Zinc in PDB 5lew: Dna Polymerase

All present enzymatic activity of Dna Polymerase:
2.7.7.7;

The structure of Dna Polymerase, PDB code: 5lew was solved by S.Banos-Mateos, U.F.Lang, S.L.Maslen, J.M.Skehel, M.H.Lamers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	143.11 / 2.80
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	256.044, 256.044, 187.350, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 23.1

The binding sites of Zinc atom in the Dna Polymerase (pdb code 5lew). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Dna Polymerase, PDB code: 5lew:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Dna Polymerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dna Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:28.1 occ:1.00 OE2 A:GLU73 1.9 30.4 1.0 ND1 A:HIS107 2.1 21.1 1.0 SG A:CYS158 2.4 29.2 1.0 O A:HOH1161 2.7 18.2 1.0 CD A:GLU73 2.8 27.2 1.0 CE1 A:HIS107 2.8 23.1 1.0 ZN A:ZN1002 3.0 25.4 1.0 OE1 A:GLU73 3.0 24.6 1.0 CG A:HIS107 3.2 24.8 1.0 CB A:CYS158 3.2 29.3 1.0 CB A:HIS107 3.7 24.5 1.0 OD2 A:ASP226 3.9 33.4 1.0 CE1 A:HIS14 3.9 34.9 1.0 NE2 A:HIS14 4.0 36.4 1.0 NE2 A:HIS107 4.1 23.7 1.0 CG A:GLU73 4.1 26.1 1.0 O A:HOH1136 4.2 29.5 1.0 CE1 A:HIS48 4.2 38.0 1.0 CD2 A:HIS107 4.2 24.4 1.0 OD1 A:ASP226 4.3 39.2 1.0 CG A:ASP226 4.5 37.6 1.0 CA A:CYS158 4.7 29.1 1.0 NE2 A:HIS16 4.8 33.8 1.0 CB A:SER160 4.9 30.5 1.0 O A:HOH1146 4.9 22.2 1.0

Zinc binding site 2 out of 3 in the Dna Polymerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dna Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:25.4 occ:1.00 NE2 A:HIS14 2.0 36.4 1.0 OD1 A:ASP226 2.0 39.2 1.0 OE1 A:GLU73 2.0 24.6 1.0 NE2 A:HIS16 2.1 33.8 1.0 O A:HOH1161 2.4 18.2 1.0 CE1 A:HIS14 2.9 34.9 1.0 CD A:GLU73 3.0 27.2 1.0 ZN A:ZN1001 3.0 28.1 1.0 CG A:ASP226 3.0 37.6 1.0 CE1 A:HIS16 3.0 34.8 1.0 CD2 A:HIS14 3.0 31.8 1.0 CD2 A:HIS16 3.1 35.3 1.0 OD2 A:ASP226 3.3 33.4 1.0 OE2 A:GLU73 3.3 30.4 1.0 CE1 A:HIS48 4.0 38.0 1.0 ND1 A:HIS14 4.0 33.0 1.0 CE1 A:HIS228 4.1 30.6 1.0 CG A:HIS14 4.1 31.6 1.0 ND1 A:HIS16 4.2 33.8 1.0 CG A:HIS16 4.2 32.8 1.0 CG A:GLU73 4.3 26.1 1.0 NE2 A:HIS48 4.3 36.7 1.0 CB A:ASP226 4.4 36.4 1.0 NE2 A:HIS228 4.6 30.2 1.0 CA A:ASP226 4.7 36.8 1.0 CB A:GLU73 4.7 25.8 1.0 ND1 A:HIS107 4.7 21.1 1.0 ZN A:ZN1003 4.8 29.9 1.0 ND1 A:HIS48 4.9 36.5 1.0 CG2 A:THR46 5.0 38.0 1.0

Zinc binding site 3 out of 3 in the Dna Polymerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Dna Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:29.9 occ:1.00 O A:HOH1106 1.7 30.7 1.0 NE2 A:HIS228 1.9 30.2 1.0 NE2 A:HIS48 2.1 36.7 1.0 OD1 A:ASP23 2.2 34.8 1.0 CE1 A:HIS228 2.8 30.6 1.0 CD2 A:HIS228 3.0 33.0 1.0 CD2 A:HIS48 3.0 33.3 1.0 CG A:ASP23 3.1 35.0 1.0 CE1 A:HIS48 3.1 38.0 1.0 O A:HOH1161 3.2 18.2 1.0 OD2 A:ASP23 3.2 41.8 1.0 ND1 A:HIS228 3.9 31.9 1.0 O2 A:SO41004 4.0 68.3 1.0 CG A:HIS228 4.1 32.2 1.0 CE1 A:HIS16 4.1 34.8 1.0 ND1 A:HIS48 4.2 36.5 1.0 CG A:HIS48 4.2 32.1 1.0 NE2 A:HIS16 4.3 33.8 1.0 ND1 A:HIS16 4.3 33.8 1.0 CZ A:PHE258 4.4 46.0 1.0 CB A:ASP23 4.4 31.6 1.0 CD2 A:HIS16 4.5 35.3 1.0 CG A:HIS16 4.6 32.8 1.0 O3 A:SO41004 4.6 53.0 1.0 ZN A:ZN1002 4.8 25.4 1.0 S A:SO41004 4.9 68.0 1.0

S.Banos-Mateos, A.M.Van Roon, U.F.Lang, S.L.Maslen, J.M.Skehel, M.H.Lamers. High-Fidelity Dna Replication in Mycobacterium Tuberculosis Relies on A Trinuclear Zinc Center. Nat Commun V. 8 855 2017.
ISSN: ESSN 2041-1723
PubMed: 29021523
DOI: 10.1038/S41467-017-00886-W