Calcium in PDB 1pvy: 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From M. Jannaschii in Complex with Ribulose 5-Phosphate

The structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From M. Jannaschii in Complex with Ribulose 5-Phosphate, PDB code: 1pvy was solved by S.Steinbacher, S.Schiffmann, G.Richter, R.Huber, A.Bacher, M.Fischer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.197, 69.272, 57.110, 90.00, 93.52, 90.00
R / Rfree (%)	21.3 / 25.9

The structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From M. Jannaschii in Complex with Ribulose 5-Phosphate also contains other interesting chemical elements:

Zinc

(Zn)

3 atoms

The binding sites of Calcium atom in the 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From M. Jannaschii in Complex with Ribulose 5-Phosphate (pdb code 1pvy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From M. Jannaschii in Complex with Ribulose 5-Phosphate, PDB code: 1pvy:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From M. Jannaschii in Complex with Ribulose 5-Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From M. Jannaschii in Complex with Ribulose 5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:27.3 occ:1.00 O A:HOH851 2.1 25.0 1.0 OE2 A:GLU26 2.3 29.9 1.0 O13 A:5RP501 2.4 26.4 1.0 OH A:TYR95 2.4 37.0 1.0 O11 A:5RP501 2.5 26.9 1.0 O4 A:5RP501 2.7 27.8 1.0 O8 A:5RP501 2.7 25.5 1.0 P9 A:5RP501 3.1 23.6 1.0 CZ A:TYR95 3.1 36.9 1.0 C5 A:5RP501 3.4 32.7 1.0 C3 A:5RP501 3.4 34.5 1.0 CE2 A:TYR95 3.4 42.5 1.0 CD A:GLU26 3.5 23.2 1.0 O10 A:5RP501 3.7 25.7 1.0 C7 A:5RP501 3.9 25.5 1.0 O A:HOH847 4.0 43.2 1.0 ZN A:ZN502 4.0 28.3 1.0 OE1 A:GLU26 4.1 21.8 1.0 O A:HOH723 4.2 23.0 1.0 CE1 A:TYR95 4.2 37.4 1.0 O A:HOH732 4.2 30.2 1.0 C6 A:5RP501 4.2 26.4 1.0 O12 A:5RP501 4.5 28.8 1.0 NH1 A:ARG161 4.6 28.3 1.0 CD2 A:TYR95 4.6 39.4 1.0 CG A:GLU26 4.7 24.6 1.0 O14 A:5RP501 4.8 23.6 1.0 C2 A:5RP501 4.9 34.1 1.0 NH1 A:ARG25 4.9 32.5 1.0

Calcium binding site 2 out of 4 in the 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From M. Jannaschii in Complex with Ribulose 5-Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From M. Jannaschii in Complex with Ribulose 5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:31.5 occ:1.00 O A:HOH769 2.2 29.2 1.0 O A:HOH774 2.3 26.0 1.0 OE1 A:GLU97 2.3 56.5 1.0 O A:HOH806 2.4 24.9 1.0 O A:HOH753 2.4 32.6 1.0 OD2 A:ASP96 2.6 44.5 1.0 CD A:GLU97 3.4 57.7 1.0 CG A:ASP96 3.6 49.1 1.0 OE2 A:GLU97 3.7 57.3 1.0 OD1 A:ASP96 4.1 39.4 1.0 O A:ASN160 4.2 40.9 1.0 OE1 A:GLN162 4.3 30.5 1.0 O A:HOH808 4.5 30.9 1.0 N A:GLU97 4.5 43.5 1.0 CA A:ARG161 4.6 31.6 1.0 CG A:GLU97 4.7 51.8 1.0 CG A:ARG161 4.8 28.3 1.0 O A:HOH762 4.8 33.8 1.0 CB A:ASP96 4.9 43.9 1.0 CB A:GLU97 4.9 50.5 1.0 O A:HOH846 4.9 38.1 1.0

Calcium binding site 3 out of 4 in the 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From M. Jannaschii in Complex with Ribulose 5-Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From M. Jannaschii in Complex with Ribulose 5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:25.1 occ:1.00 OD1 A:ASN207 2.2 28.7 1.0 O A:HOH787 2.3 40.0 1.0 O A:GLU204 2.4 22.3 1.0 CG A:ASN207 3.4 26.6 1.0 C A:GLU204 3.6 27.4 1.0 ND2 A:ASN207 3.9 25.6 1.0 CA A:GLU204 4.3 25.1 1.0 CB A:ASN207 4.6 21.7 1.0 N A:LYS205 4.6 23.4 1.0 OE2 A:GLU204 4.6 52.9 1.0 N A:ASN207 4.6 20.0 1.0 O A:LYS205 4.6 20.8 1.0 CA A:ASN207 4.6 19.6 1.0 C A:LYS205 4.8 22.2 1.0 CA A:LYS205 4.8 24.0 1.0 CB A:GLU204 4.8 31.7 1.0

Calcium binding site 4 out of 4 in the 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From M. Jannaschii in Complex with Ribulose 5-Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From M. Jannaschii in Complex with Ribulose 5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca603 b:37.9 occ:1.00 O B:HOH806 2.2 32.8 1.0 O11 B:5RP601 2.3 21.1 1.0 O B:HOH804 2.3 34.2 1.0 OE2 B:GLU26 2.3 40.9 1.0 O B:HOH764 2.7 37.9 1.0 O13 B:5RP601 2.8 23.6 1.0 O4 B:5RP601 3.0 38.2 1.0 O8 B:5RP601 3.0 20.4 1.0 P9 B:5RP601 3.1 21.8 1.0 CD B:GLU26 3.5 35.9 1.0 O10 B:5RP601 3.7 21.0 1.0 C3 B:5RP601 3.8 36.9 1.0 C5 B:5RP601 3.8 30.9 1.0 OE1 B:GLU26 4.2 27.7 1.0 O B:HOH772 4.3 48.8 1.0 NH1 B:ARG161 4.3 23.8 1.0 O B:HOH778 4.3 33.6 1.0 ZN B:ZN602 4.3 30.8 1.0 C7 B:5RP601 4.3 22.6 1.0 O12 B:5RP601 4.5 24.8 1.0 O B:HOH677 4.5 41.8 1.0 CG B:GLU26 4.6 29.5 1.0 NH2 B:ARG25 4.6 37.2 1.0 C6 B:5RP601 4.6 28.5 1.0 NH1 B:ARG25 4.7 43.2 1.0

S.Steinbacher, S.Schiffmann, G.Richter, R.Huber, A.Bacher, M.Fischer. Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From Methanococcus Jannaschii in Complex with Divalent Metal Ions and the Substrate Ribulose 5-Phosphate: Implications For the Catalytic Mechanism J.Biol.Chem. V. 278 42256 2003.
ISSN: ISSN 0021-9258
PubMed: 12904291
DOI: 10.1074/JBC.M307301200