Cobalt in PDB 7p9j: Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex

The structure of Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex, PDB code: 7p9j 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)	45.35 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	227.82, 39.5, 74.98, 90, 90, 90
R / Rfree (%)	22.8 / 25.9

The binding sites of Cobalt atom in the Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex (pdb code 7p9j). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 7 binding sites of Cobalt where determined in the Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex, PDB code: 7p9j:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7;

Cobalt binding site 1 out of 7 in the Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex


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 - Primer Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:41.3 occ:1.00 O1A A:DZ4403 2.0 50.3 1.0 O A:HOH503 2.0 39.2 1.0 O2B A:DZ4403 2.2 44.7 1.0 O1G A:DZ4403 2.2 34.2 1.0 OD1 A:ASP179 2.2 39.0 1.0 OD1 A:ASP177 2.5 41.6 1.0 OD2 A:ASP177 3.0 46.4 1.0 CG A:ASP179 3.0 45.1 1.0 CG A:ASP177 3.1 44.3 1.0 PA A:DZ4403 3.1 32.5 1.0 PB A:DZ4403 3.1 31.4 1.0 OD2 A:ASP179 3.1 52.8 1.0 PG A:DZ4403 3.3 37.7 1.0 N3A A:DZ4403 3.5 51.4 1.0 CO A:CO402 3.5 68.2 1.0 O3B A:DZ4403 3.6 32.1 1.0 O2A A:DZ4403 4.0 44.1 1.0 O2G A:DZ4403 4.0 35.3 1.0 NE A:ARG223 4.0 47.6 1.0 O5' A:DZ4403 4.2 38.8 1.0 NE2 A:HIS226 4.3 32.8 1.0 O1B A:DZ4403 4.3 39.1 1.0 C5' A:DZ4403 4.3 40.3 1.0 O3G A:DZ4403 4.4 35.5 1.0 CB A:ASP179 4.4 38.4 1.0 CB A:ASP177 4.6 40.5 1.0 CD A:ARG223 4.6 41.7 1.0 O A:ILE178 4.7 41.7 1.0 OE2 A:GLU260 4.7 61.5 1.0 NH2 A:ARG223 4.8 44.1 1.0 CD2 A:HIS226 4.8 36.5 1.0 CG2 A:THR220 4.8 34.8 1.0 CZ A:ARG223 4.8 47.4 1.0 CA A:ASP179 4.9 37.2 1.0 CG A:ARG223 5.0 40.6 1.0 OG1 A:THR220 5.0 39.4 1.0

Cobalt binding site 2 out of 7 in the Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex


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 - Primer Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co402 b:68.2 occ:1.00 OE2 A:GLU260 1.9 61.5 1.0 OD2 A:ASP177 2.2 46.4 1.0 O1A A:DZ4403 2.5 50.3 1.0 OD2 A:ASP179 2.5 52.8 1.0 CD A:GLU260 3.1 54.8 1.0 PA A:DZ4403 3.3 32.5 1.0 O5' A:DZ4403 3.3 38.8 1.0 CG A:ASP177 3.4 44.3 1.0 CG A:ASP179 3.4 45.1 1.0 CO A:CO401 3.5 41.3 1.0 O2A A:DZ4403 3.7 44.1 1.0 C5' A:DZ4403 3.8 40.3 1.0 OD1 A:ASP179 3.8 39.0 1.0 OE1 A:GLU260 3.9 60.0 1.0 OD1 A:ASP177 4.1 41.6 1.0 CG A:GLU260 4.1 46.3 1.0 CB A:ASP177 4.4 40.5 1.0 NH2 A:ARG223 4.4 44.1 1.0 CB A:ASP179 4.6 38.4 1.0 CB A:GLU260 4.7 41.7 1.0 O2B A:DZ4403 4.7 44.7 1.0 N3A A:DZ4403 4.9 51.4 1.0

Cobalt binding site 3 out of 7 in the Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex


