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Iron in PDB 6fea: A. Vinelandii Vanadium Nitrogenase, Turnover State

Enzymatic activity of A. Vinelandii Vanadium Nitrogenase, Turnover State

All present enzymatic activity of A. Vinelandii Vanadium Nitrogenase, Turnover State:
1.18.6.1;

Protein crystallography data

The structure of A. Vinelandii Vanadium Nitrogenase, Turnover State, PDB code: 6fea 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) 102.12 / 1.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 75.610, 79.750, 107.160, 84.05, 72.44, 75.25
R / Rfree (%) 11.7 / 14.5

Other elements in 6fea:

The structure of A. Vinelandii Vanadium Nitrogenase, Turnover State also contains other interesting chemical elements:

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

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Iron atom in the A. Vinelandii Vanadium Nitrogenase, Turnover State (pdb code 6fea). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 32 binding sites of Iron where determined in the A. Vinelandii Vanadium Nitrogenase, Turnover State, PDB code: 6fea:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 32 in 6fea

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Iron binding site 1 out of 32 in the A. Vinelandii Vanadium Nitrogenase, Turnover State


Mono view


Stereo pair view

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

b:9.6
occ:1.00
FE1 A:D6N502 0.0 9.6 1.0
S2A A:D6N502 2.2 9.5 1.0
SG A:CYS257 2.3 9.9 1.0
S1A A:D6N502 2.3 9.6 1.0
S4A A:D6N502 2.3 9.6 1.0
FE4 A:D6N502 2.6 9.2 1.0
FE3 A:D6N502 2.7 9.3 1.0
FE2 A:D6N502 2.7 9.3 1.0
CB A:CYS257 3.3 9.0 1.0
CX A:D6N502 3.5 8.8 1.0
OG A:SER260 3.8 9.5 1.0
CB A:SER260 4.1 9.9 1.0
O A:HOH978 4.2 11.6 1.0
O1 A:CO3503 4.2 9.8 1.0
CG A:PRO338 4.4 11.2 1.0
CE2 A:PHE211 4.6 11.0 1.0
CA A:CYS257 4.6 9.5 1.0
N2B A:D6N502 4.7 6.9 1.0
N A:SER260 4.7 9.0 1.0
O A:HOH882 4.8 11.9 1.0
S5A A:D6N502 4.8 9.4 1.0
CB A:PRO338 4.9 11.1 1.0
CD2 A:PHE211 4.9 10.1 1.0
CD A:PRO338 5.0 10.2 1.0

Iron binding site 2 out of 32 in 6fea

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Iron binding site 2 out of 32 in the A. Vinelandii Vanadium Nitrogenase, Turnover State


Mono view


Stereo pair view

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

b:9.3
occ:1.00
FE2 A:D6N502 0.0 9.3 1.0
N2B A:D6N502 2.0 6.9 1.0
CX A:D6N502 2.0 8.8 1.0
S1A A:D6N502 2.2 9.6 1.0
S2A A:D6N502 2.3 9.5 1.0
FE4 A:D6N502 2.6 9.2 1.0
FE3 A:D6N502 2.6 9.3 1.0
FE6 A:D6N502 2.6 9.3 1.0
FE1 A:D6N502 2.7 9.6 1.0
FE7 A:D6N502 3.7 9.1 1.0
FE5 A:D6N502 3.8 8.8 1.0
CZ A:PHE362 3.9 12.4 1.0
S4A A:D6N502 3.9 9.6 1.0
CG1 A:VAL57 4.0 10.8 1.0
S3B A:D6N502 4.3 9.2 1.0
S1B A:D6N502 4.4 9.0 1.0
OE1 A:GLN176 4.4 14.8 1.0
CE1 A:HIS180 4.4 10.4 1.0
O1 A:CO3503 4.4 9.8 1.0
S5A A:D6N502 4.5 9.4 1.0
CE1 A:PHE362 4.5 14.8 1.0
NE2 A:HIS180 4.5 11.1 1.0
CB A:SER260 4.7 9.9 1.0
SG A:CYS257 4.7 9.9 1.0
CE2 A:PHE362 4.8 11.3 1.0
O2 A:CO3503 5.0 9.2 1.0

Iron binding site 3 out of 32 in 6fea

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Iron binding site 3 out of 32 in the A. Vinelandii Vanadium Nitrogenase, Turnover State


