Zinc in PDB 4gdf: A Crystal Structure of SV40 Large T Antigen

The structure of A Crystal Structure of SV40 Large T Antigen, PDB code: 4gdf was solved by Y.P.Chang, M.Xu, X.S.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.633, 128.307, 166.120, 90.00, 89.91, 90.00
R / Rfree (%)	22.7 / 25.5

The binding sites of Zinc atom in the A Crystal Structure of SV40 Large T Antigen (pdb code 4gdf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the A Crystal Structure of SV40 Large T Antigen, PDB code: 4gdf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the A Crystal Structure of SV40 Large T Antigen


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A Crystal Structure of SV40 Large T Antigen within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn700 b:58.5 occ:1.00 SG A:CYS302 2.2 62.1 1.0 SG A:CYS305 2.4 66.0 1.0 ND1 A:HIS317 2.4 49.3 1.0 NE2 A:HIS313 2.5 53.0 1.0 CD2 A:HIS313 3.1 54.4 1.0 CB A:CYS305 3.2 67.1 1.0 CE1 A:HIS317 3.3 48.5 1.0 CG A:HIS317 3.4 49.0 1.0 CB A:CYS302 3.5 68.9 1.0 CE1 A:HIS313 3.6 54.8 1.0 N A:CYS305 3.6 65.9 1.0 CB A:HIS317 3.7 48.9 1.0 CA A:CYS305 3.8 67.6 1.0 CB A:LYS304 4.3 62.8 1.0 C A:LYS304 4.3 63.9 1.0 CG A:HIS313 4.3 55.2 1.0 NE2 A:HIS317 4.5 51.4 1.0 ND1 A:HIS313 4.5 55.2 1.0 CD2 A:HIS317 4.6 50.5 1.0 CD1 A:PHE299 4.7 80.9 1.0 CA A:LYS304 4.8 63.9 1.0 O A:CYS302 4.8 69.8 1.0 CA A:CYS302 4.8 70.1 1.0

Zinc binding site 2 out of 4 in the A Crystal Structure of SV40 Large T Antigen


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A Crystal Structure of SV40 Large T Antigen within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn700 b:68.7 occ:1.00 ND1 B:HIS317 2.2 59.7 1.0 SG B:CYS305 2.5 73.0 1.0 NE2 B:HIS313 2.6 71.3 1.0 SG B:CYS302 2.6 74.5 1.0 CD2 B:HIS313 2.9 70.9 1.0 CE1 B:HIS317 3.1 59.6 1.0 CG B:HIS317 3.2 59.3 1.0 CB B:CYS305 3.3 77.2 1.0 CB B:HIS317 3.5 59.1 1.0 N B:CYS305 3.6 78.3 1.0 CE1 B:HIS313 3.7 72.1 1.0 CA B:CYS305 3.8 78.1 1.0 CB B:CYS302 3.9 78.3 1.0 CG B:HIS313 4.1 72.8 1.0 NE2 B:HIS317 4.2 59.1 1.0 CD2 B:HIS317 4.3 58.8 1.0 CB B:LYS304 4.4 78.9 1.0 ND1 B:HIS313 4.5 73.6 1.0 C B:LYS304 4.5 78.0 1.0 O B:HIS313 4.8 74.8 1.0 CA B:TYR314 4.9 72.1 1.0 CA B:LYS304 4.9 78.3 1.0

Zinc binding site 3 out of 4 in the A Crystal Structure of SV40 Large T Antigen


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of A Crystal Structure of SV40 Large T Antigen within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn700 b:59.0 occ:1.00 SG E:CYS302 2.3 61.4 1.0 NE2 E:HIS313 2.4 53.0 1.0 SG E:CYS305 2.4 64.0 1.0 ND1 E:HIS317 2.5 51.1 1.0 CD2 E:HIS313 3.1 54.7 1.0 CB E:CYS305 3.2 66.4 1.0 CE1 E:HIS317 3.3 50.6 1.0 CG E:HIS317 3.5 51.3 1.0 CE1 E:HIS313 3.5 54.7 1.0 CB E:CYS302 3.5 69.2 1.0 N E:CYS305 3.6 65.6 1.0 CB E:HIS317 3.8 50.6 1.0 CA E:CYS305 3.8 67.2 1.0 CB E:LYS304 4.2 63.2 1.0 CG E:HIS313 4.3 55.8 1.0 C E:LYS304 4.3 63.9 1.0 ND1 E:HIS313 4.4 56.0 1.0 NE2 E:HIS317 4.5 52.3 1.0 CD2 E:HIS317 4.6 52.0 1.0 CA E:LYS304 4.8 63.9 1.0 CD1 E:PHE299 4.8 81.7 1.0 O E:CYS302 4.9 70.6 1.0 CA E:CYS302 4.9 70.9 1.0

Zinc binding site 4 out of 4 in the A Crystal Structure of SV40 Large T Antigen


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of A Crystal Structure of SV40 Large T Antigen within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn700 b:69.1 occ:1.00 ND1 F:HIS317 2.3 59.4 1.0 SG F:CYS302 2.4 76.1 1.0 SG F:CYS305 2.5 72.4 1.0 NE2 F:HIS313 2.6 71.7 1.0 CD2 F:HIS313 3.0 71.9 1.0 CE1 F:HIS317 3.2 59.3 1.0 CB F:CYS305 3.3 77.3 1.0 CG F:HIS317 3.4 59.6 1.0 N F:CYS305 3.5 78.0 1.0 CB F:HIS317 3.7 59.6 1.0 CE1 F:HIS313 3.7 72.0 1.0 CA F:CYS305 3.7 78.1 1.0 CB F:CYS302 3.8 78.8 1.0 CG F:HIS313 4.2 73.0 1.0 CB F:LYS304 4.3 78.9 1.0 NE2 F:HIS317 4.3 58.8 1.0 C F:LYS304 4.4 77.7 1.0 CD2 F:HIS317 4.4 59.0 1.0 ND1 F:HIS313 4.5 73.4 1.0 CA F:LYS304 4.8 78.4 1.0

Y.P.Chang, M.Xu, A.C.Machado, X.J.Yu, R.Rohs, X.S.Chen. Mechanism of Origin Dna Recognition and Assembly of An Initiator-Helicase Complex By SV40 Large Tumor Antigen. Cell Rep V. 3 1117 2013.
ISSN: ESSN 2211-1247
PubMed: 23545501
DOI: 10.1016/J.CELREP.2013.03.002