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

The structure of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp, PDB code: 1svm 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 / 1.94
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	125.021, 89.377, 148.506, 90.00, 91.31, 90.00
R / Rfree (%)	21.8 / 24.1

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

Magnesium

(Mg)

6 atoms

The binding sites of Zinc atom in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp (pdb code 1svm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp, PDB code: 1svm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp


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 Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn700 b:25.9 occ:1.00 ND1 A:HIS317 2.0 23.4 1.0 SG A:CYS305 2.2 28.0 1.0 NE2 A:HIS313 2.2 24.4 1.0 SG A:CYS302 2.3 28.9 1.0 CE1 A:HIS317 2.9 24.8 1.0 CG A:HIS317 3.0 23.5 1.0 CE1 A:HIS313 3.2 25.3 1.0 CB A:CYS302 3.2 30.0 1.0 CD2 A:HIS313 3.2 24.5 1.0 CB A:CYS305 3.3 31.6 1.0 CB A:HIS317 3.4 24.1 1.0 N A:CYS305 3.7 29.4 1.0 CA A:CYS305 3.9 32.0 1.0 NE2 A:HIS317 4.0 24.1 1.0 CD2 A:HIS317 4.1 24.3 1.0 ND1 A:HIS313 4.3 24.3 1.0 CG A:HIS313 4.3 24.4 1.0 CB A:LYS304 4.5 31.4 1.0 C A:LYS304 4.5 30.1 1.0 CA A:CYS302 4.6 29.7 1.0 O A:HOH904 4.8 42.9 1.0 CA A:PHE299 4.9 36.7 1.0 CA A:HIS317 4.9 24.7 1.0 C A:CYS302 4.9 29.5 1.0 CA A:LYS304 5.0 31.1 1.0 O A:CYS302 5.0 30.0 1.0

Zinc binding site 2 out of 6 in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp


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 Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn700 b:23.9 occ:1.00 ND1 B:HIS317 2.1 18.4 1.0 SG B:CYS302 2.2 20.5 1.0 NE2 B:HIS313 2.3 21.7 1.0 SG B:CYS305 2.3 32.6 1.0 CE1 B:HIS317 3.0 19.7 1.0 CB B:CYS302 3.1 24.9 1.0 CG B:HIS317 3.1 19.3 1.0 CD2 B:HIS313 3.2 24.1 1.0 CE1 B:HIS313 3.3 24.1 1.0 CB B:CYS305 3.3 22.7 1.0 CB B:HIS317 3.5 18.9 1.0 N B:CYS305 3.7 26.4 1.0 CA B:CYS305 4.0 26.8 1.0 NE2 B:HIS317 4.2 18.8 1.0 CD2 B:HIS317 4.2 19.0 1.0 CB B:LYS304 4.3 29.3 1.0 CG B:HIS313 4.3 24.1 1.0 ND1 B:HIS313 4.4 24.4 1.0 CA B:CYS302 4.5 26.9 1.0 C B:LYS304 4.6 28.6 1.0 CB B:PHE299 4.8 30.5 1.0 C B:CYS302 4.8 27.0 1.0 O B:CYS302 4.8 25.9 1.0 CA B:LYS304 4.9 30.6 1.0 CA B:PHE299 4.9 30.7 1.0 N B:LYS304 5.0 29.6 1.0 CA B:HIS317 5.0 22.6 1.0

Zinc binding site 3 out of 6 in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp


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 Atp within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn700 b:36.4 occ:1.00 ND1 C:HIS317 2.0 31.9 1.0 NE2 C:HIS313 2.3 36.1 1.0 SG C:CYS302 2.3 60.1 1.0 SG C:CYS305 2.3 42.1 1.0 CE1 C:HIS317 2.9 32.9 1.0 CG C:HIS317 3.0 32.9 1.0 CD2 C:HIS313 3.2 35.8 1.0 CE1 C:HIS313 3.2 34.8 1.0 CB C:CYS302 3.3 66.8 1.0 CB C:HIS317 3.4 36.1 1.0 CB C:CYS305 3.5 48.4 1.0 N C:CYS305 3.7 50.1 1.0 NE2 C:HIS317 4.0 33.4 1.0 CB C:LYS304 4.1 51.0 1.0 CA C:CYS305 4.1 50.3 1.0 CD2 C:HIS317 4.1 32.6 1.0 ND1 C:HIS313 4.3 36.1 1.0 CG C:HIS313 4.3 35.0 1.0 C C:LYS304 4.6 51.0 1.0 CD1 C:PHE299 4.6 69.9 1.0 CA C:CYS302 4.7 68.0 1.0 CA C:LYS304 4.8 52.6 1.0 O C:CYS302 4.9 65.4 1.0 CA C:HIS317 4.9 38.4 1.0 C C:CYS302 5.0 66.5 1.0

