Zinc in PDB 4pog: Mcm-Ssdna Co-Crystal Structure

The structure of Mcm-Ssdna Co-Crystal Structure, PDB code: 4pog was solved by C.A.Froelich, S.Kang, L.B.Epling, S.P.Bell, E.J.Enemark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.51 / 3.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	94.277, 113.398, 196.855, 90.00, 101.35, 90.00
R / Rfree (%)	25.7 / 29.4

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Mcm-Ssdna Co-Crystal Structure (pdb code 4pog). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Mcm-Ssdna Co-Crystal Structure, PDB code: 4pog:
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 Mcm-Ssdna Co-Crystal Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mcm-Ssdna Co-Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:0.8 occ:1.00 SG A:CYS162 2.3 0.5 1.0 SG A:CYS142 2.3 0.3 1.0 SG A:CYS139 2.3 0.7 1.0 SG A:CYS165 2.3 0.3 1.0 CB A:CYS139 3.3 0.0 1.0 CB A:CYS162 3.3 0.8 1.0 CB A:CYS142 3.4 0.7 1.0 CB A:CYS165 3.4 0.0 1.0 OG A:SER167 3.6 1.0 1.0 N A:CYS165 3.7 0.8 1.0 N A:CYS142 3.9 0.7 1.0 CA A:CYS165 4.0 0.7 1.0 CA A:CYS142 4.1 0.5 1.0 CB A:HIS144 4.2 0.5 1.0 CB A:GLN164 4.5 0.4 1.0 N A:GLY166 4.6 0.3 1.0 C A:CYS165 4.6 0.3 1.0 N A:HIS144 4.7 0.9 1.0 CB A:SER167 4.7 0.7 1.0 N A:GLY143 4.7 0.9 1.0 C A:CYS142 4.7 0.0 1.0 CA A:CYS139 4.7 0.9 1.0 N A:SER167 4.7 0.7 1.0 CA A:CYS162 4.8 0.3 1.0 CB A:ASP141 4.8 0.9 1.0 C A:GLN164 4.8 0.7 1.0 C A:ASP141 4.9 0.9 1.0

Zinc binding site 2 out of 12 in the Mcm-Ssdna Co-Crystal Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mcm-Ssdna Co-Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:0.6 occ:1.00 SG B:CYS139 2.3 0.9 1.0 SG B:CYS165 2.3 0.1 1.0 SG B:CYS142 2.3 0.6 1.0 SG B:CYS162 2.3 0.7 1.0 OG B:SER167 3.1 0.7 1.0 CB B:CYS139 3.3 0.9 1.0 CB B:CYS165 3.3 0.4 1.0 CB B:CYS162 3.4 0.5 1.0 CB B:CYS142 3.4 0.3 1.0 N B:CYS165 3.7 0.9 1.0 N B:CYS142 3.9 0.3 1.0 CA B:CYS165 4.0 0.7 1.0 CB B:SER167 4.2 0.2 1.0 CA B:CYS142 4.2 0.4 1.0 CB B:HIS144 4.5 0.2 1.0 C B:CYS165 4.5 1.0 1.0 N B:SER167 4.5 0.7 1.0 N B:GLY166 4.6 0.1 1.0 CB B:ASP141 4.6 0.1 1.0 CB B:GLN164 4.7 0.9 1.0 CA B:CYS139 4.8 0.6 1.0 CA B:CYS162 4.8 0.6 1.0 C B:ASP141 4.8 0.3 1.0 N B:GLY143 4.8 0.8 1.0 N B:HIS144 4.8 0.1 1.0 C B:CYS142 4.9 0.5 1.0 C B:GLN164 4.9 0.2 1.0 CA B:SER167 5.0 0.1 1.0

