Magnesium in PDB 3mfh: Dna Polymerase Eta in Complex with Undamaged Dna

All present enzymatic activity of Dna Polymerase Eta in Complex with Undamaged Dna:
2.7.7.7;

The structure of Dna Polymerase Eta in Complex with Undamaged Dna, PDB code: 3mfh 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)	20.00 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	88.745, 227.935, 85.967, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 22.7

The binding sites of Magnesium atom in the Dna Polymerase Eta in Complex with Undamaged Dna (pdb code 3mfh). 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 Undamaged Dna, PDB code: 3mfh:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Polymerase Eta in Complex with Undamaged Dna


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 Undamaged Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg517 b:18.4 occ:1.00 OD1 A:ASP30 2.0 24.6 1.0 O1B A:DTP514 2.1 19.1 1.0 O1G A:DTP514 2.1 22.0 1.0 O1A A:DTP514 2.1 22.3 1.0 O A:MET31 2.2 19.5 1.0 OD1 A:ASP155 2.2 19.7 1.0 CG A:ASP30 3.1 22.0 1.0 PB A:DTP514 3.1 20.4 1.0 CG A:ASP155 3.2 20.9 1.0 PA A:DTP514 3.3 21.8 1.0 PG A:DTP514 3.3 23.1 1.0 C A:MET31 3.4 19.9 1.0 OD2 A:ASP30 3.5 28.8 1.0 OD2 A:ASP155 3.5 21.0 1.0 O3A A:DTP514 3.5 20.6 1.0 O3B A:DTP514 3.6 22.2 1.0 O A:HOH694 3.7 4.4 1.0 O A:HOH736 3.9 13.8 1.0 C5' A:DTP514 3.9 22.1 1.0 N A:MET31 3.9 19.0 1.0 O3G A:DTP514 4.0 18.4 1.0 O5' A:DTP514 4.1 22.1 1.0 CA A:MET31 4.2 20.3 1.0 C A:ASP30 4.3 18.9 1.0 CB A:ASP30 4.4 18.6 1.0 N A:ASN32 4.4 19.1 1.0 N A:ALA33 4.4 19.7 1.0 O2B A:DTP514 4.5 22.3 1.0 CA A:ASN32 4.5 19.5 1.0 CB A:ASP155 4.5 19.7 1.0 O2A A:DTP514 4.6 22.2 1.0 O2G A:DTP514 4.6 22.7 1.0 MG A:MG518 4.6 51.2 1.0 CB A:MET31 4.6 20.9 1.0 N A:PHE34 4.7 19.6 1.0 C A:ASN32 4.7 19.7 1.0 O A:ASP30 4.7 18.3 1.0 CB A:PHE34 4.8 19.0 1.0 CA A:ASP30 4.8 18.6 1.0

Magnesium binding site 2 out of 2 in the Dna Polymerase Eta in Complex with Undamaged Dna


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 Undamaged Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg518 b:51.2 occ:1.00 OE1 A:GLU156 2.8 28.3 1.0 O1A A:DTP514 3.0 22.3 1.0 O A:HOH921 3.0 20.2 1.0 OD2 A:ASP30 3.0 28.8 1.0 C3' P:DOC11 3.1 45.2 1.0 OD2 A:ASP155 3.2 21.0 1.0 C4' P:DOC11 3.4 44.3 1.0 O A:HOH715 3.4 25.0 1.0 CG A:GLU156 3.5 21.3 1.0 CD A:GLU156 3.5 25.1 1.0 O2A A:DTP514 3.6 22.2 1.0 PA A:DTP514 3.6 21.8 1.0 O5' A:DTP514 3.9 22.1 1.0 C5' P:DOC11 3.9 42.6 1.0 OG A:SER153 4.1 27.4 1.0 CG A:ASP30 4.1 22.0 1.0 CG A:ASP155 4.3 20.9 1.0 C2' P:DOC11 4.5 45.4 1.0 C5' A:DTP514 4.5 22.1 1.0 OD1 A:ASP30 4.5 24.6 1.0 O A:HOH736 4.6 13.8 1.0 MG A:MG517 4.6 18.4 1.0 O4' P:DOC11 4.6 42.7 1.0 OE2 A:GLU156 4.7 26.1 1.0 OD1 A:ASP155 4.7 19.7 1.0 NZ A:LYS272 4.8 32.2 1.0 O5' P:DOC11 4.8 40.9 1.0 CB A:GLU156 4.9 18.6 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