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Zinc in PDB 1i55: Cytochrome C (Tuna) with 2ZN:1FE Mixed-Metal Porphyrins

Protein crystallography data

The structure of Cytochrome C (Tuna) with 2ZN:1FE Mixed-Metal Porphyrins, PDB code: 1i55 was solved by B.R.Crane, F.A.Tezcan, J.R.Winkler, H.B.Gray, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.64 / 2.00
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 74.359, 74.359, 35.703, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 24.7

Other elements in 1i55:

The structure of Cytochrome C (Tuna) with 2ZN:1FE Mixed-Metal Porphyrins also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Cytochrome C (Tuna) with 2ZN:1FE Mixed-Metal Porphyrins (pdb code 1i55). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cytochrome C (Tuna) with 2ZN:1FE Mixed-Metal Porphyrins, PDB code: 1i55:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1i55

Go back to Zinc Binding Sites List in 1i55
Zinc binding site 1 out of 2 in the Cytochrome C (Tuna) with 2ZN:1FE Mixed-Metal Porphyrins


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cytochrome C (Tuna) with 2ZN:1FE Mixed-Metal Porphyrins within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1105

b:13.6
occ:0.61
ZN A:ZNH1105 0.0 13.6 0.6
FE A:HEM1104 0.0 13.6 0.4
NE2 A:HIS18 2.0 13.6 1.0
ND A:HEM1104 2.0 13.5 0.4
ND A:ZNH1105 2.0 13.6 0.6
NC A:HEM1104 2.0 13.6 0.4
NC A:ZNH1105 2.0 13.6 0.6
NA A:HEM1104 2.0 13.6 0.4
NB A:ZNH1105 2.1 13.6 0.6
NA A:ZNH1105 2.1 13.7 0.6
NB A:HEM1104 2.1 13.6 0.4
SD A:MET80 2.6 13.4 1.0
CE1 A:HIS18 3.0 13.8 1.0
CD2 A:HIS18 3.0 13.9 1.0
C1D A:HEM1104 3.0 13.6 0.4
C1D A:ZNH1105 3.1 13.6 0.6
C1C A:ZNH1105 3.1 13.7 0.6
C4C A:HEM1104 3.1 13.6 0.4
C4A A:HEM1104 3.1 13.6 0.4
C4A A:ZNH1105 3.1 13.7 0.6
C1C A:HEM1104 3.1 13.7 0.4
C1B A:ZNH1105 3.1 13.7 0.6
C4D A:HEM1104 3.1 13.6 0.4
C4C A:ZNH1105 3.1 13.7 0.6
C1B A:HEM1104 3.1 13.6 0.4
C1A A:HEM1104 3.1 13.6 0.4
C4B A:ZNH1105 3.1 13.7 0.6
C4B A:HEM1104 3.1 13.6 0.4
C4D A:ZNH1105 3.1 13.6 0.6
C1A A:ZNH1105 3.1 13.7 0.6
CHB A:ZNH1105 3.4 13.7 0.6
CHD A:HEM1104 3.4 13.6 0.4
CHB A:HEM1104 3.4 13.6 0.4
CHD A:ZNH1105 3.4 13.7 0.6
CHA A:HEM1104 3.4 13.5 0.4
CHC A:ZNH1105 3.4 13.7 0.6
CHC A:HEM1104 3.4 13.6 0.4
CHA A:ZNH1105 3.4 13.6 0.6
CG A:MET80 3.5 12.9 1.0
CE A:MET80 3.6 13.0 1.0
ND1 A:HIS18 4.1 13.8 1.0
CG A:HIS18 4.1 13.9 1.0
C2D A:HEM1104 4.3 13.5 0.4
C2B A:ZNH1105 4.3 13.7 0.6
C3A A:HEM1104 4.3 13.7 0.4
C3A A:ZNH1105 4.3 13.7 0.6
C2D A:ZNH1105 4.3 13.6 0.6
C2C A:HEM1104 4.3 13.7 0.4
C2C A:ZNH1105 4.3 13.8 0.6
C2A A:HEM1104 4.3 13.7 0.4
C2B A:HEM1104 4.3 13.6 0.4
C3D A:HEM1104 4.3 13.5 0.4
C3B A:ZNH1105 4.3 13.7 0.6
C2A A:ZNH1105 4.3 13.7 0.6
C3C A:HEM1104 4.3 13.7 0.4
C3B A:HEM1104 4.3 13.6 0.4
C3C A:ZNH1105 4.3 13.7 0.6
C3D A:ZNH1105 4.3 13.6 0.6
CB A:MET80 4.4 12.8 1.0
OH A:TYR67 5.0 15.2 1.0

