii Vanadium Nitrogenase (pdb code 5n6y). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 30 binding sites of Iron where determined in the Azotobacter Vinelandii Vanadium Nitrogenase, PDB code: 5n6y:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 30 in 5n6y

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Iron binding site 1 out of 30 in the Azotobacter Vinelandii Vanadium Nitrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Azotobacter Vinelandii Vanadium Nitrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:11.2
occ:1.00
FE1 A:8P8502 0.0 11.2 1.0
S2A A:8P8502 2.3 11.2 1.0
SG A:CYS257 2.3 11.4 1.0
S1A A:8P8502 2.3 11.3 1.0
S4A A:8P8502 2.3 11.1 1.0
FE4 A:8P8502 2.6 10.7 1.0
FE3 A:8P8502 2.7 11.0 1.0
FE2 A:8P8502 2.7 10.9 1.0
CB A:CYS257 3.3 10.4 1.0
C1 A:8P8502 3.5 10.8 1.0
OG A:SER260 3.8 11.1 1.0
CB A:SER260 4.1 10.3 1.0
O1 A:CO3503 4.2 11.7 1.0
O A:HOH924 4.2 15.4 1.0
CG A:PRO338 4.4 15.2 1.0
CE2 A:PHE211 4.6 11.6 1.0
CA A:CYS257 4.6 11.3 1.0
N A:SER260 4.7 10.6 1.0
S5A A:8P8502 4.8 10.9 1.0
S2B A:8P8502 4.9 14.3 1.0
O A:HOH864 4.9 14.3 1.0
CD A:PRO338 4.9 13.5 1.0
CB A:PRO338 4.9 13.3 1.0
CD2 A:PHE211 4.9 12.5 1.0

Iron binding site 2 out of 30 in 5n6y

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Iron binding site 2 out of 30 in the Azotobacter Vinelandii Vanadium Nitrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Azotobacter Vinelandii Vanadium Nitrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:11.0
occ:1.00
FE3 A:8P8502 0.0 11.0 1.0
C1 A:8P8502 2.0 10.8 1.0
S5A A:8P8502 2.2 10.9 1.0
S2A A:8P8502 2.3 11.2 1.0
S4A A:8P8502 2.3 11.1 1.0
FE7 A:8P8502 2.6 10.5 1.0
FE4 A:8P8502 2.6 10.7 1.0
FE2 A:8P8502 2.6 10.9 1.0
FE1 A:8P8502 2.7 11.2 1.0
FE6 A:8P8502 3.7 10.6 1.0
FE5 A:8P8502 3.8 10.4 1.0
NH2 A:ARG339 3.9 12.5 1.0
S1A A:8P8502 3.9 11.3 1.0
CD2 A:PHE211 4.2 12.5 1.0
S4B A:8P8502 4.2 10.4 1.0
O A:HOH953 4.3 14.3 1.0
S3B A:8P8502 4.3 11.2 1.0
O1 A:CO3503 4.4 11.7 1.0
S2B A:8P8502 4.4 14.3 1.0
CE2 A:PHE211 4.6 11.6 1.0
CG1 A:VAL57 4.6 12.3 1.0
CZ A:ARG339 4.6 10.8 1.0
NE A:ARG339 4.7 11.6 1.0
SG A:CYS257 4.8 11.4 1.0
O A:HOH757 4.9 12.9 1.0

Iron binding site 3 out of 30 in 5n6y

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Iron binding site 3 out of 30 in the Azotobacter Vinelandii Vanadium Nitrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Azotobacter Vinelandii Vanadium Nitrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:10.7
occ:1.00
FE4 A:8P8502 0.0 10.7 1.0
O1 A:CO3503 2.0 11.7 1.0
C1 A:8P8502 2.0 10.8 1.0
S1A A:8P8502 2.3 11.3 1.0
S4A A:8P8502 2.3 11.1 1.0
FE1 A:8P8502 2.6 11.2 1.0
FE2 A:8P8502 2.6 10.9 1.0
FE3 A:8P8502 2.6 11.0 1.0
FE5 A:8P8502 2.8 10.4 1.0
C A:CO3503 2.9 10.3 1.0
O2 A:CO3503 3.1 11.0 1.0
FE7 A:8P8502 3.7 10.5 1.0
FE6 A:8P8502 3.7 10.6 1.0
S2A A:8P8502 3.8 11.2 1.0
O3 A:CO3503 4.0 10.9 1.0
NE A:ARG339 4.0 11.6 1.0
CD A:PRO338 4.1 13.5 1.0
CG A:PRO338 4.3 15.2 1.0
S4B A:8P8502 4.3 10.4 1.0
S1B A:8P8502 4.5 10.2 1.0
SG A:CYS257 4.5 11.4 1.0
S2B A:8P8502 4.5 14.3 1.0
S5A A:8P8502 4.5 10.9 1.0
NH2 A:ARG339 4.6 12.5 1.0
CZ A:ARG339 4.7 10.8 1.0
CB A:PRO338 4.7 13.3 1.0
CD A:ARG339 4.7 11.4 1.0
CZ A:PHE362 4.8 13.4 1.0
CG A:ARG339 4.9 12.7 1.0
O A:HOH924 5.0 15.4 1.0
N A:PRO338 5.0 12.3 1.0

