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Iron in PDB 2ji3: X-Ray Structure of the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) From Desulfoarculus Baarsii

Enzymatic activity of X-Ray Structure of the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) From Desulfoarculus Baarsii

All present enzymatic activity of X-Ray Structure of the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) From Desulfoarculus Baarsii:
1.15.1.2;

Protein crystallography data

The structure of X-Ray Structure of the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) From Desulfoarculus Baarsii, PDB code: 2ji3 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) 47.13 / 1.95
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 69.450, 82.900, 202.660, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 24.9

Other elements in 2ji3:

The structure of X-Ray Structure of the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) 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 the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) From Desulfoarculus Baarsii (pdb code 2ji3). 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 the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) From Desulfoarculus Baarsii, PDB code: 2ji3:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 2ji3

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Iron binding site 1 out of 8 in the X-Ray Structure of the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) 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 the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) From Desulfoarculus Baarsii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1127

b:25.0
occ:1.00
 SG A:CYS13 2.2 24.6 1.0
SG A:CYS29 2.2 22.7 1.0
SG A:CYS10 2.2 23.2 1.0
SG A:CYS30 2.4 28.2 1.0
CB A:CYS10 3.1 19.7 1.0
CB A:CYS30 3.3 28.6 1.0
CB A:CYS13 3.3 24.4 1.0
CB A:CYS29 3.3 20.1 1.0
N A:CYS30 3.6 26.3 1.0
N A:CYS13 3.7 24.8 1.0
C A:CYS29 3.7 24.2 1.0
CA B:GLY25 4.0 29.4 1.0
CA A:CYS13 4.0 22.4 1.0
CA A:CYS30 4.1 29.4 1.0
CA A:CYS29 4.1 23.4 1.0
ND2 A:ASN15 4.2 24.6 1.0
O A:CYS29 4.2 22.2 1.0
N B:GLY25 4.5 31.3 1.0
CA A:CYS10 4.6 19.4 1.0
CB A:VAL12 4.6 24.9 1.0
C A:CYS13 4.8 22.3 1.0
C B:GLY25 4.8 29.8 1.0
N A:GLY14 4.8 19.8 1.0
C A:VAL12 4.8 23.3 1.0
CG A:ASN15 4.8 25.3 1.0
CB A:ASN15 4.8 24.4 1.0

Iron binding site 2 out of 8 in 2ji3

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Iron binding site 2 out of 8 in the X-Ray Structure of the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) 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 the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) From Desulfoarculus Baarsii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1128

b:26.8
occ:1.00
 ND1 A:HIS119 2.0 24.0 1.0
NE2 A:HIS75 2.2 32.9 1.0
NE2 A:HIS49 2.2 29.0 1.0
NE2 A:HIS69 2.3 19.7 1.0
SG A:CYS116 2.5 23.5 1.0
O3 A:NO31131 2.8 79.0 1.0
CE1 A:HIS119 2.9 25.5 1.0
CE1 A:HIS75 3.1 31.1 1.0
CE1 A:HIS49 3.1 27.9 1.0
CG A:HIS119 3.2 22.9 1.0
CE1 A:HIS69 3.2 22.6 1.0
CD2 A:HIS75 3.3 31.4 1.0
CD2 A:HIS49 3.3 27.8 1.0
CD2 A:HIS69 3.3 20.3 1.0
CB A:HIS119 3.6 22.1 1.0
CB A:CYS116 3.7 21.7 1.0
N A:NO31131 4.0 80.2 1.0
NE2 A:HIS119 4.1 23.8 1.0
CD2 A:HIS119 4.2 23.3 1.0
ND1 A:HIS75 4.2 31.8 1.0
ND1 A:HIS49 4.2 30.2 1.0
N A:HIS119 4.3 24.5 1.0
ND1 A:HIS69 4.3 20.9 1.0
CG A:HIS75 4.3 31.4 1.0
CG A:HIS49 4.4 29.0 1.0
CG A:HIS69 4.4 22.6 1.0
CA A:HIS119 4.6 22.4 1.0
O2 A:NO31131 4.7 80.0 1.0
O1 A:NO31131 4.7 79.5 1.0
CB A:ILE118 4.9 23.8 1.0

