Cobalt in PDB 7qaz: 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: 7qaz 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)	56.98 / 2.11
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	227.91, 39.62, 79.77, 90, 90, 90
R / Rfree (%)	21 / 26.1

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 7qaz). 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: 7qaz:
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:38.4 occ:1.00 O A:HOH521 1.9 28.4 1.0 O2B A:DZ4402 2.2 34.6 1.0 O1A A:DZ4402 2.2 37.3 1.0 O3G A:DZ4402 2.3 31.0 1.0 OD1 A:ASP179 2.4 38.1 1.0 OD1 A:ASP177 2.4 33.0 1.0 OD2 A:ASP177 2.8 37.5 1.0 CG A:ASP177 2.9 35.2 1.0 OD2 A:ASP179 3.0 42.9 1.0 CG A:ASP179 3.0 37.7 1.0 PB A:DZ4402 3.2 30.6 1.0 PA A:DZ4402 3.2 45.4 1.0 PG A:DZ4402 3.4 28.5 1.0 N3A A:DZ4402 3.5 32.6 1.0 O A:HOH501 3.6 37.6 1.0 O3B A:DZ4402 3.6 38.9 1.0 O5' A:DZ4402 3.7 43.6 1.0 NE A:ARG223 4.2 35.7 1.0 O1G A:DZ4402 4.2 30.6 1.0 CB A:ASP177 4.4 31.8 1.0 CB A:ASP179 4.4 28.9 1.0 O1B A:DZ4402 4.5 35.3 1.0 O2G A:DZ4402 4.5 34.4 1.0 O2A A:DZ4402 4.6 44.1 1.0 NH2 A:ARG223 4.6 32.8 1.0 NE2 A:HIS226 4.6 33.4 1.0 O A:ILE178 4.6 37.2 1.0 OG1 A:THR220 4.7 31.1 1.0 CZ A:ARG223 4.7 38.9 1.0 CA A:ASP179 4.9 35.8 1.0 CG2 A:THR220 4.9 29.6 1.0 CD A:ARG223 4.9 30.7 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 B:Co401 b:60.9 occ:1.00 O3' B:GTP405 2.1 55.1 1.0 OD2 B:ASP179 2.2 43.7 1.0 OD2 B:ASP177 2.3 36.7 1.0 O1A B:DZ4404 2.7 34.6 1.0 OE1 B:GLU260 2.7 47.0 1.0 O B:HOH574 2.8 51.3 1.0 CG B:ASP177 3.4 31.7 1.0 CG B:ASP179 3.4 43.4 1.0 O B:HOH502 3.4 36.5 1.0 C3' B:GTP405 3.5 53.0 1.0 CO B:CO402 3.6 35.1 1.0 CD B:GLU260 3.6 46.3 1.0 PA B:DZ4404 3.8 31.6 1.0 O2' B:GTP405 3.8 47.9 1.0 O5' B:DZ4404 4.0 43.7 1.0 OD1 B:ASP177 4.0 34.5 1.0 C5' B:DZ4404 4.1 32.9 1.0 NH2 B:ARG223 4.1 39.2 1.0 OD1 B:ASP179 4.1 48.4 1.0 C4' B:GTP405 4.1 55.6 1.0 C2' B:GTP405 4.2 50.2 1.0 CG B:GLU260 4.3 37.0 1.0 CB B:GLU260 4.3 33.9 1.0 CB B:ASP177 4.3 36.1 1.0 CB B:ASP179 4.4 38.3 1.0 O2A B:DZ4404 4.4 41.6 1.0 OE2 B:GLU260 4.5 54.0 1.0 O2B B:DZ4404 4.8 33.0 1.0 O B:ASP177 4.8 31.2 1.0 C5' B:GTP405 4.9 61.3 1.0 CZ B:ARG223 5.0 40.9 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:Co402 b:35.1 occ:1.00 O1G B:DZ4404 2.1 33.2 1.0 O2B B:DZ4404 2.2 33.0 1.0 OD1 B:ASP179 2.2 48.4 1.0 O1A B:DZ4404 2.5 34.6 1.0 OD1 B:ASP177 2.5 34.5 1.0 O B:HOH530 2.5 31.5 1.0 OD2 B:ASP179 2.8 43.7 1.0 CG B:ASP179 2.8 43.4 1.0 OD2 B:ASP177 2.9 36.7 1.0 CG B:ASP177 3.0 31.7 1.0 PB B:DZ4404 3.2 33.3 1.0 PG B:DZ4404 3.3 32.6 1.0 PA B:DZ4404 3.4 31.6 1.0 O3B B:DZ4404 3.6 37.7 1.0 N3A B:DZ4404 3.6 26.3 1.0 CO B:CO401 3.6 60.9 1.0 O5' B:DZ4404 3.9 43.7 1.0 NE2 B:HIS226 4.1 31.4 1.0 O2G B:DZ4404 4.2 33.8 1.0 CB B:ASP179 4.3 38.3 1.0 NE B:ARG223 4.3 38.5 1.0 O3G B:DZ4404 4.4 35.9 1.0 CB B:ASP177 4.5 36.1 1.0 O1B B:DZ4404 4.5 36.1 1.0 CD2 B:HIS226 4.6 27.2 1.0 O B:ILE178 4.6 40.1 1.0 NH2 B:ARG223 4.6 39.2 1.0 OG1 B:THR220 4.7 31.3 1.0 O2A B:DZ4404 4.8 41.6 1.0 CA B:ASP179 4.8 38.7 1.0 O3' B:GTP405 4.8 55.1 1.0 CZ B:ARG223 4.9 40.9 1.0 C5' B:DZ4404 5.0 32.9 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:Co403 b:87.2 occ:1.00 OD1 B:ASP296 2.2 50.1 1.0 O3G B:DZ4406 2.6 72.4 1.0 O1A B:DZ4406 2.8 67.7 1.0 O2B B:DZ4406 3.0 73.4 1.0 CG B:ASP296 3.3 47.6 1.0 O3B B:DZ4406 3.5 78.1 1.0 PG B:DZ4406 3.6 77.8 1.0 PB B:DZ4406 3.7 80.9 1.0 OD2 B:ASP296 3.8 57.8 1.0 PA B:DZ4406 4.0 68.0 1.0 N3A B:DZ4406 4.0 74.0 1.0 O1G B:DZ4406 4.2 76.9 1.0 NZ B:LYS202 4.2 50.2 1.0 O B:HOH504 4.3 52.1 1.0 ND2 B:ASN295 4.4 50.3 1.0 CB B:ASP296 4.6 38.0 1.0 O2G B:DZ4406 4.8 70.0 1.0 CA B:ASP296 4.8 34.2 1.0 O2A B:DZ4406 4.9 66.0 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 C:Co401 b:55.5 occ:1.00 OD2 C:ASP179 1.9 38.2 1.0 OD2 C:ASP177 2.2 32.8 1.0 O2A C:DZ4403 2.4 29.9 1.0 OE1 C:GLU260 2.7 50.5 1.0 CG C:ASP179 3.0 28.9 1.0 PA C:DZ4403 3.3 31.8 1.0 CG C:ASP177 3.3 34.5 1.0 O5' C:DZ4403 3.4 31.9 1.0 OD1 C:ASP179 3.5 29.4 1.0 CO C:CO402 3.5 29.3 1.0 O1A C:DZ4403 3.6 34.2 1.0 O C:HOH578 3.6 35.9 1.0 CD C:GLU260 3.7 46.2 1.0 C5' C:DZ4403 3.8 34.5 1.0 NH2 C:ARG223 3.8 34.7 1.0 OD1 C:ASP177 3.9 28.5 1.0 CB C:ASP179 4.3 27.7 1.0 CG C:GLU260 4.3 32.2 1.0 CB C:ASP177 4.5 26.9 1.0 O2B C:DZ4403 4.7 27.4 1.0 OE2 C:GLU260 4.7 54.8 1.0 CZ C:ARG223 4.7 33.7 1.0 O3G C:DZ4403 4.7 25.8 1.0 CB C:GLU260 4.8 31.1 1.0 N3A C:DZ4403 4.8 28.5 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:Co402 b:29.3 occ:1.00 OD1 C:ASP179 1.9 29.4 1.0 O C:HOH529 2.0 24.4 1.0 O2B C:DZ4403 2.0 27.4 1.0 O2A C:DZ4403 2.1 29.9 1.0 OD1 C:ASP177 2.1 28.5 1.0 O3G C:DZ4403 2.2 25.8 1.0 CG C:ASP179 2.9 28.9 1.0 CG C:ASP177 2.9 34.5 1.0 OD2 C:ASP177 3.1 32.8 1.0 PB C:DZ4403 3.2 30.2 1.0 OD2 C:ASP179 3.2 38.2 1.0 PA C:DZ4403 3.3 31.8 1.0 PG C:DZ4403 3.3 30.6 1.0 CO C:CO401 3.5 55.5 1.0 O3B C:DZ4403 3.6 28.8 1.0 N3A C:DZ4403 3.7 28.5 1.0 O1G C:DZ4403 4.0 28.3 1.0 NE2 C:HIS226 4.3 24.4 1.0 CB C:ASP179 4.3 27.7 1.0 O1A C:DZ4403 4.3 34.2 1.0 C5' C:DZ4403 4.4 34.5 1.0 O5' C:DZ4403 4.4 31.9 1.0 CB C:ASP177 4.4 26.9 1.0 OG1 C:THR220 4.4 28.2 1.0 O1B C:DZ4403 4.5 25.0 1.0 O C:ILE178 4.5 34.0 1.0 O2G C:DZ4403 4.5 30.5 1.0 NE C:ARG223 4.6 39.2 1.0 CA C:ASP179 4.7 29.5 1.0 CD2 C:HIS226 4.7 28.0 1.0 C C:ILE178 4.8 33.4 1.0 NH2 C:ARG223 4.9 34.7 1.0 CG2 C:THR220 4.9 29.1 1.0 CB C:THR220 4.9 27.9 1.0 N C:ASP179 4.9 32.0 1.0 C C:ASP177 5.0 25.4 1.0 CA C:ASP177 5.0 28.8 1.0 CG C:ARG223 5.0 33.5 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 D:Co101 b:88.1 occ:1.00 O B:HOH617 2.2 51.5 1.0 O2B B:GTP405 2.2 71.2 1.0 N7 B:GTP405 2.4 54.7 1.0 O B:HOH510 2.6 61.5 1.0 O6 B:GTP405 3.1 52.0 1.0 C5 B:GTP405 3.3 53.8 1.0 C8 B:GTP405 3.5 55.8 1.0 PB B:GTP405 3.5 85.7 1.0 C6 B:GTP405 3.6 49.1 1.0 O3G B:GTP405 3.8 78.4 1.0 O B:HOH588 4.0 57.8 1.0 O3B B:GTP405 4.1 79.9 1.0 O3A B:GTP405 4.2 76.9 1.0 O2G B:GTP405 4.2 81.6 1.0 PG B:GTP405 4.2 88.6 1.0 C4 B:GTP405 4.5 51.8 1.0 N9 B:GTP405 4.6 55.9 1.0 O1B B:GTP405 4.7 77.2 1.0 O D:HOH203 4.8 49.1 1.0 N6 B:DZ4404 4.8 40.0 1.0 N1 B:GTP405 5.0 46.0 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