Zinc in PDB 4e2i: The Complex Structure of the SV40 Helicase Large T Antigen and P68 Subunit of Dna Polymerase Alpha-Primase

The structure of The Complex Structure of the SV40 Helicase Large T Antigen and P68 Subunit of Dna Polymerase Alpha-Primase, PDB code: 4e2i was solved by B.Zhou, D.R.Arnett, X.Yu, A.Brewster, G.A.Sowd, C.L.Xie, S.Vila, D.Gai, E.Fanning, X.S.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 5.00
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	249.098, 249.098, 387.032, 90.00, 90.00, 90.00
R / Rfree (%)	30.5 / 31.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the The Complex Structure of the SV40 Helicase Large T Antigen and P68 Subunit of Dna Polymerase Alpha-Primase (pdb code 4e2i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the The Complex Structure of the SV40 Helicase Large T Antigen and P68 Subunit of Dna Polymerase Alpha-Primase, PDB code: 4e2i:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the The Complex Structure of the SV40 Helicase Large T Antigen and P68 Subunit of Dna Polymerase Alpha-Primase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Complex Structure of the SV40 Helicase Large T Antigen and P68 Subunit of Dna Polymerase Alpha-Primase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn700 b:0.0 occ:1.00 NE2 A:HIS313 2.5 0.0 1.0 ND1 A:HIS317 2.7 0.0 1.0 CB A:CYS305 3.0 0.0 1.0 CD2 A:HIS313 3.1 0.0 1.0 CB A:CYS302 3.2 0.0 1.0 CE1 A:HIS313 3.3 0.0 1.0 SG A:CYS302 3.4 0.0 1.0 CG A:HIS317 3.6 0.0 1.0 CE1 A:HIS317 3.6 0.0 1.0 SG A:CYS305 3.7 0.0 1.0 CB A:HIS317 3.7 0.0 1.0 CA A:CYS305 3.9 0.0 1.0 CB A:PHE299 4.1 0.0 1.0 CG A:HIS313 4.1 0.0 1.0 N A:CYS305 4.1 0.0 1.0 ND1 A:HIS313 4.1 0.0 1.0 CA A:PHE299 4.1 0.0 1.0 CA A:TYR314 4.7 0.0 1.0 CA A:CYS302 4.7 0.0 1.0 O A:HIS313 4.7 0.0 1.0 NE2 A:HIS317 4.8 0.0 1.0 CD2 A:HIS317 4.8 0.0 1.0 N A:TYR314 4.8 0.0 1.0 C A:HIS313 4.8 0.0 1.0 C A:LYS304 4.9 0.0 1.0

Zinc binding site 2 out of 12 in the The Complex Structure of the SV40 Helicase Large T Antigen and P68 Subunit of Dna Polymerase Alpha-Primase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Complex Structure of the SV40 Helicase Large T Antigen and P68 Subunit of Dna Polymerase Alpha-Primase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn700 b:0.0 occ:1.00 ND1 B:HIS317 2.5 0.0 1.0 NE2 B:HIS313 2.5 0.0 1.0 CB B:CYS302 2.8 0.0 1.0 SG B:CYS302 2.9 0.0 1.0 CE1 B:HIS313 3.2 0.0 1.0 CE1 B:HIS317 3.3 0.0 1.0 CB B:CYS305 3.3 0.0 1.0 CD2 B:HIS313 3.4 0.0 1.0 CG B:HIS317 3.6 0.0 1.0 CA B:PHE299 3.9 0.0 1.0 CB B:HIS317 4.0 0.0 1.0 CB B:PHE299 4.0 0.0 1.0 SG B:CYS305 4.2 0.0 1.0 ND1 B:HIS313 4.2 0.0 1.0 N B:CYS305 4.3 0.0 1.0 CA B:CYS305 4.3 0.0 1.0 CA B:CYS302 4.3 0.0 1.0 CG B:HIS313 4.3 0.0 1.0 NE2 B:HIS317 4.5 0.0 1.0 CD2 B:HIS317 4.7 0.0 1.0 O B:SER298 4.7 0.0 1.0 N B:PHE299 4.7 0.0 1.0 C B:CYS302 4.9 0.0 1.0 O B:CYS302 4.9 0.0 1.0 C B:PHE299 5.0 0.0 1.0

