Cobalt in PDB 7nqf: Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 with Dsdna

The structure of Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 with Dsdna, PDB code: 7nqf 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)	69.44 / 2.02
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	77.041, 160.362, 39.8, 90, 90, 90
R / Rfree (%)	21.2 / 25.9

The binding sites of Cobalt atom in the Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 with Dsdna (pdb code 7nqf). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 with Dsdna, PDB code: 7nqf:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 with Dsdna


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 with Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:68.6 occ:1.00 OE2 A:GLU260 1.8 53.7 1.0 OD2 A:ASP179 2.0 56.1 1.0 OD2 A:ASP177 2.2 46.0 1.0 OP1 D:DG6 2.3 41.2 1.0 CO A:CO402 3.0 54.0 1.0 CD A:GLU260 3.0 56.1 1.0 CG A:ASP177 3.0 36.8 1.0 CG A:ASP179 3.3 48.9 1.0 O3' D:DC5 3.4 43.5 1.0 P D:DG6 3.4 36.4 1.0 OD1 A:ASP177 3.6 43.1 1.0 CG A:GLU260 3.7 43.6 1.0 C5' D:DG6 3.9 35.0 1.0 CB A:ASP177 3.9 34.5 1.0 OD1 A:ASP179 4.0 45.6 1.0 OE1 A:GLU260 4.0 44.3 1.0 O5' D:DG6 4.1 37.5 1.0 CB A:ASP179 4.3 42.5 1.0 O A:ASP177 4.6 34.8 1.0 OP2 D:DG6 4.7 40.3 1.0 C3' D:DC5 4.7 37.9 1.0 CB A:GLU260 4.8 29.2 1.0 C A:ASP177 4.9 34.0 1.0

Cobalt binding site 2 out of 4 in the Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 with Dsdna


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 with Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Co402 b:54.0 occ:1.00 OP1 D:DG6 2.2 41.2 1.0 OD1 A:ASP177 2.4 43.1 1.0 OD2 A:ASP177 2.5 46.0 1.0 OD1 A:ASP179 2.5 45.6 1.0 OD2 A:ASP179 2.6 56.1 1.0 CG A:ASP177 2.8 36.8 1.0 CG A:ASP179 2.9 48.9 1.0 CO A:CO401 3.0 68.6 1.0 P D:DG6 3.5 36.4 1.0 O D:HOH109 4.0 28.9 1.0 NE2 A:HIS226 4.0 39.0 1.0 O5' D:DG6 4.1 37.5 1.0 C5' D:DG6 4.2 35.0 1.0 OP2 D:DG6 4.2 40.3 1.0 CB A:ASP177 4.3 34.5 1.0 CB A:ASP179 4.4 42.5 1.0 CD2 A:HIS226 4.5 40.6 1.0 O3' D:DC5 4.6 43.5 1.0 OE2 A:GLU260 4.7 53.7 1.0 CG2 A:THR220 4.7 44.2 1.0

Cobalt binding site 3 out of 4 in the Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 with Dsdna


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 with Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ B:Co401 b:43.9 occ:1.00 OP1 E:DG6 1.8 50.4 1.0 OD1 B:ASP179 2.2 41.9 1.0 OD1 B:ASP177 2.2 36.7 1.0 O E:HOH105 2.9 30.5 1.0 O E:HOH104 3.0 36.4 1.0 CG B:ASP177 3.0 39.5 1.0 OD2 B:ASP177 3.0 44.8 1.0 CG B:ASP179 3.0 46.9 1.0 CO B:CO402 3.1 76.3 1.0 OD2 B:ASP179 3.2 46.5 1.0 P E:DG6 3.3 61.2 1.0 O5' E:DG6 3.9 53.5 1.0 NE B:ARG223 4.0 55.6 1.0 C5' E:DG6 4.0 55.5 1.0 NE2 B:HIS226 4.0 33.7 1.0 OP2 E:DG6 4.1 49.4 1.0 O3' E:DC5 4.1 51.2 1.0 CB B:ASP177 4.4 35.7 1.0 CB B:ASP179 4.5 36.5 1.0 CD2 B:HIS226 4.6 33.7 1.0 CD B:ARG223 4.6 47.1 1.0 NH2 B:ARG223 4.7 53.1 1.0 CG2 B:THR220 4.8 34.7 1.0 CZ B:ARG223 4.8 59.1 1.0 O B:ILE178 4.9 32.1 1.0 CE1 B:HIS226 5.0 35.5 1.0 CA B:ASP179 5.0 37.1 1.0

Cobalt binding site 4 out of 4 in the Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 with Dsdna


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 with Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ B:Co402 b:76.3 occ:1.00 OD2 B:ASP179 1.9 46.5 1.0 OD2 B:ASP177 2.0 44.8 1.0 OE2 B:GLU260 2.1 51.1 1.0 OP1 E:DG6 2.5 50.4 1.0 O3' E:DC5 2.7 51.2 1.0 CG B:ASP179 3.0 46.9 1.0 CG B:ASP177 3.1 39.5 1.0 CO B:CO401 3.1 43.9 1.0 CD B:GLU260 3.2 59.0 1.0 P E:DG6 3.2 61.2 1.0 OD1 B:ASP179 3.4 41.9 1.0 C5' E:DG6 3.5 55.5 1.0 OD1 B:ASP177 3.6 36.7 1.0 CG B:GLU260 3.7 43.3 1.0 O5' E:DG6 3.9 53.5 1.0 C3' E:DC5 3.9 63.6 1.0 C4' E:DC5 4.1 74.6 1.0 CB B:ASP179 4.2 36.5 1.0 NH2 B:ARG223 4.3 53.1 1.0 OE1 B:GLU260 4.3 50.2 1.0 CB B:ASP177 4.3 35.7 1.0 OP2 E:DG6 4.6 49.4 1.0 C2' E:DC5 4.6 57.7 1.0 C5' E:DC5 4.7 69.1 1.0 O B:ASP177 4.8 38.9 1.0 NE B:ARG223 4.8 55.6 1.0 CZ B:ARG223 4.9 59.1 1.0 C4' E:DG6 4.9 48.6 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