Iron binding site 4 out of 30 in 5n6y

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Iron binding site 4 out of 30 in the Azotobacter Vinelandii Vanadium Nitrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Azotobacter Vinelandii Vanadium Nitrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:10.4
occ:1.00
FE5 A:8P8502 0.0 10.4 1.0
O2 A:CO3503 1.9 11.0 1.0
C1 A:8P8502 2.1 10.8 1.0
S4B A:8P8502 2.3 10.4 1.0
S1B A:8P8502 2.3 10.2 1.0
FE6 A:8P8502 2.6 10.6 1.0
FE7 A:8P8502 2.6 10.5 1.0
V1 A:8P8502 2.7 10.2 1.0
FE4 A:8P8502 2.8 10.7 1.0
C A:CO3503 2.9 10.3 1.0
O1 A:CO3503 3.1 11.7 1.0
ND1 A:HIS423 3.7 10.3 1.0
FE2 A:8P8502 3.7 10.9 1.0
FE3 A:8P8502 3.8 11.0 1.0
S3B A:8P8502 3.8 11.2 1.0
O3 A:CO3503 4.1 10.9 1.0
CE1 A:HIS423 4.1 9.8 1.0
NE A:ARG339 4.1 11.6 1.0
N A:GLY336 4.1 11.9 1.0
CA A:GLY336 4.3 12.1 1.0
CZ A:ARG339 4.3 10.8 1.0
S1A A:8P8502 4.4 11.3 1.0
S2B A:8P8502 4.5 14.3 1.0
S4A A:8P8502 4.5 11.1 1.0
CD A:ARG339 4.5 11.4 1.0
NH2 A:ARG339 4.6 12.5 1.0
O7 A:HCA501 4.6 10.4 1.0
S5A A:8P8502 4.6 10.9 1.0
O5 A:HCA501 4.6 8.9 1.0
CG A:HIS423 4.7 9.4 1.0
CZ A:PHE362 4.8 13.4 1.0
NH1 A:ARG339 5.0 12.0 1.0

Iron binding site 5 out of 30 in 5n6y

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Iron binding site 5 out of 30 in the Azotobacter Vinelandii Vanadium Nitrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Azotobacter Vinelandii Vanadium Nitrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:10.9
occ:1.00
FE2 A:8P8502 0.0 10.9 1.0
C1 A:8P8502 2.0 10.8 1.0
S2B A:8P8502 2.2 14.3 1.0
S1A A:8P8502 2.2 11.3 1.0
S2A A:8P8502 2.3 11.2 1.0
FE6 A:8P8502 2.6 10.6 1.0
FE4 A:8P8502 2.6 10.7 1.0
FE3 A:8P8502 2.6 11.0 1.0
FE1 A:8P8502 2.7 11.2 1.0
FE7 A:8P8502 3.6 10.5 1.0
FE5 A:8P8502 3.7 10.4 1.0
S4A A:8P8502 3.9 11.1 1.0
CZ A:PHE362 3.9 13.4 1.0
CG1 A:VAL57 4.1 12.3 1.0
S3B A:8P8502 4.2 11.2 1.0
CE1 A:HIS180 4.3 13.2 1.0
NE2 A:HIS180 4.3 12.8 1.0
S1B A:8P8502 4.3 10.2 1.0
O1 A:CO3503 4.4 11.7 1.0
S5A A:8P8502 4.4 10.9 1.0
CE1 A:PHE362 4.5 14.8 1.0
CB A:SER260 4.7 10.3 1.0
SG A:CYS257 4.7 11.4 1.0
CE2 A:PHE362 4.9 14.3 1.0
O2 A:CO3503 4.9 11.0 1.0