Zinc binding site 3 out of 12 in the Mcm-Ssdna Co-Crystal Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mcm-Ssdna Co-Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:0.5 occ:1.00 SG C:CYS139 2.3 0.1 1.0 SG C:CYS142 2.3 0.2 1.0 SG C:CYS162 2.3 0.0 1.0 SG C:CYS165 2.3 0.2 1.0 CB C:CYS139 3.3 1.0 1.0 CB C:CYS162 3.4 0.7 1.0 CB C:CYS142 3.4 0.4 1.0 OG C:SER167 3.5 0.9 1.0 CB C:CYS165 3.5 0.4 1.0 N C:CYS165 3.8 0.5 1.0 N C:CYS142 3.9 0.3 1.0 CA C:CYS165 4.1 0.8 1.0 CA C:CYS142 4.2 0.5 1.0 CB C:HIS144 4.3 0.9 1.0 CB C:SER167 4.6 0.7 1.0 CB C:GLN164 4.6 0.4 1.0 N C:HIS144 4.7 0.9 1.0 N C:GLY166 4.7 0.9 1.0 C C:CYS165 4.7 0.3 1.0 N C:GLY143 4.7 0.6 1.0 CA C:CYS139 4.7 0.2 1.0 N C:SER167 4.8 0.4 1.0 CB C:ASP141 4.8 1.0 1.0 CA C:CYS162 4.8 0.8 1.0 C C:CYS142 4.8 0.3 1.0 C C:ASP141 4.9 0.0 1.0 C C:GLN164 4.9 0.5 1.0

Zinc binding site 4 out of 12 in the Mcm-Ssdna Co-Crystal Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Mcm-Ssdna Co-Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:0.8 occ:1.00 SG D:CYS139 2.3 0.2 1.0 SG D:CYS165 2.3 0.9 1.0 SG D:CYS162 2.3 0.5 1.0 SG D:CYS142 2.3 0.1 1.0 OG D:SER167 3.2 0.9 1.0 CB D:CYS139 3.3 0.7 1.0 CB D:CYS162 3.3 0.7 1.0 CB D:CYS142 3.4 0.1 1.0 CB D:CYS165 3.4 1.0 1.0 N D:CYS165 3.8 0.7 1.0 N D:CYS142 3.8 0.5 1.0 CA D:CYS165 4.1 0.3 1.0 CA D:CYS142 4.2 0.8 1.0 CB D:SER167 4.3 0.9 1.0 CB D:HIS144 4.5 1.0 1.0 CB D:ASP141 4.6 0.6 1.0 N D:SER167 4.6 0.8 1.0 N D:GLY166 4.6 0.1 1.0 C D:CYS165 4.7 1.0 1.0 CB D:GLN164 4.7 0.7 1.0 CA D:CYS139 4.7 0.6 1.0 N D:GLY143 4.8 0.9 1.0 CA D:CYS162 4.8 0.8 1.0 C D:CYS142 4.8 0.6 1.0 C D:ASP141 4.8 0.8 1.0 N D:HIS144 4.9 0.1 1.0 C D:GLN164 5.0 0.6 1.0

Zinc binding site 5 out of 12 in the Mcm-Ssdna Co-Crystal Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Mcm-Ssdna Co-Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn301 b:0.8 occ:1.00 SG E:CYS139 2.3 0.4 1.0 SG E:CYS162 2.3 0.3 1.0 SG E:CYS165 2.3 0.7 1.0 SG E:CYS142 2.3 0.6 1.0 CB E:CYS139 3.3 0.2 1.0 OG E:SER167 3.3 0.2 1.0 CB E:CYS162 3.3 0.3 1.0 CB E:CYS142 3.4 0.7 1.0 CB E:CYS165 3.4 0.7 1.0 N E:CYS142 3.7 0.5 1.0 N E:CYS165 3.8 0.3 1.0 CA E:CYS165 4.1 0.2 1.0 CA E:CYS142 4.1 0.3 1.0 CB E:SER167 4.3 0.7 1.0 CB E:ASP141 4.4 0.8 1.0 CB E:HIS144 4.5 0.3 1.0 N E:SER167 4.6 0.6 1.0 N E:GLY166 4.6 0.9 1.0 C E:ASP141 4.7 0.3 1.0 C E:CYS165 4.7 0.6 1.0 CA E:CYS139 4.7 1.0 1.0 N E:GLY143 4.7 0.7 1.0 C E:CYS142 4.8 0.3 1.0 CA E:CYS162 4.8 0.2 1.0 CB E:GLN164 4.8 1.0 1.0 N E:HIS144 4.8 0.2 1.0 CA E:ASP141 4.9 0.4 1.0 N E:ASP141 4.9 0.6 1.0 C E:GLN164 5.0 0.1 1.0

