Calcium in PDB 2jbh: Human Phosphoribosyl Transferase Domain Containing 1

All present enzymatic activity of Human Phosphoribosyl Transferase Domain Containing 1:
2.4.2.8;

The structure of Human Phosphoribosyl Transferase Domain Containing 1, PDB code: 2jbh was solved by M.Welin, P.Stenmark, C.Arrowsmith, H.Berglund, R.Busam, R.Collins, A.Edwards, H.Eklund, U.B.Ericsson, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, B.M.Hallberg, L.Holmberg Schiavone, M.Hogbom, I.Johansson, T.Karlberg, T.Kotenyova, M.Moche, M.E.Nilsson, T.Nyman, D.Ogg, C.Persson, J.Sagemark, M.Sundstrom, J.Uppenberg, A.G.Thorsell, S.Van Den Berg, J.Weigelt, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.44 / 1.7
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	139.232, 139.232, 52.132, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 21.5

The structure of Human Phosphoribosyl Transferase Domain Containing 1 also contains other interesting chemical elements:

Arsenic

(As)

2 atoms

The binding sites of Calcium atom in the Human Phosphoribosyl Transferase Domain Containing 1 (pdb code 2jbh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Human Phosphoribosyl Transferase Domain Containing 1, PDB code: 2jbh:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Human Phosphoribosyl Transferase Domain Containing 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Phosphoribosyl Transferase Domain Containing 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1228 b:11.6 occ:1.00 OD1 A:ASP142 2.4 10.2 1.0 O A:HOH2140 2.4 10.9 1.0 OE1 A:GLU141 2.4 13.2 1.0 O A:HOH2141 2.4 12.4 1.0 O A:HOH2143 2.5 12.0 1.0 O2' A:5GP1230 2.6 10.4 1.0 O3' A:5GP1230 2.6 11.7 1.0 OE2 A:GLU141 2.6 9.8 1.0 CD A:GLU141 2.8 10.2 1.0 CG A:ASP142 3.4 10.5 1.0 C3' A:5GP1230 3.5 12.2 1.0 C2' A:5GP1230 3.5 12.0 1.0 OD2 A:ASP142 3.7 11.3 1.0 O1 A:PO41227 4.1 13.9 1.0 CG A:GLU141 4.2 11.4 1.0 C1' A:5GP1230 4.3 12.1 1.0 O A:HOH2146 4.5 17.5 1.0 CG1 A:VAL74 4.5 11.3 1.0 N A:ASP142 4.5 9.3 1.0 O A:HOH2097 4.6 12.9 1.0 O A:VAL143 4.6 12.4 1.0 CB A:ASP142 4.8 8.7 1.0 C4' A:5GP1230 4.8 12.6 1.0 N A:VAL143 4.9 10.2 1.0 O A:HOH2145 4.9 10.9 1.0

Calcium binding site 2 out of 4 in the Human Phosphoribosyl Transferase Domain Containing 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Phosphoribosyl Transferase Domain Containing 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1229 b:12.0 occ:1.00 OD1 A:ASP201 2.4 10.2 1.0 O4 A:PO41227 2.4 11.6 1.0 O A:HOH2145 2.5 10.9 1.0 O A:HOH2127 2.5 25.5 1.0 O A:HOH2118 2.6 18.1 1.0 O3 A:PO41227 2.8 13.0 1.0 P A:PO41227 3.3 13.1 1.0 CG A:ASP201 3.3 10.2 1.0 OD2 A:ASP201 3.6 12.2 1.0 O A:HOH2142 3.8 11.1 1.0 NH2 A:ARG207 4.2 10.7 1.0 O2 A:PO41227 4.2 13.7 1.0 O A:HOH2069 4.3 57.7 1.0 O1 A:PO41227 4.4 13.9 1.0 O A:HOH2140 4.5 10.9 1.0 O A:HOH2119 4.6 15.5 1.0 N2 A:5GP1230 4.6 9.6 1.0 O A:ASP201 4.6 8.5 1.0 CB A:ASP201 4.7 10.4 1.0 NH1 A:ARG207 4.7 10.5 1.0 O A:HOH2139 4.8 32.2 1.0 N3 A:5GP1230 4.9 10.5 1.0 CZ A:ARG207 4.9 10.5 1.0