Iron binding site 3 out of 8 in 2ji3

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Iron binding site 3 out of 8 in the X-Ray Structure of the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) 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 the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) From Desulfoarculus Baarsii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1127

b:26.7
occ:1.00
 SG B:CYS13 2.2 21.8 1.0
SG B:CYS10 2.3 26.0 1.0
SG B:CYS29 2.4 23.8 1.0
SG B:CYS30 2.4 23.9 1.0
CB B:CYS13 3.2 25.9 1.0
CB B:CYS10 3.2 26.9 1.0
CB B:CYS29 3.3 22.4 1.0
CB B:CYS30 3.4 25.6 1.0
N B:CYS30 3.6 27.4 1.0
N B:CYS13 3.7 27.4 1.0
C B:CYS29 3.7 25.2 1.0
CA A:GLY25 3.9 23.7 1.0
CA B:CYS13 4.0 25.4 1.0
CA B:CYS30 4.1 29.4 1.0
CA B:CYS29 4.1 24.3 1.0
O B:CYS29 4.2 24.0 1.0
ND2 B:ASN15 4.2 18.4 1.0
N A:GLY25 4.3 26.8 1.0
C A:GLY25 4.6 24.6 1.0
CA B:CYS10 4.7 27.3 1.0
C B:CYS13 4.7 23.8 1.0
CB B:VAL12 4.7 30.8 1.0
C B:VAL12 4.8 28.6 1.0
N B:GLY14 4.8 24.3 1.0
CG B:ASN15 4.9 18.9 1.0
O A:GLY25 4.9 23.4 1.0
CB B:ASN15 5.0 20.8 1.0

Iron binding site 4 out of 8 in 2ji3

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Iron binding site 4 out of 8 in the X-Ray Structure of the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) 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 the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) From Desulfoarculus Baarsii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1128

b:28.5
occ:1.00
 O1 B:PER1130 2.0 37.2 1.0
ND1 B:HIS119 2.1 26.6 1.0
NE2 B:HIS69 2.2 22.3 1.0
NE2 B:HIS75 2.2 27.7 1.0
NE2 B:HIS49 2.3 30.1 1.0
SG B:CYS116 2.5 27.2 1.0
CE1 B:HIS119 2.9 28.9 1.0
CE1 B:HIS69 3.1 26.6 1.0
O2 B:PER1130 3.1 39.8 1.0
CE1 B:HIS75 3.2 27.3 1.0
CG B:HIS119 3.2 28.7 1.0
CD2 B:HIS75 3.3 27.8 1.0
CD2 B:HIS49 3.3 29.8 1.0
CD2 B:HIS69 3.3 24.1 1.0
CE1 B:HIS49 3.3 31.2 1.0
CB B:CYS116 3.7 26.6 1.0
CB B:HIS119 3.7 28.0 1.0
NE2 B:HIS119 4.0 31.2 1.0
CD2 B:HIS119 4.2 29.5 1.0
ND1 B:HIS69 4.2 24.4 1.0
N B:HIS119 4.3 28.1 1.0
ND1 B:HIS75 4.3 25.8 1.0
CG B:HIS75 4.4 28.0 1.0
CG B:HIS69 4.4 26.4 1.0
ND1 B:HIS49 4.4 30.6 1.0
CG B:HIS49 4.4 30.6 1.0
CA B:HIS119 4.7 28.7 1.0
CB B:ILE118 4.8 28.4 1.0

Iron binding site 5 out of 8 in 2ji3

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Iron binding site 5 out of 8 in the X-Ray Structure of the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) 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 the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) From Desulfoarculus Baarsii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1127

b:25.9
occ:1.00
 SG C:CYS10 2.2 26.9 1.0
SG C:CYS13 2.2 25.6 1.0
SG C:CYS29 2.3 24.0 1.0
SG C:CYS30 2.3 28.9 1.0
CB C:CYS10 3.2 26.3 1.0
CB C:CYS13 3.2 25.5 1.0
CB C:CYS30 3.3 28.2 1.0
CB C:CYS29 3.4 21.4 1.0
N C:CYS30 3.7 26.0 1.0
N C:CYS13 3.7 24.1 1.0
C C:CYS29 3.7 24.6 1.0
CA C:CYS13 4.0 25.6 1.0
CA D:GLY25 4.1 28.3 1.0
CA C:CYS30 4.1 28.4 1.0
CA C:CYS29 4.1 24.0 1.0
O C:CYS29 4.2 23.5 1.0
ND2 C:ASN15 4.3 24.1 1.0
N D:GLY25 4.5 29.6 1.0
CB C:VAL12 4.6 25.8 1.0
CA C:CYS10 4.6 23.1 1.0
C D:GLY25 4.8 28.3 1.0
C C:VAL12 4.8 25.2 1.0
O C:HOH2021 4.8 24.7 1.0
C C:CYS13 4.8 26.6 1.0
N C:GLY14 4.9 27.4 1.0
CB C:ASN15 5.0 24.7 1.0
CG C:ASN15 5.0 26.9 1.0

