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Zinc in PDB 1nnq: Rubrerythrin From Pyrococcus Furiosus Pfu-1210814

Protein crystallography data

The structure of Rubrerythrin From Pyrococcus Furiosus Pfu-1210814, PDB code: 1nnq was solved by Z.-J.Liu, W.Tempel, F.D.Schubot, A.Shah, W.B.Arendall Iii, J.P.Rose, D.C.Richardson, J.S.Richardson, B.-C.Wang, Southeast Collaboratory Forstructural Genomics (Secsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.54 / 2.35
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 105.918, 105.918, 81.001, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 25.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Rubrerythrin From Pyrococcus Furiosus Pfu-1210814 (pdb code 1nnq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Rubrerythrin From Pyrococcus Furiosus Pfu-1210814, PDB code: 1nnq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1nnq

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Zinc binding site 1 out of 6 in the Rubrerythrin From Pyrococcus Furiosus Pfu-1210814


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rubrerythrin From Pyrococcus Furiosus Pfu-1210814 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn200

b:27.5
occ:0.90
SG A:CYS142 2.2 27.6 1.0
SG A:CYS157 2.3 29.4 1.0
SG A:CYS145 2.3 26.9 1.0
SG A:CYS160 2.3 34.8 1.0
CB A:CYS157 3.2 29.7 1.0
CB A:CYS142 3.2 27.0 1.0
CB A:CYS145 3.3 28.4 1.0
CB A:CYS160 3.4 33.5 1.0
N A:CYS145 3.7 29.2 1.0
N A:CYS160 3.8 33.8 1.0
CA A:CYS145 4.1 29.4 1.0
CA A:CYS160 4.1 35.4 1.0
CB A:ILE144 4.3 31.7 1.0
CB A:TYR147 4.4 32.5 1.0
CB A:ALA162 4.6 33.0 1.0
CA A:CYS142 4.6 27.2 1.0
CA A:CYS157 4.6 29.6 1.0
CB A:VAL159 4.7 33.2 1.0
C A:ILE144 4.7 28.7 1.0
C A:CYS145 4.7 30.3 1.0
C A:CYS160 4.8 37.1 1.0
N A:GLY146 4.8 31.6 1.0
C A:VAL159 4.8 33.0 1.0
N A:GLY161 4.8 36.5 1.0
N A:TYR147 4.9 31.9 1.0
N A:ALA162 4.9 35.4 1.0
CA A:ILE144 4.9 28.5 1.0
CG2 A:ILE144 5.0 29.2 1.0
N A:ILE144 5.0 28.0 1.0

Zinc binding site 2 out of 6 in 1nnq

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Zinc binding site 2 out of 6 in the Rubrerythrin From Pyrococcus Furiosus Pfu-1210814


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rubrerythrin From Pyrococcus Furiosus Pfu-1210814 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:22.4
occ:0.40
OE2 B:GLU52 2.0 25.1 1.0
OE2 A:GLU114 2.1 29.0 1.0
OE2 A:GLU80 2.4 23.8 1.0
OE1 A:GLU80 2.4 24.3 1.0
ND1 A:HIS117 2.5 11.2 1.0
CD A:GLU80 2.7 25.2 1.0
CD B:GLU52 2.9 23.8 1.0
OE1 B:GLU52 3.0 27.1 1.0
CD A:GLU114 3.3 30.5 1.0
CE1 A:HIS117 3.3 13.4 1.0
CG A:HIS117 3.5 14.7 1.0
ZN B:ZN202 3.8 27.8 0.4
CB A:HIS117 3.8 13.8 1.0
OE1 A:GLU114 4.0 31.8 1.0
OE2 A:GLU83 4.1 35.1 1.0
CA A:GLU114 4.2 26.6 1.0
CG A:GLU80 4.2 23.1 1.0
CG B:GLU52 4.3 21.1 1.0
CB A:GLU114 4.4 27.1 1.0
CG A:GLU114 4.4 28.6 1.0
CG2 B:ILE48 4.4 17.2 1.0
NE2 A:HIS117 4.5 14.1 1.0
CE1 B:TYR26 4.6 16.9 1.0
CD2 A:HIS117 4.6 13.2 1.0
OH B:TYR26 4.7 16.4 1.0
N A:GLU114 4.9 25.8 1.0

