Calcium in PDB 5l2x: Crystal Structure of Human Primpol Ternary Complex

The structure of Crystal Structure of Human Primpol Ternary Complex, PDB code: 5l2x was solved by O.Rechkoblit, Y.K.Gupta, R.Malik, K.R.Rajashankar, R.E.Johnson, L.Prakash, S.Prakash, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.35 / 2.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.723, 65.212, 72.463, 67.89, 85.22, 86.65
R / Rfree (%)	20.6 / 25.5

The structure of Crystal Structure of Human Primpol Ternary Complex also contains other interesting chemical elements:

Iodine

(I)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Human Primpol Ternary Complex (pdb code 5l2x). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Human Primpol Ternary Complex, PDB code: 5l2x:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Human Primpol Ternary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human Primpol Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:44.7 occ:1.00 OE2 A:GLU116 2.1 59.6 1.0 O2A A:DTP401 2.2 37.1 1.0 O2B A:DTP401 2.3 39.2 1.0 O A:HOH514 2.3 39.6 1.0 O2G A:DTP401 2.4 52.9 1.0 OD1 A:ASP114 2.4 40.7 1.0 OD2 A:ASP114 2.5 44.1 1.0 CG A:ASP114 2.8 47.1 1.0 CD A:GLU116 3.4 61.1 1.0 PB A:DTP401 3.5 37.6 1.0 PA A:DTP401 3.6 43.5 1.0 PG A:DTP401 3.6 42.1 1.0 O3B A:DTP401 4.0 58.3 1.0 O3A A:DTP401 4.0 48.8 1.0 NZ A:LYS165 4.1 53.2 1.0 CG A:GLU116 4.2 45.9 1.0 NE2 A:HIS169 4.2 38.6 1.0 OE1 A:GLU116 4.2 73.4 1.0 OG A:SER167 4.3 54.3 1.0 CB A:GLU116 4.3 51.0 1.0 CB A:ASP114 4.3 38.6 1.0 O3G A:DTP401 4.4 48.0 1.0 C5' A:DTP401 4.5 37.2 1.0 O5' A:DTP401 4.5 48.6 1.0 CE A:LYS165 4.6 61.6 1.0 O1A A:DTP401 4.7 39.0 1.0 OD2 A:ASP280 4.7 54.1 1.0 CD2 A:HIS169 4.7 39.1 1.0 O1B A:DTP401 4.7 39.5 1.0 O1G A:DTP401 4.7 46.2 1.0 O A:LEU115 4.8 51.5 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Human Primpol Ternary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human Primpol Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:36.5 occ:1.00 OE2 B:GLU116 2.1 42.1 1.0 O2A B:DTP401 2.1 37.7 1.0 O2G B:DTP401 2.3 42.4 1.0 O2B B:DTP401 2.3 34.6 1.0 O B:HOH503 2.3 35.6 1.0 OD1 B:ASP114 2.5 44.5 1.0 OD2 B:ASP114 2.5 36.9 1.0 CG B:ASP114 2.9 45.6 1.0 CD B:GLU116 3.3 48.5 1.0 PB B:DTP401 3.4 38.2 1.0 PA B:DTP401 3.4 32.4 1.0 PG B:DTP401 3.5 34.4 1.0 O3A B:DTP401 3.8 37.6 1.0 O3B B:DTP401 3.8 43.8 1.0 NZ B:LYS165 4.0 40.3 1.0 OE1 B:GLU116 4.2 60.2 1.0 C5' B:DTP401 4.2 37.0 1.0 O5' B:DTP401 4.2 36.2 1.0 CG B:GLU116 4.2 39.5 1.0 O3G B:DTP401 4.3 36.1 1.0 OG B:SER167 4.3 41.5 1.0 NE2 B:HIS169 4.3 34.1 1.0 CB B:ASP114 4.4 43.2 1.0 CB B:GLU116 4.5 41.8 1.0 O1A B:DTP401 4.5 36.7 1.0 O1G B:DTP401 4.6 47.9 1.0 OD2 B:ASP280 4.7 42.5 1.0 O1B B:DTP401 4.7 30.9 1.0 CE B:LYS165 4.8 38.8 1.0 CD2 B:HIS169 4.9 38.9 1.0

O.Rechkoblit, Y.K.Gupta, R.Malik, K.R.Rajashankar, R.E.Johnson, L.Prakash, S.Prakash, A.K.Aggarwal. Structure and Mechanism of Human Primpol, A Dna Polymerase with Primase Activity. Sci Adv V. 2 01317 2016.
ISSN: ESSN 2375-2548
PubMed: 27819052
DOI: 10.1126/SCIADV.1601317