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Iron in PDB 1vzg: 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: 1vzg 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) 37.49 / 1.69
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.130, 67.650, 82.190, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 24.9

Other elements in 1vzg:

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:

Calcium (Ca) 1 atom

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 1vzg). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 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: 1vzg:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 1vzg

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Iron binding site 1 out of 6 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:Fe1127

b:18.8
occ:0.37
 SG A:CYS10 1.7 11.5 0.3
SG A:CYS29 2.0 10.7 0.3
SG A:CYS13 2.0 20.5 0.4
SG A:CYS10 2.0 12.9 0.4
SG A:CYS29 2.2 9.8 0.4
SG A:CYS30 2.2 15.5 0.4
SG A:CYS29 2.3 18.4 0.3
CB A:CYS13 2.3 10.7 0.6
SG A:CYS30 2.7 10.9 0.6
CB A:CYS13 3.1 17.5 0.4
SG A:CYS13 3.1 11.8 0.6
CB A:CYS10 3.2 10.7 0.3
CB A:CYS30 3.2 12.8 0.6
CB A:CYS10 3.2 15.6 0.3
CB A:CYS10 3.2 9.6 0.4
CB A:CYS30 3.2 13.7 0.4
SG A:CYS10 3.4 18.7 0.3
CB A:CYS29 3.5 11.4 0.4
CA B:GLY25 3.5 17.6 1.0
CB A:CYS29 3.6 11.8 0.3
CB A:CYS29 3.6 15.7 0.3
C A:CYS29 3.6 12.2 0.3
CA A:CYS13 3.6 10.8 0.6
ND2 A:ASN15 3.6 12.7 0.6
N A:CYS30 3.6 13.1 0.6
N A:CYS30 3.6 12.5 0.4
C A:CYS29 3.7 12.2 0.4
C A:CYS29 3.7 13.8 0.3
O A:CYS29 3.9 11.9 0.4
O A:GLU11 3.9 13.9 0.4
N A:CYS13 4.0 12.0 0.6
CA A:CYS30 4.0 12.8 0.4
CA A:CYS30 4.0 12.6 0.6
N B:GLY25 4.0 18.5 1.0
O A:CYS29 4.0 13.5 0.3
CA A:CYS29 4.1 14.6 0.3
N A:CYS13 4.1 16.3 0.4
CA A:CYS29 4.1 12.5 0.3
CA A:CYS29 4.1 12.4 0.4
CA A:CYS13 4.2 16.5 0.4
C A:CYS13 4.2 12.0 0.6
ND2 A:ASN15 4.3 11.7 0.4
C B:GLY25 4.4 18.8 1.0
CG A:ASN15 4.4 9.2 0.4
O A:GLU11 4.4 16.5 0.6
O A:CYS29 4.4 11.7 0.3
CA A:CYS10 4.4 14.7 0.3
CA A:CYS10 4.4 11.8 0.3
CA A:CYS10 4.5 11.1 0.4
O A:CYS10 4.5 11.6 0.4
OD1 A:ASN15 4.5 7.9 0.4
C A:CYS10 4.6 11.2 0.4
N A:GLY14 4.7 15.1 0.4
O A:CYS13 4.7 12.8 0.6
C A:CYS10 4.7 14.6 0.3
C A:CYS10 4.7 11.9 0.3
N A:GLY14 4.8 12.1 0.6
CG A:ASN15 4.8 14.6 0.6
C A:CYS13 4.9 16.7 0.4
CB A:ASN15 4.9 10.6 0.4
O A:CYS10 4.9 15.1 0.3
O B:GLY25 4.9 17.5 1.0
N B:GLU26 5.0 17.8 1.0
N A:ASN15 5.0 11.5 0.4

