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Iron in PDB 3mps: Peroxide Bound Oxidized Rubrerythrin From Pyrococcus Furiosus

Protein crystallography data

The structure of Peroxide Bound Oxidized Rubrerythrin From Pyrococcus Furiosus, PDB code: 3mps was solved by B.D.Dillard, M.W.W.Adams, W.N.Lanzilotta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 105.41 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.398, 105.164, 105.220, 90.00, 90.13, 90.00
R / Rfree (%) 24.2 / 29.1

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the Peroxide Bound Oxidized Rubrerythrin From Pyrococcus Furiosus (pdb code 3mps). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Peroxide Bound Oxidized Rubrerythrin From Pyrococcus Furiosus, PDB code: 3mps:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in 3mps

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Iron binding site 1 out of 24 in the Peroxide Bound Oxidized Rubrerythrin From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Peroxide Bound Oxidized Rubrerythrin From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe172

b:22.4
occ:1.00
 SG A:CYS145 2.3 21.2 1.0
SG A:CYS160 2.3 20.5 1.0
SG A:CYS142 2.3 20.8 1.0
SG A:CYS157 2.3 23.2 1.0
CB A:CYS157 3.2 22.5 1.0
CB A:CYS142 3.2 20.0 1.0
CB A:CYS160 3.3 21.7 1.0
CB A:CYS145 3.5 20.6 1.0
N A:CYS160 3.7 21.9 1.0
N A:CYS145 3.9 20.2 1.0
CA A:CYS160 4.0 22.1 1.0
CA A:CYS145 4.3 20.2 1.0
CB A:ILE144 4.3 21.6 1.0
CB A:ALA162 4.4 23.4 1.0
CB A:TYR147 4.5 21.3 1.0
CB A:VAL159 4.5 21.6 1.0
CA A:CYS157 4.6 22.3 1.0
CA A:CYS142 4.6 20.4 1.0
C A:CYS160 4.7 22.8 1.0
N A:ALA162 4.7 23.3 1.0
N A:GLY161 4.8 23.0 1.0
C A:VAL159 4.8 21.8 1.0
CG2 A:ILE144 4.8 21.6 1.0
C A:CYS145 4.8 20.0 1.0
C A:ILE144 4.9 20.9 1.0
N A:GLY146 4.9 20.0 1.0
CA A:ILE144 5.0 21.2 1.0
N A:ILE144 5.0 21.4 1.0
N A:TYR147 5.0 20.6 1.0

Iron binding site 2 out of 24 in 3mps

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Iron binding site 2 out of 24 in the Peroxide Bound Oxidized Rubrerythrin From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Peroxide Bound Oxidized Rubrerythrin From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe173

b:22.4
occ:1.00
 FE1 A:FEO173 0.0 22.4 1.0
ND1 A:HIS117 1.9 24.1 1.0
OE2 B:GLU52 2.0 23.9 1.0
OE2 A:GLU114 2.0 25.4 1.0
OE1 A:GLU80 2.1 23.2 1.0
OE2 A:GLU80 2.1 23.5 1.0
O A:FEO173 2.1 17.6 1.0
CD A:GLU80 2.4 20.7 1.0
CE1 A:HIS117 2.6 24.8 1.0
CD B:GLU52 3.0 23.3 1.0
CD A:GLU114 3.1 25.4 1.0
CG A:HIS117 3.1 24.3 1.0
OE1 B:GLU52 3.3 24.7 1.0
FE2 A:FEO173 3.4 21.5 1.0
OE1 A:GLU114 3.5 24.9 1.0
CB A:HIS117 3.8 24.8 1.0
NE2 A:HIS117 3.8 25.3 1.0
CG A:GLU80 3.9 21.6 1.0
CD2 A:HIS117 4.1 24.2 1.0
CG B:GLU52 4.3 20.9 1.0
CG2 B:ILE48 4.3 19.7 1.0
CG A:GLU114 4.4 25.0 1.0
OE2 A:GLU83 4.5 25.4 1.0
CB A:GLU114 4.7 25.0 1.0
CE1 B:TYR26 4.7 20.2 1.0
O A:GLU114 4.7 24.7 1.0
CA A:GLU114 4.8 25.2 1.0
CB A:GLU80 4.8 20.5 1.0
OH B:TYR26 4.8 18.7 1.0
O A:HOH198 4.9 20.5 1.0

