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Iron in PDB 4tku: Reactivated Nitrogenase Mofe-Protein From A. Vinelandii

Enzymatic activity of Reactivated Nitrogenase Mofe-Protein From A. Vinelandii

All present enzymatic activity of Reactivated Nitrogenase Mofe-Protein From A. Vinelandii:
1.18.6.1;

Protein crystallography data

The structure of Reactivated Nitrogenase Mofe-Protein From A. Vinelandii, PDB code: 4tku was solved by T.Spatzal, K.Perez, O.Einsle, J.B.Howard, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.65 / 1.43
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.941, 130.785, 107.005, 90.00, 110.58, 90.00
R / Rfree (%) 13.2 / 14.2

Other elements in 4tku:

The structure of Reactivated Nitrogenase Mofe-Protein From A. Vinelandii also contains other interesting chemical elements:

Molybdenum (Mo) 2 atoms
Chlorine (Cl) 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 Reactivated Nitrogenase Mofe-Protein From A. Vinelandii (pdb code 4tku). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 32 binding sites of Iron where determined in the Reactivated Nitrogenase Mofe-Protein From A. Vinelandii, PDB code: 4tku:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 32 in 4tku

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Iron binding site 1 out of 32 in the Reactivated Nitrogenase Mofe-Protein From A. Vinelandii


Mono view


Stereo pair view

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

b:9.1
occ:1.00
 FE1 A:ICS502 0.0 9.1 1.0
S2A A:ICS502 2.2 8.9 1.0
SG A:CYS275 2.3 8.7 1.0
S4A A:ICS502 2.3 8.9 1.0
S1A A:ICS502 2.3 8.9 1.0
FE4 A:ICS502 2.7 8.8 1.0
FE3 A:ICS502 2.7 8.6 1.0
FE2 A:ICS502 2.7 8.4 1.0
CB A:CYS275 3.3 8.6 1.0
CX A:ICS502 3.5 8.3 1.0
OG A:SER278 4.1 8.1 1.0
CB A:LEU358 4.1 8.6 1.0
CB A:SER278 4.4 8.1 1.0
CA A:CYS275 4.5 8.2 1.0
CE2 A:TYR229 4.5 8.2 1.0
CD2 A:LEU358 4.7 9.2 1.0
S2B A:ICS502 4.8 8.8 1.0
S3A A:ICS502 4.8 8.8 1.0
S5A A:ICS502 4.8 8.6 1.0
N A:SER278 4.9 8.5 1.0
CD2 A:TYR229 5.0 8.2 1.0
N A:LEU358 5.0 8.4 1.0
FE7 A:ICS502 5.0 8.1 1.0

Iron binding site 2 out of 32 in 4tku

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Iron binding site 2 out of 32 in the Reactivated Nitrogenase Mofe-Protein From A. Vinelandii


Mono view


Stereo pair view

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

b:8.4
occ:1.00
 FE2 A:ICS502 0.0 8.4 1.0
CX A:ICS502 2.0 8.3 1.0
S2B A:ICS502 2.2 8.8 1.0
S2A A:ICS502 2.2 8.9 1.0
S1A A:ICS502 2.2 8.9 1.0
FE6 A:ICS502 2.6 8.2 1.0
FE4 A:ICS502 2.6 8.8 1.0
FE3 A:ICS502 2.7 8.6 1.0
FE1 A:ICS502 2.7 9.1 1.0
FE7 A:ICS502 3.7 8.1 1.0
FE5 A:ICS502 3.7 8.5 1.0
S4A A:ICS502 3.9 8.9 1.0
CZ A:PHE381 4.0 8.7 1.0
NE2 A:HIS195 4.1 9.6 1.0
S1B A:ICS502 4.2 8.4 1.0
S3B A:ICS502 4.2 8.1 1.0
CE1 A:HIS195 4.2 9.0 1.0
CG1 A:VAL70 4.5 11.6 1.0
S3A A:ICS502 4.5 8.8 1.0
S5A A:ICS502 4.5 8.6 1.0
CE1 A:PHE381 4.5 8.9 1.0
SG A:CYS275 4.6 8.7 1.0
CG2 A:VAL70 5.0 10.7 1.0
N A:GLY357 5.0 8.3 1.0

Iron binding site 3 out of 32 in 4tku

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Iron binding site 3 out of 32 in the Reactivated Nitrogenase Mofe-Protein From A. Vinelandii