Iron binding site 2 out of 6 in 1vzg

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Iron binding site 2 out of 6 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:Fe1129

b:18.9
occ:1.00
 ND1 A:HIS119 2.1 14.8 1.0
NE2 A:HIS69 2.2 14.6 1.0
NE2 A:HIS75 2.2 17.9 1.0
NE2 A:HIS49 2.3 16.9 1.0
N24 A:FC61130 2.4 30.6 1.0
SG A:CYS116 2.6 17.5 1.0
CE1 A:HIS119 2.9 17.3 1.0
CE1 A:HIS75 3.1 17.1 1.0
CE1 A:HIS49 3.1 17.3 1.0
CE1 A:HIS69 3.1 15.3 1.0
CD2 A:HIS69 3.2 14.5 1.0
CG A:HIS119 3.3 16.2 1.0
CD2 A:HIS49 3.3 17.2 1.0
CD2 A:HIS75 3.3 18.3 1.0
C24 A:FC61130 3.4 29.3 1.0
CB A:HIS119 3.8 15.7 1.0
CB A:CYS116 3.9 16.0 1.0
NE2 A:HIS119 4.1 17.4 1.0
ND1 A:HIS69 4.3 13.6 1.0
ND1 A:HIS49 4.3 19.1 1.0
ND1 A:HIS75 4.3 18.8 1.0
CD2 A:HIS119 4.3 18.9 1.0
CG A:HIS69 4.3 14.2 1.0
CG A:HIS49 4.4 16.4 1.0
CG A:HIS75 4.4 18.9 1.0
N A:HIS119 4.4 15.7 1.0
CA A:HIS119 4.8 15.4 1.0
C26 A:FC61130 5.0 30.5 1.0

Iron binding site 3 out of 6 in 1vzg

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Iron binding site 3 out of 6 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
A:Fe1130

b:30.5
occ:1.00
 FE2 A:FC61130 0.0 30.5 1.0
C22 A:FC61130 1.9 30.4 1.0
C26 A:FC61130 1.9 30.5 1.0
C23 A:FC61130 1.9 31.1 1.0
C11 A:FC61130 1.9 30.8 1.0
C24 A:FC61130 1.9 29.3 1.0
C21 A:FC61130 1.9 30.0 1.0
N22 A:FC61130 3.0 32.9 1.0
N11 A:FC61130 3.1 32.0 1.0
N23 A:FC61130 3.1 30.3 1.0
N21 A:FC61130 3.1 32.2 1.0
N24 A:FC61130 3.1 30.6 1.0
N25 A:FC61130 3.1 29.6 1.0
CE1 A:HIS119 4.3 17.3 1.0
CE1 A:HIS75 4.5 17.1 1.0
CD A:LYS48 4.6 23.9 1.0
CE1 A:HIS49 4.7 17.3 1.0
NZ A:LYS48 4.8 27.6 1.0
NE2 A:HIS119 4.8 17.4 1.0

Iron binding site 4 out of 6 in 1vzg

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Iron binding site 4 out of 6 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:18.8
occ:0.70
 SG B:CYS29 1.8 16.5 0.3
SG B:CYS10 2.1 18.4 0.7
SG B:CYS13 2.2 20.4 0.7
SG B:CYS29 2.2 14.5 0.7
CB B:CYS13 2.2 23.3 0.3
SG B:CYS30 2.5 21.4 0.7
SG B:CYS30 2.7 22.6 0.3
SG B:CYS10 2.9 16.6 0.3
SG B:CYS13 3.1 24.1 0.3
CB B:CYS10 3.1 18.1 0.7
CB B:CYS10 3.2 17.2 0.3
CB B:CYS30 3.3 20.6 0.3
CB B:CYS30 3.3 18.9 0.7
CB B:CYS29 3.4 16.1 0.7
CB B:CYS13 3.4 21.3 0.7
CB B:CYS29 3.4 16.7 0.3
CA B:CYS13 3.6 23.4 0.3
N B:CYS30 3.6 18.6 0.3
N B:CYS30 3.7 18.1 0.7
C B:CYS29 3.7 16.4 0.7
CA A:GLY25 3.7 24.7 1.0
N B:CYS13 3.7 21.7 0.7
C B:CYS29 3.7 17.3 0.3
ND2 B:ASN15 4.0 21.6 0.3
N B:CYS13 4.0 24.3 0.3
CA B:CYS29 4.0 16.6 0.3
CA B:CYS30 4.1 19.5 0.3
CA B:CYS29 4.1 16.1 0.7
CA B:CYS30 4.1 18.6 0.7
O B:CYS29 4.1 17.3 0.7
CA B:CYS13 4.1 20.5 0.7
C B:CYS13 4.2 22.7 0.3
ND2 B:ASN15 4.2 14.7 0.7
O B:CYS29 4.2 17.7 0.3
O B:CYS13 4.3 22.4 0.3
N A:GLY25 4.4 25.9 1.0
C A:GLY25 4.5 24.1 1.0
CB B:VAL12 4.5 22.5 0.7
CA B:CYS10 4.5 18.0 0.3
CA B:CYS10 4.5 17.6 0.7
C B:VAL12 4.8 22.9 0.7
CG B:ASN15 4.9 16.4 0.7
C B:CYS13 4.9 20.2 0.7
CB B:ASN15 4.9 14.9 0.7
N B:GLY14 5.0 18.0 0.7
C B:CYS10 5.0 19.3 0.7
O A:GLY25 5.0 20.8 1.0

