Manganese in PDB 7nqe: Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 with Dgtp

The structure of Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 with Dgtp, PDB code: 7nqe was solved by A.W.H.Li, A.J.Doherty, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.90 / 1.28
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.953, 62.675, 82.484, 90, 90, 90
R / Rfree (%)	16.3 / 19

The binding sites of Manganese atom in the Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 with Dgtp (pdb code 7nqe). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 with Dgtp, PDB code: 7nqe:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 with Dgtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 with Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:10.9 occ:1.00 OD1 A:ASP179 2.1 12.6 1.0 O1B A:DGT401 2.2 12.1 1.0 OD1 A:ASP177 2.2 11.7 1.0 O3G A:DGT401 2.2 11.4 1.0 O A:HOH608 2.2 14.1 1.0 O2A A:DGT401 2.3 11.5 1.0 CG A:ASP179 3.1 12.1 1.0 CG A:ASP177 3.1 12.1 1.0 PB A:DGT401 3.2 227.1 1.0 PA A:DGT401 3.4 11.8 1.0 PG A:DGT401 3.4 11.9 1.0 OD2 A:ASP177 3.4 12.7 1.0 O3A A:DGT401 3.5 11.0 1.0 OD2 A:ASP179 3.5 13.6 1.0 MN A:MN403 3.6 11.8 1.0 O3B A:DGT401 3.7 9.1 1.0 NE A:ARG223 4.0 14.3 1.0 NE2 A:HIS226 4.1 12.9 1.0 O1G A:DGT401 4.1 12.7 1.0 O A:ILE178 4.4 12.0 1.0 O1A A:DGT401 4.4 13.4 1.0 OG1 A:THR220 4.4 14.5 1.0 CB A:ASP179 4.5 11.4 1.0 O5' A:DGT401 4.5 12.1 1.0 CB A:ASP177 4.5 10.0 1.0 C5' A:DGT401 4.5 10.9 1.0 CD2 A:HIS226 4.5 11.5 1.0 CD A:ARG223 4.6 14.1 1.0 O2G A:DGT401 4.6 12.6 1.0 O2B A:DGT401 4.7 12.3 1.0 C A:ILE178 4.7 11.1 1.0 CA A:ASP179 4.7 10.6 1.0 CZ A:ARG223 4.9 13.2 1.0 C A:ASP177 4.9 10.4 1.0 N A:ILE178 4.9 10.5 1.0 CA A:ASP177 5.0 9.8 1.0 N A:ASP179 5.0 12.0 1.0 CG2 A:THR220 5.0 13.7 1.0 CB A:THR220 5.0 14.0 1.0 NH2 A:ARG223 5.0 13.7 1.0

Manganese binding site 2 out of 2 in the Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 with Dgtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 with Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:11.8 occ:1.00 OD2 A:ASP179 2.1 13.6 1.0 OD2 A:ASP177 2.1 12.7 1.0 OE2 A:GLU260 2.2 13.6 1.0 O1 A:EDO408 2.2 13.7 1.0 O2 A:EDO408 2.2 15.3 1.0 O2A A:DGT401 2.3 11.5 1.0 C2 A:EDO408 3.1 17.6 1.0 CG A:ASP179 3.1 12.1 1.0 C1 A:EDO408 3.1 19.1 1.0 CD A:GLU260 3.1 13.7 1.0 CG A:ASP177 3.2 12.1 1.0 PA A:DGT401 3.3 11.8 1.0 OD1 A:ASP179 3.5 12.6 1.0 OE1 A:GLU260 3.5 14.5 1.0 MN A:MN402 3.6 10.9 1.0 OD1 A:ASP177 3.6 11.7 1.0 O5' A:DGT401 3.7 12.1 1.0 O1A A:DGT401 3.9 13.4 1.0 C5' A:DGT401 3.9 10.9 1.0 O A:HOH643 4.0 33.6 1.0 O A:HOH618 4.1 14.2 1.0 NH2 A:ARG223 4.3 13.7 1.0 CG A:GLU260 4.4 13.0 1.0 CB A:ASP179 4.4 11.4 1.0 CB A:ASP177 4.5 10.0 1.0 O3A A:DGT401 4.8 11.0 1.0 O3G A:DGT401 4.8 11.4 1.0 O1B A:DGT401 4.8 12.1 1.0 CZ A:ARG223 4.8 13.2 1.0 CB A:GLU260 4.9 13.1 1.0 NE A:ARG223 4.9 14.3 1.0

A.W.H.Li, K.Zabrady, L.J.Bainbridge, M.Zabrady, S.Naseem-Khan, M.B.Berger, P.Kolesar, G.A.Cisneros, A.J.Doherty. Molecular Basis For the Initiation of Dna Primer Synthesis. Nature V. 605 767 2022.
ISSN: ESSN 1476-4687
PubMed: 35508653
DOI: 10.1038/S41586-022-04695-0