Iron binding site 6 out of 30 in 5n6y

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Iron binding site 6 out of 30 in the Azotobacter Vinelandii Vanadium Nitrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Azotobacter Vinelandii Vanadium Nitrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:10.6
occ:1.00
FE6 A:8P8502 0.0 10.6 1.0
C1 A:8P8502 2.0 10.8 1.0
S2B A:8P8502 2.2 14.3 1.0
S3B A:8P8502 2.2 11.2 1.0
S1B A:8P8502 2.2 10.2 1.0
FE7 A:8P8502 2.6 10.5 1.0
FE5 A:8P8502 2.6 10.4 1.0
FE2 A:8P8502 2.6 10.9 1.0
V1 A:8P8502 2.8 10.2 1.0
FE3 A:8P8502 3.7 11.0 1.0
FE4 A:8P8502 3.7 10.7 1.0
S4B A:8P8502 3.8 10.4 1.0
O7 A:HCA501 3.9 10.4 1.0
CZ A:PHE362 4.0 13.4 1.0
CE2 A:PHE362 4.3 14.3 1.0
O2 A:CO3503 4.3 11.0 1.0
S1A A:8P8502 4.3 11.3 1.0
S2A A:8P8502 4.4 11.2 1.0
S5A A:8P8502 4.5 10.9 1.0
CG2 A:VAL57 4.5 13.3 1.0
CG1 A:VAL57 4.5 12.3 1.0
O5 A:HCA501 4.5 8.9 1.0
O1 A:HCA501 4.6 13.1 1.0
ND1 A:HIS423 4.8 10.3 1.0
C3 A:HCA501 4.9 10.0 1.0

Iron binding site 7 out of 30 in 5n6y

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Iron binding site 7 out of 30 in the Azotobacter Vinelandii Vanadium Nitrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Azotobacter Vinelandii Vanadium Nitrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:10.5
occ:1.00
FE7 A:8P8502 0.0 10.5 1.0
C1 A:8P8502 2.0 10.8 1.0
S4B A:8P8502 2.2 10.4 1.0
S3B A:8P8502 2.2 11.2 1.0
S5A A:8P8502 2.3 10.9 1.0
FE6 A:8P8502 2.6 10.6 1.0
FE3 A:8P8502 2.6 11.0 1.0
FE5 A:8P8502 2.6 10.4 1.0
V1 A:8P8502 2.7 10.2 1.0
FE2 A:8P8502 3.6 10.9 1.0
FE4 A:8P8502 3.7 10.7 1.0
O5 A:HCA501 3.7 8.9 1.0
NZ A:LYS83 3.8 14.5 1.0
S1B A:8P8502 3.8 10.2 1.0
NH2 A:ARG339 3.8 12.5 1.0
O A:HOH760 3.9 12.5 1.0
S4A A:8P8502 4.3 11.1 1.0
S2A A:8P8502 4.3 11.2 1.0
S2B A:8P8502 4.3 14.3 1.0
CZ A:ARG339 4.3 10.8 1.0
O2 A:CO3503 4.5 11.0 1.0
O7 A:HCA501 4.6 10.4 1.0
O A:HOH757 4.6 12.9 1.0
ND1 A:HIS423 4.7 10.3 1.0
NE A:ARG339 4.7 11.6 1.0
C7 A:HCA501 4.8 8.7 1.0
CG1 A:VAL57 4.9 12.3 1.0
O1 A:CO3503 5.0 11.7 1.0
NH1 A:ARG339 5.0 12.0 1.0

