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Calcium in PDB 1wnd: Escherichia Coli Ydcw Gene Product Is A Medium-Chain Aldehyde Dehydrogenase As Determined By Kinetics and Crystal Structure

Enzymatic activity of Escherichia Coli Ydcw Gene Product Is A Medium-Chain Aldehyde Dehydrogenase As Determined By Kinetics and Crystal Structure

All present enzymatic activity of Escherichia Coli Ydcw Gene Product Is A Medium-Chain Aldehyde Dehydrogenase As Determined By Kinetics and Crystal Structure:
1.2.1.8;

Protein crystallography data

The structure of Escherichia Coli Ydcw Gene Product Is A Medium-Chain Aldehyde Dehydrogenase As Determined By Kinetics and Crystal Structure, PDB code: 1wnd was solved by A.Gruez, V.Roig-Zamboni, M.Tegoni, C.Cambillau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.036, 79.680, 158.669, 90.00, 95.77, 90.00
R / Rfree (%) 18.4 / 21.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Escherichia Coli Ydcw Gene Product Is A Medium-Chain Aldehyde Dehydrogenase As Determined By Kinetics and Crystal Structure (pdb code 1wnd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Escherichia Coli Ydcw Gene Product Is A Medium-Chain Aldehyde Dehydrogenase As Determined By Kinetics and Crystal Structure, PDB code: 1wnd:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1wnd

Go back to Calcium Binding Sites List in 1wnd
Calcium binding site 1 out of 4 in the Escherichia Coli Ydcw Gene Product Is A Medium-Chain Aldehyde Dehydrogenase As Determined By Kinetics and Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Escherichia Coli Ydcw Gene Product Is A Medium-Chain Aldehyde Dehydrogenase As Determined By Kinetics and Crystal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca475

b:25.9
occ:1.00
 O A:HOH497 2.9 27.4 1.0
N A:LYS250 3.1 20.5 1.0
N A:LEU406 3.1 16.9 1.0
N A:ALA407 3.4 15.6 1.0
O A:ALA407 3.5 15.0 1.0
CA A:GLY249 3.5 21.9 1.0
CE2 A:TYR427 3.6 14.8 1.0
CB A:LEU406 3.6 16.8 1.0
N A:ALA251 3.7 18.4 1.0
C A:LYS250 3.7 19.9 1.0
CD2 A:TYR427 3.7 16.6 1.0
CA A:LEU406 3.7 16.8 1.0
CB A:TYR404 3.8 19.3 1.0
C A:GLY249 3.8 21.3 1.0
N A:GLY405 3.9 18.4 1.0
CA A:ALA251 3.9 18.3 1.0
O A:LYS250 4.0 19.8 1.0
CA A:LYS250 4.1 20.6 1.0
C A:LEU406 4.1 16.6 1.0
C A:GLY405 4.1 17.9 1.0
CA A:GLY405 4.3 17.7 1.0
C A:TYR404 4.3 18.9 1.0
C A:ALA407 4.4 15.8 1.0
CA A:ALA407 4.5 15.8 1.0
OG A:SER450 4.5 18.4 1.0
CD A:PRO252 4.6 17.8 1.0
CB A:ALA251 4.6 18.1 1.0
CA A:TYR404 4.7 19.5 1.0
CG A:TYR404 4.8 20.3 1.0
CB A:LYS250 4.9 20.8 1.0
CZ A:TYR427 4.9 17.2 1.0
CG A:LEU406 4.9 16.3 1.0
N A:GLY249 4.9 22.6 1.0
O A:CYS280 4.9 21.3 1.0
O A:TYR404 5.0 18.9 1.0

Calcium binding site 2 out of 4 in 1wnd

Go back to Calcium Binding Sites List in 1wnd
Calcium binding site 2 out of 4 in the Escherichia Coli Ydcw Gene Product Is A Medium-Chain Aldehyde Dehydrogenase As Determined By Kinetics and Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Escherichia Coli Ydcw Gene Product Is A Medium-Chain Aldehyde Dehydrogenase As Determined By Kinetics and Crystal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca475

b:27.4
occ:1.00
 N B:LEU406 3.1 16.9 1.0
N B:LYS250 3.1 20.3 1.0
N B:ALA407 3.3 15.7 1.0
CA B:GLY249 3.5 21.7 1.0
CB B:LEU406 3.6 16.4 1.0
O B:ALA407 3.6 15.0 1.0
CE2 B:TYR427 3.6 14.6 1.0
CA B:LEU406 3.7 16.9 1.0
CD2 B:TYR427 3.7 14.2 1.0
C B:LYS250 3.7 19.6 1.0
N B:ALA251 3.7 18.4 1.0
CB B:TYR404 3.8 19.5 1.0
C B:GLY249 3.8 21.2 1.0
N B:GLY405 3.8 18.5 1.0
CA B:ALA251 4.0 18.3 1.0
C B:LEU406 4.0 17.0 1.0
O B:LYS250 4.0 19.4 1.0
C B:GLY405 4.1 18.0 1.0
CA B:LYS250 4.1 20.4 1.0
CA B:GLY405 4.3 17.5 1.0
C B:TYR404 4.3 18.9 1.0
C B:ALA407 4.4 15.9 1.0
CA B:ALA407 4.4 16.1 1.0
OG B:SER450 4.5 19.7 1.0
CB B:ALA251 4.7 17.4 1.0
CA B:TYR404 4.7 19.5 1.0
CD B:PRO252 4.7 18.0 1.0
CB B:LYS250 4.8 20.2 1.0
CG B:LEU406 4.8 18.3 1.0
CG B:TYR404 4.8 20.6 1.0
CZ B:TYR427 4.9 16.6 1.0
N B:GLY249 4.9 22.6 1.0
O B:CYS280 4.9 21.0 1.0
O B:TYR404 4.9 18.5 1.0
O B:GLY248 5.0 24.0 1.0

