Calcium in PDB 3oyr: Crystal Structure of Polyprenyl Synthase From Caulobacter Crescentus CB15 Complexed with Calcium and Isoprenyl Diphosphate

The structure of Crystal Structure of Polyprenyl Synthase From Caulobacter Crescentus CB15 Complexed with Calcium and Isoprenyl Diphosphate, PDB code: 3oyr was solved by Y.Patskovsky, R.Toro, M.Rutter, J.M.Sauder, S.K.Burley, C.D.Poulter, J.A.Gerlt, S.C.Almo, New York Sgx Research Center For Structuralgenomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.894, 72.438, 125.854, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 24.7

The binding sites of Calcium atom in the Crystal Structure of Polyprenyl Synthase From Caulobacter Crescentus CB15 Complexed with Calcium and Isoprenyl Diphosphate (pdb code 3oyr). 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 Polyprenyl Synthase From Caulobacter Crescentus CB15 Complexed with Calcium and Isoprenyl Diphosphate, PDB code: 3oyr:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Polyprenyl Synthase From Caulobacter Crescentus CB15 Complexed with Calcium and Isoprenyl Diphosphate


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 Polyprenyl Synthase From Caulobacter Crescentus CB15 Complexed with Calcium and Isoprenyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca337 b:33.2 occ:1.00 OD2 B:ASP95 2.3 37.6 1.0 O2A B:DMA339 2.3 42.3 1.0 O3B B:DMA339 2.3 33.6 1.0 O B:HOH347 2.3 28.0 1.0 OD1 B:ASP99 2.4 49.9 1.0 O B:HOH365 2.5 31.2 1.0 CG B:ASP95 3.3 43.8 1.0 PB B:DMA339 3.5 38.0 1.0 PA B:DMA339 3.5 32.4 1.0 CG B:ASP99 3.5 44.1 1.0 O3A B:DMA339 3.6 35.5 1.0 OD1 B:ASP95 3.7 37.7 1.0 O B:HOH467 3.9 45.3 1.0 CB B:ASP99 4.0 39.8 1.0 O B:HOH388 4.0 33.0 1.0 O2B B:DMA339 4.1 37.2 1.0 NH2 B:ARG104 4.4 26.7 1.0 OG B:SER101 4.4 38.2 1.0 NZ B:LYS246 4.4 44.8 1.0 O B:HOH352 4.5 35.1 1.0 O1A B:DMA339 4.5 32.5 1.0 O B:ASP95 4.6 35.9 1.0 OD2 B:ASP99 4.6 47.7 1.0 C2 B:DMA339 4.6 55.5 1.0 OD1 B:ASP96 4.6 36.0 1.0 CB B:ASP95 4.6 32.3 1.0 O1 B:DMA339 4.7 40.2 1.0 O1B B:DMA339 4.7 33.1 1.0 C B:ASP95 4.8 33.8 1.0 C1 B:DMA339 4.9 47.5 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Polyprenyl Synthase From Caulobacter Crescentus CB15 Complexed with Calcium and Isoprenyl Diphosphate


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 Polyprenyl Synthase From Caulobacter Crescentus CB15 Complexed with Calcium and Isoprenyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca338 b:40.0 occ:1.00 O2B B:DMA339 2.2 37.2 1.0 OD1 B:ASP222 2.3 33.6 1.0 O B:HOH395 2.3 40.3 1.0 O B:HOH360 2.4 35.4 1.0 O1A B:DMA339 2.4 32.5 1.0 O B:HOH352 2.4 35.1 1.0 CG B:ASP222 3.4 39.3 1.0 PA B:DMA339 3.4 32.4 1.0 PB B:DMA339 3.4 38.0 1.0 O3A B:DMA339 3.5 35.5 1.0 OD1 B:ASP226 3.9 41.6 1.0 OD2 B:ASP222 3.9 37.7 1.0 O B:HOH394 4.0 50.9 1.0 O B:ASP222 4.2 35.5 1.0 OD1 B:ASP241 4.2 46.3 1.0 NZ B:LYS236 4.2 27.8 1.0 OD2 B:ASP241 4.2 45.1 1.0 O2A B:DMA339 4.2 42.3 1.0 OD1 B:ASP223 4.3 38.1 1.0 CE B:LYS236 4.4 33.0 1.0 O1B B:DMA339 4.4 33.1 1.0 O3B B:DMA339 4.4 33.6 1.0 CG B:ASP226 4.5 43.4 1.0 NE2 B:GLN219 4.5 29.6 1.0 O B:HOH365 4.6 31.2 1.0 O B:HOH398 4.6 36.9 1.0 CB B:ASP222 4.6 30.1 1.0 C B:ASP222 4.6 32.5 1.0 O1 B:DMA339 4.7 40.2 1.0 CG B:ASP241 4.7 52.4 1.0 CB B:ASP226 4.7 34.9 1.0 O B:HOH388 4.9 33.0 1.0

F.H.Wallrapp, J.J.Pan, G.Ramamoorthy, D.E.Almonacid, B.S.Hillerich, R.Seidel, Y.Patskovsky, P.C.Babbitt, S.C.Almo, M.P.Jacobson, C.D.Poulter. Prediction of Function For the Polyprenyl Transferase Subgroup in the Isoprenoid Synthase Superfamily. Proc.Natl.Acad.Sci.Usa V. 110 E1196 2013.
ISSN: ISSN 0027-8424
PubMed: 23493556
DOI: 10.1073/PNAS.1300632110