Calcium in PDB 1snn: 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From Methanococcus Jannaschii

The structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From Methanococcus Jannaschii, PDB code: 1snn was solved by S.Steinbacher, S.Schiffmann, 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 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.395, 69.366, 57.574, 90.00, 93.58, 90.00
R / Rfree (%)	20 / 23.4

The structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From Methanococcus Jannaschii 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 Methanococcus Jannaschii (pdb code 1snn). 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 Methanococcus Jannaschii, PDB code: 1snn:
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 Methanococcus Jannaschii


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 Methanococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:20.3 occ:1.00 O A:HOH750 2.3 26.9 1.0 OE2 A:GLU26 2.3 23.9 1.0 O13 A:5RP401 2.4 21.2 1.0 OH A:TYR95 2.4 25.8 1.0 O11 A:5RP401 2.5 20.7 1.0 O A:HOH668 2.6 27.7 1.0 O4 A:5RP401 2.6 24.1 1.0 O8 A:5RP401 2.7 18.4 1.0 P9 A:5RP401 3.2 17.6 1.0 CZ A:TYR95 3.2 23.9 1.0 C3 A:5RP401 3.4 21.8 1.0 C5 A:5RP401 3.4 22.8 1.0 CD A:GLU26 3.5 20.8 1.0 CE2 A:TYR95 3.6 22.1 1.0 O10 A:5RP401 3.8 18.5 1.0 C7 A:5RP401 3.9 20.8 1.0 O A:HOH746 4.0 26.9 1.0 ZN A:ZN402 4.0 18.9 1.0 O A:HOH623 4.0 18.4 1.0 OE1 A:GLU26 4.1 19.9 1.0 O A:HOH633 4.1 33.7 1.0 C6 A:5RP401 4.2 17.4 1.0 CE1 A:TYR95 4.3 22.9 1.0 O12 A:5RP401 4.6 21.1 1.0 CG A:GLU26 4.7 18.6 1.0 NH1 A:ARG161 4.7 20.3 1.0 O14 A:5RP401 4.8 20.0 1.0 C2 A:5RP401 4.8 26.0 1.0 CD2 A:TYR95 4.9 21.3 1.0 NH1 A:ARG25 4.9 20.7 1.0

Calcium binding site 2 out of 4 in the 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From Methanococcus Jannaschii


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 Methanococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:24.7 occ:1.00 O A:HOH671 2.2 27.2 1.0 O A:HOH654 2.3 26.7 1.0 O A:HOH676 2.4 25.7 1.0 OE1 A:GLU97 2.4 31.6 1.0 O A:HOH706 2.4 23.1 1.0 OD2 A:ASP96 2.5 24.5 1.0 CD A:GLU97 3.5 39.0 1.0 CG A:ASP96 3.6 26.9 1.0 OE2 A:GLU97 3.9 44.8 1.0 OD1 A:ASP96 4.0 24.9 1.0 O A:HOH708 4.2 23.8 1.0 O A:ASN160 4.4 25.9 1.0 N A:GLU97 4.5 25.9 1.0 OE1 A:GLN162 4.6 26.1 1.0 O A:HOH663 4.7 31.2 1.0 CA A:ARG161 4.7 23.3 1.0 O A:HOH745 4.7 38.6 1.0 CG A:GLU97 4.7 36.2 1.0 CG A:ARG161 4.8 20.0 1.0 CB A:ASP96 4.8 24.9 1.0 CA A:ASP96 4.9 25.5 1.0

Calcium binding site 3 out of 4 in the 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From Methanococcus Jannaschii


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 Methanococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:20.6 occ:1.00 OD1 A:ASN207 2.3 21.6 1.0 O A:HOH688 2.3 33.2 1.0 O A:GLU204 2.4 19.4 1.0 CG A:ASN207 3.4 19.0 1.0 C A:GLU204 3.6 22.3 1.0 ND2 A:ASN207 4.0 20.8 1.0 CA A:GLU204 4.3 23.8 1.0 OE2 A:GLU204 4.5 50.0 1.0 O A:LYS205 4.6 17.4 1.0 N A:LYS205 4.6 19.7 1.0 N A:ASN207 4.6 18.4 1.0 CB A:ASN207 4.6 18.2 1.0 CA A:ASN207 4.7 19.3 1.0 C A:LYS205 4.7 18.6 1.0 CA A:LYS205 4.8 20.9 1.0 CB A:GLU204 4.8 27.0 1.0

Calcium binding site 4 out of 4 in the 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From Methanococcus Jannaschii


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 Methanococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:28.5 occ:1.00 O B:HOH707 2.3 37.8 1.0 O B:HOH705 2.3 31.9 1.0 OE2 B:GLU26 2.4 27.3 1.0 O11 B:5RP501 2.4 22.2 1.0 O B:HOH664 2.5 32.3 1.0 O13 B:5RP501 2.6 21.8 1.0 O4 B:5RP501 2.7 27.7 1.0 O8 B:5RP501 2.9 19.0 1.0 P9 B:5RP501 3.1 19.4 1.0 C3 B:5RP501 3.5 28.8 1.0 CD B:GLU26 3.5 27.8 1.0 C5 B:5RP501 3.5 24.8 1.0 O10 B:5RP501 3.8 16.2 1.0 OE1 B:GLU26 4.1 19.2 1.0 C7 B:5RP501 4.1 18.0 1.0 O B:HOH679 4.1 26.9 1.0 O B:HOH672 4.2 41.0 1.0 ZN B:ZN502 4.2 21.8 1.0 O B:HOH632 4.4 54.9 1.0 NH1 B:ARG161 4.4 20.4 1.0 C6 B:5RP501 4.4 23.5 1.0 O12 B:5RP501 4.5 20.2 1.0 O B:HOH576 4.5 46.3 1.0 NH1 B:ARG25 4.7 31.2 1.0 CG B:GLU26 4.7 22.1 1.0 NH2 B:ARG25 4.9 26.7 1.0 C2 B:5RP501 5.0 31.2 1.0 O14 B:5RP501 5.0 19.4 1.0

S.Steinbacher, S.Schiffmann, A.Bacher, M.Fischer. Metal Sites in 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From Methanococcus Jannaschii in Complex with the Substrate Ribulose 5-Phosphate. Acta Crystallogr.,Sect.D V. 60 1338 2004.
ISSN: ISSN 0907-4449
PubMed: 15213409
DOI: 10.1107/S0907444904009862