Iron binding site 6 out of 8 in 2ji3

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Iron binding site 6 out of 8 in the X-Ray Structure of the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) 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 the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) From Desulfoarculus Baarsii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1128

b:29.4
occ:1.00
 O1 C:PER1130 2.0 37.6 1.0
ND1 C:HIS119 2.3 26.3 1.0
NE2 C:HIS69 2.3 31.1 1.0
NE2 C:HIS75 2.4 32.2 1.0
NE2 C:HIS49 2.4 33.2 1.0
SG C:CYS116 2.5 26.1 1.0
O2 C:PER1130 3.1 40.9 1.0
CE1 C:HIS69 3.2 32.4 1.0
CE1 C:HIS119 3.2 28.3 1.0
CE1 C:HIS49 3.2 32.2 1.0
CD2 C:HIS75 3.3 30.8 1.0
CG C:HIS119 3.3 25.0 1.0
CD2 C:HIS69 3.4 31.3 1.0
CE1 C:HIS75 3.4 31.2 1.0
CD2 C:HIS49 3.4 33.1 1.0
CB C:HIS119 3.6 23.7 1.0
CB C:CYS116 3.6 24.6 1.0
N C:HIS119 4.2 26.2 1.0
ND1 C:HIS69 4.3 30.4 1.0
NE2 C:HIS119 4.3 27.7 1.0
ND1 C:HIS49 4.4 33.2 1.0
CD2 C:HIS119 4.4 26.0 1.0
CG C:HIS69 4.5 31.9 1.0
CG C:HIS75 4.5 32.8 1.0
ND1 C:HIS75 4.5 31.6 1.0
CG C:HIS49 4.5 34.8 1.0
CA C:HIS119 4.6 24.9 1.0
CB C:ILE118 4.9 28.4 1.0

Iron binding site 7 out of 8 in 2ji3

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Iron binding site 7 out of 8 in the X-Ray Structure of the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) 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 the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) From Desulfoarculus Baarsii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1127

b:26.8
occ:1.00
 SG D:CYS13 2.2 26.5 1.0
SG D:CYS10 2.2 30.9 1.0
SG D:CYS30 2.2 25.9 1.0
SG D:CYS29 2.3 24.7 1.0
CB D:CYS10 3.2 25.5 1.0
CB D:CYS13 3.3 25.9 1.0
CB D:CYS29 3.3 22.9 1.0
CB D:CYS30 3.3 23.9 1.0
N D:CYS30 3.6 25.0 1.0
N D:CYS13 3.7 27.1 1.0
C D:CYS29 3.7 25.6 1.0
CA C:GLY25 3.9 27.1 1.0
CA D:CYS29 4.0 24.9 1.0
CA D:CYS13 4.0 25.7 1.0
CA D:CYS30 4.0 26.1 1.0
O D:CYS29 4.2 24.8 1.0
ND2 D:ASN15 4.3 24.9 1.0
N C:GLY25 4.5 27.8 1.0
CB D:VAL12 4.5 30.4 1.0
CA D:CYS10 4.6 27.2 1.0
C C:GLY25 4.7 28.1 1.0
C D:VAL12 4.8 29.8 1.0
C D:CYS13 4.8 25.4 1.0
N D:GLY14 4.9 25.2 1.0
CG D:ASN15 4.9 25.9 1.0
CB D:ASN15 5.0 25.5 1.0

Iron binding site 8 out of 8 in 2ji3

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Iron binding site 8 out of 8 in the X-Ray Structure of the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) 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 the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) From Desulfoarculus Baarsii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1128

b:39.3
occ:1.00
 O1 D:PER1129 2.0 45.4 1.0
NE2 D:HIS49 2.2 44.4 1.0
NE2 D:HIS69 2.2 42.6 1.0
ND1 D:HIS119 2.3 39.0 1.0
NE2 D:HIS75 2.3 48.7 1.0
SG D:CYS116 2.6 38.1 1.0
CE1 D:HIS119 3.0 38.8 1.0
CE1 D:HIS49 3.0 45.9 1.0
O2 D:PER1129 3.1 46.2 1.0
CE1 D:HIS75 3.1 48.9 1.0
CD2 D:HIS69 3.2 42.2 1.0
CD2 D:HIS49 3.2 44.9 1.0
CG D:HIS119 3.2 38.7 1.0
CE1 D:HIS69 3.3 44.1 1.0
CD2 D:HIS75 3.4 50.1 1.0
CB D:HIS119 3.7 38.4 1.0
CB D:CYS116 3.8 38.8 1.0
NE2 D:HIS119 4.1 39.2 1.0
ND1 D:HIS49 4.2 45.0 1.0
CD2 D:HIS119 4.2 38.1 1.0
ND1 D:HIS75 4.3 49.5 1.0
N D:HIS119 4.3 37.7 1.0
CG D:HIS49 4.3 44.4 1.0
CG D:HIS69 4.3 43.5 1.0
ND1 D:HIS69 4.3 44.5 1.0
CG D:HIS75 4.5 49.2 1.0
CA D:HIS119 4.6 38.4 1.0
O D:HOH2058 4.7 55.9 1.0
CB D:ILE118 4.8 39.4 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: Sun Dec 13 14:48:07 2020

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