Iron binding site 3 out of 24 in 3mps

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Iron binding site 3 out of 24 in the Peroxide Bound Oxidized Rubrerythrin From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Peroxide Bound Oxidized Rubrerythrin From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe173

b:21.5
occ:1.00
 FE2 A:FEO173 0.0 21.5 1.0
OE2 A:GLU83 2.0 25.4 1.0
OE1 A:GLU114 2.0 24.9 1.0
OE1 B:GLU19 2.0 18.9 1.0
OE1 B:GLU52 2.0 24.7 1.0
OE2 B:GLU19 2.1 18.8 1.0
O A:FEO173 2.1 17.6 1.0
CD B:GLU19 2.3 18.2 1.0
CD A:GLU83 3.0 25.9 1.0
CD B:GLU52 3.0 23.3 1.0
CD A:GLU114 3.0 25.4 1.0
OE1 A:GLU83 3.3 28.3 1.0
OE2 A:GLU114 3.3 25.4 1.0
FE1 A:FEO173 3.4 22.4 1.0
OE2 B:GLU52 3.5 23.9 1.0
CG B:GLU19 3.9 18.3 1.0
ND1 B:HIS55 4.1 20.0 1.0
CG B:GLU52 4.2 20.9 1.0
CG A:GLU83 4.3 23.7 1.0
CG A:GLU114 4.4 25.0 1.0
OE2 A:GLU80 4.5 23.5 1.0
CE2 A:TYR88 4.5 18.6 1.0
CB B:GLU52 4.7 20.2 1.0
CB A:GLU83 4.7 22.4 1.0
OE1 A:GLU80 4.7 23.2 1.0
CB B:GLU19 4.7 16.6 1.0
CB B:ALA22 4.8 18.2 1.0
CE1 B:HIS55 4.8 18.2 1.0
OH A:TYR88 4.8 17.7 1.0
CD A:GLU80 4.9 20.7 1.0
CA B:GLU52 5.0 19.6 1.0
CA B:GLU19 5.0 17.3 1.0

Iron binding site 4 out of 24 in 3mps

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Iron binding site 4 out of 24 in the Peroxide Bound Oxidized Rubrerythrin From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Peroxide Bound Oxidized Rubrerythrin From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe172

b:20.9
occ:1.00
 SG B:CYS142 2.3 18.0 1.0
SG B:CYS157 2.3 23.1 1.0
SG B:CYS160 2.3 20.1 1.0
SG B:CYS145 2.3 21.0 1.0
CB B:CYS142 3.2 18.4 1.0
CB B:CYS157 3.2 21.0 1.0
CB B:CYS160 3.3 20.5 1.0
CB B:CYS145 3.5 18.7 1.0
N B:CYS160 3.8 20.1 1.0
N B:CYS145 3.9 18.2 1.0
CA B:CYS160 4.1 20.3 1.0
CA B:CYS145 4.2 18.7 1.0
CB B:ALA162 4.3 21.6 1.0
CB B:TYR147 4.5 22.3 1.0
CA B:CYS142 4.6 18.7 1.0
CB B:ILE144 4.6 19.4 1.0
CA B:CYS157 4.6 21.6 1.0
C B:CYS160 4.7 21.2 1.0
C B:ILE144 4.8 18.3 1.0
N B:GLY161 4.8 21.2 1.0
N B:ALA162 4.8 21.8 1.0
CB B:VAL159 4.8 19.9 1.0
C B:CYS145 4.9 18.2 1.0
C B:VAL159 4.9 19.9 1.0
N B:TYR147 4.9 20.4 1.0
N B:GLY146 4.9 18.5 1.0