Mono view


Stereo pair view

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

b:8.6
occ:1.00
 FE3 A:ICS502 0.0 8.6 1.0
CX A:ICS502 2.0 8.3 1.0
S5A A:ICS502 2.2 8.6 1.0
S4A A:ICS502 2.2 8.9 1.0
S2A A:ICS502 2.3 8.9 1.0
FE7 A:ICS502 2.6 8.1 1.0
FE4 A:ICS502 2.6 8.8 1.0
FE2 A:ICS502 2.7 8.4 1.0
FE1 A:ICS502 2.7 9.1 1.0
FE6 A:ICS502 3.7 8.2 1.0
FE5 A:ICS502 3.7 8.5 1.0
S1A A:ICS502 3.8 8.9 1.0
O A:HOH689 4.1 9.5 1.0
NH2 A:ARG96 4.1 8.7 1.0
CD2 A:TYR229 4.2 8.2 1.0
S3B A:ICS502 4.2 8.1 1.0
S4B A:ICS502 4.2 8.2 1.0
S2B A:ICS502 4.5 8.8 1.0
CE2 A:TYR229 4.5 8.2 1.0
S3A A:ICS502 4.5 8.8 1.0
SG A:CYS275 4.8 8.7 1.0

Iron binding site 4 out of 32 in 4tku

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Iron binding site 4 out of 32 in the Reactivated Nitrogenase Mofe-Protein From A. Vinelandii


Mono view


Stereo pair view

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

b:8.8
occ:1.00
 FE4 A:ICS502 0.0 8.8 1.0
CX A:ICS502 2.0 8.3 1.0
S3A A:ICS502 2.2 8.8 1.0
S1A A:ICS502 2.3 8.9 1.0
S4A A:ICS502 2.3 8.9 1.0
FE5 A:ICS502 2.6 8.5 1.0
FE2 A:ICS502 2.6 8.4 1.0
FE3 A:ICS502 2.6 8.6 1.0
FE1 A:ICS502 2.7 9.1 1.0
FE7 A:ICS502 3.7 8.1 1.0
FE6 A:ICS502 3.7 8.2 1.0
S2A A:ICS502 3.8 8.9 1.0
N A:LEU358 4.0 8.4 1.0
N A:GLY357 4.0 8.3 1.0
CB A:LEU358 4.1 8.6 1.0
S4B A:ICS502 4.2 8.2 1.0
S1B A:ICS502 4.3 8.4 1.0
S5A A:ICS502 4.5 8.6 1.0
S2B A:ICS502 4.5 8.8 1.0
N A:ARG359 4.6 7.6 1.0
CA A:LEU358 4.6 7.7 1.0
C A:GLY357 4.6 9.4 1.0
SG A:CYS275 4.6 8.7 1.0
CA A:GLY357 4.7 8.7 1.0
CG A:ARG359 4.8 7.4 1.0
CD A:ARG359 4.9 7.8 1.0
CA A:GLY356 4.9 8.2 1.0
C A:GLY356 5.0 8.3 1.0

Iron binding site 5 out of 32 in 4tku

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Iron binding site 5 out of 32 in the Reactivated Nitrogenase Mofe-Protein From A. Vinelandii


Mono view


Stereo pair view

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

b:8.5
occ:1.00
 FE5 A:ICS502 0.0 8.5 1.0
CX A:ICS502 2.0 8.3 1.0
S4B A:ICS502 2.2 8.2 1.0
S1B A:ICS502 2.3 8.4 1.0
S3A A:ICS502 2.3 8.8 1.0
FE4 A:ICS502 2.6 8.8 1.0
FE7 A:ICS502 2.6 8.1 1.0
FE6 A:ICS502 2.6 8.2 1.0
MO1 A:ICS502 2.7 8.1 1.0
FE2 A:ICS502 3.7 8.4 1.0
FE3 A:ICS502 3.7 8.6 1.0
ND1 A:HIS442 3.8 7.8 1.0
S3B A:ICS502 3.9 8.1 1.0
N A:GLY356 4.1 8.2 1.0
CG2 A:ILE355 4.1 8.4 1.0
CA A:GLY356 4.2 8.2 1.0
CE1 A:HIS442 4.2 8.3 1.0
S1A A:ICS502 4.3 8.9 1.0
S4A A:ICS502 4.4 8.9 1.0
S2B A:ICS502 4.5 8.8 1.0
S5A A:ICS502 4.5 8.6 1.0
O7 A:HCA501 4.7 7.7 1.0
CG A:HIS442 4.7 7.7 1.0
N A:GLY357 4.7 8.3 1.0
O5 A:HCA501 4.7 8.0 1.0
CD A:ARG359 4.8 7.8 1.0
CZ A:PHE381 5.0 8.7 1.0

