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Iron in PDB 2ji2: X-Ray Structure of E114A Mutant of Superoxide Reductase From Desulfoarculus Baarsii in the Native, Reduced Form

Enzymatic activity of X-Ray Structure of E114A Mutant of Superoxide Reductase From Desulfoarculus Baarsii in the Native, Reduced Form

All present enzymatic activity of X-Ray Structure of E114A Mutant of Superoxide Reductase From Desulfoarculus Baarsii in the Native, Reduced Form:
1.15.1.2;

Protein crystallography data

The structure of X-Ray Structure of E114A Mutant of Superoxide Reductase From Desulfoarculus Baarsii in the Native, Reduced Form, PDB code: 2ji2 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) 47.40 / 1.70
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 70.470, 82.870, 201.950, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 22.2

Other elements in 2ji2:

The structure of X-Ray Structure of E114A Mutant of Superoxide Reductase From Desulfoarculus Baarsii in the Native, Reduced Form 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 E114A Mutant of Superoxide Reductase From Desulfoarculus Baarsii in the Native, Reduced Form (pdb code 2ji2). 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 E114A Mutant of Superoxide Reductase From Desulfoarculus Baarsii in the Native, Reduced Form, PDB code: 2ji2:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 2ji2

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Iron binding site 1 out of 8 in the X-Ray Structure of E114A Mutant of Superoxide Reductase From Desulfoarculus Baarsii in the Native, Reduced Form


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 E114A Mutant of Superoxide Reductase From Desulfoarculus Baarsii in the Native, Reduced Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1000

b:17.7
occ:1.00
 SG A:CYS13 2.3 17.3 1.0
SG A:CYS10 2.3 16.1 1.0
SG A:CYS30 2.3 19.3 1.0
SG A:CYS29 2.3 16.0 1.0
CB A:CYS10 3.2 16.6 1.0
CB A:CYS30 3.3 19.9 1.0
CB A:CYS13 3.3 17.0 1.0
CB A:CYS29 3.3 15.6 1.0
N A:CYS30 3.6 17.6 1.0
C A:CYS29 3.7 16.7 1.0
N A:CYS13 3.7 17.0 1.0
CA B:GLY25 3.9 20.8 1.0
CA A:CYS30 4.0 20.4 1.0
CA A:CYS29 4.1 15.2 1.0
CA A:CYS13 4.1 15.6 1.0
O A:CYS29 4.2 16.8 1.0
ND2 A:ASN15 4.3 17.1 1.0
N B:GLY25 4.5 21.5 1.0
CB A:VAL12 4.6 18.9 1.0
CA A:CYS10 4.6 13.9 1.0
C B:GLY25 4.7 20.4 1.0
C A:CYS13 4.8 16.7 1.0
C A:VAL12 4.8 17.2 1.0
CB A:ASN15 4.9 16.2 1.0
CG A:ASN15 4.9 16.1 1.0
N A:GLY14 4.9 14.8 1.0
O A:HOH2045 5.0 15.8 1.0

Iron binding site 2 out of 8 in 2ji2

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Iron binding site 2 out of 8 in the X-Ray Structure of E114A Mutant of Superoxide Reductase From Desulfoarculus Baarsii in the Native, Reduced Form


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 E114A Mutant of Superoxide Reductase From Desulfoarculus Baarsii in the Native, Reduced Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2000