Mono view


Stereo pair view

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

b:9.3
occ:1.00
FE3 A:D6N502 0.0 9.3 1.0
CX A:D6N502 2.0 8.8 1.0
S5A A:D6N502 2.2 9.4 1.0
S2A A:D6N502 2.3 9.5 1.0
S4A A:D6N502 2.3 9.6 1.0
FE7 A:D6N502 2.6 9.1 1.0
FE4 A:D6N502 2.6 9.2 1.0
FE2 A:D6N502 2.6 9.3 1.0
FE1 A:D6N502 2.7 9.6 1.0
FE6 A:D6N502 3.7 9.3 1.0
FE5 A:D6N502 3.8 8.8 1.0
NH2 A:ARG339 3.8 10.7 1.0
S1A A:D6N502 3.9 9.6 1.0
CD2 A:PHE211 4.2 10.1 1.0
O A:HOH1014 4.2 11.7 1.0
N2B A:D6N502 4.2 6.9 1.0
S4B A:D6N502 4.3 8.6 1.0
S3B A:D6N502 4.3 9.2 1.0
O1 A:CO3503 4.4 9.8 1.0
CZ A:ARG339 4.6 8.6 1.0
CE2 A:PHE211 4.6 11.0 1.0
CG1 A:VAL57 4.6 10.8 1.0
NE A:ARG339 4.7 9.2 1.0
O A:HOH724 4.8 10.8 1.0
SG A:CYS257 4.9 9.9 1.0

Iron binding site 4 out of 32 in 6fea

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Iron binding site 4 out of 32 in the A. Vinelandii Vanadium Nitrogenase, Turnover State


Mono view


Stereo pair view

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

b:9.2
occ:1.00
FE4 A:D6N502 0.0 9.2 1.0
O1 A:CO3503 2.0 9.8 1.0
CX A:D6N502 2.0 8.8 1.0
S1A A:D6N502 2.3 9.6 1.0
S4A A:D6N502 2.3 9.6 1.0
FE1 A:D6N502 2.6 9.6 1.0
FE2 A:D6N502 2.6 9.3 1.0
FE3 A:D6N502 2.6 9.3 1.0
FE5 A:D6N502 2.8 8.8 1.0
C A:CO3503 2.9 9.1 1.0
O2 A:CO3503 3.2 9.2 1.0
FE7 A:D6N502 3.7 9.1 1.0
FE6 A:D6N502 3.8 9.3 1.0
S2A A:D6N502 3.8 9.5 1.0
NE A:ARG339 4.0 9.2 1.0
O3 A:CO3503 4.0 9.4 1.0
CD A:PRO338 4.2 10.2 1.0
N2B A:D6N502 4.3 6.9 1.0
CG A:PRO338 4.3 11.2 1.0
S4B A:D6N502 4.4 8.6 1.0
SG A:CYS257 4.5 9.9 1.0
S1B A:D6N502 4.5 9.0 1.0
S5A A:D6N502 4.6 9.4 1.0
NH2 A:ARG339 4.6 10.7 1.0
CB A:PRO338 4.6 11.1 1.0
CZ A:ARG339 4.6 8.6 1.0
CD A:ARG339 4.7 9.2 1.0
CZ A:PHE362 4.8 12.4 1.0
CG A:ARG339 4.9 10.6 1.0
O A:HOH978 4.9 11.6 1.0
N A:PRO338 5.0 10.1 1.0

Iron binding site 5 out of 32 in 6fea

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Iron binding site 5 out of 32 in the A. Vinelandii Vanadium Nitrogenase, Turnover State


Mono view


Stereo pair view

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

b:8.8
occ:1.00
FE5 A:D6N502 0.0 8.8 1.0
O2 A:CO3503 2.0 9.2 1.0
CX A:D6N502 2.1 8.8 1.0
S4B A:D6N502 2.3 8.6 1.0
S1B A:D6N502 2.3 9.0 1.0
FE6 A:D6N502 2.6 9.3 1.0
FE7 A:D6N502 2.6 9.1 1.0
V1 A:D6N502 2.7 8.6 1.0
FE4 A:D6N502 2.8 9.2 1.0
C A:CO3503 2.9 9.1 1.0
O1 A:CO3503 3.2 9.8 1.0
ND1 A:HIS423 3.7 8.2 1.0
FE2 A:D6N502 3.8 9.3 1.0
FE3 A:D6N502 3.8 9.3 1.0
S3B A:D6N502 3.8 9.2 1.0
NE A:ARG339 4.0 9.2 1.0
O3 A:CO3503 4.1 9.4 1.0
CE1 A:HIS423 4.1 9.0 1.0
N A:GLY336 4.1 9.3 1.0
N2B A:D6N502 4.2 6.9 1.0
CZ A:ARG339 4.3 8.6 1.0
CA A:GLY336 4.3 10.3 1.0
S1A A:D6N502 4.5 9.6 1.0
S4A A:D6N502 4.5 9.6 1.0
CD A:ARG339 4.5 9.2 1.0
O7 A:HCA501 4.6 8.5 1.0
NH2 A:ARG339 4.6 10.7 1.0
S5A A:D6N502 4.6 9.4 1.0
O5 A:HCA501 4.6 8.4 1.0
CG A:HIS423 4.7 8.6 1.0
CZ A:PHE362 4.9 12.4 1.0
NH1 A:ARG339 4.9 9.6 1.0

Iron binding site 6 out of 32 in 6fea

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Iron binding site 6 out of 32 in the A. Vinelandii Vanadium Nitrogenase, Turnover State


Mono view


Stereo pair view

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

b:9.3
occ:1.00
FE6 A:D6N502 0.0 9.3 1.0
N2B A:D6N502 2.0 6.9 1.0
CX A:D6N502 2.0 8.8 1.0
S3B A:D6N502 2.2 9.2 1.0
S1B A:D6N502 2.2 9.0 1.0
FE7 A:D6N502 2.6 9.1 1.0
FE5 A:D6N502 2.6 8.8 1.0
FE2 A:D6N502 2.6 9.3 1.0
V1 A:D6N502 2.8 8.6 1.0
FE3 A:D6N502 3.7 9.3 1.0
FE4 A:D6N502 3.8 9.2 1.0
S4B A:D6N502 3.8 8.6 1.0
O7 A:HCA501 3.9 8.5 1.0
OE1 A:GLN176 4.0 14.8 1.0
CZ A:PHE362 4.0 12.4 1.0
NE2 A:GLN176 4.2 16.9 1.0
CE2 A:PHE362 4.2 11.3 1.0
O2 A:CO3503 4.3 9.2 1.0
S1A A:D6N502 4.3 9.6 1.0
S2A A:D6N502 4.4 9.5 1.0
CD A:GLN176 4.4 15.4 1.0
S5A A:D6N502 4.5 9.4 1.0
CG1 A:VAL57 4.5 10.8 1.0
CG2 A:VAL57 4.5 10.4 1.0
O5 A:HCA501 4.5 8.4 1.0
O1 A:HCA501 4.6 10.7 1.0
ND1 A:HIS423 4.7 8.2 1.0
C3 A:HCA501 5.0 8.0 1.0

Iron binding site 7 out of 32 in 6fea

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Iron binding site 7 out of 32 in the A. Vinelandii Vanadium Nitrogenase, Turnover State


Mono view


Stereo pair view

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

b:9.1
occ:1.00
FE7 A:D6N502 0.0 9.1 1.0
CX A:D6N502 2.0 8.8 1.0
S4B A:D6N502 2.2 8.6 1.0
S5A A:D6N502 2.2 9.4 1.0
S3B A:D6N502 2.3 9.2 1.0
FE6 A:D6N502 2.6 9.3 1.0
FE3 A:D6N502 2.6 9.3 1.0
FE5 A:D6N502 2.6 8.8 1.0
V1 A:D6N502 2.8 8.6 1.0
FE2 A:D6N502 3.7 9.3 1.0
O5 A:HCA501 3.7 8.4 1.0
FE4 A:D6N502 3.7 9.2 1.0
NH2 A:ARG339 3.8 10.7 1.0
NZ A:LYS83 3.8 11.5 1.0
S1B A:D6N502 3.8 9.0 1.0
O A:HOH788 3.9 10.0 1.0
N2B A:D6N502 4.1 6.9 1.0
CZ A:ARG339 4.3 8.6 1.0
S4A A:D6N502 4.3 9.6 1.0
S2A A:D6N502 4.3 9.5 1.0
O2 A:CO3503 4.5 9.2 1.0
O A:HOH724 4.6 10.8 1.0
O7 A:HCA501 4.7 8.5 1.0
ND1 A:HIS423 4.7 8.2 1.0
NE A:ARG339 4.7 9.2 1.0
C7 A:HCA501 4.7 8.1 1.0
CG1 A:VAL57 5.0 10.8 1.0
NH1 A:ARG339 5.0 9.6 1.0