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 - Primer Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Co401 b:44.3 occ:1.00 OD1 B:ASP179 2.2 51.4 1.0 O1A B:DZ4403 2.3 45.3 1.0 O2B B:DZ4403 2.3 39.1 1.0 O1G B:DZ4403 2.3 44.3 1.0 OD1 B:ASP177 2.3 47.6 1.0 O B:HOH529 2.5 38.8 1.0 CG B:ASP177 3.1 45.5 1.0 CG B:ASP179 3.1 53.1 1.0 OD2 B:ASP177 3.1 47.1 1.0 PB B:DZ4403 3.3 42.4 1.0 PG B:DZ4403 3.4 44.2 1.0 OD2 B:ASP179 3.4 54.2 1.0 PA B:DZ4403 3.4 45.9 1.0 CO B:CO402 3.4 62.9 1.0 O3B B:DZ4403 3.7 42.3 1.0 N3A B:DZ4403 3.7 40.1 1.0 O2G B:DZ4403 4.0 45.9 1.0 NE B:ARG223 4.1 51.8 1.0 NE2 B:HIS226 4.2 35.3 1.0 O2A B:DZ4403 4.3 44.3 1.0 C5' B:DZ4403 4.4 35.2 1.0 O5' B:DZ4403 4.4 35.9 1.0 O1B B:DZ4403 4.5 39.1 1.0 CB B:ASP179 4.5 48.0 1.0 O B:ILE178 4.5 43.5 1.0 O3G B:DZ4403 4.5 43.6 1.0 CB B:ASP177 4.6 37.4 1.0 CD2 B:HIS226 4.6 33.6 1.0 CD B:ARG223 4.8 45.4 1.0 CA B:ASP179 4.8 47.1 1.0 NH2 B:ARG223 4.8 53.0 1.0 C B:ILE178 4.9 46.2 1.0 CZ B:ARG223 4.9 46.7 1.0 OG1 B:THR220 5.0 46.1 1.0

Cobalt binding site 4 out of 7 in the Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex


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 - Primer Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Co402 b:62.9 occ:1.00 OD2 B:ASP177 2.2 47.1 1.0 OE2 B:GLU260 2.3 56.1 1.0 O3' B:GTP404 2.3 52.1 1.0 O1A B:DZ4403 2.3 45.3 1.0 OD2 B:ASP179 2.4 54.2 1.0 O2' B:GTP404 3.1 55.1 1.0 CG B:ASP179 3.1 53.1 1.0 OD1 B:ASP179 3.2 51.4 1.0 CD B:GLU260 3.2 57.3 1.0 CG B:ASP177 3.3 45.5 1.0 PA B:DZ4403 3.4 45.9 1.0 CO B:CO401 3.4 44.3 1.0 C3' B:GTP404 3.5 58.0 1.0 O5' B:DZ4403 3.6 35.9 1.0 OE1 B:GLU260 3.7 54.8 1.0 C2' B:GTP404 3.7 56.5 1.0 O2A B:DZ4403 3.8 44.3 1.0 OD1 B:ASP177 3.9 47.6 1.0 C5' B:DZ4403 3.9 35.2 1.0 C4' B:GTP404 4.2 64.2 1.0 NH2 B:ARG223 4.3 53.0 1.0 OD1 B:ASP258 4.3 61.5 1.0 CB B:ASP179 4.3 48.0 1.0 CG B:GLU260 4.4 46.1 1.0 CB B:ASP177 4.5 37.4 1.0 O2B B:DZ4403 4.7 39.1 1.0 CB B:GLU260 4.7 43.6 1.0 O1G B:DZ4403 4.9 44.3 1.0 N3A B:DZ4403 4.9 40.1 1.0 CZ B:ARG223 4.9 46.7 1.0

Cobalt binding site 5 out of 7 in the Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Co406 b:78.9 occ:1.00 O3B B:DZ4405 2.2 79.6 1.0 OD1 B:ASP296 2.5 50.7 1.0 O1A B:DZ4405 2.6 67.2 1.0 O1B B:DZ4405 2.7 72.1 1.0 CG B:ASP296 2.9 50.0 1.0 PB B:DZ4405 2.9 83.4 1.0 OD2 B:ASP296 2.9 51.8 1.0 PG B:DZ4405 3.4 74.9 1.0 O1G B:DZ4405 3.7 83.1 1.0 PA B:DZ4405 3.7 76.1 1.0 N3A B:DZ4405 3.8 74.6 1.0 O2G B:DZ4405 4.0 77.9 1.0 CB B:ASP296 4.1 51.0 1.0 O2B B:DZ4405 4.1 76.7 1.0 C5' B:DZ4405 4.5 65.3 1.0 O2A B:DZ4405 4.7 73.4 1.0 O3G B:DZ4405 4.7 71.7 1.0 O5' B:DZ4405 4.7 73.3 1.0 CE B:LYS202 4.8 59.7 1.0 NZ B:LYS202 4.9 55.9 1.0

