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

Protein crystallography data

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

Other elements in 1pvy:

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:

Calcium (Ca) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 3 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 1pvy

Go back to Zinc Binding Sites List in 1pvy
Zinc binding site 1 out of 3 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 Zinc with other atoms in the Zn 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:Zn502

b:28.3
occ:1.00
OE1 A:GLU26 1.8 21.8 1.0
O A:HOH852 2.1 22.1 1.0
ND1 A:HIS164 2.1 21.9 1.0
O14 A:5RP501 2.2 23.6 1.0
O10 A:5RP501 2.2 25.7 1.0
O13 A:5RP501 2.5 26.4 1.0
CD A:GLU26 2.8 23.2 1.0
CE1 A:HIS164 3.0 23.4 1.0
C6 A:5RP501 3.0 26.4 1.0
OE2 A:GLU26 3.2 29.9 1.0
CG A:HIS164 3.2 24.0 1.0
C5 A:5RP501 3.2 32.7 1.0
P9 A:5RP501 3.3 23.6 1.0
O8 A:5RP501 3.4 25.5 1.0
CB A:HIS164 3.5 23.0 1.0
C7 A:5RP501 3.6 25.5 1.0
OD2 A:ASP30 3.9 21.4 1.0
CA A:CA503 4.0 27.3 1.0
O11 A:5RP501 4.1 26.9 1.0
CG A:GLU26 4.1 24.6 1.0
NE2 A:HIS164 4.1 24.2 1.0
OD1 A:ASP30 4.1 17.5 1.0
CD2 A:HIS164 4.2 27.4 1.0
N A:HIS164 4.2 24.7 1.0
NH2 A:ARG25 4.3 27.9 1.0
CG A:ASP30 4.4 18.9 1.0
O A:HOH723 4.4 23.0 1.0
O12 A:5RP501 4.5 28.8 1.0
OE2 A:GLU28 4.5 21.0 1.0
CA A:HIS164 4.5 20.8 1.0
C3 A:5RP501 4.6 34.5 1.0
CB A:GLU26 4.7 30.2 1.0
O A:HOH851 4.9 25.0 1.0
OD2 A:ASP21 4.9 24.1 1.0
O4 A:5RP501 5.0 27.8 1.0

Zinc binding site 2 out of 3 in 1pvy

Go back to Zinc Binding Sites List in 1pvy
Zinc binding site 2 out of 3 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 Zinc with other atoms in the Zn 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:Zn703

b:23.6
occ:1.00
ND1 A:HIS206 2.1 23.3 1.0
CG A:HIS206 3.0 18.2 1.0
CE1 A:HIS206 3.1 20.6 1.0
CB A:HIS206 3.2 23.1 1.0
CA A:HIS206 3.7 22.3 1.0
CD2 A:HIS206 4.2 18.3 1.0
O A:HOH713 4.2 25.1 1.0
NE2 A:HIS206 4.2 22.1 1.0
O A:HIS206 4.4 20.7 1.0
C A:HIS206 4.5 20.2 1.0
O A:HOH829 4.7 37.1 1.0
N A:HIS206 4.8 17.7 1.0
O A:LYS205 4.9 20.8 1.0

Zinc binding site 3 out of 3 in 1pvy

Go back to Zinc Binding Sites List in 1pvy
Zinc binding site 3 out of 3 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 Zinc with other atoms in the Zn 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
B:Zn602

b:30.8
occ:1.00
OE1 B:GLU26 1.9 27.7 1.0
O10 B:5RP601 2.1 21.0 1.0
O B:HOH805 2.1 36.5 1.0
ND1 B:HIS164 2.2 19.2 1.0
O14 B:5RP601 2.4 31.7 1.0
O13 B:5RP601 2.5 23.6 1.0
CD B:GLU26 2.9 35.9 1.0
CE1 B:HIS164 3.0 23.1 1.0
OE2 B:GLU26 3.2 40.9 1.0
CG B:HIS164 3.3 22.5 1.0
C6 B:5RP601 3.3 28.5 1.0
P9 B:5RP601 3.3 21.8 1.0
C5 B:5RP601 3.3 30.9 1.0
O8 B:5RP601 3.6 20.4 1.0
CB B:HIS164 3.7 19.8 1.0
C7 B:5RP601 3.9 22.6 1.0
N B:HIS164 4.0 16.5 1.0
O11 B:5RP601 4.1 21.1 1.0
OD1 B:ASP30 4.1 22.4 1.0
OD2 B:ASP30 4.2 14.8 1.0
NE2 B:HIS164 4.2 17.6 1.0
CG B:GLU26 4.2 29.5 1.0
CD2 B:HIS164 4.3 17.5 1.0
NH2 B:ARG25 4.3 37.2 1.0
CA B:CA603 4.3 37.9 1.0
O B:HOH778 4.4 33.6 1.0
O12 B:5RP601 4.5 24.8 1.0
CG B:ASP30 4.5 17.9 1.0
CA B:HIS164 4.5 18.0 1.0
OE2 B:GLU28 4.6 32.2 1.0
CB B:GLU26 4.6 36.0 1.0
C3 B:5RP601 4.7 36.9 1.0
OD2 B:ASP21 5.0 52.5 1.0

Reference:

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
Page generated: Wed Dec 16 03:01:09 2020

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