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Iron in PDB 1vzi: Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray Induced Photoreduction

Enzymatic activity of Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray Induced Photoreduction

All present enzymatic activity of Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray Induced Photoreduction:
1.15.1.2;

Protein crystallography data

The structure of Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray Induced Photoreduction, PDB code: 1vzi was solved by V.Adam, A.Royant, V.Niviere, F.P.Molina-Heredia, D.Bourgeois, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.00 / 1.15
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 123.608, 123.608, 73.016, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1vzi:

The structure of Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray Induced Photoreduction also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms
Calcium (Ca) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray Induced Photoreduction (pdb code 1vzi). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray Induced Photoreduction, PDB code: 1vzi:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1vzi

Go back to Iron Binding Sites List in 1vzi
Iron binding site 1 out of 4 in the Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray Induced Photoreduction


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray Induced Photoreduction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1131

b:13.2
occ:1.00
 SG A:CYS28 2.3 13.5 1.0
SG A:CYS29 2.3 15.0 1.0
SG A:CYS9 2.3 12.5 1.0
SG A:CYS12 2.4 14.3 1.0
CB A:CYS9 3.2 11.8 1.0
CB A:CYS28 3.3 13.2 1.0
CB A:CYS12 3.3 14.4 1.0
CB A:CYS29 3.4 15.1 1.0
N A:CYS29 3.6 13.5 1.0
C A:CYS28 3.7 12.2 1.0
N A:CYS12 3.8 14.2 1.0
CA B:GLY24 4.0 15.3 1.0
CA A:CYS28 4.0 12.4 1.0
CA A:CYS29 4.0 14.7 1.0
CA A:CYS12 4.1 13.8 1.0
O A:CYS28 4.2 12.9 1.0
ND2 A:ASN14 4.2 13.1 1.0
N B:GLY24 4.4 14.5 1.0
CB A:VAL11 4.6 14.2 1.0
CA A:CYS9 4.7 11.3 1.0
C B:GLY24 4.7 14.4 1.0
C A:CYS12 4.7 13.4 1.0
CB A:ASN14 4.8 11.6 1.0
N A:GLY13 4.8 13.5 1.0
CG A:ASN14 4.8 12.9 1.0
C A:VAL11 4.9 13.1 1.0

Iron binding site 2 out of 4 in 1vzi

Go back to Iron Binding Sites List in 1vzi
Iron binding site 2 out of 4 in the Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray Induced Photoreduction


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray Induced Photoreduction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1132

b:11.9
occ:1.00
 NE2 A:HIS68 2.1 11.2 1.0
ND1 A:HIS118 2.2 11.2 1.0
NE2 A:HIS48 2.2 11.7 1.0
NE2 A:HIS74 2.2 11.7 1.0
SG A:CYS115 2.4 11.0 1.0
CE1 A:HIS68 3.0 11.6 1.0
CE1 A:HIS48 3.1 11.8 1.0
CE1 A:HIS118 3.1 12.2 1.0
CE1 A:HIS74 3.1 13.1 1.0
CG A:HIS118 3.2 11.5 1.0
CD2 A:HIS68 3.3 11.4 1.0
CD2 A:HIS48 3.3 11.4 1.0
CD2 A:HIS74 3.3 12.2 1.0
CB A:CYS115 3.5 11.0 1.0
CB A:HIS118 3.5 11.7 1.0
ND1 A:HIS68 4.2 11.5 1.0
N A:HIS118 4.2 11.7 1.0
CL A:CL1128 4.2 19.6 1.0
ND1 A:HIS48 4.3 12.2 1.0
ND1 A:HIS74 4.3 12.9 1.0
NE2 A:HIS118 4.3 11.9 1.0
CD2 A:HIS118 4.3 12.9 1.0
CG A:HIS68 4.3 10.7 1.0
CG A:HIS48 4.4 10.8 1.0
CG A:HIS74 4.4 12.8 1.0
CA A:HIS118 4.5 11.1 1.0
CB A:ILE117 4.8 14.4 1.0
CA A:CYS115 4.9 10.5 1.0
CD1 A:ILE76 4.9 11.9 1.0