Iron binding site 6 out of 32 in 4tku

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Iron binding site 6 out of 32 in the Reactivated Nitrogenase Mofe-Protein From A. Vinelandii


Mono view


Stereo pair view

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

b:8.2
occ:1.00
 FE6 A:ICS502 0.0 8.2 1.0
CX A:ICS502 2.0 8.3 1.0
S2B A:ICS502 2.2 8.8 1.0
S1B A:ICS502 2.2 8.4 1.0
S3B A:ICS502 2.2 8.1 1.0
FE2 A:ICS502 2.6 8.4 1.0
FE7 A:ICS502 2.6 8.1 1.0
FE5 A:ICS502 2.6 8.5 1.0
MO1 A:ICS502 2.7 8.1 1.0
FE3 A:ICS502 3.7 8.6 1.0
FE4 A:ICS502 3.7 8.8 1.0
O7 A:HCA501 3.8 7.7 1.0
S4B A:ICS502 3.8 8.2 1.0
CZ A:PHE381 4.1 8.7 1.0
S2A A:ICS502 4.3 8.9 1.0
S1A A:ICS502 4.3 8.9 1.0
CG2 A:VAL70 4.4 10.7 1.0
S5A A:ICS502 4.5 8.6 1.0
O5 A:HCA501 4.5 8.0 1.0
S3A A:ICS502 4.5 8.8 1.0
CE2 A:PHE381 4.6 8.8 1.0
O1 A:HCA501 4.6 10.0 1.0
ND1 A:HIS442 4.7 7.8 1.0
C3 A:HCA501 4.8 7.3 1.0

Iron binding site 7 out of 32 in 4tku

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Iron binding site 7 out of 32 in the Reactivated Nitrogenase Mofe-Protein From A. Vinelandii


Mono view


Stereo pair view

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

b:8.1
occ:1.00
 FE7 A:ICS502 0.0 8.1 1.0
CX A:ICS502 2.0 8.3 1.0
S5A A:ICS502 2.2 8.6 1.0
S4B A:ICS502 2.2 8.2 1.0
S3B A:ICS502 2.2 8.1 1.0
FE3 A:ICS502 2.6 8.6 1.0
FE6 A:ICS502 2.6 8.2 1.0
FE5 A:ICS502 2.6 8.5 1.0
MO1 A:ICS502 2.7 8.1 1.0
FE2 A:ICS502 3.7 8.4 1.0
FE4 A:ICS502 3.7 8.8 1.0
O A:HOH643 3.7 10.6 1.0
O5 A:HCA501 3.7 8.0 1.0
S1B A:ICS502 3.8 8.4 1.0
NE A:ARG96 4.1 9.2 1.0
NH2 A:ARG96 4.2 8.7 1.0
S2A A:ICS502 4.3 8.9 1.0
S4A A:ICS502 4.3 8.9 1.0
S2B A:ICS502 4.4 8.8 1.0
S3A A:ICS502 4.5 8.8 1.0
O7 A:HCA501 4.6 7.7 1.0
CZ A:ARG96 4.7 8.3 1.0
ND1 A:HIS442 4.7 7.8 1.0
C7 A:HCA501 4.7 7.5 1.0
NH1 A:ARG359 4.8 7.9 1.0
CZ A:ARG359 4.8 8.1 1.0
FE1 A:ICS502 5.0 9.1 1.0

Iron binding site 8 out of 32 in 4tku

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Iron binding site 8 out of 32 in the Reactivated Nitrogenase Mofe-Protein From A. Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Reactivated Nitrogenase Mofe-Protein From A. Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:8.3
occ:1.00
 FE1 B:CLF601 0.0 8.3 1.0
S3A B:CLF601 2.3 8.4 1.0
S2A B:CLF601 2.3 8.6 1.0
SG B:CYS95 2.3 8.1 1.0
S1 B:CLF601 2.5 8.3 1.0
FE2 B:CLF601 2.5 8.4 1.0
FE4 B:CLF601 2.6 8.3 1.0
FE3 B:CLF601 2.8 8.6 1.0
FE8 B:CLF601 2.9 8.4 1.0
N B:CYS95 3.3 6.9 1.0
CB B:CYS95 3.5 7.1 1.0
CA B:CYS95 3.6 7.1 1.0
FE5 B:CLF601 3.8 8.9 1.0
S4A B:CLF601 3.8 8.2 1.0
S4B B:CLF601 4.0 8.2 1.0
C B:GLY94 4.0 7.5 1.0
O B:HOH750 4.4 11.3 1.0
CA B:GLY94 4.5 7.7 1.0
SG A:CYS154 4.5 8.7 1.0
CB B:SER92 4.6 10.8 1.0
FE6 B:CLF601 4.6 9.6 1.0
SG A:CYS88 4.6 8.4 1.0
O B:GLY94 4.7 7.8 1.0
SG A:CYS62 4.7 8.9 1.0
N B:GLY94 4.9 7.5 1.0
O B:SER92 4.9 9.3 1.0

