Zinc in PDB 4tkp: Complex of UBC13 with the Ring Domain of the TRIM5ALPHA Retroviral Restriction Factor

All present enzymatic activity of Complex of UBC13 with the Ring Domain of the TRIM5ALPHA Retroviral Restriction Factor:
6.3.2.19;

The structure of Complex of UBC13 with the Ring Domain of the TRIM5ALPHA Retroviral Restriction Factor, PDB code: 4tkp was solved by R.Johnson, A.B.Taylor, P.J.Hart, D.N.Ivanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.93 / 2.08
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.170, 78.170, 82.562, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 25.5

The binding sites of Zinc atom in the Complex of UBC13 with the Ring Domain of the TRIM5ALPHA Retroviral Restriction Factor (pdb code 4tkp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Complex of UBC13 with the Ring Domain of the TRIM5ALPHA Retroviral Restriction Factor, PDB code: 4tkp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Complex of UBC13 with the Ring Domain of the TRIM5ALPHA Retroviral Restriction Factor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complex of UBC13 with the Ring Domain of the TRIM5ALPHA Retroviral Restriction Factor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:59.7 occ:1.00 ND1 B:HIS32 2.1 45.0 1.0 SG B:CYS59 2.3 52.0 1.0 SG B:CYS56 2.4 46.9 1.0 SG B:CYS30 2.4 49.3 1.0 CE1 B:HIS32 3.1 59.0 1.0 CG B:HIS32 3.2 54.5 1.0 CB B:CYS56 3.2 47.5 1.0 CB B:CYS59 3.2 40.4 1.0 CB B:CYS30 3.4 56.3 1.0 CB B:HIS32 3.5 49.6 1.0 N B:CYS59 3.6 47.1 1.0 CA B:CYS59 4.0 50.8 1.0 NE2 B:HIS32 4.2 50.6 1.0 CD2 B:HIS32 4.3 51.1 1.0 CB B:VAL58 4.4 50.3 1.0 CD1 B:LEU28 4.4 57.7 1.0 N B:HIS32 4.6 49.2 1.0 C B:VAL58 4.7 53.4 1.0 CA B:HIS32 4.7 41.0 1.0 CA B:CYS56 4.7 63.4 1.0 CA B:CYS30 4.7 57.6 1.0 C B:CYS59 4.7 45.0 1.0 N B:ARG60 4.8 49.0 1.0 CG1 B:VAL58 4.9 46.2 1.0 C B:CYS30 4.9 53.2 1.0 CA B:VAL58 4.9 46.2 1.0 N B:VAL58 5.0 49.8 1.0

Zinc binding site 2 out of 2 in the Complex of UBC13 with the Ring Domain of the TRIM5ALPHA Retroviral Restriction Factor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complex of UBC13 with the Ring Domain of the TRIM5ALPHA Retroviral Restriction Factor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:75.3 occ:1.00 SG B:CYS18 2.3 59.0 1.0 SG B:CYS38 2.3 62.3 1.0 SG B:CYS15 2.5 50.0 1.0 SG B:CYS35 2.8 55.8 1.0 CB B:CYS18 3.0 60.6 1.0 CB B:CYS15 3.1 51.1 1.0 CB B:CYS35 3.2 47.7 1.0 N B:CYS18 3.5 53.9 1.0 CB B:CYS38 3.7 62.3 1.0 CA B:CYS18 3.9 50.6 1.0 N B:CYS35 4.2 59.1 1.0 CA B:CYS35 4.3 64.7 1.0 CB B:ILE17 4.5 52.5 1.0 CA B:CYS15 4.6 53.4 1.0 C B:ILE17 4.7 55.5 1.0 C B:CYS18 4.7 54.8 1.0 N B:LEU19 4.9 45.2 1.0 O B:CYS15 4.9 61.6 1.0 C B:CYS15 4.9 58.8 1.0 CA B:CYS38 5.0 73.3 1.0 CA B:ILE17 5.0 50.6 1.0

Z.Yudina, R.Johnson, A.Roa, N.Biris, V.Tsiperson, A.B.Taylor, P.J.Hart, B.Demeler, F.Diaz-Griffero, D.N.Ivanov. Activation of the UBC13-Ub Adduct By the Ring Domain of the TRIM5ALPHA Retroviral Restriction Factor Offers Insight Into the Mechanism of Molecular Pattern Recognition By Trim Proteins Cell Rep 2015.
ISSN: ESSN 2211-1247