Iron binding site 8 out of 30 in 5n6y

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Iron binding site 8 out of 30 in the Azotobacter Vinelandii Vanadium Nitrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Azotobacter Vinelandii Vanadium Nitrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe504

b:11.3
occ:1.00
FE1 A:CLF504 0.0 11.3 1.0
S3A A:CLF504 2.3 10.8 1.0
S2A A:CLF504 2.3 11.2 1.0
SG A:CYS138 2.3 11.8 1.0
S1 A:CLF504 2.4 11.2 1.0
FE2 A:CLF504 2.5 11.7 1.0
FE4 A:CLF504 2.6 11.0 1.0
FE3 A:CLF504 2.8 11.0 1.0
CB A:CYS138 3.5 12.8 1.0
S4A A:CLF504 3.8 11.1 1.0
O B:HOH725 3.8 13.2 1.0
N A:CYS138 3.9 10.8 1.0
CA A:GLY170 3.9 15.5 1.0
N A:GLY170 4.0 14.6 1.0
SG B:CYS56 4.1 11.7 1.0
CA A:CYS138 4.3 9.7 1.0
FE8 A:CLF504 4.4 12.4 1.0
SG A:CYS75 4.5 10.7 1.0
FE5 A:CLF504 4.6 11.9 1.0
FE6 A:CLF504 4.9 14.7 1.0
SG A:CYS49 4.9 11.7 1.0
C A:GLY170 4.9 16.3 1.0

Iron binding site 9 out of 30 in 5n6y

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Iron binding site 9 out of 30 in the Azotobacter Vinelandii Vanadium Nitrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Azotobacter Vinelandii Vanadium Nitrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe504

b:11.7
occ:1.00
FE2 A:CLF504 0.0 11.7 1.0
S2A A:CLF504 2.3 11.2 1.0
S4A A:CLF504 2.3 11.1 1.0
SG B:CYS56 2.4 11.7 1.0
S1 A:CLF504 2.5 11.2 1.0
FE1 A:CLF504 2.5 11.3 1.0
FE4 A:CLF504 2.6 11.0 1.0
FE3 A:CLF504 2.8 11.0 1.0
FE8 A:CLF504 2.9 12.4 1.0
N B:CYS56 3.2 10.1 1.0
CB B:CYS56 3.7 11.3 1.0
CA B:CYS56 3.7 10.4 1.0
S4B A:CLF504 3.8 11.5 1.0
FE5 A:CLF504 3.8 11.9 1.0
S3A A:CLF504 3.8 10.8 1.0
C B:GLY55 3.9 11.3 1.0
CA B:GLY55 4.2 11.2 1.0
O B:HOH725 4.3 13.2 1.0
N B:GLY55 4.4 11.1 1.0
O B:GLY53 4.5 11.8 1.0
SG A:CYS138 4.6 11.8 1.0
FE6 A:CLF504 4.6 14.7 1.0
SG A:CYS75 4.7 10.7 1.0
O B:GLY55 4.7 12.4 1.0
C B:GLY53 4.8 10.8 1.0
SG A:CYS49 4.8 11.7 1.0

Iron binding site 10 out of 30 in 5n6y

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Iron binding site 10 out of 30 in the Azotobacter Vinelandii Vanadium Nitrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Azotobacter Vinelandii Vanadium Nitrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe504

b:11.0
occ:1.00
FE3 A:CLF504 0.0 11.0 1.0
S4A A:CLF504 2.3 11.1 1.0
SG A:CYS49 2.3 11.7 1.0
S3A A:CLF504 2.3 10.8 1.0
S2A A:CLF504 2.3 11.2 1.0
FE4 A:CLF504 2.7 11.0 1.0
FE1 A:CLF504 2.8 11.3 1.0
FE2 A:CLF504 2.8 11.7 1.0
CB A:CYS49 3.3 11.8 1.0
CA A:GLY170 3.9 15.5 1.0
CD2 A:PHE51 4.1 12.8 1.0
CA B:GLY55 4.1 11.2 1.0
CB A:PHE51 4.2 10.8 1.0
S1 A:CLF504 4.3 11.2 1.0
N B:GLY55 4.4 11.1 1.0
N A:GLY170 4.5 14.6 1.0
CG A:PHE51 4.6 11.2 1.0
C B:GLY55 4.7 11.3 1.0
CA A:CYS49 4.7 11.5 1.0
N B:CYS56 4.8 10.1 1.0
CE2 B:PHE59 4.8 10.5 1.0
SG A:CYS138 4.8 11.8 1.0
SG A:CYS75 5.0 10.7 1.0

Reference:

D.Sippel, O.Einsle. The Structure of Vanadium Nitrogenase Reveals An Unusual Bridging Ligand. Nat. Chem. Biol. V. 13 956 2017.
ISSN: ESSN 1552-4469
PubMed: 28692069
DOI: 10.1038/NCHEMBIO.2428
Page generated: Sun Dec 13 16:09:10 2020

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