b:19.4
occ:1.00
 NE2 A:HIS69 2.2 16.0 1.0
ND1 A:HIS119 2.2 18.3 1.0
NE2 A:HIS49 2.2 18.9 1.0
NE2 A:HIS75 2.2 21.8 1.0
SG A:CYS116 2.4 16.2 1.0
O3 A:NO31127 2.8 41.9 1.0
CE1 A:HIS49 3.1 15.8 1.0
CE1 A:HIS119 3.1 22.0 1.0
CE1 A:HIS69 3.1 16.5 1.0
CE1 A:HIS75 3.1 22.0 1.0
CD2 A:HIS69 3.2 14.0 1.0
CG A:HIS119 3.2 17.8 1.0
CD2 A:HIS49 3.3 17.7 1.0
CD2 A:HIS75 3.3 20.9 1.0
CB A:HIS119 3.6 17.5 1.0
CB A:CYS116 3.6 14.5 1.0
N A:NO31127 4.0 43.1 1.0
N A:HIS119 4.2 15.6 1.0
ND1 A:HIS49 4.2 16.9 1.0
ND1 A:HIS69 4.2 17.1 1.0
NE2 A:HIS119 4.2 20.1 1.0
ND1 A:HIS75 4.3 21.9 1.0
CD2 A:HIS119 4.3 18.5 1.0
CG A:HIS69 4.3 13.7 1.0
CG A:HIS49 4.3 17.6 1.0
CG A:HIS75 4.4 21.7 1.0
CA A:HIS119 4.6 17.6 1.0
O1 A:NO31127 4.7 41.3 1.0
O2 A:NO31127 4.7 44.2 1.0
CB A:ILE118 4.9 19.2 1.0
CA A:CYS116 5.0 15.0 1.0

Iron binding site 3 out of 8 in 2ji2

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Iron binding site 3 out of 8 in the X-Ray Structure of E114A Mutant of Superoxide Reductase From Desulfoarculus Baarsii in the Native, Reduced Form


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 E114A Mutant of Superoxide Reductase From Desulfoarculus Baarsii in the Native, Reduced Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1001

b:17.1
occ:1.00
 SG B:CYS10 2.2 16.8 1.0
SG B:CYS13 2.3 17.4 1.0
SG B:CYS30 2.3 17.3 1.0
SG B:CYS29 2.3 16.1 1.0
CB B:CYS10 3.2 15.6 1.0
CB B:CYS13 3.3 15.2 1.0
CB B:CYS29 3.3 14.1 1.0
CB B:CYS30 3.3 19.8 1.0
N B:CYS30 3.6 18.1 1.0
C B:CYS29 3.6 16.9 1.0
N B:CYS13 3.7 16.9 1.0
CA A:GLY25 3.9 17.1 1.0
O B:CYS29 4.0 19.3 1.0
CA B:CYS29 4.0 15.9 1.0
CA B:CYS30 4.1 20.5 1.0
CA B:CYS13 4.1 15.8 1.0
ND2 B:ASN15 4.3 14.1 1.0
N A:GLY25 4.4 18.2 1.0
CB B:VAL12 4.6 21.2 1.0
CA B:CYS10 4.6 17.0 1.0
C A:GLY25 4.7 18.5 1.0
C B:VAL12 4.8 19.0 1.0
C B:CYS13 4.8 14.7 1.0
CG B:ASN15 4.9 14.7 1.0
CB B:ASN15 4.9 14.3 1.0
N B:GLY14 4.9 16.0 1.0
O A:GLY25 5.0 18.6 1.0

Iron binding site 4 out of 8 in 2ji2

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Iron binding site 4 out of 8 in the X-Ray Structure of E114A Mutant of Superoxide Reductase From Desulfoarculus Baarsii in the Native, Reduced Form


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 E114A Mutant of Superoxide Reductase From Desulfoarculus Baarsii in the Native, Reduced Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1129

b:16.3
occ:1.00
 ND1 B:HIS119 2.1 16.0 1.0
NE2 B:HIS69 2.2 16.5 1.0
NE2 B:HIS75 2.3 15.4 1.0
NE2 B:HIS49 2.3 14.9 1.0
SG B:CYS116 2.4 14.4 1.0
O1 B:NO31127 2.7 49.2 1.0
CE1 B:HIS119 3.0 18.6 1.0
CE1 B:HIS69 3.1 16.0 1.0
CE1 B:HIS75 3.2 15.0 1.0
CE1 B:HIS49 3.2 15.0 1.0
CG B:HIS119 3.2 17.0 1.0
CD2 B:HIS69 3.2 15.3 1.0
CD2 B:HIS49 3.3 17.3 1.0
CD2 B:HIS75 3.3 16.2 1.0
CB B:CYS116 3.6 11.3 1.0
CB B:HIS119 3.6 15.2 1.0
N B:NO31127 3.9 50.6 1.0
NE2 B:HIS119 4.1 19.9 1.0
N B:HIS119 4.2 14.9 1.0
ND1 B:HIS69 4.3 16.0 1.0
CD2 B:HIS119 4.3 18.3 1.0
ND1 B:HIS75 4.3 16.6 1.0
ND1 B:HIS49 4.3 16.4 1.0
CG B:HIS69 4.4 15.4 1.0
CG B:HIS49 4.4 17.7 1.0
CG B:HIS75 4.4 15.5 1.0
O3 B:NO31127 4.5 50.9 1.0
CA B:HIS119 4.6 16.6 1.0
CB B:ILE118 4.7 17.3 1.0
O2 B:NO31127 4.7 50.0 1.0
CA B:CYS116 4.9 12.6 1.0

