Zinc in PDB 1pvw: 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From M. Jannaschii

The structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From M. Jannaschii, PDB code: 1pvw 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 / 2.45
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	66.315, 154.205, 133.152, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 28.9

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

Calcium

(Ca)

1 atom

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

Zinc binding site 1 out of 2 in the 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From M. 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 M. Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:28.9 occ:1.00 OE1 A:GLU26 2.0 33.9 1.0 O1 A:PO4409 2.0 34.6 1.0 O A:HOH404 2.1 33.7 1.0 ND1 A:HIS164 2.1 36.0 1.0 O A:HOH403 2.2 40.4 1.0 CD A:GLU26 3.0 33.1 1.0 CE1 A:HIS164 3.1 35.7 1.0 CG A:HIS164 3.1 32.8 1.0 P A:PO4409 3.2 35.8 1.0 OE2 A:GLU26 3.3 35.0 1.0 O2 A:PO4409 3.3 35.2 1.0 CB A:HIS164 3.5 31.9 1.0 CA A:CA402 3.6 33.7 1.0 NH2 A:ARG25 3.9 35.8 1.0 OD2 A:ASP30 3.9 34.4 1.0 N A:HIS164 4.0 31.1 1.0 NE2 A:HIS164 4.2 36.9 1.0 O A:HOH408 4.2 34.2 1.0 O4 A:PO4409 4.2 39.5 1.0 CD2 A:HIS164 4.2 33.0 1.0 O3 A:PO4409 4.2 33.9 1.0 CG A:GLU26 4.3 37.8 1.0 CA A:HIS164 4.4 31.3 1.0 OD1 A:ASP30 4.5 30.1 1.0 CG A:ASP30 4.6 32.0 1.0 O A:HOH406 4.6 30.4 1.0 CB A:GLU26 4.7 37.3 1.0 CZ A:ARG25 5.0 38.0 1.0

Zinc binding site 2 out of 2 in the 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase From M. 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 M. Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:40.3 occ:1.00 OE2 B:GLU132 2.2 33.4 1.0 OE2 B:GLU128 2.6 49.5 1.0 CD B:GLU128 2.8 46.9 1.0 OE1 B:GLU132 2.9 39.9 1.0 CD B:GLU132 2.9 37.2 1.0 CG B:GLU128 3.3 45.5 1.0 OE1 B:GLU128 3.4 54.8 1.0 NH1 B:ARG134 4.4 31.1 1.0 CG B:GLU132 4.4 37.5 1.0 CB B:GLU128 4.7 40.3 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