Zinc binding site 3 out of 6 in 1nnq

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Zinc binding site 3 out of 6 in the Rubrerythrin From Pyrococcus Furiosus Pfu-1210814


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rubrerythrin From Pyrococcus Furiosus Pfu-1210814 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:27.8
occ:0.40
OE1 B:GLU114 2.1 28.8 1.0
OE2 A:GLU52 2.2 34.2 1.0
OE2 A:GLU19 2.3 29.8 1.0
OE1 A:GLU19 2.3 28.3 1.0
ND1 A:HIS55 2.5 30.4 1.0
CD A:GLU19 2.6 26.2 1.0
CD B:GLU114 2.8 24.6 1.0
OE2 B:GLU114 2.8 23.5 1.0
CD A:GLU52 3.3 30.1 1.0
CE1 A:HIS55 3.3 31.4 1.0
CG A:HIS55 3.6 30.5 1.0
ZN B:ZN201 3.7 27.6 0.4
OE1 B:GLU83 3.8 42.1 1.0
OE1 A:GLU52 3.8 32.4 1.0
OE2 B:GLU83 3.8 44.4 1.0
CB A:HIS55 3.9 27.4 1.0
CG A:GLU19 4.2 23.6 1.0
CD B:GLU83 4.2 38.8 1.0
CG B:GLU114 4.2 22.0 1.0
CA A:GLU52 4.3 26.5 1.0
CG A:GLU52 4.4 28.2 1.0
NE2 A:HIS55 4.5 33.0 1.0
CB A:GLU52 4.5 25.4 1.0
OH B:TYR88 4.6 15.7 1.0
CD2 A:HIS55 4.7 30.6 1.0
CB B:ALA110 4.7 20.6 1.0
CE2 B:TYR88 4.7 13.9 1.0
N A:GLU52 4.9 26.2 1.0
CB A:GLU19 5.0 21.4 1.0

Zinc binding site 4 out of 6 in 1nnq

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Zinc binding site 4 out of 6 in the Rubrerythrin From Pyrococcus Furiosus Pfu-1210814


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rubrerythrin From Pyrococcus Furiosus Pfu-1210814 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn200

b:29.8
occ:0.90
SG B:CYS142 2.3 26.9 1.0
SG B:CYS160 2.3 31.2 1.0
SG B:CYS145 2.3 28.9 1.0
SG B:CYS157 2.3 35.2 1.0
CB B:CYS142 3.2 30.9 1.0
CB B:CYS157 3.2 33.0 1.0
CB B:CYS160 3.3 27.3 1.0
CB B:CYS145 3.3 28.4 1.0
N B:CYS145 3.7 28.4 1.0
N B:CYS160 3.9 27.1 1.0
CA B:CYS145 4.0 29.3 1.0
CA B:CYS160 4.2 28.9 1.0
CB B:TYR147 4.4 38.1 1.0
CB B:ILE144 4.5 32.3 1.0
CA B:CYS142 4.6 30.6 1.0
CB B:ALA162 4.6 36.6 1.0
CB B:VAL159 4.6 27.9 1.0
C B:ILE144 4.7 30.1 1.0
CA B:CYS157 4.7 33.0 1.0
C B:CYS145 4.7 27.4 1.0
N B:GLY146 4.8 28.3 1.0
N B:TYR147 4.8 32.8 1.0
C B:CYS160 4.9 29.9 1.0
N B:GLY161 4.9 31.2 1.0
C B:VAL159 4.9 26.7 1.0
N B:ILE144 4.9 30.7 1.0
CA B:ILE144 5.0 30.3 1.0
CG2 B:ILE144 5.0 29.7 1.0

Zinc binding site 5 out of 6 in 1nnq

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Zinc binding site 5 out of 6 in the Rubrerythrin From Pyrococcus Furiosus Pfu-1210814


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rubrerythrin From Pyrococcus Furiosus Pfu-1210814 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:27.6
occ:0.40
OE1 A:GLU52 2.0 32.4 1.0
OE2 B:GLU114 2.1 23.5 1.0
OE1 B:GLU80 2.2 27.1 1.0
OE2 B:GLU80 2.3 28.9 1.0
ND1 B:HIS117 2.5 22.7 1.0
CD B:GLU80 2.6 28.5 1.0
CD A:GLU52 2.9 30.1 1.0
OE2 A:GLU52 3.0 34.2 1.0
CD B:GLU114 3.3 24.6 1.0
CE1 B:HIS117 3.3 22.3 1.0
OE1 B:GLU83 3.3 42.1 1.0
CG B:HIS117 3.5 23.0 1.0
ZN A:ZN202 3.7 27.8 0.4
CB B:HIS117 3.9 22.7 1.0
OE1 B:GLU114 4.0 28.8 1.0
CG B:GLU80 4.1 26.7 1.0
CB B:GLU114 4.2 23.7 1.0
CA B:GLU114 4.3 23.8 1.0
CG A:GLU52 4.3 28.2 1.0
CG B:GLU114 4.3 22.0 1.0
CD B:GLU83 4.4 38.8 1.0
CG2 A:ILE48 4.5 29.8 1.0
NE2 B:HIS117 4.5 22.2 1.0
CE1 A:TYR26 4.6 20.8 1.0
OH A:TYR26 4.6 21.9 1.0
CD2 B:HIS117 4.6 21.3 1.0
OE2 B:GLU83 4.8 44.4 1.0
CB B:GLU80 5.0 24.8 1.0

Zinc binding site 6 out of 6 in 1nnq

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Zinc binding site 6 out of 6 in the Rubrerythrin From Pyrococcus Furiosus Pfu-1210814


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rubrerythrin From Pyrococcus Furiosus Pfu-1210814 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:27.8
occ:0.40
OE1 A:GLU114 2.0 31.8 1.0
OE1 B:GLU52 2.3 27.1 1.0
ND1 B:HIS55 2.3 19.5 1.0
OE1 B:GLU19 2.3 30.4 1.0
OE2 B:GLU19 2.5 22.8 1.0
CD B:GLU19 2.8 25.7 1.0
CD A:GLU114 2.8 30.5 1.0
OE2 A:GLU114 3.0 29.0 1.0
CE1 B:HIS55 3.1 17.9 1.0
CD B:GLU52 3.3 23.8 1.0
CG B:HIS55 3.4 19.5 1.0
ZN A:ZN201 3.8 22.4 0.4
CB B:HIS55 3.8 18.0 1.0
OE2 B:GLU52 3.9 25.1 1.0
OE2 A:GLU83 4.0 35.1 1.0
CA B:GLU52 4.2 20.4 1.0
CG B:GLU19 4.3 23.4 1.0
CG A:GLU114 4.3 28.6 1.0
NE2 B:HIS55 4.3 20.5 1.0
CD2 B:HIS55 4.4 20.2 1.0
CG B:GLU52 4.4 21.1 1.0
CB B:GLU52 4.5 20.7 1.0
CB A:ALA110 4.6 19.6 1.0
OH A:TYR88 4.7 15.6 1.0
CE2 A:TYR88 4.8 16.9 1.0
N B:GLU52 4.9 19.3 1.0
CD A:GLU83 4.9 33.2 1.0
O B:ALA51 4.9 21.1 1.0
O A:ALA110 4.9 23.0 1.0

Reference:

W.Tempel, Z.-J.Liu, F.D.Schubot, A.Shah, M.V.Weinberg, F.E.Jenney Jr., W.B.Arendall Iii, M.W.Adams, J.S.Richardson, D.C.Richardson, J.P.Rose, B.-C.Wang. Structural Genomics of Pyrococcus Furiosus: X-Ray Crystallography Reveals 3D Domain Swapping in Rubrerythrin Proteins V. 57 878 2004.
ISSN: ISSN 0887-3585
PubMed: 15468318
DOI: 10.1002/PROT.20280
Page generated: Wed Dec 16 02:58:44 2020

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