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Iron in PDB 7ady: Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein

Enzymatic activity of Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein

All present enzymatic activity of Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein:
1.18.6.1;

Protein crystallography data

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

Resolution Low / High (Å) 46.66 / 1.05
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 75.576, 80.027, 107.200, 83.99, 72.48, 75.03
R / Rfree (%) 12.1 / 14.1

Other elements in 7ady:

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

Iron binding site 1 out of 32 in 7ady

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Iron binding site 1 out of 32 in the Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein


Mono view


Stereo pair view

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

b:8.7
occ:1.00
 FE1 A:D6N501 0.0 8.7 1.0
S2A A:D6N501 2.3 9.0 1.0
SG A:CYS257 2.3 8.8 1.0
S1A A:D6N501 2.3 8.6 1.0
S4A A:D6N501 2.3 8.8 1.0
FE4 A:D6N501 2.6 8.2 1.0
FE3 A:D6N501 2.7 8.3 1.0
FE2 A:D6N501 2.7 8.4 1.0
CB A:CYS257 3.3 8.5 1.0
CX A:D6N501 3.5 8.7 1.0
OG A:SER260 3.8 9.5 1.0
CB A:SER260 4.1 8.5 1.0
O1 A:BCT503 4.1 9.2 1.0
O A:HOH979 4.2 10.8 1.0
CG A:PRO338 4.4 10.8 1.0
CE2 A:PHE211 4.5 9.4 1.0
CA A:CYS257 4.6 8.8 1.0
N A:SER260 4.7 8.2 1.0
O A:HOH607 4.7 8.7 1.0
O A:HOH881 4.8 10.1 1.0
S5A A:D6N501 4.8 8.7 1.0
CB A:PRO338 4.9 10.1 1.0
CD2 A:PHE211 4.9 9.5 1.0
CD A:PRO338 4.9 10.2 1.0

Iron binding site 2 out of 32 in 7ady

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Iron binding site 2 out of 32 in the Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein


Mono view


Stereo pair view

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

b:8.4
occ:1.00
 FE2 A:D6N501 0.0 8.4 1.0
CX A:D6N501 2.1 8.7 1.0
O A:HOH607 2.1 8.7 1.0
S1A A:D6N501 2.2 8.6 1.0
S2A A:D6N501 2.3 9.0 1.0
FE4 A:D6N501 2.6 8.2 1.0
FE3 A:D6N501 2.6 8.3 1.0
FE6 A:D6N501 2.6 8.2 1.0
FE1 A:D6N501 2.7 8.7 1.0
FE7 A:D6N501 3.7 8.0 1.0
FE5 A:D6N501 3.8 7.9 1.0
CZ A:PHE362 3.9 11.2 1.0
S4A A:D6N501 3.9 8.8 1.0
CG1 A:VAL57 4.0 9.8 1.0
S3B A:D6N501 4.3 8.7 1.0
OE1 A:GLN176 4.4 13.9 1.0
S1B A:D6N501 4.4 8.2 1.0
O1 A:BCT503 4.4 9.2 1.0
CE1 A:HIS180 4.4 10.3 1.0
S5A A:D6N501 4.5 8.7 1.0
NE2 A:HIS180 4.5 10.5 1.0
CE1 A:PHE362 4.5 13.0 1.0
CB A:SER260 4.7 8.5 1.0
SG A:CYS257 4.7 8.8 1.0
CE2 A:PHE362 4.8 10.5 1.0
O2 A:BCT503 5.0 9.3 1.0

Iron binding site 3 out of 32 in 7ady

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Iron binding site 3 out of 32 in the Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein


Mono view


Stereo pair view

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

b:8.3
occ:1.00
 FE3 A:D6N501 0.0 8.3 1.0
CX A:D6N501 2.1 8.7 1.0
S5A A:D6N501 2.2 8.7 1.0
S4A A:D6N501 2.3 8.8 1.0
S2A A:D6N501 2.3 9.0 1.0
FE7 A:D6N501 2.6 8.0 1.0
FE2 A:D6N501 2.6 8.4 1.0
FE4 A:D6N501 2.7 8.2 1.0
FE1 A:D6N501 2.7 8.7 1.0
FE6 A:D6N501 3.7 8.2 1.0
FE5 A:D6N501 3.8 7.9 1.0
NH2 A:ARG339 3.8 9.1 1.0
S1A A:D6N501 3.9 8.6 1.0
CD2 A:PHE211 4.2 9.5 1.0
O A:HOH1018 4.2 10.6 1.0
S4B A:D6N501 4.3 7.9 1.0
O A:HOH607 4.3 8.7 1.0
S3B A:D6N501 4.3 8.7 1.0
O1 A:BCT503 4.4 9.2 1.0
CE2 A:PHE211 4.6 9.4 1.0
CG1 A:VAL57 4.6 9.8 1.0
CZ A:ARG339 4.6 8.0 1.0
NE A:ARG339 4.7 8.7 1.0
O A:HOH746 4.8 9.9 1.0
SG A:CYS257 4.9 8.8 1.0