Zinc binding site 4 out of 6 in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn700 b:35.0 occ:1.00 ND1 D:HIS317 1.9 23.8 1.0 NE2 D:HIS313 2.2 30.4 1.0 SG D:CYS302 2.3 30.9 1.0 SG D:CYS305 2.4 34.0 1.0 CE1 D:HIS317 2.9 23.6 1.0 CG D:HIS317 3.0 24.8 1.0 CE1 D:HIS313 3.1 28.4 1.0 CB D:CYS302 3.2 35.7 1.0 CD2 D:HIS313 3.2 28.9 1.0 CB D:HIS317 3.4 26.3 1.0 CB D:CYS305 3.4 34.9 1.0 N D:CYS305 3.7 35.2 1.0 NE2 D:HIS317 4.0 24.3 1.0 CA D:CYS305 4.0 36.9 1.0 CD2 D:HIS317 4.0 22.9 1.0 ND1 D:HIS313 4.2 29.1 1.0 CG D:HIS313 4.3 29.4 1.0 CB D:LYS304 4.3 35.2 1.0 C D:LYS304 4.5 35.8 1.0 CA D:CYS302 4.6 36.1 1.0 CA D:LYS304 4.9 36.2 1.0 CA D:HIS317 4.9 25.7 1.0 O D:CYS302 4.9 35.1 1.0 C D:CYS302 4.9 36.2 1.0 CA D:PHE299 4.9 37.7 1.0 N D:LYS304 5.0 36.6 1.0

Zinc binding site 5 out of 6 in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn700 b:27.8 occ:1.00 CD2 E:HIS317 2.0 15.6 1.0 SG E:CYS302 2.3 24.0 1.0 NE2 E:HIS313 2.3 24.0 1.0 SG E:CYS305 2.3 23.6 1.0 CG E:HIS317 3.0 17.5 1.0 NE2 E:HIS317 3.1 19.9 1.0 CB E:CYS302 3.2 26.6 1.0 CD2 E:HIS313 3.2 24.4 1.0 CB E:CYS305 3.3 24.5 1.0 CE1 E:HIS313 3.3 24.1 1.0 CB E:HIS317 3.4 19.1 1.0 N E:CYS305 3.7 23.9 1.0 CA E:CYS305 4.0 24.3 1.0 ND1 E:HIS317 4.1 20.5 1.0 CE1 E:HIS317 4.2 14.9 1.0 CB E:LYS304 4.3 27.6 1.0 CG E:HIS313 4.3 23.4 1.0 ND1 E:HIS313 4.4 24.5 1.0 C E:LYS304 4.5 25.0 1.0 CA E:CYS302 4.6 25.0 1.0 O E:CYS302 4.8 23.5 1.0 CB E:PHE299 4.8 30.1 1.0 C E:CYS302 4.9 24.0 1.0 CA E:LYS304 4.9 26.5 1.0 CA E:HIS317 4.9 22.2 1.0 CA E:PHE299 4.9 30.8 1.0 N E:LYS304 5.0 26.0 1.0

Zinc binding site 6 out of 6 in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn700 b:38.2 occ:1.00 ND1 F:HIS317 1.9 36.2 1.0 NE2 F:HIS313 2.2 31.9 1.0 SG F:CYS302 2.2 55.0 1.0 SG F:CYS305 2.3 44.7 1.0 CE1 F:HIS317 2.8 36.1 1.0 CG F:HIS317 3.0 34.8 1.0 CE1 F:HIS313 3.1 32.0 1.0 CD2 F:HIS313 3.2 33.3 1.0 CB F:CYS302 3.2 62.0 1.0 CB F:HIS317 3.4 36.1 1.0 CB F:CYS305 3.4 51.3 1.0 N F:CYS305 3.7 53.1 1.0 NE2 F:HIS317 4.0 35.8 1.0 CD2 F:HIS317 4.1 35.1 1.0 CA F:CYS305 4.1 53.2 1.0 ND1 F:HIS313 4.2 32.6 1.0 CB F:LYS304 4.2 57.9 1.0 CG F:HIS313 4.3 31.4 1.0 C F:LYS304 4.5 54.4 1.0 CD1 F:PHE299 4.6 68.2 1.0 CA F:CYS302 4.6 63.9 1.0 CA F:LYS304 4.8 56.2 1.0 C F:CYS302 4.9 61.7 1.0 O F:CYS302 4.9 60.1 1.0 CA F:HIS317 4.9 37.9 1.0 N F:LYS304 4.9 57.3 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