Calcium binding site 3 out of 4 in the Human Phosphoribosyl Transferase Domain Containing 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Phosphoribosyl Transferase Domain Containing 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1228 b:19.1 occ:1.00 O B:HOH2143 2.3 25.1 1.0 OD1 B:ASP201 2.4 11.5 1.0 O B:HOH2147 2.4 16.0 1.0 O3 B:PO41227 2.5 20.5 1.0 O B:HOH2128 2.5 29.4 1.0 O B:HOH2127 2.5 16.6 1.0 O4 B:PO41227 2.9 22.2 1.0 CG B:ASP201 3.2 11.7 1.0 P B:PO41227 3.3 20.0 1.0 OD2 B:ASP201 3.3 15.2 1.0 O B:HOH2108 3.8 12.2 1.0 NH1 B:ARG207 4.1 11.6 1.0 O1 B:PO41227 4.3 19.1 1.0 O B:HOH2151 4.3 38.3 1.0 O B:HOH2129 4.4 18.9 1.0 O2 B:PO41227 4.4 18.6 1.0 O B:HOH2142 4.5 13.0 1.0 N2 B:5GP1230 4.6 13.6 1.0 O B:ASP201 4.7 11.5 1.0 CB B:ASP201 4.7 11.3 1.0 O B:HOH2145 4.8 33.6 1.0 NH2 B:ARG207 4.8 12.1 1.0 N3 B:5GP1230 4.9 13.7 1.0 CZ B:ARG207 4.9 12.1 1.0

Calcium binding site 4 out of 4 in the Human Phosphoribosyl Transferase Domain Containing 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human Phosphoribosyl Transferase Domain Containing 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1229 b:13.9 occ:1.00 OE2 B:GLU141 2.4 14.3 1.0 O B:HOH2144 2.4 11.7 1.0 OD1 B:ASP142 2.4 9.8 1.0 O B:HOH2142 2.4 13.0 1.0 O B:HOH2153 2.4 16.6 1.0 O3' B:5GP1230 2.6 13.0 1.0 O2' B:5GP1230 2.6 13.1 1.0 OE1 B:GLU141 2.7 11.6 1.0 CD B:GLU141 2.8 12.7 1.0 CG B:ASP142 3.4 11.4 1.0 C3' B:5GP1230 3.5 14.3 1.0 C2' B:5GP1230 3.6 14.0 1.0 OD2 B:ASP142 3.7 12.4 1.0 O2 B:PO41227 4.1 18.6 1.0 CG B:GLU141 4.2 12.6 1.0 C1' B:5GP1230 4.3 14.9 1.0 CG1 B:VAL74 4.4 10.8 1.0 O B:HOH2107 4.5 15.0 1.0 N B:ASP142 4.6 9.7 1.0 O B:HOH2152 4.6 23.9 1.0 O B:VAL143 4.6 11.7 1.0 CB B:ASP142 4.8 11.5 1.0 C4' B:5GP1230 4.8 14.0 1.0 N B:VAL143 4.8 11.8 1.0 O B:HOH2147 4.9 16.0 1.0 O B:HOH2053 5.0 15.4 1.0

M.Welin, L.Egeblad, A.Johansson, P.Stenmark, L.Wang, S.Flodin, T.Nyman, L.Tresaugues, T.Kotenyova, I.Johansson, S.Eriksson, H.Eklund, P.Nordlund. Structural and Functional Studies of the Human Phosphoribosyltransferase Domain Containing Protein 1. Febs J. V. 277 4920 2010.
ISSN: ISSN 1742-464X
PubMed: 21054786
DOI: 10.1111/J.1742-4658.2010.07897.X