Iron binding site 3 out of 4 in 1vzi

Go back to Iron Binding Sites List in 1vzi
Iron binding site 3 out of 4 in the Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray Induced Photoreduction


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray Induced Photoreduction within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1127

b:14.4
occ:1.00
 SG B:CYS9 2.3 14.1 1.0
SG B:CYS29 2.3 16.7 1.0
SG B:CYS28 2.3 14.5 1.0
SG B:CYS12 2.3 13.8 1.0
CB B:CYS9 3.2 13.4 1.0
CB B:CYS28 3.3 14.2 1.0
CB B:CYS29 3.3 17.2 1.0
CB B:CYS12 3.4 15.5 1.0
N B:CYS29 3.6 16.9 1.0
C B:CYS28 3.7 14.9 1.0
N B:CYS12 3.7 14.5 1.0
CA A:GLY24 3.8 15.4 1.0
CA B:CYS28 4.0 14.4 1.0
CA B:CYS29 4.1 17.4 1.0
CA B:CYS12 4.1 14.7 1.0
O B:CYS28 4.1 15.7 1.0
ND2 B:ASN14 4.2 12.4 1.0
N A:GLY24 4.4 13.7 1.0
CA B:CYS9 4.6 14.4 1.0
CB B:VAL11 4.7 18.2 1.0
C A:GLY24 4.7 12.5 1.0
C B:CYS12 4.8 12.7 1.0
CG B:ASN14 4.8 12.5 1.0
CB B:ASN14 4.8 11.6 1.0
C B:VAL11 4.9 14.3 1.0
N B:GLY13 4.9 12.9 1.0
O B:HOH2088 5.0 14.6 1.0

Iron binding site 4 out of 4 in 1vzi

Go back to Iron Binding Sites List in 1vzi
Iron binding site 4 out of 4 in the Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray Induced Photoreduction


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray Induced Photoreduction within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1128

b:14.6
occ:1.00
 NE2 B:HIS48 2.2 13.7 1.0
NE2 B:HIS68 2.2 14.3 1.0
ND1 B:HIS118 2.2 14.4 1.0
NE2 B:HIS74 2.2 14.9 1.0
SG B:CYS115 2.4 13.6 1.0
CE1 B:HIS68 3.0 14.1 1.0
CE1 B:HIS48 3.1 14.2 1.0
CE1 B:HIS74 3.2 14.9 1.0
CE1 B:HIS118 3.2 16.1 1.0
CG B:HIS118 3.2 14.4 1.0
CD2 B:HIS74 3.2 14.0 1.0
CD2 B:HIS68 3.3 14.7 1.0
CD2 B:HIS48 3.3 13.8 1.0
CB B:CYS115 3.5 14.0 1.0
CB B:HIS118 3.5 14.6 1.0
N B:HIS118 4.2 13.8 1.0
ND1 B:HIS48 4.2 13.8 1.0
ND1 B:HIS68 4.2 14.1 1.0
NE2 B:HIS118 4.3 16.2 1.0
ND1 B:HIS74 4.3 13.7 1.0
CG B:HIS68 4.3 15.2 1.0
CG B:HIS48 4.4 13.7 1.0
CG B:HIS74 4.4 14.7 1.0
CD2 B:HIS118 4.4 16.4 1.0
CL B:CL1126 4.4 22.3 0.5
CA B:HIS118 4.5 13.9 1.0
CA B:CYS115 4.9 12.5 1.0
CD1 B:ILE76 4.9 13.2 1.0
CB B:ILE117 5.0 15.7 1.0

Reference:

V.Adam, A.Royant, V.Niviere, F.P.Molina-Heredia, D.Bourgeois. Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray-Induced Photo-Reduction. Structure V. 12 1729 2004.
ISSN: ISSN 0969-2126
PubMed: 15341736
DOI: 10.1016/J.STR.2004.07.013
Page generated: Sat Aug 3 16:23:59 2024

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