Iron binding site 5 out of 8 in 2ji2

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Iron binding site 5 out of 8 in the X-Ray Structure of E114A Mutant of Superoxide Reductase From Desulfoarculus Baarsii in the Native, Reduced Form


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 E114A Mutant of Superoxide Reductase From Desulfoarculus Baarsii in the Native, Reduced Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1002

b:19.8
occ:1.00
 SG C:CYS10 2.3 17.4 1.0
SG C:CYS29 2.3 17.7 1.0
SG C:CYS30 2.3 21.6 1.0
SG C:CYS13 2.3 19.4 1.0
CB C:CYS10 3.2 15.2 1.0
CB C:CYS30 3.3 21.4 1.0
CB C:CYS13 3.4 18.6 1.0
CB C:CYS29 3.4 16.4 1.0
N C:CYS30 3.6 19.7 1.0
C C:CYS29 3.7 17.2 1.0
N C:CYS13 3.8 17.2 1.0
CA D:GLY25 3.9 22.5 1.0
CA C:CYS30 4.0 21.9 1.0
CA C:CYS29 4.1 17.9 1.0
CA C:CYS13 4.1 17.3 1.0
O C:CYS29 4.2 17.4 1.0
ND2 C:ASN15 4.2 16.6 1.0
N D:GLY25 4.3 24.0 1.0
CB C:VAL12 4.5 19.8 1.0
CA C:CYS10 4.6 14.4 1.0
C D:GLY25 4.7 22.4 1.0
C C:VAL12 4.8 18.9 1.0
C C:CYS13 4.9 17.9 1.0
CB C:ASN15 4.9 16.7 1.0
CG C:ASN15 4.9 19.9 1.0
N C:GLY14 4.9 17.6 1.0
O C:HOH2050 5.0 16.7 1.0

Iron binding site 6 out of 8 in 2ji2

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Iron binding site 6 out of 8 in the X-Ray Structure of E114A Mutant of Superoxide Reductase From Desulfoarculus Baarsii in the Native, Reduced Form


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 E114A Mutant of Superoxide Reductase From Desulfoarculus Baarsii in the Native, Reduced Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1131

b:21.1
occ:1.00
 ND1 C:HIS119 2.2 19.6 1.0
NE2 C:HIS69 2.2 19.6 1.0
NE2 C:HIS49 2.2 20.0 1.0
NE2 C:HIS75 2.4 22.2 1.0
SG C:CYS116 2.5 18.8 1.0
O1 C:NO31127 2.9 49.3 1.0
CE1 C:HIS119 3.0 21.5 1.0
CE1 C:HIS49 3.1 18.9 1.0
CE1 C:HIS69 3.1 19.3 1.0
CG C:HIS119 3.2 19.3 1.0
CD2 C:HIS69 3.2 18.5 1.0
CD2 C:HIS49 3.3 19.2 1.0
CE1 C:HIS75 3.3 22.5 1.0
CD2 C:HIS75 3.4 22.4 1.0
CB C:HIS119 3.6 17.3 1.0
CB C:CYS116 3.6 16.5 1.0
N C:NO31127 4.0 49.9 1.0
NE2 C:HIS119 4.2 21.9 1.0
N C:HIS119 4.2 19.5 1.0
ND1 C:HIS49 4.3 20.8 1.0
ND1 C:HIS69 4.3 19.1 1.0
CD2 C:HIS119 4.3 19.9 1.0
CG C:HIS69 4.4 19.2 1.0
CG C:HIS49 4.4 20.5 1.0
ND1 C:HIS75 4.5 22.5 1.0
CG C:HIS75 4.5 24.2 1.0
CA C:HIS119 4.5 18.9 1.0
O2 C:NO31127 4.7 48.7 1.0
O3 C:NO31127 4.8 50.0 1.0
CB C:ILE118 4.9 20.7 1.0
CA C:CYS116 5.0 15.5 1.0

