Manganese in PDB 6m7o: Human Dna Polymerase Eta Ternary Complex with MN2+ and Dtmpnpp Oppositing Cda

All present enzymatic activity of Human Dna Polymerase Eta Ternary Complex with MN2+ and Dtmpnpp Oppositing Cda:
2.7.7.7;

The structure of Human Dna Polymerase Eta Ternary Complex with MN2+ and Dtmpnpp Oppositing Cda, PDB code: 6m7o was solved by P.Weng, Y.Gao, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.44 / 3.00
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.900, 98.900, 81.060, 90.00, 90.00, 120.00
R / Rfree (%)	23.1 / 27.3

The binding sites of Manganese atom in the Human Dna Polymerase Eta Ternary Complex with MN2+ and Dtmpnpp Oppositing Cda (pdb code 6m7o). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Human Dna Polymerase Eta Ternary Complex with MN2+ and Dtmpnpp Oppositing Cda, PDB code: 6m7o:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Human Dna Polymerase Eta Ternary Complex with MN2+ and Dtmpnpp Oppositing Cda


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Human Dna Polymerase Eta Ternary Complex with MN2+ and Dtmpnpp Oppositing Cda within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:63.3 occ:1.00 O3G A:1FZ503 1.9 72.0 1.0 O2B A:1FZ503 2.0 69.3 1.0 OD1 A:ASP115 2.1 57.0 1.0 O1A A:1FZ503 2.1 59.0 1.0 O A:MET14 2.1 56.3 1.0 OD1 A:ASP13 2.2 71.7 1.0 PB A:1FZ503 3.0 74.0 1.0 PG A:1FZ503 3.0 58.7 1.0 O3B A:1FZ503 3.1 70.3 1.0 CG A:ASP115 3.2 61.4 1.0 CG A:ASP13 3.2 67.1 1.0 C A:MET14 3.3 62.6 1.0 PA A:1FZ503 3.4 64.5 1.0 OD2 A:ASP115 3.5 69.4 1.0 N3A A:1FZ503 3.6 52.3 1.0 OD2 A:ASP13 3.7 69.9 1.0 MN A:MN502 3.7 60.9 1.0 C5' A:1FZ503 3.9 66.7 1.0 N A:MET14 3.9 68.0 1.0 O1G A:1FZ503 4.0 43.1 1.0 NZ A:LYS231 4.1 65.4 1.0 CA A:MET14 4.1 59.3 1.0 O5' A:1FZ503 4.1 63.4 1.0 O2G A:1FZ503 4.1 65.7 1.0 O1B A:1FZ503 4.2 66.8 1.0 N A:ASP15 4.4 63.1 1.0 C A:ASP13 4.4 63.3 1.0 N A:CYS16 4.5 66.4 1.0 O2A A:1FZ503 4.5 91.3 1.0 CB A:ASP115 4.5 57.2 1.0 CA A:ASP15 4.5 69.1 1.0 CB A:ASP13 4.5 51.6 1.0 CB A:MET14 4.6 57.1 1.0 N A:PHE17 4.6 61.0 1.0 C A:ASP15 4.6 65.6 1.0 CB A:PHE17 4.8 56.1 1.0 CA A:ASP13 4.9 54.3 1.0 O A:ASP13 5.0 58.4 1.0

Manganese binding site 2 out of 2 in the Human Dna Polymerase Eta Ternary Complex with MN2+ and Dtmpnpp Oppositing Cda


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Human Dna Polymerase Eta Ternary Complex with MN2+ and Dtmpnpp Oppositing Cda within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:60.9 occ:1.00 O3' P:DG9 1.9 75.3 1.0 OD2 A:ASP13 2.2 69.9 1.0 OE2 A:GLU116 2.2 61.5 1.0 O1A A:1FZ503 2.3 59.0 1.0 OD2 A:ASP115 2.3 69.4 1.0 PA A:1FZ503 3.1 64.5 1.0 CG A:ASP13 3.2 67.1 1.0 C3' P:DG9 3.2 60.8 1.0 O5' A:1FZ503 3.2 63.4 1.0 CD A:GLU116 3.3 62.1 1.0 CG A:ASP115 3.3 61.4 1.0 O2A A:1FZ503 3.4 91.3 1.0 OG A:SER113 3.5 58.5 1.0 OD1 A:ASP13 3.5 71.7 1.0 O P:HOH101 3.5 70.0 1.0 C5' A:1FZ503 3.6 66.7 1.0 OD1 A:ASP115 3.7 57.0 1.0 MN A:MN501 3.7 63.3 1.0 C4' P:DG9 4.0 56.7 1.0 CG A:GLU116 4.1 57.7 1.0 OE1 A:GLU116 4.1 63.8 1.0 CB A:GLU116 4.2 61.7 1.0 C2' P:DG9 4.3 59.2 1.0 O2B A:1FZ503 4.5 69.3 1.0 CB A:ASP13 4.5 51.6 1.0 CB A:SER113 4.6 61.0 1.0 N3A A:1FZ503 4.6 52.3 1.0 NZ A:LYS224 4.6 55.5 1.0 C A:ASP115 4.6 59.4 1.0 CB A:ASP115 4.6 57.2 1.0 C5' P:DG9 4.7 67.8 0.5 O3G A:1FZ503 4.7 72.0 1.0 C5' P:DG9 4.7 67.3 0.5 N A:GLU116 4.7 57.4 1.0 O5' P:DG9 4.8 73.3 0.5 O A:ASP115 4.8 54.8 1.0 O5' P:DG9 4.9 73.1 0.5

P.J.Weng, Y.Gao, M.T.Gregory, P.Wang, Y.Wang, W.Yang. Bypassing A 8,5'-Cyclo-2'-Deoxyadenosine Lesion By Human Dna Polymerase Eta at Atomic Resolution. Proc. Natl. Acad. Sci. V. 115 10660 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30275308
DOI: 10.1073/PNAS.1812856115