Cobalt binding site 6 out of 7 in the Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Co401 b:39.7 occ:1.00 OD1 C:ASP179 2.0 35.0 1.0 O1A C:DZ4403 2.0 38.9 1.0 OD1 C:ASP177 2.2 32.2 1.0 O2B C:DZ4403 2.2 35.1 1.0 O1G C:DZ4403 2.3 34.5 1.0 CG C:ASP179 3.0 36.8 1.0 CG C:ASP177 3.0 40.6 1.0 PA C:DZ4403 3.2 39.6 1.0 OD2 C:ASP177 3.2 38.3 1.0 CO C:CO402 3.3 57.5 1.0 OD2 C:ASP179 3.3 46.4 1.0 PB C:DZ4403 3.3 36.1 1.0 PG C:DZ4403 3.4 40.6 1.0 N3A C:DZ4403 3.7 39.4 1.0 O3B C:DZ4403 3.7 35.0 1.0 NE2 C:HIS226 3.9 38.8 1.0 O2G C:DZ4403 4.0 37.7 1.0 O2A C:DZ4403 4.0 44.7 1.0 NE C:ARG223 4.2 40.7 1.0 O5' C:DZ4403 4.3 39.9 1.0 C5' C:DZ4403 4.3 37.4 1.0 CB C:ASP179 4.4 32.5 1.0 CB C:ASP177 4.4 32.9 1.0 CD2 C:HIS226 4.5 34.5 1.0 O3G C:DZ4403 4.5 37.7 1.0 O1B C:DZ4403 4.5 36.2 1.0 O C:ILE178 4.6 40.8 1.0 CA C:ASP179 4.7 40.4 1.0 CG2 C:THR220 4.8 36.3 1.0 C C:ILE178 4.8 37.1 1.0 CD C:ARG223 4.8 44.0 1.0 NH2 C:ARG223 4.9 36.6 1.0 CE1 C:HIS226 4.9 35.2 1.0 CZ C:ARG223 4.9 32.0 1.0 N C:ASP179 5.0 33.8 1.0 C C:ASP177 5.0 27.8 1.0

Cobalt binding site 7 out of 7 in the Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Co402 b:57.5 occ:1.00 OD2 C:ASP179 2.1 46.4 1.0 OD2 C:ASP177 2.1 38.3 1.0 OE2 C:GLU260 2.2 56.1 1.0 O1A C:DZ4403 2.3 38.9 1.0 CG C:ASP179 3.0 36.8 1.0 CG C:ASP177 3.1 40.6 1.0 O C:HOH516 3.1 61.6 1.0 CD C:GLU260 3.2 58.9 1.0 PA C:DZ4403 3.2 39.6 1.0 CO C:CO401 3.3 39.7 1.0 OD1 C:ASP179 3.4 35.0 1.0 O5' C:DZ4403 3.4 39.9 1.0 OD1 C:ASP177 3.5 32.2 1.0 O2A C:DZ4403 3.6 44.7 1.0 C5' C:DZ4403 3.7 37.4 1.0 OE1 C:GLU260 3.7 56.4 1.0 NH2 C:ARG223 4.1 36.6 1.0 CG C:GLU260 4.2 45.7 1.0 CB C:ASP179 4.4 32.5 1.0 CB C:ASP177 4.4 32.9 1.0 O1G C:DZ4403 4.6 34.5 1.0 O2B C:DZ4403 4.7 35.1 1.0 N3A C:DZ4403 4.8 39.4 1.0 CZ C:ARG223 4.8 32.0 1.0 CB C:GLU260 4.9 42.9 1.0 NE C:ARG223 5.0 40.7 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