Iron binding site 5 out of 24 in 3mps

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Iron binding site 5 out of 24 in the Peroxide Bound Oxidized Rubrerythrin From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Peroxide Bound Oxidized Rubrerythrin From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe173

b:22.6
occ:1.00
 FE1 B:FEO173 0.0 22.6 1.0
OE1 B:GLU83 2.0 23.4 1.0
OE2 A:GLU19 2.0 19.7 1.0
OE2 A:GLU52 2.1 20.4 1.0
OE1 B:GLU114 2.1 23.6 1.0
O B:FEO173 2.1 19.3 1.0
OE1 A:GLU19 2.4 17.9 1.0
CD A:GLU19 2.5 17.9 1.0
CD B:GLU83 2.9 23.2 1.0
CD B:GLU114 2.9 22.9 1.0
CD A:GLU52 3.0 17.8 1.0
OE2 B:GLU83 3.1 25.2 1.0
OE2 B:GLU114 3.2 23.0 1.0
FE2 B:FEO173 3.5 16.9 1.0
OE1 A:GLU52 3.5 19.8 1.0
CG A:GLU19 4.0 16.5 1.0
CG A:GLU52 4.1 17.1 1.0
CG B:GLU114 4.1 24.0 1.0
CG B:GLU83 4.3 20.8 1.0
ND1 A:HIS55 4.3 17.5 1.0
CE2 B:TYR88 4.3 16.1 1.0
OE1 B:GLU80 4.6 15.4 1.0
CB B:GLU83 4.6 18.6 1.0
OH B:TYR88 4.7 15.2 1.0
CB A:GLU52 4.7 17.0 1.0
CB A:GLU19 4.8 15.3 1.0
OE2 B:GLU80 4.9 16.2 1.0
CB A:ALA22 4.9 14.2 1.0

Iron binding site 6 out of 24 in 3mps

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Iron binding site 6 out of 24 in the Peroxide Bound Oxidized Rubrerythrin From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Peroxide Bound Oxidized Rubrerythrin From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe173

b:16.9
occ:1.00
 FE2 B:FEO173 0.0 16.9 1.0
ND1 B:HIS117 1.9 18.8 1.0
O B:FEO173 2.0 19.3 1.0
OE1 A:GLU52 2.0 19.8 1.0
OE2 B:GLU114 2.0 23.0 1.0
OE2 B:GLU80 2.1 16.2 1.0
OE1 B:GLU80 2.1 15.4 1.0
CD B:GLU80 2.4 13.2 1.0
CE1 B:HIS117 2.6 19.3 1.0
CD B:GLU114 2.8 22.9 1.0
CD A:GLU52 2.9 17.8 1.0
CG B:HIS117 3.2 18.9 1.0
OE2 A:GLU52 3.2 20.4 1.0
FE1 B:FEO173 3.5 22.6 1.0
OE1 B:GLU114 3.5 23.6 1.0
CG B:GLU114 3.6 24.0 1.0
CB B:HIS117 3.8 19.8 1.0
NE2 B:HIS117 3.8 18.6 1.0
CG B:GLU80 4.0 14.2 1.0
CD2 B:HIS117 4.1 19.1 1.0
CG A:GLU52 4.2 17.1 1.0
O B:HOH198 4.2 26.4 1.0
CG2 A:ILE48 4.3 18.0 1.0
OH A:TYR26 4.5 24.4 1.0
CE1 A:TYR26 4.6 23.9 1.0
O B:GLU114 4.7 21.9 1.0
CB B:GLU114 4.7 22.6 1.0
OE2 B:GLU83 4.7 25.2 1.0
OE1 B:GLU83 4.8 23.4 1.0
CA B:GLU114 4.8 22.7 1.0
CB B:GLU80 4.8 16.4 1.0
CD B:GLU83 5.0 23.2 1.0

