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Iron in PDB 2ji1: X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii

Enzymatic activity of X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii

All present enzymatic activity of X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii:
1.15.1.2;

Protein crystallography data

The structure of X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii, PDB code: 2ji1 was solved by G.Katona, P.Carpentier, V.Niviere, P.Amara, V.Adam, J.Ohana, N.Tsanov, D.Bourgeois, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.81 / 1.70
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 70.393, 82.985, 204.349, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 23.4

Other elements in 2ji1:

The structure of X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii (pdb code 2ji1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii, PDB code: 2ji1:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 2ji1

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Iron binding site 1 out of 8 in the X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1127

b:14.2
occ:1.00
 SG A:CYS10 2.2 12.8 1.0
SG A:CYS13 2.3 13.6 1.0
SG A:CYS29 2.3 12.7 1.0
SG A:CYS30 2.3 13.5 1.0
CB A:CYS10 3.1 9.9 1.0
CB A:CYS30 3.3 12.9 1.0
CB A:CYS13 3.3 12.8 1.0
CB A:CYS29 3.3 9.6 1.0
N A:CYS30 3.6 12.2 1.0
N A:CYS13 3.7 12.3 1.0
C A:CYS29 3.7 13.2 1.0
CA B:GLY25 3.9 15.0 1.0
CA A:CYS30 4.0 13.4 1.0
CA A:CYS13 4.0 12.2 1.0
CA A:CYS29 4.1 12.5 1.0
O A:CYS29 4.2 11.9 1.0
ND2 A:ASN15 4.4 11.0 1.0
N B:GLY25 4.5 15.2 1.0
CB A:VAL12 4.6 13.3 1.0
CA A:CYS10 4.6 9.6 1.0
C B:GLY25 4.7 15.2 1.0
C A:VAL12 4.8 11.8 1.0
C A:CYS13 4.8 12.2 1.0
CG A:ASN15 4.8 11.9 1.0
N A:GLY14 4.9 12.4 1.0
CB A:ASN15 4.9 12.1 1.0

Iron binding site 2 out of 8 in 2ji1

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Iron binding site 2 out of 8 in the X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1130

b:14.8
occ:1.00
 ND1 A:HIS119 2.1 13.2 1.0
NE2 A:HIS75 2.1 17.1 1.0
NE2 A:HIS49 2.2 14.8 1.0
NE2 A:HIS69 2.2 11.6 1.0
SG A:CYS116 2.4 12.9 1.0
CE1 A:HIS119 3.0 14.7 1.0
CE1 A:HIS75 3.0 16.9 1.0
CE1 A:HIS49 3.1 15.9 1.0
CE1 A:HIS69 3.1 13.4 1.0
CG A:HIS119 3.2 14.6 1.0
CD2 A:HIS49 3.2 12.9 1.0
CD2 A:HIS69 3.2 10.0 1.0
CD2 A:HIS75 3.2 17.3 1.0
CB A:HIS119 3.6 14.4 1.0
CB A:CYS116 3.6 10.8 1.0
NE2 A:HIS119 4.2 15.2 1.0
N A:HIS119 4.2 13.8 1.0
ND1 A:HIS75 4.2 18.1 1.0
ND1 A:HIS49 4.2 13.3 1.0
ND1 A:HIS69 4.2 11.5 1.0
CD2 A:HIS119 4.3 14.8 1.0
CG A:HIS75 4.3 17.7 1.0
CG A:HIS49 4.3 14.1 1.0
CG A:HIS69 4.3 11.7 1.0
CA A:HIS119 4.5 13.7 1.0
O A:HOH2108 4.6 26.8 1.0
CB A:ILE118 4.8 15.6 1.0
CA A:CYS116 4.9 11.3 1.0

Iron binding site 3 out of 8 in 2ji1

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Iron binding site 3 out of 8 in the X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1127

b:13.2
occ:1.00
 SG B:CYS13 2.3 13.1 1.0
SG B:CYS30 2.3 14.1 1.0
SG B:CYS10 2.3 13.6 1.0
SG B:CYS29 2.3 13.5 1.0
CB B:CYS10 3.2 12.3 1.0
CB B:CYS13 3.2 12.7 1.0
CB B:CYS30 3.3 13.8 1.0
CB B:CYS29 3.3 8.8 1.0
N B:CYS30 3.6 12.6 1.0
N B:CYS13 3.7 14.2 1.0
C B:CYS29 3.7 13.5 1.0
CA B:CYS13 4.0 13.3 1.0
CA B:CYS30 4.1 14.7 1.0
CA B:CYS29 4.1 12.2 1.0
CA A:GLY25 4.1 14.9 1.0
O B:CYS29 4.1 12.0 1.0
ND2 B:ASN15 4.3 10.6 1.0
N A:GLY25 4.5 15.4 1.0
CB B:VAL12 4.6 14.8 1.0
CA B:CYS10 4.6 11.5 1.0
C A:GLY25 4.7 14.6 1.0
C B:CYS13 4.7 13.2 1.0
C B:VAL12 4.8 15.1 1.0
N B:GLY14 4.8 13.5 1.0
CG B:ASN15 4.9 13.4 1.0
O B:HOH2100 5.0 12.5 1.0

