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Zinc in PDB 3eb5: Structure of the CIAP2 Ring Domain

Protein crystallography data

The structure of Structure of the CIAP2 Ring Domain, PDB code: 3eb5 was solved by P.D.Mace, K.Linke, C.A.Smith, C.L.Day, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.69 / 2.00
Space group C 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 34.869, 66.474, 77.465, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 27.5

Other elements in 3eb5:

The structure of Structure of the CIAP2 Ring Domain also contains other interesting chemical elements:

Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the CIAP2 Ring Domain (pdb code 3eb5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of the CIAP2 Ring Domain, PDB code: 3eb5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3eb5

Go back to Zinc Binding Sites List in 3eb5
Zinc binding site 1 out of 2 in the Structure of the CIAP2 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the CIAP2 Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:65.0
occ:1.00
SG A:CYS581 2.2 65.5 1.0
SG A:CYS578 2.2 66.3 1.0
SG A:CYS557 2.4 58.5 1.0
SG A:CYS560 2.5 62.2 1.0
CB A:CYS557 3.1 60.6 1.0
CB A:CYS581 3.2 64.1 1.0
CB A:CYS560 3.3 63.0 1.0
CB A:CYS578 3.4 64.8 1.0
N A:CYS578 3.8 65.0 1.0
N A:CYS560 3.9 62.9 1.0
CA A:CYS578 4.2 65.3 1.0
CA A:CYS560 4.2 63.1 1.0
N A:CYS581 4.2 65.0 1.0
CG2 A:VAL559 4.3 61.7 1.0
CA A:CYS581 4.3 64.2 1.0
CA A:CYS557 4.6 60.7 1.0
C A:CYS578 4.7 65.5 1.0
O A:CYS578 4.8 64.5 1.0
CB A:LYS563 4.9 64.4 1.0
C A:VAL577 5.0 64.7 1.0

Zinc binding site 2 out of 2 in 3eb5

Go back to Zinc Binding Sites List in 3eb5
Zinc binding site 2 out of 2 in the Structure of the CIAP2 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the CIAP2 Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:60.5
occ:1.00
ND1 A:HIS574 2.0 65.4 1.0
SG A:CYS591 2.1 52.6 1.0
SG A:CYS572 2.2 58.9 1.0
SG A:CYS588 2.4 59.2 1.0
CE1 A:HIS574 3.0 65.1 1.0
CB A:CYS572 3.0 62.7 1.0
CB A:CYS588 3.0 60.8 1.0
CG A:HIS574 3.1 64.2 1.0
CB A:HIS574 3.5 64.1 1.0
CB A:CYS591 3.7 59.4 1.0
OG A:SER593 3.9 61.4 0.3
N A:CYS591 4.0 61.3 1.0
NE2 A:HIS574 4.1 65.3 1.0
CD2 A:HIS574 4.2 64.5 1.0
CA A:CYS591 4.4 59.8 1.0
N A:HIS574 4.4 63.1 1.0
CA A:CYS572 4.4 62.8 1.0
CA A:CYS588 4.5 61.5 1.0
CA A:HIS574 4.6 63.6 1.0
C A:CYS591 4.6 60.7 1.0
CD2 A:PHE569 4.6 65.1 1.0
OG A:SER593 4.7 61.3 0.7
C A:CYS572 4.7 62.9 1.0
CB A:ILE590 4.7 63.3 1.0
CB A:SER593 4.8 61.8 0.1
N A:SER593 4.9 61.9 1.0
O A:CYS591 4.9 61.8 1.0
NA A:NA1 5.0 49.3 1.0
O A:CYS572 5.0 63.0 1.0
N A:ARG592 5.0 61.4 1.0

Reference:

P.D.Mace, K.Linke, R.Feltham, F.R.Schumacher, C.A.Smith, D.L.Vaux, J.Silke, C.L.Day. Structures of the CIAP2 Ring Domain Reveal Conformational Changes Associated with Ubiquitin-Conjugating Enzyme (E2) Recruitment. J.Biol.Chem. V. 283 31633 2008.
ISSN: ISSN 0021-9258
PubMed: 18784070
DOI: 10.1074/JBC.M804753200
Page generated: Wed Dec 16 04:15:22 2020

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