Iron in PDB 7aiz: Vanadium Nitrogenase Vfe Protein, High Co State

Enzymatic activity of Vanadium Nitrogenase Vfe Protein, High Co State

All present enzymatic activity of Vanadium Nitrogenase Vfe Protein, High Co State:
1.18.6.1;

Protein crystallography data

The structure of Vanadium Nitrogenase Vfe Protein, High Co State, PDB code: 7aiz was solved by M.Rohde, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.39 / 1.05
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 75.521, 80.041, 107.21, 84, 72.48, 75.03
R / Rfree (%) 12.4 / 14.6

Other elements in 7aiz:

The structure of Vanadium Nitrogenase Vfe Protein, High Co State 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; Page 4, Binding sites: 31 - 32;

Binding sites:

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

Iron binding site 1 out of 32 in 7aiz

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Iron binding site 1 out of 32 in the Vanadium Nitrogenase Vfe Protein, High Co State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Vanadium Nitrogenase Vfe Protein, High Co State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:9.8
occ:1.00
 FE1 A:D6N501 0.0 9.8 1.0
S2A A:D6N501 2.2 10.2 1.0
SG A:CYS257 2.3 10.4 1.0
S1A A:D6N501 2.3 10.0 1.0
S4A A:D6N501 2.3 10.1 1.0
FE4 A:D6N501 2.6 9.6 1.0
FE3 A:D6N501 2.7 9.6 1.0
FE2 A:D6N501 2.7 9.6 1.0
CB A:CYS257 3.3 9.4 1.0
CX A:D6N501 3.5 9.7 1.0
OG A:SER260 3.9 10.4 1.0
CB A:SER260 4.1 10.2 1.0
O1 A:BCT503 4.2 10.4 1.0
O A:HOH977 4.2 11.8 1.0
CG A:PRO338 4.4 11.7 1.0
CE2 A:PHE211 4.6 10.9 1.0
C A:CMO504 4.6 9.2 1.0
CA A:CYS257 4.6 9.8 1.0
N A:SER260 4.7 9.6 1.0
S5A A:D6N501 4.8 9.7 1.0
CB A:PRO338 4.8 11.3 1.0
CD A:PRO338 4.9 11.2 1.0
O A:HOH881 4.9 11.5 1.0
CD2 A:PHE211 4.9 10.7 1.0
FE7 A:D6N501 5.0 9.3 1.0

Iron binding site 2 out of 32 in 7aiz

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Iron binding site 2 out of 32 in the Vanadium Nitrogenase Vfe Protein, High Co State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Vanadium Nitrogenase Vfe Protein, High Co State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:9.6
occ:1.00
 FE2 A:D6N501 0.0 9.6 1.0
CX A:D6N501 2.0 9.7 1.0
C A:CMO504 2.0 9.2 1.0
S1A A:D6N501 2.2 10.0 1.0
S2A A:D6N501 2.3 10.2 1.0
FE6 A:D6N501 2.6 9.7 1.0
FE4 A:D6N501 2.6 9.6 1.0
FE3 A:D6N501 2.6 9.6 1.0
FE1 A:D6N501 2.7 9.8 1.0
O A:CMO504 2.8 21.0 1.0
FE7 A:D6N501 3.6 9.3 1.0
FE5 A:D6N501 3.7 9.2 1.0
C A:CMO505 3.8 11.9 0.5
S4A A:D6N501 3.9 10.1 1.0
CZ A:PHE362 4.0 12.1 1.0
CG1 A:VAL57 4.1 10.7 1.0
S3B A:D6N501 4.2 9.8 1.0
S1B A:D6N501 4.3 9.4 1.0
S5A A:D6N501 4.4 9.7 1.0
O1 A:BCT503 4.4 10.4 1.0
CE1 A:HIS180 4.5 13.2 1.0
NE2 A:HIS180 4.5 14.1 1.0
CE1 A:PHE362 4.5 13.7 1.0
SG A:CYS257 4.7 10.4 1.0
O A:CMO505 4.7 12.8 0.5
CB A:SER260 4.8 10.2 1.0
CE2 A:PHE362 4.9 12.1 1.0
O2 A:BCT503 4.9 9.8 1.0

Iron binding site 3 out of 32 in 7aiz

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Iron binding site 3 out of 32 in the Vanadium Nitrogenase Vfe Protein, High Co State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Vanadium Nitrogenase Vfe Protein, High Co State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:9.6
occ:1.00
 FE3 A:D6N501 0.0 9.6 1.0
CX A:D6N501 2.1 9.7 1.0
S5A A:D6N501 2.2 9.7 1.0
S2A A:D6N501 2.3 10.2 1.0
S4A A:D6N501 2.3 10.1 1.0
FE7 A:D6N501 2.6 9.3 1.0
FE2 A:D6N501 2.6 9.6 1.0
FE4 A:D6N501 2.7 9.6 1.0
FE1 A:D6N501 2.7 9.8 1.0
FE6 A:D6N501 3.8 9.7 1.0
FE5 A:D6N501 3.8 9.2 1.0
NH2 A:ARG339 3.8 10.6 1.0
S1A A:D6N501 3.9 10.0 1.0
CD2 A:PHE211 4.2 10.7 1.0
C A:CMO504 4.2 9.2 1.0
O A:HOH1005 4.2 11.4 1.0
S4B A:D6N501 4.2 9.2 1.0
S3B A:D6N501 4.3 9.8 1.0
O1 A:BCT503 4.4 10.4 1.0
CE2 A:PHE211 4.6 10.9 1.0
CZ A:ARG339 4.6 9.4 1.0
CG1 A:VAL57 4.6 10.7 1.0
NE A:ARG339 4.7 9.9 1.0
O A:HOH753 4.8 11.2 1.0
SG A:CYS257 4.9 10.4 1.0

Iron binding site 4 out of 32 in 7aiz

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Iron binding site 4 out of 32 in the Vanadium Nitrogenase Vfe Protein, High Co State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Vanadium Nitrogenase Vfe Protein, High Co State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:9.6
occ:1.00
 FE4 A:D6N501 0.0 9.6 1.0
O1 A:BCT503 2.0 10.4 1.0
CX A:D6N501 2.0 9.7 1.0
S1A A:D6N501 2.3 10.0 1.0
S4A A:D6N501 2.3 10.1 1.0
FE1 A:D6N501 2.6 9.8 1.0
FE2 A:D6N501 2.6 9.6 1.0
FE3 A:D6N501 2.7 9.6 1.0
FE5 A:D6N501 2.8 9.2 1.0
C A:BCT503 2.9 9.3 1.0
O2 A:BCT503 3.2 9.8 1.0
FE7 A:D6N501 3.7 9.3 1.0
FE6 A:D6N501 3.8 9.7 1.0
S2A A:D6N501 3.8 10.2 1.0
NE A:ARG339 4.0 9.9 1.0
O3 A:BCT503 4.0 9.7 1.0
CD A:PRO338 4.1 11.2 1.0
C A:CMO504 4.3 9.2 1.0
CG A:PRO338 4.4 11.7 1.0
S4B A:D6N501 4.4 9.2 1.0
S1B A:D6N501 4.5 9.4 1.0
SG A:CYS257 4.5 10.4 1.0
S5A A:D6N501 4.6 9.7 1.0
NH2 A:ARG339 4.6 10.6 1.0
CB A:PRO338 4.6 11.3 1.0
CZ A:ARG339 4.7 9.4 1.0
CD A:ARG339 4.7 9.7 1.0
CZ A:PHE362 4.9 12.1 1.0
CG A:ARG339 4.9 10.5 1.0
O A:HOH977 5.0 11.8 1.0
N A:PRO338 5.0 10.4 1.0

Iron binding site 5 out of 32 in 7aiz

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Iron binding site 5 out of 32 in the Vanadium Nitrogenase Vfe Protein, High Co State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Vanadium Nitrogenase Vfe Protein, High Co State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:9.2
occ:1.00
 FE5 A:D6N501 0.0 9.2 1.0
O2 A:BCT503 2.0 9.8 1.0
CX A:D6N501 2.0 9.7 1.0
S4B A:D6N501 2.3 9.2 1.0
S1B A:D6N501 2.3 9.4 1.0
FE6 A:D6N501 2.6 9.7 1.0
FE7 A:D6N501 2.6 9.3 1.0
V1 A:D6N501 2.7 8.9 1.0
FE4 A:D6N501 2.8 9.6 1.0
C A:BCT503 2.9 9.3 1.0
O1 A:BCT503 3.2 10.4 1.0
ND1 A:HIS423 3.7 8.9 1.0
FE2 A:D6N501 3.7 9.6 1.0
FE3 A:D6N501 3.8 9.6 1.0
S3B A:D6N501 3.8 9.8 1.0
NE A:ARG339 4.0 9.9 1.0
CE1 A:HIS423 4.1 9.7 1.0
O3 A:BCT503 4.1 9.7 1.0
N A:GLY336 4.1 9.8 1.0
CZ A:ARG339 4.3 9.4 1.0
C A:CMO504 4.3 9.2 1.0
CA A:GLY336 4.3 9.9 1.0
C A:CMO505 4.3 11.9 0.5
S1A A:D6N501 4.4 10.0 1.0
S4A A:D6N501 4.5 10.1 1.0
CD A:ARG339 4.5 9.7 1.0
NH2 A:ARG339 4.6 10.6 1.0
O7 A:HCA502 4.6 8.9 1.0
S5A A:D6N501 4.6 9.7 1.0
O5 A:HCA502 4.6 8.7 1.0
CG A:HIS423 4.7 9.3 1.0
CZ A:PHE362 4.9 12.1 1.0
NH1 A:ARG339 5.0 9.9 1.0