Iron binding site 4 out of 8 in 2ji1

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Iron binding site 4 out of 8 in the X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1128

b:13.5
occ:1.00
 ND1 B:HIS119 2.1 8.8 1.0
NE2 B:HIS69 2.2 10.5 1.0
NE2 B:HIS75 2.2 9.7 1.0
NE2 B:HIS49 2.2 10.1 1.0
SG B:CYS116 2.4 12.7 1.0
CE1 B:HIS119 2.9 12.1 1.0
CE1 B:HIS69 3.1 12.0 1.0
CE1 B:HIS75 3.1 10.4 1.0
CE1 B:HIS49 3.1 12.1 1.0
CG B:HIS119 3.2 11.5 1.0
CD2 B:HIS69 3.2 11.4 1.0
CD2 B:HIS49 3.3 11.4 1.0
CD2 B:HIS75 3.3 11.2 1.0
CB B:CYS116 3.6 12.3 1.0
CB B:HIS119 3.6 11.4 1.0
NE2 B:HIS119 4.1 14.8 1.0
N B:HIS119 4.2 13.3 1.0
O B:HOH2066 4.2 30.6 1.0
CD2 B:HIS119 4.2 12.8 1.0
ND1 B:HIS69 4.3 12.1 1.0
ND1 B:HIS75 4.3 12.9 1.0
ND1 B:HIS49 4.3 9.8 1.0
CG B:HIS69 4.3 12.1 1.0
CG B:HIS49 4.4 10.6 1.0
CG B:HIS75 4.4 11.4 1.0
CA B:HIS119 4.5 12.4 1.0
CB B:ILE118 4.7 14.8 1.0
CA B:CYS116 4.9 13.1 1.0

Iron binding site 5 out of 8 in 2ji1

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Iron binding site 5 out of 8 in the X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1127

b:15.1
occ:1.00
 SG C:CYS13 2.3 12.9 1.0
SG C:CYS10 2.3 13.7 1.0
SG C:CYS29 2.3 14.5 1.0
SG C:CYS30 2.3 15.5 1.0
CB C:CYS10 3.2 10.3 1.0
CB C:CYS30 3.3 15.0 1.0
CB C:CYS13 3.3 15.0 1.0
CB C:CYS29 3.4 12.5 1.0
N C:CYS30 3.6 15.5 1.0
N C:CYS13 3.7 15.2 1.0
C C:CYS29 3.7 14.5 1.0
CA D:GLY25 4.0 16.5 1.0
CA C:CYS30 4.0 15.5 1.0
CA C:CYS13 4.1 14.3 1.0
O C:CYS29 4.1 14.6 1.0
CA C:CYS29 4.1 14.1 1.0
ND2 C:ASN15 4.1 15.2 1.0
N D:GLY25 4.5 17.0 1.0
CB C:VAL12 4.6 15.0 1.0
CA C:CYS10 4.6 10.6 1.0
C D:GLY25 4.7 15.4 1.0
C C:VAL12 4.8 15.1 1.0
CG C:ASN15 4.8 14.6 1.0
C C:CYS13 4.8 14.9 1.0
CB C:ASN15 4.9 11.6 1.0
N C:GLY14 4.9 14.2 1.0

Iron binding site 6 out of 8 in 2ji1

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Iron binding site 6 out of 8 in the X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1130

