Magnesium in PDB 3mfi: Dna Polymerase Eta in Complex with A Cis-Syn Thymidine Dimer

All present enzymatic activity of Dna Polymerase Eta in Complex with A Cis-Syn Thymidine Dimer:
2.7.7.7;

The structure of Dna Polymerase Eta in Complex with A Cis-Syn Thymidine Dimer, PDB code: 3mfi was solved by T.D.Silverstein, R.E.Johnson, R.Jain, L.Prakash, S.Prakash, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.00 / 1.76
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	88.087, 226.962, 85.919, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 18.7

The binding sites of Magnesium atom in the Dna Polymerase Eta in Complex with A Cis-Syn Thymidine Dimer (pdb code 3mfi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Dna Polymerase Eta in Complex with A Cis-Syn Thymidine Dimer, PDB code: 3mfi:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Polymerase Eta in Complex with A Cis-Syn Thymidine Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Polymerase Eta in Complex with A Cis-Syn Thymidine Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg515 b:12.3 occ:1.00 O1G A:DTP514 2.0 12.7 1.0 OD1 A:ASP30 2.0 13.5 1.0 O1B A:DTP514 2.1 11.2 1.0 OD1 A:ASP155 2.1 12.7 1.0 O1A A:DTP514 2.1 14.0 1.0 O A:MET31 2.1 11.4 1.0 CG A:ASP30 3.1 13.2 1.0 PB A:DTP514 3.1 13.2 1.0 CG A:ASP155 3.2 11.9 1.0 PA A:DTP514 3.3 13.1 1.0 C A:MET31 3.3 11.7 1.0 PG A:DTP514 3.3 13.2 1.0 O3A A:DTP514 3.5 14.6 1.0 OD2 A:ASP30 3.5 18.0 1.0 OD2 A:ASP155 3.5 13.9 1.0 O3B A:DTP514 3.6 13.1 1.0 O A:HOH723 3.8 4.3 1.0 O A:HOH756 3.8 8.0 1.0 N A:MET31 3.9 11.2 1.0 C5' A:DTP514 4.0 12.8 1.0 O3G A:DTP514 4.1 12.2 1.0 O5' A:DTP514 4.1 13.3 1.0 CA A:MET31 4.1 11.6 1.0 C A:ASP30 4.2 10.2 1.0 N A:ASN32 4.3 10.7 1.0 CB A:ASP30 4.3 10.2 1.0 N A:ALA33 4.4 11.1 1.0 CA A:ASN32 4.5 10.7 1.0 CB A:ASP155 4.5 12.9 1.0 CB A:MET31 4.5 12.9 1.0 O2G A:DTP514 4.5 14.0 1.0 O2B A:DTP514 4.5 14.5 1.0 C A:ASN32 4.5 11.1 1.0 O2A A:DTP514 4.6 13.4 1.0 N A:PHE34 4.6 10.2 1.0 O A:ASP30 4.6 10.4 1.0 CB A:PHE34 4.7 10.4 1.0 CA A:ASP30 4.7 10.2 1.0 MG A:MG516 4.9 33.8 1.0 O A:ASP155 4.9 12.8 1.0

Magnesium binding site 2 out of 2 in the Dna Polymerase Eta in Complex with A Cis-Syn Thymidine Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dna Polymerase Eta in Complex with A Cis-Syn Thymidine Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg516 b:33.8 occ:1.00 OE1 A:GLU156 2.7 23.9 1.0 OD2 A:ASP30 3.1 18.0 1.0 O A:HOH1060 3.2 22.0 1.0 O1A A:DTP514 3.2 14.0 1.0 O A:HOH862 3.2 10.8 1.0 OD2 A:ASP155 3.2 13.9 1.0 C3' P:DOC11 3.3 45.8 1.0 C4' P:DOC11 3.4 45.2 1.0 CD A:GLU156 3.5 21.2 1.0 CG A:GLU156 3.5 18.2 1.0 O2A A:DTP514 3.5 13.4 1.0 PA A:DTP514 3.6 13.1 1.0 O A:HOH856 3.7 12.1 1.0 O5' A:DTP514 3.8 13.3 1.0 C5' P:DOC11 3.9 45.5 1.0 OG A:SER153 3.9 21.8 1.0 CG A:ASP30 4.3 13.2 1.0 CG A:ASP155 4.4 11.9 1.0 C5' A:DTP514 4.5 12.8 1.0 OE2 A:GLU156 4.7 20.8 1.0 O4' P:DOC11 4.7 43.1 1.0 C2' P:DOC11 4.7 44.8 1.0 OD1 A:ASP30 4.7 13.5 1.0 O A:HOH756 4.7 8.0 1.0 OD1 A:ASP155 4.8 12.7 1.0 MG A:MG515 4.9 12.3 1.0 CB A:GLU156 4.9 13.5 1.0 NZ A:LYS272 4.9 29.0 1.0 O5' P:DOC11 4.9 43.3 1.0

T.D.Silverstein, R.E.Johnson, R.Jain, L.Prakash, S.Prakash, A.K.Aggarwal. Structural Basis For the Suppression of Skin Cancers By Dna Polymerase Eta. Nature V. 465 1039 2010.
ISSN: ISSN 0028-0836
PubMed: 20577207
DOI: 10.1038/NATURE09104