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Zinc in PDB 3cvd: Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization

Protein crystallography data

The structure of Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization, PDB code: 3cvd was solved by P.B.Crowley, P.M.Matias, H.Mi, S.J.Firbank, M.J.Banfield, C.Dennison, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.77 / 1.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 85.843, 85.843, 90.282, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 18.4

Other elements in 3cvd:

The structure of Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization also contains other interesting chemical elements:

Copper (Cu) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization (pdb code 3cvd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization, PDB code: 3cvd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3cvd

Go back to Zinc Binding Sites List in 3cvd
Zinc binding site 1 out of 4 in the Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn107

b:12.2
occ:1.00
OD1 A:ASP44 2.0 11.4 1.0
O A:HOH226 2.0 13.5 1.0
OD1 A:ASP45 2.1 10.8 1.0
O A:HOH225 2.2 13.9 1.0
CG A:ASP44 2.7 12.0 1.0
OD2 A:ASP44 2.9 12.6 1.0
CG A:ASP45 3.1 11.7 1.0
OD2 A:ASP45 3.5 13.6 1.0
O A:HOH212 4.1 16.4 1.0
N A:ASP45 4.1 11.4 1.0
CB A:ASP44 4.2 10.5 1.0
CB A:ASP45 4.4 11.4 1.0
CA A:ASP44 4.8 10.8 1.0
N A:LYS46 4.8 12.0 1.0
CA A:ASP45 4.8 11.7 1.0
C A:ASP44 4.9 11.3 1.0
O A:HOH121 4.9 20.7 1.0

Zinc binding site 2 out of 4 in 3cvd

Go back to Zinc Binding Sites List in 3cvd
Zinc binding site 2 out of 4 in the Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn108

b:18.8
occ:0.50
NE2 A:HIS24 2.1 27.1 1.0
O A:HOH275 2.1 17.5 0.5
CE1 A:HIS24 3.0 27.0 1.0
CD2 A:HIS24 3.1 25.1 1.0
O A:GLU104 4.1 30.7 1.0
ND1 A:HIS24 4.1 25.4 1.0
CG A:HIS24 4.2 24.7 1.0
C A:GLU104 4.7 28.6 1.0

Zinc binding site 3 out of 4 in 3cvd

Go back to Zinc Binding Sites List in 3cvd
Zinc binding site 3 out of 4 in the Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn106

b:14.8
occ:1.00
OD1 C:ASP44 2.0 14.8 1.0
O C:HOH181 2.0 16.3 1.0
NE2 A:HIS61 2.0 12.4 1.0
O C:HOH182 2.1 17.6 1.0
OD1 C:ASP45 2.1 14.6 1.0
CG C:ASP44 2.8 14.9 1.0
OD2 C:ASP44 2.9 16.6 1.0
CE1 A:HIS61 3.0 13.4 1.0
CD2 A:HIS61 3.0 12.9 1.0
CG C:ASP45 3.1 15.3 1.0
OD2 C:ASP45 3.5 16.2 1.0
O C:HOH116 4.1 18.3 1.0
ND1 A:HIS61 4.1 12.3 1.0
N C:ASP45 4.1 14.0 1.0
CG A:HIS61 4.2 11.7 1.0
O A:HOH173 4.2 28.4 1.0
CB C:ASP44 4.2 15.0 1.0
CB C:ASP45 4.4 14.9 1.0
O A:SER71 4.6 15.6 1.0
CA C:ASP45 4.8 15.4 1.0
CA C:ASP44 4.8 14.4 1.0
N C:LYS46 4.8 17.0 1.0
C C:ASP44 4.9 14.4 1.0
SD A:MET65 5.0 18.9 0.5

Zinc binding site 4 out of 4 in 3cvd

Go back to Zinc Binding Sites List in 3cvd
Zinc binding site 4 out of 4 in the Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn108

b:14.7
occ:1.00
NE2 C:HIS61 2.1 14.0 1.0
O C:HOH180 2.1 17.9 1.0
CE1 C:HIS61 3.0 12.0 1.0
CD2 C:HIS61 3.1 13.9 1.0
O C:HOH223 3.8 34.8 1.0
ND1 C:HIS61 4.2 11.7 1.0
CG C:HIS61 4.2 12.2 1.0
O C:HOH192 4.3 41.1 1.0
O C:SER71 4.9 19.8 1.0
SD C:MET65 4.9 19.3 0.4
CG C:MET65 5.0 16.3 0.4

Reference:

P.B.Crowley, P.M.Matias, H.Mi, S.J.Firbank, M.J.Banfield, C.Dennison. Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization. Biochemistry V. 47 6583 2008.
ISSN: ISSN 0006-2960
PubMed: 18479147
DOI: 10.1021/BI800125H
Page generated: Wed Dec 16 04:11:25 2020

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