Iron binding site 4 out of 32 in 7ady

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Iron binding site 4 out of 32 in the Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein


Mono view


Stereo pair view

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

b:8.2
occ:1.00
 FE4 A:D6N501 0.0 8.2 1.0
O1 A:BCT503 1.9 9.2 1.0
CX A:D6N501 2.0 8.7 1.0
S1A A:D6N501 2.3 8.6 1.0
S4A A:D6N501 2.3 8.8 1.0
FE1 A:D6N501 2.6 8.7 1.0
FE2 A:D6N501 2.6 8.4 1.0
FE3 A:D6N501 2.7 8.3 1.0
FE5 A:D6N501 2.8 7.9 1.0
C A:BCT503 2.9 8.6 1.0
O2 A:BCT503 3.2 9.3 1.0
FE7 A:D6N501 3.8 8.0 1.0
FE6 A:D6N501 3.8 8.2 1.0
S2A A:D6N501 3.8 9.0 1.0
NE A:ARG339 4.0 8.7 1.0
O3 A:BCT503 4.0 8.6 1.0
CD A:PRO338 4.1 10.2 1.0
O A:HOH607 4.3 8.7 1.0
CG A:PRO338 4.4 10.8 1.0
S4B A:D6N501 4.4 7.9 1.0
SG A:CYS257 4.5 8.8 1.0
S1B A:D6N501 4.5 8.2 1.0
S5A A:D6N501 4.6 8.7 1.0
NH2 A:ARG339 4.6 9.1 1.0
CB A:PRO338 4.6 10.1 1.0
CZ A:ARG339 4.7 8.0 1.0
CD A:ARG339 4.7 8.5 1.0
CZ A:PHE362 4.8 11.2 1.0
CG A:ARG339 4.8 9.1 1.0
O A:HOH979 4.9 10.8 1.0
N A:PRO338 5.0 9.2 1.0

Iron binding site 5 out of 32 in 7ady

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Iron binding site 5 out of 32 in the Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein


Mono view


Stereo pair view

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

b:7.9
occ:1.00
 FE5 A:D6N501 0.0 7.9 1.0
O2 A:BCT503 2.0 9.3 1.0
CX A:D6N501 2.0 8.7 1.0
S4B A:D6N501 2.3 7.9 1.0
S1B A:D6N501 2.3 8.2 1.0
FE6 A:D6N501 2.6 8.2 1.0
FE7 A:D6N501 2.7 8.0 1.0
V1 A:D6N501 2.7 7.8 1.0
FE4 A:D6N501 2.8 8.2 1.0
C A:BCT503 2.9 8.6 1.0
O1 A:BCT503 3.1 9.2 1.0
ND1 A:HIS423 3.7 7.6 1.0
FE2 A:D6N501 3.8 8.4 1.0
FE3 A:D6N501 3.8 8.3 1.0
S3B A:D6N501 3.8 8.7 1.0
NE A:ARG339 4.0 8.7 1.0
O3 A:BCT503 4.1 8.6 1.0
N A:GLY336 4.1 8.8 1.0
CE1 A:HIS423 4.1 8.3 1.0
O A:HOH607 4.3 8.7 1.0
CZ A:ARG339 4.3 8.0 1.0
CA A:GLY336 4.3 9.1 1.0
S1A A:D6N501 4.5 8.6 1.0
S4A A:D6N501 4.5 8.8 1.0
CD A:ARG339 4.5 8.5 1.0
NH2 A:ARG339 4.6 9.1 1.0
O7 A:HCA502 4.6 7.6 1.0
S5A A:D6N501 4.6 8.7 1.0
O5 A:HCA502 4.6 7.6 1.0
CG A:HIS423 4.7 7.8 1.0
CZ A:PHE362 4.9 11.2 1.0
NH1 A:ARG339 4.9 8.7 1.0