Zinc binding site 3 out of 12 in the The Complex Structure of the SV40 Helicase Large T Antigen and P68 Subunit of Dna Polymerase Alpha-Primase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Complex Structure of the SV40 Helicase Large T Antigen and P68 Subunit of Dna Polymerase Alpha-Primase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn700 b:0.0 occ:1.00 ND1 C:HIS317 2.4 0.0 1.0 NE2 C:HIS313 2.8 0.0 1.0 CB C:CYS302 3.0 0.0 1.0 SG C:CYS302 3.1 0.0 1.0 CB C:CYS305 3.2 0.0 1.0 CE1 C:HIS317 3.3 0.0 1.0 CG C:HIS317 3.4 0.0 1.0 CE1 C:HIS313 3.5 0.0 1.0 CD2 C:HIS313 3.5 0.0 1.0 CA C:PHE299 3.7 0.0 1.0 CB C:PHE299 3.7 0.0 1.0 CB C:HIS317 3.7 0.0 1.0 SG C:CYS305 3.9 0.0 1.0 CA C:CYS305 4.3 0.0 1.0 N C:CYS305 4.4 0.0 1.0 ND1 C:HIS313 4.4 0.0 1.0 NE2 C:HIS317 4.4 0.0 1.0 CG C:HIS313 4.5 0.0 1.0 CA C:CYS302 4.5 0.0 1.0 CD2 C:HIS317 4.5 0.0 1.0 N C:PHE299 4.6 0.0 1.0 O C:SER298 4.7 0.0 1.0 C C:PHE299 4.8 0.0 1.0 O C:PHE299 4.8 0.0 1.0 C C:SER298 5.0 0.0 1.0

Zinc binding site 4 out of 12 in the The Complex Structure of the SV40 Helicase Large T Antigen and P68 Subunit of Dna Polymerase Alpha-Primase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Complex Structure of the SV40 Helicase Large T Antigen and P68 Subunit of Dna Polymerase Alpha-Primase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn700 b:0.7 occ:1.00 ND1 D:HIS317 2.5 0.0 1.0 NE2 D:HIS313 2.8 0.0 1.0 CB D:CYS305 3.0 0.0 1.0 CD2 D:HIS313 3.3 0.0 1.0 CB D:CYS302 3.3 0.0 1.0 CG D:HIS317 3.4 0.0 1.0 CE1 D:HIS313 3.5 0.0 1.0 CB D:HIS317 3.5 0.0 1.0 CE1 D:HIS317 3.6 0.0 1.0 SG D:CYS305 3.6 0.0 1.0 SG D:CYS302 3.6 0.0 1.0 CB D:PHE299 3.8 0.0 1.0 CA D:PHE299 4.0 0.0 1.0 CA D:CYS305 4.0 0.0 1.0 CG D:HIS313 4.2 0.0 1.0 N D:CYS305 4.3 0.0 1.0 ND1 D:HIS313 4.3 0.0 1.0 CA D:TYR314 4.6 0.0 1.0 CD2 D:HIS317 4.6 0.0 1.0 O D:HIS313 4.6 0.0 1.0 NE2 D:HIS317 4.6 0.0 1.0 CA D:CYS302 4.8 0.0 1.0 C D:HIS313 4.8 0.0 1.0 N D:TYR314 4.8 0.0 1.0 N D:PHE299 4.9 0.0 1.0

Zinc binding site 5 out of 12 in the The Complex Structure of the SV40 Helicase Large T Antigen and P68 Subunit of Dna Polymerase Alpha-Primase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Complex Structure of the SV40 Helicase Large T Antigen and P68 Subunit of Dna Polymerase Alpha-Primase within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn700 b:0.0 occ:1.00 ND1 E:HIS317 2.5 0.0 1.0 NE2 E:HIS313 2.7 0.0 1.0 CB E:CYS305 3.0 0.0 1.0 CB E:CYS302 3.1 0.0 1.0 SG E:CYS302 3.4 0.0 1.0 CD2 E:HIS313 3.4 0.0 1.0 CE1 E:HIS317 3.5 0.0 1.0 CG E:HIS317 3.5 0.0 1.0 CE1 E:HIS313 3.5 0.0 1.0 SG E:CYS305 3.7 0.0 1.0 CB E:HIS317 3.7 0.0 1.0 CB E:PHE299 3.8 0.0 1.0 CA E:PHE299 3.9 0.0 1.0 CA E:CYS305 4.1 0.0 1.0 N E:CYS305 4.2 0.0 1.0 CG E:HIS313 4.3 0.0 1.0 ND1 E:HIS313 4.4 0.0 1.0 CA E:CYS302 4.6 0.0 1.0 NE2 E:HIS317 4.6 0.0 1.0 CD2 E:HIS317 4.6 0.0 1.0 N E:PHE299 4.8 0.0 1.0 CA E:TYR314 4.8 0.0 1.0 O E:HIS313 4.8 0.0 1.0 C E:PHE299 4.9 0.0 1.0 O E:PHE299 4.9 0.0 1.0 O E:SER298 5.0 0.0 1.0 O E:CYS302 5.0 0.0 1.0