Iron binding site 7 out of 24 in 3mps

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Iron binding site 7 out of 24 in the Peroxide Bound Oxidized Rubrerythrin From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Peroxide Bound Oxidized Rubrerythrin From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1

b:23.2
occ:1.00
 OE1 D:GLU114 2.0 21.8 1.0
OE1 D:GLU83 2.0 26.0 1.0
OE2 I:GLU19 2.0 24.1 1.0
OE2 I:GLU52 2.2 24.9 1.0
OE1 I:GLU19 2.4 16.1 1.0
CD I:GLU19 2.5 21.0 1.0
CD D:GLU114 2.9 25.6 1.0
CD D:GLU83 3.0 25.4 1.0
CD I:GLU52 3.1 22.4 1.0
OE2 D:GLU114 3.1 23.4 1.0
OE2 D:GLU83 3.3 26.9 1.0
FE D:FE172 3.4 22.6 1.0
OE1 I:GLU52 3.6 23.2 1.0
CG I:GLU19 4.0 19.1 1.0
CG I:GLU52 4.1 19.7 1.0
ND1 I:HIS55 4.2 21.7 1.0
CG D:GLU114 4.3 25.6 1.0
CG D:GLU83 4.4 24.8 1.0
OE1 D:GLU80 4.4 21.4 1.0
CE2 D:TYR88 4.5 19.5 1.0
CB I:GLU52 4.5 19.3 1.0
CB D:GLU83 4.6 24.3 1.0
CB I:ALA22 4.8 18.9 1.0
OH D:TYR88 4.8 18.7 1.0
CB I:GLU19 4.8 18.1 1.0
OE2 D:GLU80 4.8 19.8 1.0
CE1 I:HIS55 4.9 19.8 1.0
CD D:GLU80 4.9 19.5 1.0
CA I:GLU52 5.0 19.5 1.0

Iron binding site 8 out of 24 in 3mps

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Iron binding site 8 out of 24 in the Peroxide Bound Oxidized Rubrerythrin From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Peroxide Bound Oxidized Rubrerythrin From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe172

b:22.6
occ:1.00
 ND1 D:HIS117 1.9 24.7 1.0
OE2 D:GLU114 2.0 23.4 1.0
OE1 I:GLU52 2.0 23.2 1.0
OE2 D:GLU80 2.1 19.8 1.0
OE1 D:GLU80 2.1 21.4 1.0
CD D:GLU80 2.4 19.5 1.0
CE1 D:HIS117 2.6 26.8 1.0
CD I:GLU52 2.9 22.4 1.0
CG D:HIS117 3.1 26.0 1.0
CD D:GLU114 3.1 25.6 1.0
OE2 I:GLU52 3.2 24.9 1.0
FE D:FE1 3.4 23.2 1.0
OE1 D:GLU114 3.6 21.8 1.0
CB D:HIS117 3.7 26.7 1.0
NE2 D:HIS117 3.8 27.1 1.0
CG D:GLU80 3.9 21.6 1.0
CD2 D:HIS117 4.1 26.4 1.0
CG I:GLU52 4.2 19.7 1.0
CG2 I:ILE48 4.4 20.1 1.0
CG D:GLU114 4.4 25.6 1.0
CB D:GLU114 4.6 25.9 1.0
OE1 D:GLU83 4.6 26.0 1.0
CE1 I:TYR26 4.7 22.2 1.0
O D:GLU114 4.8 26.5 1.0
CA D:GLU114 4.8 26.1 1.0
CB D:GLU80 4.8 21.5 1.0
OH I:TYR26 4.9 22.0 1.0