Zinc binding site 6 out of 12 in the Mcm-Ssdna Co-Crystal Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Mcm-Ssdna Co-Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:0.9 occ:1.00 SG F:CYS162 2.3 0.0 1.0 SG F:CYS139 2.3 0.3 1.0 SG F:CYS142 2.3 0.8 1.0 SG F:CYS165 2.3 0.4 1.0 CB F:CYS162 3.3 0.2 1.0 CB F:CYS139 3.4 0.4 1.0 CB F:CYS142 3.4 0.1 1.0 CB F:CYS165 3.4 1.0 1.0 OG F:SER167 3.6 0.2 1.0 N F:CYS165 3.7 0.8 1.0 N F:CYS142 3.9 0.1 1.0 CA F:CYS165 4.1 1.0 1.0 CA F:CYS142 4.2 0.3 1.0 CB F:HIS144 4.3 0.2 1.0 CB F:SER167 4.5 0.5 1.0 N F:GLY166 4.6 0.1 1.0 CB F:GLN164 4.6 0.9 1.0 C F:CYS165 4.7 0.9 1.0 CB F:ASP141 4.7 0.2 1.0 N F:SER167 4.7 0.4 1.0 N F:HIS144 4.8 0.3 1.0 CA F:CYS162 4.8 0.4 1.0 C F:GLN164 4.8 0.2 1.0 CA F:CYS139 4.8 0.7 1.0 C F:ASP141 4.8 0.9 1.0 N F:GLY143 4.8 0.8 1.0 C F:CYS142 4.9 0.3 1.0

Zinc binding site 7 out of 12 in the Mcm-Ssdna Co-Crystal Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Mcm-Ssdna Co-Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn301 b:0.2 occ:1.00 SG G:CYS142 2.3 0.4 1.0 SG G:CYS165 2.3 0.2 1.0 SG G:CYS162 2.3 0.8 1.0 SG G:CYS139 2.3 0.9 1.0 CB G:CYS139 3.3 0.6 1.0 CB G:CYS142 3.3 0.5 1.0 CB G:CYS162 3.3 0.6 1.0 CB G:CYS165 3.3 0.7 1.0 OG G:SER167 3.5 0.9 1.0 N G:CYS165 3.7 0.3 1.0 N G:CYS142 3.9 0.5 1.0 CA G:CYS165 4.0 0.9 1.0 CA G:CYS142 4.2 0.9 1.0 CB G:HIS144 4.2 0.1 1.0 CB G:SER167 4.6 0.5 1.0 N G:GLY166 4.6 0.7 1.0 CB G:GLN164 4.6 0.4 1.0 N G:HIS144 4.6 0.2 1.0 C G:CYS165 4.7 0.8 1.0 N G:GLY143 4.7 0.8 1.0 CA G:CYS139 4.7 0.9 1.0 N G:SER167 4.7 0.6 1.0 CA G:CYS162 4.8 0.1 1.0 C G:CYS142 4.8 0.2 1.0 C G:GLN164 4.8 0.7 1.0 CB G:ASP141 4.9 0.6 1.0 C G:ASP141 4.9 0.4 1.0 CD1 G:ILE170 5.0 0.9 1.0

Zinc binding site 8 out of 12 in the Mcm-Ssdna Co-Crystal Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Mcm-Ssdna Co-Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn301 b:0.5 occ:1.00 SG H:CYS165 2.3 0.5 1.0 SG H:CYS142 2.3 0.1 1.0 SG H:CYS139 2.3 0.9 1.0 SG H:CYS162 2.3 0.2 1.0 CB H:CYS139 3.3 0.8 1.0 OG H:SER167 3.4 0.4 1.0 CB H:CYS162 3.4 0.4 1.0 CB H:CYS165 3.4 0.3 1.0 CB H:CYS142 3.4 0.9 1.0 N H:CYS165 3.7 0.2 1.0 N H:CYS142 3.8 0.4 1.0 CA H:CYS165 4.1 0.3 1.0 CA H:CYS142 4.1 0.0 1.0 CB H:HIS144 4.2 0.2 1.0 CB H:SER167 4.5 0.2 1.0 N H:HIS144 4.6 0.7 1.0 CB H:GLN164 4.6 0.2 1.0 C H:CYS142 4.7 0.8 1.0 N H:GLY166 4.7 0.2 1.0 N H:GLY143 4.7 0.5 1.0 C H:CYS165 4.7 0.6 1.0 CB H:ASP141 4.7 0.5 1.0 N H:SER167 4.7 0.7 1.0 CA H:CYS139 4.8 0.6 1.0 C H:ASP141 4.8 0.5 1.0 CA H:CYS162 4.8 0.0 1.0 C H:GLN164 4.9 0.9 1.0