Iron binding site 6 out of 32 in 7ady

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Iron binding site 6 out of 32 in the Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein


Mono view


Stereo pair view

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

b:8.2
occ:1.00
 FE6 A:D6N501 0.0 8.2 1.0
CX A:D6N501 2.0 8.7 1.0
O A:HOH607 2.1 8.7 1.0
S3B A:D6N501 2.2 8.7 1.0
S1B A:D6N501 2.3 8.2 1.0
FE7 A:D6N501 2.6 8.0 1.0
FE5 A:D6N501 2.6 7.9 1.0
FE2 A:D6N501 2.6 8.4 1.0
V1 A:D6N501 2.8 7.8 1.0
FE3 A:D6N501 3.7 8.3 1.0
FE4 A:D6N501 3.8 8.2 1.0
S4B A:D6N501 3.8 7.9 1.0
O7 A:HCA502 3.9 7.6 1.0
OE1 A:GLN176 4.0 13.9 1.0
CZ A:PHE362 4.0 11.2 1.0
NE2 A:GLN176 4.1 15.0 1.0
CE2 A:PHE362 4.2 10.5 1.0
O2 A:BCT503 4.3 9.3 1.0
S1A A:D6N501 4.3 8.6 1.0
CD A:GLN176 4.4 12.8 1.0
S2A A:D6N501 4.4 9.0 1.0
S5A A:D6N501 4.5 8.7 1.0
CG1 A:VAL57 4.5 9.8 1.0
CG2 A:VAL57 4.5 9.3 1.0
O5 A:HCA502 4.5 7.6 1.0
O1 A:HCA502 4.6 10.0 1.0
ND1 A:HIS423 4.7 7.6 1.0
C3 A:HCA502 5.0 8.1 1.0
O1 A:BCT503 5.0 9.2 1.0

Iron binding site 7 out of 32 in 7ady

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Iron binding site 7 out of 32 in the Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein


Mono view


Stereo pair view

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

b:8.0
occ:1.00
 FE7 A:D6N501 0.0 8.0 1.0
CX A:D6N501 2.0 8.7 1.0
S4B A:D6N501 2.2 7.9 1.0
S5A A:D6N501 2.2 8.7 1.0
S3B A:D6N501 2.3 8.7 1.0
FE6 A:D6N501 2.6 8.2 1.0
FE3 A:D6N501 2.6 8.3 1.0
FE5 A:D6N501 2.7 7.9 1.0
V1 A:D6N501 2.8 7.8 1.0
FE2 A:D6N501 3.7 8.4 1.0
O5 A:HCA502 3.7 7.6 1.0
FE4 A:D6N501 3.8 8.2 1.0
NZ A:LYS83 3.8 10.0 1.0
NH2 A:ARG339 3.8 9.1 1.0
O A:HOH845 3.9 9.5 1.0
S1B A:D6N501 3.9 8.2 1.0
O A:HOH607 4.2 8.7 1.0
CZ A:ARG339 4.3 8.0 1.0
S4A A:D6N501 4.3 8.8 1.0
S2A A:D6N501 4.3 9.0 1.0
O2 A:BCT503 4.5 9.3 1.0
O A:HOH746 4.6 9.9 1.0
O7 A:HCA502 4.6 7.6 1.0
ND1 A:HIS423 4.7 7.6 1.0
NE A:ARG339 4.7 8.7 1.0
C7 A:HCA502 4.8 7.8 1.0
CG1 A:VAL57 4.9 9.8 1.0
NH1 A:ARG339 5.0 8.7 1.0
O1 A:BCT503 5.0 9.2 1.0

Iron binding site 8 out of 32 in 7ady

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Iron binding site 8 out of 32 in the Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein


Mono view


Stereo pair view

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

b:8.4
occ:1.00
 FE1 B:CLF501 0.0 8.4 1.0
S3A B:CLF501 2.3 8.4 1.0
S2A B:CLF501 2.3 8.7 1.0
SG A:CYS138 2.3 9.0 1.0
S1 B:CLF501 2.4 8.4 1.0
FE2 B:CLF501 2.5 8.6 1.0
FE4 B:CLF501 2.6 8.2 1.0
FE3 B:CLF501 2.8 8.4 1.0
CB A:CYS138 3.5 8.7 1.0
S4A B:CLF501 3.8 8.4 1.0
O B:HOH731 3.8 9.7 1.0
N A:CYS138 3.9 8.6 1.0
CA A:GLY170 4.0 12.1 1.0
N A:GLY170 4.0 10.3 1.0
SG B:CYS56 4.1 8.6 1.0
CA A:CYS138 4.3 8.3 1.0
FE8 B:CLF501 4.4 8.9 1.0
SG A:CYS75 4.5 8.2 1.0
FE5 B:CLF501 4.6 8.6 1.0
FE6 B:CLF501 4.8 6.9 0.6
C A:GLY170 4.9 14.5 1.0
SG A:CYS49 4.9 8.9 1.0
SG B:CYS115 5.0 9.4 1.0

Iron binding site 9 out of 32 in 7ady

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Iron binding site 9 out of 32 in the Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein


Mono view


Stereo pair view

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

b:8.6
occ:1.00
 FE2 B:CLF501 0.0 8.6 1.0
S2A B:CLF501 2.3 8.7 1.0
S4A B:CLF501 2.3 8.4 1.0
SG B:CYS56 2.4 8.6 1.0
S1 B:CLF501 2.5 8.4 1.0
FE1 B:CLF501 2.5 8.4 1.0
FE4 B:CLF501 2.6 8.2 1.0
FE3 B:CLF501 2.8 8.4 1.0
FE8 B:CLF501 2.9 8.9 1.0
N B:CYS56 3.3 7.7 1.0
CB B:CYS56 3.7 8.1 1.0
CA B:CYS56 3.7 8.2 1.0
FE5 B:CLF501 3.7 8.6 1.0
S4B B:CLF501 3.8 8.7 1.0
S3A B:CLF501 3.9 8.4 1.0
C B:GLY55 3.9 7.9 1.0
CA B:GLY55 4.2 8.5 1.0
O B:HOH731 4.3 9.7 1.0
N B:GLY55 4.4 8.1 1.0
FE6 B:CLF501 4.5 6.9 0.6
O B:GLY53 4.6 8.9 1.0
SG A:CYS138 4.6 9.0 1.0
SG A:CYS75 4.6 8.2 1.0
O B:GLY55 4.7 8.5 1.0
C B:GLY53 4.8 8.7 1.0
SG A:CYS49 4.8 8.9 1.0
FE6 B:CLF501 5.0 15.2 0.4

Iron binding site 10 out of 32 in 7ady

Go back to Iron Binding Sites List in 7ady
Iron binding site 10 out of 32 in the Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein


Mono view


Stereo pair view

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

b:8.4
occ:1.00
 FE3 B:CLF501 0.0 8.4 1.0
S4A B:CLF501 2.3 8.4 1.0
SG A:CYS49 2.3 8.9 1.0
S2A B:CLF501 2.3 8.7 1.0
S3A B:CLF501 2.3 8.4 1.0
FE4 B:CLF501 2.7 8.2 1.0
FE1 B:CLF501 2.8 8.4 1.0
FE2 B:CLF501 2.8 8.6 1.0
CB A:CYS49 3.3 8.7 1.0
CA A:GLY170 3.9 12.1 1.0
CD2 A:PHE51 4.0 10.2 1.0
CA B:GLY55 4.1 8.5 1.0
CB A:PHE51 4.2 9.3 1.0
S1 B:CLF501 4.3 8.4 1.0
N B:GLY55 4.4 8.1 1.0
N A:GLY170 4.5 10.3 1.0
CG A:PHE51 4.6 8.8 1.0
C B:GLY55 4.7 7.9 1.0
CE2 B:PHE59 4.7 8.1 1.0
CA A:CYS49 4.8 8.4 1.0
N B:CYS56 4.8 7.7 1.0
SG A:CYS138 4.8 9.0 1.0
SG A:CYS75 4.9 8.2 1.0

Reference:

M.Rohde, K.Grunau, O.Einsle. Co Binding to the Fev Cofactor of Co-Reducing Vanadium Nitrogenase at Atomic Resolution. Angew.Chem.Int.Ed.Engl. 2020.
ISSN: ESSN 1521-3773
PubMed: 32915491
DOI: 10.1002/ANIE.202010790
Page generated: Wed Aug 7 22:03:06 2024

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