Iron binding site 9 out of 24 in 3mps

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Iron binding site 9 out of 24 in the Peroxide Bound Oxidized Rubrerythrin From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Peroxide Bound Oxidized Rubrerythrin From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe173

b:22.4
occ:1.00
 SG D:CYS157 2.3 22.5 1.0
SG D:CYS160 2.3 19.2 1.0
SG D:CYS145 2.3 22.3 1.0
SG D:CYS142 2.3 21.1 1.0
CB D:CYS157 3.2 23.8 1.0
CB D:CYS160 3.3 19.8 1.0
CB D:CYS142 3.3 21.1 1.0
CB D:CYS145 3.5 21.2 1.0
N D:CYS160 3.8 20.7 1.0
N D:CYS145 4.0 21.4 1.0
CA D:CYS160 4.0 20.1 1.0
CB D:ILE144 4.3 22.0 1.0
CA D:CYS145 4.3 21.6 1.0
CB D:TYR147 4.3 24.3 1.0
CB D:ALA162 4.6 22.0 1.0
CA D:CYS157 4.6 23.3 1.0
CA D:CYS142 4.7 20.7 1.0
CB D:VAL159 4.7 21.7 1.0
C D:CYS160 4.8 19.7 1.0
C D:VAL159 4.8 21.0 1.0
C D:ILE144 4.8 21.8 1.0
CG2 D:ILE144 4.9 22.3 1.0
N D:TYR147 4.9 22.8 1.0
C D:CYS145 4.9 21.3 1.0
CA D:ILE144 4.9 22.0 1.0
N D:GLY161 5.0 19.7 1.0
N D:ILE144 5.0 21.4 1.0
N D:GLY146 5.0 21.4 1.0

Iron binding site 10 out of 24 in 3mps

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Iron binding site 10 out of 24 in the Peroxide Bound Oxidized Rubrerythrin From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Peroxide Bound Oxidized Rubrerythrin From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe172

b:24.8
occ:1.00
 SG F:CYS160 2.3 26.2 1.0
SG F:CYS145 2.3 21.9 1.0
SG F:CYS142 2.3 25.3 1.0
SG F:CYS157 2.4 24.9 1.0
CG2 F:ILE144 2.7 26.1 1.0
CB F:CYS142 3.1 25.5 1.0
CB F:CYS157 3.2 25.9 1.0
CB F:CYS160 3.4 25.3 1.0
CB F:CYS145 3.5 23.6 1.0
N F:CYS160 3.8 25.4 1.0
N F:CYS145 4.0 24.1 1.0
CA F:CYS160 4.1 25.6 1.0
CB F:ILE144 4.2 24.8 1.0
CA F:CYS145 4.3 23.8 1.0
CB F:TYR147 4.4 24.8 1.0
CB F:ALA162 4.5 29.3 1.0
CA F:CYS142 4.5 26.0 1.0
CA F:CYS157 4.7 25.7 1.0
CA F:ILE144 4.7 24.9 1.0
N F:ILE144 4.7 25.4 1.0
C F:ILE144 4.8 24.4 1.0
N F:TYR147 4.8 24.3 1.0
C F:CYS160 4.8 25.9 1.0
C F:VAL159 4.8 24.9 1.0
N F:GLY161 4.8 26.1 1.0
C F:CYS145 4.8 23.6 1.0
CB F:VAL159 4.8 24.7 1.0
N F:GLY146 4.9 23.6 1.0
N F:ALA162 4.9 28.6 1.0
C F:CYS142 4.9 25.6 1.0

Reference:

B.D.Dillard, J.M.Demick, M.W.Adams, W.N.Lanzilotta. A Cryo-Crystallographic Time Course For Peroxide Reduction By Rubrerythrin From Pyrococcus Furiosus. J.Biol.Inorg.Chem. V. 16 949 2011.
ISSN: ISSN 0949-8257
PubMed: 21647777
DOI: 10.1007/S00775-011-0795-6
Page generated: Sun Dec 13 15:12:52 2020

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