Iron binding site 5 out of 6 in 1vzg

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Iron binding site 5 out of 6 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 5 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:Fe1129

b:22.7
occ:1.00
 FE2 B:FC61129 0.0 22.7 1.0
C22 B:FC61129 1.9 25.6 1.0
C23 B:FC61129 1.9 24.9 1.0
C26 B:FC61129 1.9 25.1 1.0
C11 B:FC61129 1.9 24.1 1.0
C24 B:FC61129 1.9 24.1 1.0
C21 B:FC61129 1.9 24.2 1.0
N22 B:FC61129 3.0 26.3 1.0
N23 B:FC61129 3.1 28.0 1.0
N11 B:FC61129 3.1 25.5 1.0
N21 B:FC61129 3.1 23.7 1.0
N24 B:FC61129 3.1 23.6 1.0
N25 B:FC61129 3.1 24.3 1.0
CE1 B:HIS119 4.4 20.7 1.0
CE1 B:HIS75 4.5 16.2 1.0
CD B:LYS48 4.7 18.6 1.0
CE1 B:HIS49 4.8 14.8 1.0
NE2 B:HIS119 4.9 19.9 1.0

Iron binding site 6 out of 6 in 1vzg

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Iron binding site 6 out of 6 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 6 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:Fe1130

b:17.4
occ:1.00
 ND1 B:HIS119 2.1 19.2 1.0
N24 B:FC61129 2.2 23.6 1.0
NE2 B:HIS69 2.2 12.7 1.0
NE2 B:HIS75 2.2 17.2 1.0
NE2 B:HIS49 2.2 14.3 1.0
SG B:CYS116 2.5 16.1 1.0
CE1 B:HIS119 3.0 20.7 1.0
CE1 B:HIS75 3.1 16.2 1.0
CE1 B:HIS49 3.1 14.8 1.0
CD2 B:HIS69 3.1 13.6 1.0
CE1 B:HIS69 3.2 12.3 1.0
CG B:HIS119 3.2 19.0 1.0
C24 B:FC61129 3.2 24.1 1.0
CD2 B:HIS49 3.3 12.2 1.0
CD2 B:HIS75 3.3 16.2 1.0
CB B:HIS119 3.7 16.4 1.0
CB B:CYS116 3.8 13.6 1.0
NE2 B:HIS119 4.1 19.9 1.0
ND1 B:HIS75 4.3 16.9 1.0
ND1 B:HIS69 4.3 13.6 1.0
CD2 B:HIS119 4.3 21.3 1.0
ND1 B:HIS49 4.3 13.7 1.0
CG B:HIS69 4.3 13.9 1.0
N B:HIS119 4.4 14.8 1.0
CG B:HIS49 4.4 13.9 1.0
CG B:HIS75 4.4 16.6 1.0
CA B:HIS119 4.7 16.1 1.0
C21 B:FC61129 5.0 24.2 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 Photoreduction Structure V. 12 1729 2004.
ISSN: ISSN 0969-2126
PubMed: 15341736
DOI: 10.1016/J.STR.2004.07.013
Page generated: Sat Aug 3 16:23:48 2024

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