Zinc binding site 6 out of 12 in the The Complex Structure of the SV40 Helicase Large T Antigen and P68 Subunit of Dna Polymerase Alpha-Primase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Complex Structure of the SV40 Helicase Large T Antigen and P68 Subunit of Dna Polymerase Alpha-Primase within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn700 b:0.0 occ:1.00 NE2 F:HIS313 2.7 0.0 1.0 ND1 F:HIS317 2.7 0.0 1.0 CB F:CYS305 2.9 0.0 1.0 CB F:CYS302 3.0 0.0 1.0 CD2 F:HIS313 3.3 0.0 1.0 SG F:CYS302 3.3 0.0 1.0 CE1 F:HIS313 3.5 0.0 1.0 CE1 F:HIS317 3.6 0.0 1.0 SG F:CYS305 3.7 0.0 1.0 CG F:HIS317 3.7 0.0 1.0 CB F:HIS317 3.9 0.0 1.0 CA F:CYS305 3.9 0.0 1.0 CB F:PHE299 3.9 0.0 1.0 CA F:PHE299 4.0 0.0 1.0 N F:CYS305 4.0 0.0 1.0 CG F:HIS313 4.3 0.0 1.0 ND1 F:HIS313 4.3 0.0 1.0 CA F:CYS302 4.5 0.0 1.0 NE2 F:HIS317 4.8 0.0 1.0 CA F:TYR314 4.8 0.0 1.0 CD2 F:HIS317 4.8 0.0 1.0 O F:CYS302 4.8 0.0 1.0 N F:PHE299 4.9 0.0 1.0 O F:HIS313 4.9 0.0 1.0 O F:PHE299 4.9 0.0 1.0 C F:LYS304 4.9 0.0 1.0 C F:CYS302 4.9 0.0 1.0 C F:PHE299 4.9 0.0 1.0

Zinc binding site 7 out of 12 in the The Complex Structure of the SV40 Helicase Large T Antigen and P68 Subunit of Dna Polymerase Alpha-Primase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Complex Structure of the SV40 Helicase Large T Antigen and P68 Subunit of Dna Polymerase Alpha-Primase within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn700 b:0.0 occ:1.00 ND1 G:HIS317 2.3 0.0 1.0 NE2 G:HIS313 2.5 0.0 1.0 CE1 G:HIS313 3.2 0.0 1.0 CD2 G:HIS313 3.2 0.0 1.0 CG G:HIS317 3.3 0.0 1.0 CB G:CYS302 3.3 0.0 1.0 CE1 G:HIS317 3.3 0.0 1.0 CB G:CYS305 3.3 0.0 1.0 SG G:CYS302 3.4 0.0 1.0 CB G:HIS317 3.5 0.0 1.0 CB G:PHE299 4.0 0.0 1.0 SG G:CYS305 4.0 0.0 1.0 ND1 G:HIS313 4.0 0.0 1.0 CA G:PHE299 4.1 0.0 1.0 CG G:HIS313 4.1 0.0 1.0 CA G:CYS305 4.3 0.0 1.0 N G:CYS305 4.4 0.0 1.0 NE2 G:HIS317 4.4 0.0 1.0 CD2 G:HIS317 4.4 0.0 1.0 O G:HIS313 4.6 0.0 1.0 CA G:TYR314 4.8 0.0 1.0 CA G:CYS302 4.8 0.0 1.0 C G:HIS313 4.9 0.0 1.0 N G:PHE299 4.9 0.0 1.0 N G:TYR314 4.9 0.0 1.0 CA G:HIS317 5.0 0.0 1.0

Zinc binding site 8 out of 12 in the The Complex Structure of the SV40 Helicase Large T Antigen and P68 Subunit of Dna Polymerase Alpha-Primase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Complex Structure of the SV40 Helicase Large T Antigen and P68 Subunit of Dna Polymerase Alpha-Primase within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn700 b:0.0 occ:1.00 NE2 H:HIS313 2.7 0.0 1.0 ND1 H:HIS317 2.7 0.0 1.0 CB H:CYS302 2.8 0.0 1.0 CB H:CYS305 2.9 0.0 1.0 SG H:CYS302 3.2 0.0 1.0 CD2 H:HIS313 3.4 0.0 1.0 CE1 H:HIS313 3.5 0.0 1.0 CE1 H:HIS317 3.6 0.0 1.0 CG H:HIS317 3.7 0.0 1.0 SG H:CYS305 3.7 0.0 1.0 CA H:PHE299 3.9 0.0 1.0 CB H:PHE299 3.9 0.0 1.0 CA H:CYS305 3.9 0.0 1.0 CB H:HIS317 4.0 0.0 1.0 N H:CYS305 4.0 0.0 1.0 CA H:CYS302 4.3 0.0 1.0 CG H:HIS313 4.4 0.0 1.0 ND1 H:HIS313 4.4 0.0 1.0 NE2 H:HIS317 4.7 0.0 1.0 O H:CYS302 4.7 0.0 1.0 N H:PHE299 4.8 0.0 1.0 C H:CYS302 4.8 0.0 1.0 C H:PHE299 4.8 0.0 1.0 CD2 H:HIS317 4.8 0.0 1.0 O H:PHE299 4.8 0.0 1.0 O H:SER298 4.9 0.0 1.0 C H:LYS304 4.9 0.0 1.0 CA H:TYR314 5.0 0.0 1.0 N H:CYS302 5.0 0.0 1.0