Iron binding site 9 out of 32 in 4tku

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Iron binding site 9 out of 32 in the Reactivated Nitrogenase Mofe-Protein From A. Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Reactivated Nitrogenase Mofe-Protein From A. Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:8.4
occ:1.00
 FE2 B:CLF601 0.0 8.4 1.0
S4A B:CLF601 2.3 8.2 1.0
S2A B:CLF601 2.3 8.6 1.0
SG A:CYS154 2.3 8.7 1.0
S1 B:CLF601 2.5 8.3 1.0
FE1 B:CLF601 2.5 8.3 1.0
FE4 B:CLF601 2.6 8.3 1.0
FE3 B:CLF601 2.8 8.6 1.0
CB A:CYS154 3.4 8.3 1.0
S3A B:CLF601 3.8 8.4 1.0
O B:HOH750 3.8 11.3 1.0
N A:CYS154 3.8 7.8 1.0
CA A:GLY185 4.0 9.4 1.0
N A:GLY185 4.1 8.9 1.0
CA A:CYS154 4.2 7.8 1.0
SG B:CYS95 4.2 8.1 1.0
FE8 B:CLF601 4.4 8.4 1.0
FE5 B:CLF601 4.5 8.9 1.0
CB B:SER92 4.6 10.8 1.0
SG A:CYS88 4.6 8.4 1.0
OG B:SER92 4.7 11.3 0.6
C A:GLY185 4.7 10.0 1.0
FE6 B:CLF601 4.8 9.6 1.0
SG A:CYS62 4.9 8.9 1.0
SG B:CYS153 4.9 9.8 1.0
C A:GLU153 5.0 8.3 1.0

Iron binding site 10 out of 32 in 4tku

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Iron binding site 10 out of 32 in the Reactivated Nitrogenase Mofe-Protein From A. Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Reactivated Nitrogenase Mofe-Protein From A. Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:8.6
occ:1.00
 FE3 B:CLF601 0.0 8.6 1.0
S3A B:CLF601 2.2 8.4 1.0
SG A:CYS62 2.3 8.9 1.0
S2A B:CLF601 2.3 8.6 1.0
S4A B:CLF601 2.3 8.2 1.0
FE4 B:CLF601 2.7 8.3 1.0
FE1 B:CLF601 2.8 8.3 1.0
FE2 B:CLF601 2.8 8.4 1.0
CB A:CYS62 3.4 7.7 1.0
CA A:GLY185 3.9 9.4 1.0
CB A:TYR64 4.1 8.0 1.0
S1 B:CLF601 4.2 8.3 1.0
CA B:GLY94 4.4 7.7 1.0
N A:GLY185 4.5 8.9 1.0
C B:GLY94 4.5 7.5 1.0
CD1 A:TYR64 4.6 7.1 1.0
CG A:TYR64 4.6 7.8 1.0
N B:CYS95 4.7 6.9 1.0
O B:HOH808 4.8 11.4 1.0
CA A:CYS62 4.8 7.4 1.0
SG A:CYS154 4.8 8.7 1.0
N A:TYR64 4.9 8.6 1.0
SG A:CYS88 4.9 8.4 1.0
CE2 B:TYR98 5.0 9.2 1.0
SG B:CYS95 5.0 8.1 1.0

Reference:

T.Spatzal, K.A.Perez, O.Einsle, J.B.Howard, D.C.Rees. Ligand Binding to the Femo-Cofactor: Structures of Co-Bound and Reactivated Nitrogenase. Science V. 345 1620 2014.
ISSN: ESSN 1095-9203
PubMed: 25258081
DOI: 10.1126/SCIENCE.1256679
Page generated: Sun Dec 13 15:46:49 2020

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