Calcium in PDB 7rr3: Structure of Deep-Sea Phage Nrs-1 Primase-Polymerase N300 in Complex with Calcium and Ddctp

The structure of Structure of Deep-Sea Phage Nrs-1 Primase-Polymerase N300 in Complex with Calcium and Ddctp, PDB code: 7rr3 was solved by L.Wang, C.Yu, P.Sliz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.10 / 2.24
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.452, 71.58, 72.962, 90, 90, 90
R / Rfree (%)	23.5 / 28.7

The binding sites of Calcium atom in the Structure of Deep-Sea Phage Nrs-1 Primase-Polymerase N300 in Complex with Calcium and Ddctp (pdb code 7rr3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of Deep-Sea Phage Nrs-1 Primase-Polymerase N300 in Complex with Calcium and Ddctp, PDB code: 7rr3:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structure of Deep-Sea Phage Nrs-1 Primase-Polymerase N300 in Complex with Calcium and Ddctp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Deep-Sea Phage Nrs-1 Primase-Polymerase N300 in Complex with Calcium and Ddctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:40.4 occ:1.00 O A:ASP72 2.3 41.9 1.0 O A:GLU142 2.4 42.8 1.0 O A:HOH417 2.4 37.2 1.0 O A:THR69 2.5 42.3 1.0 C A:GLU142 3.5 39.9 1.0 C A:ASP72 3.6 42.7 1.0 C A:THR69 3.6 43.6 1.0 O A:PHE74 3.9 38.6 1.0 OD2 A:ASP72 4.0 45.9 1.0 N A:THR69 4.3 39.4 1.0 CA A:GLU142 4.3 43.0 1.0 CG A:ASP72 4.3 45.6 1.0 N A:PHE74 4.3 41.0 1.0 CA A:PRO73 4.4 41.2 1.0 CB A:SER143 4.4 40.8 1.0 N A:PRO73 4.4 44.0 1.0 CB A:GLU142 4.4 49.0 1.0 N A:ASP72 4.4 46.1 1.0 CA A:LYS70 4.4 44.8 1.0 OD1 A:ASP72 4.4 47.7 1.0 N A:LYS70 4.4 39.2 1.0 N A:SER143 4.5 38.4 1.0 C A:PRO73 4.5 43.1 1.0 CA A:ASP72 4.5 46.3 1.0 O A:HOH409 4.6 42.6 1.0 CA A:THR69 4.6 42.7 1.0 CA A:SER143 4.6 43.1 1.0 C A:LYS70 4.6 47.7 1.0 C A:PHE74 4.8 38.9 1.0 CB A:LEU68 4.9 39.6 1.0 C A:LEU68 4.9 39.1 1.0 N A:SER71 4.9 44.8 1.0 CG A:GLU142 4.9 43.6 1.0

Calcium binding site 2 out of 3 in the Structure of Deep-Sea Phage Nrs-1 Primase-Polymerase N300 in Complex with Calcium and Ddctp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Deep-Sea Phage Nrs-1 Primase-Polymerase N300 in Complex with Calcium and Ddctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:58.2 occ:1.00 OE2 A:GLU139 2.5 58.6 1.0 OD2 A:ASP80 2.5 46.6 1.0 O A:HOH422 2.8 56.2 1.0 O A:HOH434 2.8 58.3 1.0 OD2 A:ASP78 2.8 44.1 1.0 O1A A:DCT304 2.8 49.8 1.0 OD1 A:ASP80 3.2 46.4 1.0 CD A:GLU139 3.2 56.6 1.0 CG A:ASP80 3.2 44.9 1.0 O5' A:DCT304 3.3 49.4 1.0 PA A:DCT304 3.5 49.6 1.0 OE1 A:GLU139 3.7 56.7 1.0 O2A A:DCT304 3.8 48.0 1.0 CA A:CA303 4.0 43.0 1.0 CG A:ASP78 4.1 40.8 1.0 C5' A:DCT304 4.1 51.1 1.0 CG A:GLU139 4.2 47.2 1.0 NZ A:LYS129 4.4 60.0 1.0 CB A:ASP80 4.7 45.3 1.0 OD1 A:ASP78 4.9 44.0 1.0 CB A:ASP78 4.9 38.7 1.0 O3A A:DCT304 5.0 48.5 1.0

Calcium binding site 3 out of 3 in the Structure of Deep-Sea Phage Nrs-1 Primase-Polymerase N300 in Complex with Calcium and Ddctp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Deep-Sea Phage Nrs-1 Primase-Polymerase N300 in Complex with Calcium and Ddctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:43.0 occ:1.00 O1G A:DCT304 2.1 48.4 1.0 O1B A:DCT304 2.3 43.5 1.0 OD1 A:ASP80 2.3 46.4 1.0 OD1 A:ASP78 2.3 44.0 1.0 O1A A:DCT304 2.4 49.8 1.0 OD2 A:ASP78 2.5 44.1 1.0 CG A:ASP78 2.8 40.8 1.0 CG A:ASP80 3.5 44.9 1.0 PB A:DCT304 3.5 41.4 1.0 PG A:DCT304 3.5 51.9 1.0 PA A:DCT304 3.7 49.6 1.0 NE2 A:HIS115 3.8 44.8 1.0 CA A:CA302 4.0 58.2 1.0 O3B A:DCT304 4.0 47.2 1.0 O3A A:DCT304 4.1 48.5 1.0 OD2 A:ASP80 4.1 46.6 1.0 CD2 A:HIS115 4.2 41.9 1.0 CB A:ASP78 4.3 38.7 1.0 O5' A:DCT304 4.4 49.4 1.0 C5' A:DCT304 4.4 51.1 1.0 O2G A:DCT304 4.4 55.3 1.0 CA A:ASP80 4.4 41.2 1.0 CB A:SER108 4.4 41.4 1.0 CB A:ASP80 4.5 45.3 1.0 O3G A:DCT304 4.5 39.6 1.0 OG A:SER108 4.5 40.4 1.0 N A:ASP80 4.6 39.5 1.0 O A:LEU79 4.6 42.2 1.0 C A:LEU79 4.7 39.2 1.0 O2B A:DCT304 4.7 52.1 1.0 O2A A:DCT304 4.8 48.0 1.0 O A:LEU114 4.9 43.3 1.0 N A:LEU79 5.0 39.5 1.0 CA A:ASP78 5.0 39.9 1.0

F.Huang, X.Lu, C.Yu, P.Sliz, L.Wang, B.Zhu. Molecular Dissection of the Primase and Polymerase Activities of Deep-Sea Phage Nrs-1 Primase-Polymerase. Front Microbiol V. 12 66612 2021.
ISSN: ESSN 1664-302X
PubMed: 34975792
DOI: 10.3389/FMICB.2021.766612