Iron binding site 6 out of 32 in 7aiz

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Iron binding site 6 out of 32 in the Vanadium Nitrogenase Vfe Protein, High Co State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Vanadium Nitrogenase Vfe Protein, High Co State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:9.7
occ:1.00
 FE6 A:D6N501 0.0 9.7 1.0
C A:CMO505 2.0 11.9 0.5
CX A:D6N501 2.0 9.7 1.0
C A:CMO504 2.0 9.2 1.0
S3B A:D6N501 2.2 9.8 1.0
S1B A:D6N501 2.3 9.4 1.0
FE2 A:D6N501 2.6 9.6 1.0
FE7 A:D6N501 2.6 9.3 1.0
FE5 A:D6N501 2.6 9.2 1.0
V1 A:D6N501 2.8 8.9 1.0
O A:CMO504 3.1 21.0 1.0
O A:CMO505 3.1 12.8 0.5
FE3 A:D6N501 3.8 9.6 1.0
FE4 A:D6N501 3.8 9.6 1.0
S4B A:D6N501 3.8 9.2 1.0
O7 A:HCA502 3.9 8.9 1.0
CZ A:PHE362 3.9 12.1 1.0
CE2 A:PHE362 4.2 12.1 1.0
S1A A:D6N501 4.3 10.0 1.0
S2A A:D6N501 4.4 10.2 1.0
O2 A:BCT503 4.4 9.8 1.0
CG2 A:VAL57 4.4 11.1 1.0
S5A A:D6N501 4.5 9.7 1.0
O5 A:HCA502 4.6 8.7 1.0
CG1 A:VAL57 4.6 10.7 1.0
O1 A:HCA502 4.7 10.8 1.0
ND1 A:HIS423 4.8 8.9 1.0
C3 A:HCA502 5.0 9.0 1.0

Iron binding site 7 out of 32 in 7aiz

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Iron binding site 7 out of 32 in the Vanadium Nitrogenase Vfe Protein, High Co State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Vanadium Nitrogenase Vfe Protein, High Co State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:9.3
occ:1.00
 FE7 A:D6N501 0.0 9.3 1.0
CX A:D6N501 2.0 9.7 1.0
S4B A:D6N501 2.2 9.2 1.0
S5A A:D6N501 2.2 9.7 1.0
S3B A:D6N501 2.3 9.8 1.0
FE3 A:D6N501 2.6 9.6 1.0
FE6 A:D6N501 2.6 9.7 1.0
FE5 A:D6N501 2.6 9.2 1.0
V1 A:D6N501 2.7 8.9 1.0
FE2 A:D6N501 3.6 9.6 1.0
O5 A:HCA502 3.7 8.7 1.0
FE4 A:D6N501 3.7 9.6 1.0
NZ A:LYS83 3.8 10.6 1.0
S1B A:D6N501 3.8 9.4 1.0
NH2 A:ARG339 3.8 10.6 1.0
O A:HOH836 3.9 11.0 1.0
C A:CMO504 4.2 9.2 1.0
S2A A:D6N501 4.3 10.2 1.0
CZ A:ARG339 4.3 9.4 1.0
S4A A:D6N501 4.3 10.1 1.0
C A:CMO505 4.4 11.9 0.5
O2 A:BCT503 4.5 9.8 1.0
O A:HOH753 4.6 11.2 1.0
O7 A:HCA502 4.6 8.9 1.0
ND1 A:HIS423 4.7 8.9 1.0
NE A:ARG339 4.7 9.9 1.0
C7 A:HCA502 4.8 9.2 1.0
FE1 A:D6N501 5.0 9.8 1.0
NH1 A:ARG339 5.0 9.9 1.0

Iron binding site 8 out of 32 in 7aiz

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Iron binding site 8 out of 32 in the Vanadium Nitrogenase Vfe Protein, High Co State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Vanadium Nitrogenase Vfe Protein, High Co State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:9.8
occ:1.00
 FE1 B:CLF501 0.0 9.8 1.0
S3A B:CLF501 2.3 9.8 1.0
SG A:CYS138 2.3 10.6 1.0
S2A B:CLF501 2.3 10.1 1.0
S1 B:CLF501 2.4 9.8 1.0
FE2 B:CLF501 2.5 10.0 1.0
FE4 B:CLF501 2.6 9.7 1.0
FE3 B:CLF501 2.8 9.8 1.0
CB A:CYS138 3.5 10.2 1.0
O B:HOH732 3.8 11.0 1.0
S4A B:CLF501 3.8 9.9 1.0
N A:CYS138 3.9 10.1 1.0
CA A:GLY170 4.0 13.3 1.0
N A:GLY170 4.0 12.3 1.0
SG B:CYS56 4.1 10.0 1.0
CA A:CYS138 4.3 9.9 1.0
FE8 B:CLF501 4.4 10.3 1.0
SG A:CYS75 4.5 9.6 1.0
FE5 B:CLF501 4.6 10.0 1.0
FE6 B:CLF501 4.8 9.0 0.8
C A:GLY170 4.8 14.8 1.0
SG A:CYS49 4.9 10.2 1.0

Iron binding site 9 out of 32 in 7aiz

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Iron binding site 9 out of 32 in the Vanadium Nitrogenase Vfe Protein, High Co State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Vanadium Nitrogenase Vfe Protein, High Co State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:10.0
occ:1.00
 FE2 B:CLF501 0.0 10.0 1.0
S2A B:CLF501 2.3 10.1 1.0
S4A B:CLF501 2.3 9.9 1.0
SG B:CYS56 2.4 10.0 1.0
S1 B:CLF501 2.5 9.8 1.0
FE1 B:CLF501 2.5 9.8 1.0
FE4 B:CLF501 2.6 9.7 1.0
FE3 B:CLF501 2.8 9.8 1.0
FE8 B:CLF501 2.9 10.3 1.0
N B:CYS56 3.3 9.1 1.0
CB B:CYS56 3.7 9.7 1.0
CA B:CYS56 3.7 9.2 1.0
FE5 B:CLF501 3.7 10.0 1.0
S4B B:CLF501 3.8 10.3 1.0
S3A B:CLF501 3.9 9.8 1.0
C B:GLY55 3.9 9.3 1.0
CA B:GLY55 4.2 9.5 1.0
O B:HOH732 4.3 11.0 1.0
N B:GLY55 4.4 9.4 1.0
FE6 B:CLF501 4.5 9.0 0.8
O B:GLY53 4.5 10.1 1.0
SG A:CYS138 4.5 10.6 1.0
SG A:CYS75 4.6 9.6 1.0
O B:GLY55 4.7 10.0 1.0
SG A:CYS49 4.9 10.2 1.0
C B:GLY53 4.9 10.2 1.0

Iron binding site 10 out of 32 in 7aiz

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Iron binding site 10 out of 32 in the Vanadium Nitrogenase Vfe Protein, High Co State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Vanadium Nitrogenase Vfe Protein, High Co State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:9.8
occ:1.00
 FE3 B:CLF501 0.0 9.8 1.0
S4A B:CLF501 2.3 9.9 1.0
SG A:CYS49 2.3 10.2 1.0
S2A B:CLF501 2.3 10.1 1.0
S3A B:CLF501 2.3 9.8 1.0
FE4 B:CLF501 2.7 9.7 1.0
FE1 B:CLF501 2.8 9.8 1.0
FE2 B:CLF501 2.8 10.0 1.0
CB A:CYS49 3.3 11.1 1.0
CA A:GLY170 3.9 13.3 1.0
CD2 A:PHE51 4.1 11.3 1.0
CA B:GLY55 4.1 9.5 1.0
CB A:PHE51 4.2 10.8 1.0
S1 B:CLF501 4.3 9.8 1.0
N B:GLY55 4.3 9.4 1.0
N A:GLY170 4.5 12.3 1.0
CG A:PHE51 4.6 10.8 1.0
CE2 B:PHE59 4.7 9.3 1.0
C B:GLY55 4.7 9.3 1.0
CA A:CYS49 4.8 10.4 1.0
N B:CYS56 4.8 9.1 1.0
SG A:CYS138 4.8 10.6 1.0
SG A:CYS75 4.9 9.6 1.0

Reference:

M.Rohde, K.Laun, I.Zebger, S.T.Stripp, O.Einsle. Two Ligand-Binding Sites in Co-Reducing V Nitrogenase Reveal A General Mechanistic Principle Sci Adv 2021.
ISSN: ESSN 2375-2548
DOI: 10.1126/SCIADV.ABG4474
Page generated: Sat Jul 10 15:11:56 2021

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