Zinc 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:

Calcium

(Ca)

4 atoms

The binding sites of Zinc 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 Zinc atom.
In total 3 binding sites of Zinc where determined in the 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From Methanococcus Jannaschii, PDB code: 1snn:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From Methanococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn402 b:18.9 occ:1.00 OE1 A:GLU26 1.9 19.9 1.0 O10 A:5RP401 2.1 18.5 1.0 ND1 A:HIS164 2.2 17.0 1.0 O A:HOH751 2.2 19.3 1.0 O14 A:5RP401 2.2 20.0 1.0 O13 A:5RP401 2.4 21.2 1.0 CD A:GLU26 2.9 20.8 1.0 CE1 A:HIS164 3.0 16.9 1.0 C6 A:5RP401 3.1 17.4 1.0 C5 A:5RP401 3.2 22.8 1.0 OE2 A:GLU26 3.2 23.9 1.0 P9 A:5RP401 3.2 17.6 1.0 CG A:HIS164 3.2 18.1 1.0 O8 A:5RP401 3.4 18.4 1.0 C7 A:5RP401 3.6 20.8 1.0 CB A:HIS164 3.7 19.9 1.0 OD2 A:ASP30 3.9 19.0 1.0 O11 A:5RP401 4.0 20.7 1.0 CA A:CA403 4.0 20.3 1.0 OD1 A:ASP30 4.1 17.6 1.0 NE2 A:HIS164 4.2 17.7 1.0 NH2 A:ARG25 4.2 16.4 1.0 N A:HIS164 4.3 21.1 1.0 CG A:GLU26 4.3 18.6 1.0 CD2 A:HIS164 4.3 19.5 1.0 CG A:ASP30 4.4 17.7 1.0 O A:HOH623 4.4 18.4 1.0 O12 A:5RP401 4.5 21.1 1.0 C3 A:5RP401 4.5 21.8 1.0 OE2 A:GLU28 4.6 19.6 1.0 CA A:HIS164 4.6 18.8 1.0 CB A:GLU26 4.8 17.9 1.0 O4 A:5RP401 4.9 24.1 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn603 b:17.9 occ:1.00 ND1 A:HIS206 2.0 18.3 1.0 CE1 A:HIS206 3.0 17.1 1.0 CG A:HIS206 3.0 18.2 1.0 CB A:HIS206 3.4 14.7 1.0 CA A:HIS206 3.8 15.6 1.0 O A:HOH612 4.0 25.5 1.0 NE2 A:HIS206 4.1 21.1 1.0 CD2 A:HIS206 4.2 17.7 1.0 O A:HIS206 4.4 18.9 1.0 C A:HIS206 4.6 16.3 1.0 N A:HIS206 4.8 19.7 1.0 O A:LYS205 4.8 17.4 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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 B:Zn502 b:21.8 occ:1.00 OE1 B:GLU26 2.0 19.2 1.0 O10 B:5RP501 2.1 16.2 1.0 O B:HOH706 2.1 21.8 1.0 O14 B:5RP501 2.2 19.4 1.0 ND1 B:HIS164 2.3 19.5 1.0 O13 B:5RP501 2.4 21.8 1.0 CD B:GLU26 3.0 27.8 1.0 C6 B:5RP501 3.1 23.5 1.0 CE1 B:HIS164 3.1 16.3 1.0 C5 B:5RP501 3.2 24.8 1.0 P9 B:5RP501 3.2 19.4 1.0 CG B:HIS164 3.3 17.4 1.0 OE2 B:GLU26 3.3 27.3 1.0 O8 B:5RP501 3.5 19.0 1.0 CB B:HIS164 3.6 12.9 1.0 C7 B:5RP501 3.7 18.0 1.0 O11 B:5RP501 4.0 22.2 1.0 OD2 B:ASP30 4.1 17.4 1.0 OD1 B:ASP30 4.1 19.2 1.0 N B:HIS164 4.1 14.3 1.0 NH2 B:ARG25 4.2 26.7 1.0 CA B:CA503 4.2 28.5 1.0 NE2 B:HIS164 4.3 15.1 1.0 OE2 B:GLU28 4.3 23.8 1.0 O B:HOH679 4.3 26.9 1.0 CG B:GLU26 4.4 22.1 1.0 CD2 B:HIS164 4.4 16.6 1.0 CG B:ASP30 4.4 14.9 1.0 O12 B:5RP501 4.4 20.2 1.0 CA B:HIS164 4.5 15.9 1.0 C3 B:5RP501 4.6 28.8 1.0 CB B:GLU26 4.8 24.5 1.0 OD2 B:ASP21 5.0 26.8 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