Zinc binding site 9 out of 12 in the Mcm-Ssdna Co-Crystal Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Mcm-Ssdna Co-Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn301 b:0.2 occ:1.00 SG I:CYS165 2.3 0.7 1.0 SG I:CYS139 2.3 0.1 1.0 SG I:CYS162 2.3 0.8 1.0 SG I:CYS142 2.3 0.5 1.0 OG I:SER167 3.1 0.8 1.0 CB I:CYS139 3.3 0.4 1.0 CB I:CYS162 3.3 1.0 1.0 CB I:CYS165 3.4 0.8 1.0 CB I:CYS142 3.4 0.3 1.0 N I:CYS142 3.8 0.4 1.0 N I:CYS165 3.8 0.4 1.0 CA I:CYS165 4.1 0.1 1.0 CA I:CYS142 4.2 0.2 1.0 CB I:SER167 4.3 0.6 1.0 CB I:HIS144 4.4 0.9 1.0 CB I:ASP141 4.5 0.0 1.0 N I:SER167 4.6 0.7 1.0 N I:GLY166 4.6 0.6 1.0 C I:CYS165 4.7 0.5 1.0 N I:GLY143 4.7 0.1 1.0 N I:HIS144 4.8 1.0 1.0 CA I:CYS139 4.8 0.8 1.0 C I:ASP141 4.8 0.1 1.0 CA I:CYS162 4.8 0.4 1.0 C I:CYS142 4.8 0.7 1.0 CB I:GLN164 4.9 0.0 1.0 C I:GLN164 5.0 0.0 1.0

Zinc binding site 10 out of 12 in the Mcm-Ssdna Co-Crystal Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Mcm-Ssdna Co-Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn301 b:0.2 occ:1.00 SG J:CYS139 2.3 0.7 1.0 SG J:CYS165 2.3 1.0 1.0 SG J:CYS142 2.3 0.1 1.0 SG J:CYS162 2.3 0.5 1.0 CB J:CYS139 3.3 0.6 1.0 OG J:SER167 3.3 0.7 1.0 CB J:CYS162 3.3 0.5 1.0 CB J:CYS142 3.4 0.1 1.0 CB J:CYS165 3.5 0.1 1.0 N J:CYS142 3.8 0.9 1.0 N J:CYS165 3.8 0.3 1.0 CA J:CYS165 4.1 0.9 1.0 CA J:CYS142 4.2 0.3 1.0 CB J:SER167 4.3 0.2 1.0 CB J:ASP141 4.5 0.5 1.0 CB J:HIS144 4.5 0.2 1.0 N J:SER167 4.6 0.9 1.0 C J:CYS165 4.6 0.4 1.0 N J:GLY166 4.6 0.3 1.0 CB J:GLN164 4.7 0.9 1.0 C J:ASP141 4.7 1.0 1.0 CA J:CYS139 4.7 0.8 1.0 CA J:CYS162 4.8 0.7 1.0 N J:GLY143 4.8 0.6 1.0 C J:CYS142 4.9 0.1 1.0 N J:HIS144 4.9 0.3 1.0 N J:ASP141 5.0 0.8 1.0 CA J:ASP141 5.0 0.5 1.0 C J:GLN164 5.0 0.8 1.0

C.A.Froelich, S.Kang, L.B.Epling, S.P.Bell, E.J.Enemark. A Conserved Mcm Single-Stranded Dna Binding Element Is Essential For Replication Initiation Elife V. 3 01993 2014.
ISSN: ESSN 2050-084X
DOI: 10.7554/ELIFE.01993