Zinc binding site 2 out of 2 in 1i55

Go back to Zinc Binding Sites List in 1i55
Zinc binding site 2 out of 2 in the Cytochrome C (Tuna) with 2ZN:1FE Mixed-Metal Porphyrins


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cytochrome C (Tuna) with 2ZN:1FE Mixed-Metal Porphyrins within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1107

b:14.2
occ:0.61
ZN B:ZNH1107 0.0 14.2 0.6
FE B:HEM1106 0.0 14.0 0.4
NB B:HEM1106 2.0 14.1 0.4
NE2 B:HIS18 2.0 14.4 1.0
NB B:ZNH1107 2.0 14.1 0.6
NA B:HEM1106 2.0 14.0 0.4
NA B:ZNH1107 2.0 14.1 0.6
NC B:ZNH1107 2.1 14.1 0.6
ND B:ZNH1107 2.1 13.9 0.6
NC B:HEM1106 2.1 14.0 0.4
ND B:HEM1106 2.1 13.9 0.4
SD B:MET80 2.4 13.7 1.0
CD2 B:HIS18 3.0 14.8 1.0
CE1 B:HIS18 3.0 14.8 1.0
C1B B:HEM1106 3.0 14.1 0.4
C4A B:HEM1106 3.0 14.1 0.4
C4A B:ZNH1107 3.1 14.2 0.6
C1B B:ZNH1107 3.1 14.2 0.6
C4B B:HEM1106 3.1 14.2 0.4
C4B B:ZNH1107 3.1 14.2 0.6
C1A B:HEM1106 3.1 14.0 0.4
C4D B:ZNH1107 3.1 13.9 0.6
C1C B:ZNH1107 3.1 14.1 0.6
C1D B:ZNH1107 3.1 13.9 0.6
C1C B:HEM1106 3.1 14.1 0.4
C1A B:ZNH1107 3.1 14.1 0.6
C4D B:HEM1106 3.1 13.9 0.4
C4C B:ZNH1107 3.1 14.1 0.6
C1D B:HEM1106 3.1 13.9 0.4
C4C B:HEM1106 3.1 14.0 0.4
CHB B:HEM1106 3.4 14.1 0.4
CHB B:ZNH1107 3.4 14.2 0.6
CHA B:ZNH1107 3.4 14.0 0.6
CHD B:ZNH1107 3.4 14.0 0.6
CHA B:HEM1106 3.4 13.9 0.4
CE B:MET80 3.4 13.4 1.0
CHC B:HEM1106 3.4 14.1 0.4
CHD B:HEM1106 3.4 13.9 0.4
CHC B:ZNH1107 3.4 14.2 0.6
CG B:MET80 3.5 13.2 1.0
ND1 B:HIS18 4.1 14.8 1.0
CG B:HIS18 4.1 14.9 1.0
C2B B:HEM1106 4.3 14.2 0.4
C3A B:HEM1106 4.3 14.1 0.4
C3A B:ZNH1107 4.3 14.2 0.6
C3D B:ZNH1107 4.3 13.9 0.6
C2A B:HEM1106 4.3 14.1 0.4
C2B B:ZNH1107 4.3 14.3 0.6
C2D B:ZNH1107 4.3 13.9 0.6
C3B B:HEM1106 4.3 14.2 0.4
C3D B:HEM1106 4.3 13.8 0.4
C2A B:ZNH1107 4.3 14.2 0.6
C3B B:ZNH1107 4.3 14.3 0.6
C2D B:HEM1106 4.3 13.8 0.4
C2C B:ZNH1107 4.3 14.1 0.6
C2C B:HEM1106 4.3 14.1 0.4
C3C B:ZNH1107 4.3 14.1 0.6
C3C B:HEM1106 4.3 14.0 0.4
CB B:MET80 4.4 13.2 1.0
OH B:TYR67 4.9 13.7 1.0

Reference:

F.A.Tezcan, B.R.Crane, J.R.Winkler, H.B.Gray. Electron Tunneling in Protein Crystals. Proc.Natl.Acad.Sci.Usa V. 98 5002 2001.
ISSN: ISSN 0027-8424
PubMed: 11296248
DOI: 10.1073/PNAS.081072898
Page generated: Wed Dec 16 02:52:17 2020

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