Calcium in PDB 2gse: Crystal Structure of Human Dihydropyrimidinease-Like 2

All present enzymatic activity of Crystal Structure of Human Dihydropyrimidinease-Like 2:
3.5.2.2;

The structure of Crystal Structure of Human Dihydropyrimidinease-Like 2, PDB code: 2gse was solved by D.Ogg, P.Stenmark, C.Arrowsmith, H.Berglund, R.Collins, A.Edwards, M.Ehn, S.Flodin, A.Flores, S.Graslund, B.M.Hallberg, M.Hammarstrom, T.Kotenyova, P.Kursula, P.Nilsson-Ehle, T.Nyman, C.Persson, J.Sagemark, M.Sundstrom, L.Holmberg-Schiavone, A.G.Thorsell, J.Uppenberg, S.Van Den Berg, J.Weigelt, P.Nordlund, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.31 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.400, 126.100, 102.900, 90.00, 113.00, 90.00
R / Rfree (%)	16.9 / 24.5

The binding sites of Calcium atom in the Crystal Structure of Human Dihydropyrimidinease-Like 2 (pdb code 2gse). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Human Dihydropyrimidinease-Like 2, PDB code: 2gse:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Human Dihydropyrimidinease-Like 2


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 Dihydropyrimidinease-Like 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1000 b:42.6 occ:1.00 O A:THR349 2.2 20.3 1.0 O A:HOH1215 2.4 25.8 1.0 O A:HOH1202 2.6 42.8 1.0 O A:HOH1089 3.1 14.4 1.0 C A:THR349 3.5 19.4 1.0 OE1 A:GLN81 3.6 42.7 1.0 O A:HOH1218 4.1 30.7 1.0 CA A:THR349 4.4 19.2 1.0 N A:LEU350 4.4 19.0 1.0 CA A:LEU350 4.4 18.8 1.0 O A:HOH1092 4.5 20.4 1.0 OE1 A:GLU353 4.6 22.4 1.0 CD A:GLN81 4.7 38.6 1.0 O A:HOH1134 4.7 25.4 1.0 O A:ILE351 4.7 18.6 1.0 CB A:THR349 4.8 19.3 1.0 C A:LEU350 4.9 18.5 1.0 CD A:GLU353 4.9 22.0 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Human Dihydropyrimidinease-Like 2


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 Dihydropyrimidinease-Like 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:32.9 occ:1.00 O B:THR349 2.4 19.9 1.0 O B:HOH1178 2.4 25.5 1.0 O B:HOH1175 2.4 29.4 1.0 O B:HOH1061 2.5 29.3 1.0 O B:HOH1141 2.8 28.1 1.0 O B:HOH1099 3.0 25.5 1.0 C B:THR349 3.6 19.6 1.0 O B:HOH1098 4.1 23.9 1.0 OE1 B:GLU353 4.1 16.3 1.0 CA B:THR349 4.4 18.7 1.0 N B:LEU350 4.5 20.2 1.0 O B:HOH1023 4.6 16.2 1.0 CA B:LEU350 4.6 19.8 1.0 CD B:GLU353 4.7 19.9 1.0 CB B:THR349 4.8 18.7 1.0 O B:ILE351 4.9 18.1 1.0 OE1 B:GLN81 5.0 40.9 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Human Dihydropyrimidinease-Like 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human Dihydropyrimidinease-Like 2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1002 b:36.9 occ:1.00 O C:HOH1206 2.2 19.4 1.0 O C:THR349 2.3 23.1 1.0 O C:HOH1222 2.5 31.7 1.0 O C:HOH1122 2.5 14.7 1.0 C C:THR349 3.4 21.7 1.0 O C:HOH1113 3.7 22.5 1.0 O C:HOH1030 4.0 28.9 1.0 CA C:THR349 4.3 21.5 1.0 N C:LEU350 4.3 21.1 1.0 NE2 C:GLN81 4.3 38.7 1.0 CA C:LEU350 4.4 20.5 1.0 O C:ILE351 4.4 19.7 1.0 OE2 C:GLU353 4.4 25.8 1.0 O C:HOH1211 4.5 21.3 1.0 CD C:GLU353 4.5 22.3 1.0 OE1 C:GLU353 4.6 23.5 1.0 CD C:GLN81 4.6 38.4 1.0 C C:LEU350 4.7 20.6 1.0 OE1 C:GLN81 4.8 36.2 1.0 CB C:THR349 4.9 21.6 1.0 N C:ILE351 5.0 20.8 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Human Dihydropyrimidinease-Like 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human Dihydropyrimidinease-Like 2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1003 b:28.1 occ:1.00 O D:THR349 2.1 22.0 1.0 O D:HOH1215 2.2 29.2 1.0 O D:HOH1158 2.6 31.5 1.0 C D:THR349 3.2 20.4 1.0 O D:HOH1089 3.3 33.0 1.0 CA D:THR349 3.9 20.1 1.0 O D:HOH1042 4.3 24.2 1.0 N D:LEU350 4.3 21.0 1.0 OE1 D:GLU353 4.4 25.8 1.0 CB D:THR349 4.4 20.4 1.0 O D:HOH1046 4.4 29.6 1.0 OE1 D:GLN81 4.5 40.6 1.0 CD D:GLU353 4.5 22.8 1.0 O D:ILE351 4.5 19.5 1.0 CA D:LEU350 4.6 20.9 1.0 OE2 D:GLU353 4.6 23.3 1.0 O D:HOH1081 4.8 43.5 1.0 C D:LEU350 4.9 20.7 1.0

P.Stenmark, D.Ogg, S.Flodin, A.Flores, T.Kotenyova, T.Nyman, P.Nordlund, P.Kursula. The Structure of Human Collapsin Response Mediator Protein 2, A Regulator of Axonal Growth. J.Neurochem. V. 101 906 2007.
ISSN: ISSN 0022-3042
PubMed: 17250651
DOI: 10.1111/J.1471-4159.2006.04401.X