Iron binding site 7 out of 8 in 2ji2

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Iron binding site 7 out of 8 in the X-Ray Structure of E114A Mutant of Superoxide Reductase From Desulfoarculus Baarsii in the Native, Reduced Form


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 E114A Mutant of Superoxide Reductase From Desulfoarculus Baarsii in the Native, Reduced Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1003

b:18.2
occ:1.00
 SG D:CYS10 2.2 17.0 1.0
SG D:CYS30 2.3 18.9 1.0
SG D:CYS29 2.3 16.2 1.0
SG D:CYS13 2.3 18.9 1.0
CB D:CYS10 3.2 17.1 1.0
CB D:CYS30 3.3 16.9 1.0
CB D:CYS29 3.3 17.4 1.0
CB D:CYS13 3.4 17.2 1.0
N D:CYS30 3.6 17.1 1.0
C D:CYS29 3.7 16.7 1.0
N D:CYS13 3.7 18.9 1.0
CA C:GLY25 3.9 19.0 1.0
CA D:CYS30 4.0 19.6 1.0
O D:CYS29 4.0 17.2 1.0
CA D:CYS29 4.1 16.1 1.0
CA D:CYS13 4.1 18.2 1.0
ND2 D:ASN15 4.3 17.1 1.0
N C:GLY25 4.4 17.9 1.0
CB D:VAL12 4.5 21.4 1.0
CA D:CYS10 4.6 16.7 1.0
C C:GLY25 4.7 18.6 1.0
C D:VAL12 4.8 22.0 1.0
C D:CYS13 4.9 18.1 1.0
CB D:ASN15 4.9 15.9 1.0
CG D:ASN15 4.9 16.1 1.0
N D:GLY14 4.9 18.3 1.0

Iron binding site 8 out of 8 in 2ji2

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Iron binding site 8 out of 8 in the X-Ray Structure of E114A Mutant of Superoxide Reductase From Desulfoarculus Baarsii in the Native, Reduced Form


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 E114A Mutant of Superoxide Reductase From Desulfoarculus Baarsii in the Native, Reduced Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1128

b:24.5
occ:1.00
 NE2 D:HIS69 2.2 23.1 1.0
ND1 D:HIS119 2.2 22.4 1.0
NE2 D:HIS49 2.2 23.8 1.0
NE2 D:HIS75 2.2 26.4 1.0
SG D:CYS116 2.5 20.3 1.0
O3 D:NO31127 2.7 52.1 1.0
CE1 D:HIS119 3.0 23.3 1.0
CE1 D:HIS69 3.1 21.1 1.0
CE1 D:HIS75 3.1 28.3 1.0
CE1 D:HIS49 3.2 23.9 1.0
CD2 D:HIS69 3.2 20.6 1.0
CD2 D:HIS49 3.2 24.0 1.0
CG D:HIS119 3.2 22.3 1.0
CD2 D:HIS75 3.3 26.1 1.0
CB D:CYS116 3.6 19.5 1.0
CB D:HIS119 3.6 21.5 1.0
N D:NO31127 3.9 53.5 1.0
NE2 D:HIS119 4.2 23.1 1.0
ND1 D:HIS69 4.2 21.8 1.0
ND1 D:HIS75 4.3 28.3 1.0
N D:HIS119 4.3 22.3 1.0
ND1 D:HIS49 4.3 22.4 1.0
CD2 D:HIS119 4.3 23.3 1.0
CG D:HIS69 4.3 23.2 1.0
CG D:HIS49 4.3 22.8 1.0
CG D:HIS75 4.4 27.3 1.0
O2 D:NO31127 4.6 53.3 1.0
CA D:HIS119 4.6 21.6 1.0
O1 D:NO31127 4.6 52.8 1.0
CB D:ILE118 4.8 23.9 1.0
CA D:CYS116 5.0 19.0 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 23:40:36 2024

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