b:18.8
occ:1.00
 ND1 C:HIS119 2.2 19.3 1.0
NE2 C:HIS49 2.2 18.3 1.0
NE2 C:HIS69 2.2 15.4 1.0
NE2 C:HIS75 2.3 22.2 1.0
SG C:CYS116 2.4 16.4 1.0
CE1 C:HIS49 3.1 16.8 1.0
CE1 C:HIS119 3.1 18.0 1.0
CE1 C:HIS69 3.2 15.8 1.0
CE1 C:HIS75 3.2 20.6 1.0
CD2 C:HIS69 3.2 14.3 1.0
CG C:HIS119 3.2 19.0 1.0
CD2 C:HIS49 3.2 17.6 1.0
CD2 C:HIS75 3.3 21.1 1.0
CB C:CYS116 3.5 16.6 1.0
CB C:HIS119 3.6 16.6 1.0
N C:HIS119 4.2 16.8 1.0
ND1 C:HIS49 4.2 18.2 1.0
NE2 C:HIS119 4.2 20.2 1.0
ND1 C:HIS69 4.3 13.9 1.0
CD2 C:HIS119 4.3 17.7 1.0
CG C:HIS49 4.3 17.2 1.0
ND1 C:HIS75 4.4 21.6 1.0
CG C:HIS69 4.4 16.3 1.0
O C:HOH2038 4.4 31.9 1.0
CG C:HIS75 4.4 22.4 1.0
CA C:HIS119 4.5 16.5 1.0
CB C:ILE118 4.8 17.9 1.0
CA C:CYS116 4.9 14.1 1.0

Iron binding site 7 out of 8 in 2ji1

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Iron binding site 7 out of 8 in the X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1127

b:14.0
occ:1.00
 SG D:CYS13 2.2 13.9 1.0
SG D:CYS10 2.3 15.9 1.0
SG D:CYS30 2.3 14.6 1.0
SG D:CYS29 2.3 14.4 1.0
CB D:CYS10 3.2 14.4 1.0
CB D:CYS13 3.3 16.4 1.0
CB D:CYS30 3.3 15.3 1.0
CB D:CYS29 3.3 14.1 1.0
N D:CYS30 3.6 15.2 1.0
N D:CYS13 3.7 16.0 1.0
C D:CYS29 3.7 14.8 1.0
CA C:GLY25 3.9 15.8 1.0
CA D:CYS13 4.0 15.5 1.0
CA D:CYS30 4.1 16.2 1.0
O D:CYS29 4.1 14.8 1.0
CA D:CYS29 4.1 13.5 1.0
ND2 D:ASN15 4.3 13.2 1.0
N C:GLY25 4.4 14.7 1.0
CB D:VAL12 4.5 17.1 1.0
CA D:CYS10 4.6 13.2 1.0
C C:GLY25 4.6 13.6 1.0
C D:VAL12 4.7 17.8 1.0
C D:CYS13 4.8 15.5 1.0
CG D:ASN15 4.9 11.9 1.0
CB D:ASN15 4.9 12.0 1.0
N D:GLY14 4.9 15.6 1.0

Iron binding site 8 out of 8 in 2ji1

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Iron binding site 8 out of 8 in the X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of X-Ray Structure of Wild-Type Superoxide Reductase From Desulfoarculus Baarsii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1128

b:17.8
occ:1.00
 ND1 D:HIS119 2.1 17.1 1.0
NE2 D:HIS69 2.2 14.8 1.0
NE2 D:HIS49 2.2 16.7 1.0
NE2 D:HIS75 2.3 19.1 1.0
SG D:CYS116 2.4 17.2 1.0
CE1 D:HIS119 2.9 19.6 1.0
CD2 D:HIS69 3.2 17.3 1.0
CE1 D:HIS69 3.2 15.2 1.0
CG D:HIS119 3.2 17.4 1.0
CE1 D:HIS49 3.2 18.1 1.0
CE1 D:HIS75 3.2 21.5 1.0
CD2 D:HIS49 3.2 17.6 1.0
CD2 D:HIS75 3.3 22.0 1.0
CB D:CYS116 3.6 16.7 1.0
CB D:HIS119 3.6 15.7 1.0
O D:HOH2054 3.9 30.6 1.0
NE2 D:HIS119 4.1 19.6 1.0
N D:HIS119 4.1 16.1 1.0
CD2 D:HIS119 4.2 18.6 1.0
ND1 D:HIS69 4.3 17.2 1.0
ND1 D:HIS49 4.3 15.9 1.0
CG D:HIS69 4.3 17.8 1.0
ND1 D:HIS75 4.4 21.0 1.0
CG D:HIS49 4.4 17.0 1.0
CG D:HIS75 4.4 21.1 1.0
CA D:HIS119 4.6 15.7 1.0
CB D:ILE118 4.7 19.3 1.0
CA D:CYS116 5.0 16.3 1.0

Reference:

G.Katona, P.Carpentier, V.Niviere, P.Amara, V.Adam, J.Ohana, N.Tsanov, D.Bourgeois. Raman-Assisted Crystallography Reveals End-on Peroxide Intermediates in A Nonheme Iron Enzyme. Science V. 316 449 2007.
ISSN: ESSN 1095-9203
PubMed: 17446401
DOI: 10.1126/SCIENCE.1138885
Page generated: Sat Aug 3 23:40:32 2024

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