Zinc in PDB 1svl: Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Adp

The structure of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Adp, PDB code: 1svl was solved by D.Gai, R.Zhao, C.V.Finkielstein, X.S.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	195.812, 86.442, 128.601, 90.00, 129.00, 90.00
R / Rfree (%)	23.6 / 26.4

The structure of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Adp also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

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

Zinc binding site 1 out of 3 in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Adp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn700 b:33.4 occ:1.00 ND1 A:HIS317 2.0 23.6 1.0 NE2 A:HIS313 2.2 33.7 1.0 SG A:CYS305 2.2 38.1 1.0 SG A:CYS302 2.3 31.8 1.0 CE1 A:HIS317 2.9 25.4 1.0 CG A:HIS317 3.0 25.6 1.0 CD2 A:HIS313 3.1 32.4 1.0 CE1 A:HIS313 3.2 33.1 1.0 CB A:CYS302 3.2 38.0 1.0 CB A:CYS305 3.3 40.6 1.0 CB A:HIS317 3.4 27.4 1.0 N A:CYS305 3.6 40.8 1.0 CA A:CYS305 3.9 41.3 1.0 NE2 A:HIS317 4.0 23.6 1.0 CD2 A:HIS317 4.1 23.9 1.0 CG A:HIS313 4.2 31.9 1.0 ND1 A:HIS313 4.2 31.7 1.0 CB A:LYS304 4.4 42.0 1.0 C A:LYS304 4.4 40.6 1.0 CD1 A:PHE299 4.4 48.4 1.0 CA A:CYS302 4.6 37.6 1.0 CA A:LYS304 4.8 41.6 1.0 O A:HOH168 4.9 40.6 1.0 CA A:HIS317 4.9 29.8 1.0 C A:CYS302 5.0 38.1 1.0 CE1 A:PHE299 5.0 48.8 1.0 N A:LYS304 5.0 40.8 1.0 O A:CYS302 5.0 35.7 1.0

Zinc binding site 2 out of 3 in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Adp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn700 b:36.1 occ:1.00 SG B:CYS305 2.0 36.8 1.0 SG B:CYS302 2.2 44.0 1.0 ND1 B:HIS317 2.2 31.3 1.0 NE2 B:HIS313 2.3 35.4 1.0 CD2 B:HIS313 3.1 36.7 1.0 CG B:HIS317 3.1 31.3 1.0 CE1 B:HIS317 3.2 33.5 1.0 CB B:CYS302 3.2 49.1 1.0 CE1 B:HIS313 3.3 36.6 1.0 CB B:CYS305 3.3 42.0 1.0 CB B:HIS317 3.4 32.8 1.0 N B:CYS305 3.7 41.9 1.0 CA B:CYS305 4.0 42.0 1.0 NE2 B:HIS317 4.3 30.8 1.0 CD2 B:HIS317 4.3 30.4 1.0 CG B:HIS313 4.3 35.8 1.0 CB B:LYS304 4.3 43.9 1.0 ND1 B:HIS313 4.4 36.7 1.0 CD1 B:PHE299 4.5 57.5 1.0 C B:LYS304 4.5 41.8 1.0 CA B:CYS302 4.6 49.7 1.0 CA B:LYS304 4.8 42.9 1.0 CA B:HIS317 4.9 34.2 1.0 C B:CYS302 4.9 47.8 1.0 O B:CYS302 4.9 46.2 1.0 N B:LYS304 5.0 45.0 1.0 CE1 B:PHE299 5.0 57.4 1.0

Zinc binding site 3 out of 3 in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Adp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Adp within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn700 b:24.4 occ:1.00 SG C:CYS302 1.9 21.4 1.0 CD2 C:HIS317 2.2 13.7 1.0 NE2 C:HIS313 2.3 25.3 1.0 SG C:CYS305 2.4 26.3 1.0 CG C:HIS317 3.1 16.5 1.0 CD2 C:HIS313 3.1 21.0 1.0 CB C:CYS302 3.2 26.8 1.0 CB C:CYS305 3.2 26.1 1.0 NE2 C:HIS317 3.2 18.3 1.0 CE1 C:HIS313 3.3 26.3 1.0 CB C:HIS317 3.5 15.3 1.0 N C:CYS305 3.6 27.1 1.0 CA C:CYS305 3.9 25.2 1.0 ND1 C:HIS317 4.2 18.9 1.0 CG C:HIS313 4.3 24.4 1.0 CE1 C:HIS317 4.3 13.1 1.0 CB C:LYS304 4.3 27.8 1.0 ND1 C:HIS313 4.3 25.7 1.0 C C:LYS304 4.5 28.4 1.0 CA C:CYS302 4.6 29.1 1.0 CB C:PHE299 4.8 28.0 1.0 O C:CYS302 4.9 30.5 1.0 C C:CYS302 4.9 29.5 1.0 CA C:LYS304 4.9 28.6 1.0 CA C:PHE299 5.0 29.7 1.0 O C:HOH60 5.0 27.7 1.0 CA C:HIS317 5.0 22.1 1.0

D.Gai, R.Zhao, D.Li, C.V.Finkielstein, X.S.Chen. Mechanisms of Conformational Change For A Replicative Hexameric Helicase of SV40 Large Tumor Antigen. Cell(Cambridge,Mass.) V. 119 47 2004.
ISSN: ISSN 0092-8674
PubMed: 15454080
DOI: 10.1016/J.CELL.2004.09.017