Atomistry » Zinc » PDB 1cp6-1d4u » 1cpr
Atomistry »
  Zinc »
    PDB 1cp6-1d4u »
      1cpr »

Zinc in PDB 1cpr: St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus

Protein crystallography data

The structure of St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus, PDB code: 1cpr was solved by T.H.Tahirov, S.Misaki, T.E.Meyer, M.A.Cusanovich, N.Yasuoka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.680, 46.850, 40.750, 90.00, 110.94, 90.00
R / Rfree (%) 18.4 / n/a

Other elements in 1cpr:

The structure of St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus also contains other interesting chemical elements:

Iron (Fe) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus (pdb code 1cpr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus, PDB code: 1cpr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1cpr

Go back to Zinc Binding Sites List in 1cpr
Zinc binding site 1 out of 6 in the St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn130

b:16.1
occ:1.00
OE1 A:GLU34 2.0 8.7 1.0
OD1 A:ASP32 2.1 11.4 1.0
CG A:ASP32 2.9 14.2 1.0
OD2 A:ASP32 3.0 12.5 1.0
ZN A:ZN131 3.2 23.0 0.3
CD A:GLU34 3.2 12.6 1.0
CG A:GLU34 3.8 12.5 1.0
CB A:GLU34 3.9 10.4 1.0
O A:HOH137 4.0 5.6 1.0
OE2 A:GLU34 4.2 16.4 1.0
N A:GLU34 4.3 9.6 1.0
CB A:ASP32 4.4 13.0 1.0
CA A:GLU34 4.7 12.3 1.0
N A:ALA33 4.8 10.5 1.0
CA A:ASP32 5.0 13.2 1.0

Zinc binding site 2 out of 6 in 1cpr

Go back to Zinc Binding Sites List in 1cpr
Zinc binding site 2 out of 6 in the St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn131

b:23.0
occ:0.35
O A:HOH137 2.9 5.6 1.0
ZN A:ZN130 3.2 16.1 1.0
OE1 A:GLU34 3.7 8.7 1.0
CD A:GLU34 4.5 12.6 1.0
OD1 A:ASP32 4.7 11.4 1.0
OE2 A:GLU34 4.8 16.4 1.0

Zinc binding site 3 out of 6 in 1cpr

Go back to Zinc Binding Sites List in 1cpr
Zinc binding site 3 out of 6 in the St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn132

b:13.5
occ:0.70
ND1 A:HIS122 2.1 7.5 1.0
O A:HOH148 2.4 15.0 1.0
CE1 A:HIS122 3.1 9.4 1.0
CG A:HIS122 3.1 6.3 1.0
CB A:HIS122 3.5 9.0 1.0
NE2 A:HIS122 4.2 8.5 1.0
CD2 A:HIS122 4.3 6.6 1.0
NH1 A:ARG126 4.3 20.2 1.0
O A:CYS118 4.5 8.8 1.0
CA A:LYS119 4.6 11.5 1.0
C A:CYS118 4.7 9.9 1.0
N A:LYS119 4.8 8.8 1.0

Zinc binding site 4 out of 6 in 1cpr

Go back to Zinc Binding Sites List in 1cpr
Zinc binding site 4 out of 6 in the St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn133

b:28.2
occ:0.45
OE2 A:GLU11 2.1 29.5 1.0
O2A A:HEM136 2.1 32.6 1.0
O1A A:HEM136 2.4 31.0 1.0
CGA A:HEM136 2.6 25.6 1.0
CD A:GLU11 3.2 27.6 1.0
CG A:GLU11 3.6 23.8 1.0
CE A:LYS15 4.1 35.8 1.0
CBA A:HEM136 4.1 22.5 1.0
O A:HOH179 4.1 42.0 1.0
OE1 A:GLU11 4.3 30.9 1.0
NZ A:LYS15 4.7 41.9 1.0
CB A:GLU11 4.7 12.1 1.0
CAA A:HEM136 4.8 13.7 1.0

Zinc binding site 5 out of 6 in 1cpr

Go back to Zinc Binding Sites List in 1cpr
Zinc binding site 5 out of 6 in the St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn134

b:27.8
occ:0.31
ND1 A:HIS89 2.1 28.0 1.0
CG A:HIS89 3.0 24.6 1.0
O A:HOH182 3.1 36.1 1.0
CB A:HIS89 3.2 19.0 1.0
CE1 A:HIS89 3.2 27.8 1.0
O A:LEU47 3.8 22.1 1.0
O A:HOH141 4.0 32.5 1.0
CA A:HIS89 4.1 16.7 1.0
CB A:LEU47 4.2 16.9 1.0
CD2 A:HIS89 4.2 27.6 1.0
NE2 A:HIS89 4.3 29.9 1.0
O A:HIS89 4.5 16.9 1.0
C A:HIS89 4.6 15.8 1.0
C A:LEU47 4.7 22.2 1.0
CD1 A:LEU47 4.7 17.1 1.0
CG A:LEU47 5.0 15.9 1.0

Zinc binding site 6 out of 6 in 1cpr

Go back to Zinc Binding Sites List in 1cpr
Zinc binding site 6 out of 6 in the St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn135

b:28.1
occ:0.25
NE2 A:HIS89 2.1 29.9 1.0
O A:HOH183 2.5 31.3 1.0
O A:HOH172 2.6 41.3 1.0
CE1 A:HIS89 3.0 27.8 1.0
CD2 A:HIS89 3.2 27.6 1.0
OH A:TYR13 3.2 12.6 1.0
O A:THR49 3.6 25.7 1.0
CG1 A:VAL51 3.9 30.0 1.0
CG2 A:VAL51 4.0 31.4 1.0
ND1 A:HIS89 4.2 28.0 1.0
CZ A:TYR13 4.3 10.6 1.0
CG A:HIS89 4.3 24.6 1.0
CE A:MET88 4.4 13.1 1.0
CB A:VAL51 4.6 30.3 1.0
N A:VAL51 4.7 27.1 1.0
O A:LEU47 4.8 22.1 1.0
C A:THR49 4.8 28.7 1.0
O A:GLY85 5.0 16.5 1.0
CE1 A:TYR13 5.0 10.2 1.0

Reference:

T.H.Tahirov, S.Misaki, T.E.Meyer, M.A.Cusanovich, Y.Higuchi, N.Yasuoka. Structure of Cytochrome C' From Rhodobacter Capsulatus Strain St Louis: An Unusual Molecular Association Induced By Bridging Zn Ions. Acta Crystallogr.,Sect.D V. 53 658 1997.
ISSN: ISSN 0907-4449
PubMed: 15299853
DOI: 10.1107/S0907444997005805
Page generated: Mon Jan 25 16:08:06 2021

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy