Sodium in PDB 3blj: Crystal Structure of Human Poly(Adp-Ribose) Polymerase 15, Catalytic Fragment

All present enzymatic activity of Crystal Structure of Human Poly(Adp-Ribose) Polymerase 15, Catalytic Fragment:
2.4.2.30;

The structure of Crystal Structure of Human Poly(Adp-Ribose) Polymerase 15, Catalytic Fragment, PDB code: 3blj was solved by T.Karlberg, L.Lehtio, C.H.Arrowsmith, H.Berglund, R.D.Busam, R.Collins, L.G.Dahlgren, A.M.Edwards, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, I.Johansson, A.Kallas, T.Kotenyova, M.Moche, M.E.Nilsson, P.Nordlund, T.Nyman, C.Persson, J.Sagemark, L.Svensson, A.G.Thorsell, L.Tresaugues, S.Van Den Berg, M.Welin, J.Weigelt, Structural Genomics Consortium(Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.78 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.210, 68.120, 158.280, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 24.3

The structure of Crystal Structure of Human Poly(Adp-Ribose) Polymerase 15, Catalytic Fragment also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Human Poly(Adp-Ribose) Polymerase 15, Catalytic Fragment (pdb code 3blj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human Poly(Adp-Ribose) Polymerase 15, Catalytic Fragment, PDB code: 3blj:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Poly(Adp-Ribose) Polymerase 15, Catalytic Fragment


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Poly(Adp-Ribose) Polymerase 15, Catalytic Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Na701 b:55.5 occ:1.00 O A:ASN526 2.3 37.7 1.0 O A:HOH931 2.6 42.6 1.0 O A:ASP523 2.7 26.6 1.0 O A:ILE524 3.3 29.2 1.0 C A:ASN526 3.5 39.1 1.0 C A:ILE524 3.8 28.9 1.0 N A:HIS528 3.9 49.7 1.0 C A:ASP523 3.9 26.2 1.0 CA A:ILE524 4.0 27.0 1.0 O A:HOH816 4.0 34.5 1.0 CA A:ASP527 4.2 47.4 1.0 N A:ASP527 4.3 43.6 1.0 N A:ASN526 4.3 34.1 1.0 N A:ILE524 4.4 27.0 1.0 CA A:ASN526 4.5 35.9 1.0 C A:ASP527 4.5 48.8 1.0 N A:LYS525 4.7 29.6 1.0 C A:LYS525 4.7 32.6 1.0 CA A:HIS528 4.8 50.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Poly(Adp-Ribose) Polymerase 15, Catalytic Fragment


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human Poly(Adp-Ribose) Polymerase 15, Catalytic Fragment within 5.0Å range: probe atom residue distance (Å) B Occ B:Na701 b:40.6 occ:1.00 O B:HOH950 2.3 28.4 1.0 O B:HOH902 2.3 38.7 1.0 O B:ASN526 2.4 26.4 1.0 O B:ILE524 2.6 19.7 1.0 O B:ASP523 2.7 17.7 1.0 C B:ILE524 3.4 18.6 1.0 C B:ASN526 3.6 27.0 1.0 CA B:ILE524 3.7 15.6 1.0 C B:ASP523 3.8 16.7 1.0 O B:HOH951 4.0 28.9 1.0 O B:HOH819 4.2 19.1 1.0 N B:HIS528 4.2 32.2 1.0 N B:ILE524 4.2 16.7 1.0 N B:ASN526 4.3 23.5 1.0 CA B:ASP527 4.3 31.3 1.0 N B:LYS525 4.4 19.9 1.0 N B:ASP527 4.4 28.7 1.0 C B:LYS525 4.5 22.5 1.0 CA B:ASN526 4.6 25.0 1.0 O B:HOH862 4.6 32.6 1.0 C B:ASP527 4.8 32.1 1.0 O B:LYS525 4.8 24.1 1.0 CA B:LYS525 5.0 22.1 1.0

T.Karlberg, M.Klepsch, A.G.Thorsell, C.D.Andersson, A.Linusson, H.Schuler. Structural Basis For Lack of Adp-Ribosyltransferase Activity in Poly(Adp-Ribose) Polymerase-13/Zinc Finger Antiviral Protein. J.Biol.Chem. V. 290 7336 2015.
ISSN: ISSN 0021-9258
PubMed: 25635049
DOI: 10.1074/JBC.M114.630160