Iron binding site 8 out of 32 in 6fea

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Iron binding site 8 out of 32 in the A. Vinelandii Vanadium Nitrogenase, Turnover State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of A. Vinelandii Vanadium Nitrogenase, Turnover State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe506

b:9.6
occ:1.00
FE1 A:CLF506 0.0 9.6 1.0
S3A A:CLF506 2.3 9.5 1.0
S2A A:CLF506 2.3 9.7 1.0
SG A:CYS138 2.3 10.2 1.0
S1 A:CLF506 2.4 9.9 1.0
FE2 A:CLF506 2.5 10.0 1.0
FE4 A:CLF506 2.6 9.4 1.0
FE3 A:CLF506 2.8 9.5 1.0
CB A:CYS138 3.5 11.1 1.0
S4A A:CLF506 3.8 9.4 1.0
O B:HOH749 3.8 10.9 1.0
N A:CYS138 3.9 9.1 1.0
CA A:GLY170 4.0 13.5 1.0
N A:GLY170 4.0 11.8 1.0
SG B:CYS56 4.1 9.8 1.0
CA A:CYS138 4.3 8.9 1.0
FE8 A:CLF506 4.4 10.2 1.0
SG A:CYS75 4.5 9.4 1.0
FE5 A:CLF506 4.6 9.9 1.0
FE6 A:CLF506 4.8 7.9 0.6
C A:GLY170 4.9 14.4 1.0
SG A:CYS49 4.9 9.8 1.0
C A:THR137 5.0 10.4 1.0

Iron binding site 9 out of 32 in 6fea

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Iron binding site 9 out of 32 in the A. Vinelandii Vanadium Nitrogenase, Turnover State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of A. Vinelandii Vanadium Nitrogenase, Turnover State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe506

b:10.0
occ:1.00
FE2 A:CLF506 0.0 10.0 1.0
S4A A:CLF506 2.3 9.4 1.0
S2A A:CLF506 2.3 9.7 1.0
SG B:CYS56 2.4 9.8 1.0
S1 A:CLF506 2.5 9.9 1.0
FE1 A:CLF506 2.5 9.6 1.0
FE4 A:CLF506 2.6 9.4 1.0
FE3 A:CLF506 2.8 9.5 1.0
FE8 A:CLF506 2.9 10.2 1.0
N B:CYS56 3.2 8.3 1.0
CA B:CYS56 3.7 8.9 1.0
CB B:CYS56 3.7 8.9 1.0
S4B A:CLF506 3.8 9.8 1.0
FE5 A:CLF506 3.8 9.9 1.0
C B:GLY55 3.8 8.9 1.0
S3A A:CLF506 3.9 9.5 1.0
CA B:GLY55 4.2 9.5 1.0
O B:HOH749 4.2 10.9 1.0
N B:GLY55 4.4 8.9 1.0
FE6 A:CLF506 4.5 7.9 0.6
O B:GLY53 4.5 9.7 1.0
SG A:CYS138 4.5 10.2 1.0
SG A:CYS75 4.6 9.4 1.0
O B:GLY55 4.7 9.8 1.0
SG A:CYS49 4.8 9.8 1.0
C B:GLY53 4.8 9.0 1.0

Iron binding site 10 out of 32 in 6fea

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Iron binding site 10 out of 32 in the A. Vinelandii Vanadium Nitrogenase, Turnover State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of A. Vinelandii Vanadium Nitrogenase, Turnover State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe506

b:9.5
occ:1.00
FE3 A:CLF506 0.0 9.5 1.0
S4A A:CLF506 2.3 9.4 1.0
SG A:CYS49 2.3 9.8 1.0
S2A A:CLF506 2.3 9.7 1.0
S3A A:CLF506 2.3 9.5 1.0
FE4 A:CLF506 2.7 9.4 1.0
FE1 A:CLF506 2.8 9.6 1.0
FE2 A:CLF506 2.8 10.0 1.0
CB A:CYS49 3.3 10.3 1.0
CA A:GLY170 4.0 13.5 1.0
CD2 A:PHE51 4.1 11.0 1.0
CA B:GLY55 4.1 9.5 1.0
CB A:PHE51 4.2 10.1 1.0
S1 A:CLF506 4.3 9.9 1.0
N B:GLY55 4.4 8.9 1.0
N A:GLY170 4.5 11.8 1.0
CG A:PHE51 4.6 10.2 1.0
C B:GLY55 4.7 8.9 1.0
CE2 B:PHE59 4.7 9.7 1.0
CA A:CYS49 4.7 10.0 1.0
N B:CYS56 4.8 8.3 1.0
SG A:CYS138 4.8 10.2 1.0
SG A:CYS75 5.0 9.4 1.0

Reference:

D.Sippel, M.Rohde, J.Netzer, C.Trncik, J.Gies, K.Grunau, I.Djurdjevic, L.Decamps, S.L.A.Andrade, O.Einsle. A Bound Reaction Intermediate Sheds Light on the Mechanism of Nitrogenase. Science V. 359 1484 2018.
ISSN: ESSN 1095-9203
PubMed: 29599235
DOI: 10.1126/SCIENCE.AAR2765
Page generated: Sun Dec 13 16:26:00 2020

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