Zinc binding site 9 out of 12 in the The Complex Structure of the SV40 Helicase Large T Antigen and P68 Subunit of Dna Polymerase Alpha-Primase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The Complex Structure of the SV40 Helicase Large T Antigen and P68 Subunit of Dna Polymerase Alpha-Primase within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn700 b:0.0 occ:1.00 ND1 I:HIS317 2.5 0.0 1.0 NE2 I:HIS313 2.6 0.0 1.0 CB I:CYS302 3.1 0.0 1.0 CB I:CYS305 3.1 0.0 1.0 SG I:CYS302 3.3 0.0 1.0 CD2 I:HIS313 3.3 0.0 1.0 CE1 I:HIS313 3.3 0.0 1.0 CE1 I:HIS317 3.5 0.0 1.0 CG I:HIS317 3.5 0.0 1.0 CB I:HIS317 3.7 0.0 1.0 SG I:CYS305 3.8 0.0 1.0 CB I:PHE299 3.9 0.0 1.0 CA I:PHE299 4.0 0.0 1.0 CA I:CYS305 4.1 0.0 1.0 N I:CYS305 4.2 0.0 1.0 ND1 I:HIS313 4.2 0.0 1.0 CG I:HIS313 4.2 0.0 1.0 CA I:CYS302 4.6 0.0 1.0 NE2 I:HIS317 4.6 0.0 1.0 CD2 I:HIS317 4.6 0.0 1.0 N I:PHE299 4.9 0.0 1.0 O I:HIS313 4.9 0.0 1.0 CA I:TYR314 4.9 0.0 1.0 O I:SER298 5.0 0.0 1.0 C I:PHE299 5.0 0.0 1.0

Zinc binding site 10 out of 12 in the The Complex Structure of the SV40 Helicase Large T Antigen and P68 Subunit of Dna Polymerase Alpha-Primase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of The Complex Structure of the SV40 Helicase Large T Antigen and P68 Subunit of Dna Polymerase Alpha-Primase within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn700 b:0.0 occ:1.00 NE2 J:HIS313 2.6 0.0 1.0 CB J:CYS305 2.8 0.0 1.0 ND1 J:HIS317 2.8 0.0 1.0 CD2 J:HIS313 3.1 0.0 1.0 CB J:CYS302 3.3 0.0 1.0 SG J:CYS305 3.4 0.0 1.0 CE1 J:HIS313 3.5 0.0 1.0 CG J:HIS317 3.7 0.0 1.0 SG J:CYS302 3.7 0.0 1.0 CB J:HIS317 3.7 0.0 1.0 CA J:CYS305 3.7 0.0 1.0 CE1 J:HIS317 3.8 0.0 1.0 N J:CYS305 4.0 0.0 1.0 CB J:PHE299 4.0 0.0 1.0 CG J:HIS313 4.1 0.0 1.0 CA J:PHE299 4.2 0.0 1.0 ND1 J:HIS313 4.2 0.0 1.0 CA J:TYR314 4.4 0.0 1.0 O J:HIS313 4.6 0.0 1.0 N J:TYR314 4.7 0.0 1.0 C J:HIS313 4.7 0.0 1.0 CA J:CYS302 4.8 0.0 1.0 C J:LYS304 4.8 0.0 1.0 CD2 J:HIS317 4.9 0.0 1.0 CB J:TYR314 4.9 0.0 1.0 NE2 J:HIS317 4.9 0.0 1.0 O J:CYS302 5.0 0.0 1.0

B.Zhou, D.R.Arnett, X.Yu, A.Brewster, G.A.Sowd, C.L.Xie, S.Vila, D.Gai, E.Fanning, X.S.Chen. Structural Basis For the Interaction of A Hexameric Replicative Helicase with the Regulatory Subunit of Human Dna Polymerase Alpha-Primase. J.Biol.Chem. V. 287 26854 2012.
ISSN: ISSN 0021-9258
PubMed: 22700977
DOI: 10.1074/JBC.M112.363655