Calcium binding site 3 out of 4 in 1wnd

Go back to Calcium Binding Sites List in 1wnd
Calcium binding site 3 out of 4 in the Escherichia Coli Ydcw Gene Product Is A Medium-Chain Aldehyde Dehydrogenase As Determined By Kinetics and Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Escherichia Coli Ydcw Gene Product Is A Medium-Chain Aldehyde Dehydrogenase As Determined By Kinetics and Crystal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca475

b:26.7
occ:1.00
 N C:LEU406 3.1 17.0 1.0
N C:LYS250 3.1 20.6 1.0
N C:ALA407 3.4 16.0 1.0
O C:ALA407 3.5 15.2 1.0
N C:ALA251 3.5 18.4 1.0
CA C:GLY249 3.6 21.8 1.0
CE2 C:TYR427 3.6 18.2 1.0
CD2 C:TYR427 3.6 17.0 1.0
C C:LYS250 3.7 19.6 1.0
CB C:LEU406 3.7 16.3 1.0
CA C:LEU406 3.7 16.9 1.0
CB C:TYR404 3.8 19.4 1.0
N C:GLY405 3.9 18.4 1.0
C C:GLY249 3.9 21.4 1.0
CA C:ALA251 3.9 18.5 1.0
CA C:LYS250 4.0 20.5 1.0
C C:LEU406 4.1 16.8 1.0
C C:GLY405 4.1 18.0 1.0
O C:LYS250 4.2 19.2 1.0
CA C:GLY405 4.2 17.7 1.0
C C:TYR404 4.3 18.8 1.0
C C:ALA407 4.4 16.0 1.0
CA C:ALA407 4.4 15.9 1.0
OG C:SER450 4.5 19.4 1.0
CD C:PRO252 4.6 17.5 1.0
CB C:ALA251 4.7 18.6 1.0
CA C:TYR404 4.7 19.7 1.0
CG C:TYR404 4.8 17.8 1.0
CB C:LYS250 4.8 20.8 1.0
CZ C:TYR427 4.9 18.1 1.0
CG C:LEU406 4.9 16.2 1.0
O C:TYR404 5.0 18.9 1.0
N C:GLY249 5.0 22.6 1.0
O C:CYS280 5.0 21.2 1.0
CG C:TYR427 5.0 18.8 1.0

Calcium binding site 4 out of 4 in 1wnd

Go back to Calcium Binding Sites List in 1wnd
Calcium binding site 4 out of 4 in the Escherichia Coli Ydcw Gene Product Is A Medium-Chain Aldehyde Dehydrogenase As Determined By Kinetics and Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Escherichia Coli Ydcw Gene Product Is A Medium-Chain Aldehyde Dehydrogenase As Determined By Kinetics and Crystal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca475

b:26.0
occ:1.00
 N D:LYS250 3.1 20.4 1.0
N D:LEU406 3.1 17.1 1.0
N D:ALA407 3.4 15.6 1.0
O D:ALA407 3.5 15.4 1.0
CA D:GLY249 3.6 21.6 1.0
CE2 D:TYR427 3.6 16.3 1.0
C D:LYS250 3.6 19.9 1.0
N D:ALA251 3.6 18.5 1.0
CD2 D:TYR427 3.7 16.5 1.0
CB D:LEU406 3.7 17.4 1.0
CA D:LEU406 3.8 17.1 1.0
C D:GLY249 3.8 21.3 1.0
CB D:TYR404 3.8 19.2 1.0
CA D:ALA251 3.9 18.2 1.0
N D:GLY405 3.9 18.3 1.0
O D:LYS250 3.9 19.7 1.0
CA D:LYS250 4.0 20.6 1.0
C D:LEU406 4.1 16.8 1.0
C D:GLY405 4.1 17.9 1.0
CA D:GLY405 4.3 17.5 1.0
C D:ALA407 4.4 16.0 1.0
C D:TYR404 4.4 18.8 1.0
CA D:ALA407 4.4 16.0 1.0
CB D:ALA251 4.5 16.6 1.0
OG D:SER450 4.5 18.2 1.0
CD D:PRO252 4.5 16.6 1.0
CA D:TYR404 4.7 19.4 1.0
CB D:LYS250 4.8 21.0 1.0
CZ D:TYR427 4.8 17.0 1.0
CG D:TYR404 4.9 19.9 1.0
CG D:LEU406 4.9 18.2 1.0
N D:GLY249 4.9 22.6 1.0
O D:CYS280 4.9 21.0 1.0
CG D:TYR427 5.0 16.9 1.0

Reference:

A.Gruez, V.Roig-Zamboni, S.Grisel, A.Salomoni, C.Valencia, V.Campanacci, M.Tegoni, C.Cambillau. Crystal Structure and Kinetics Identify Escherichia Coli Ydcw Gene Product As A Medium-Chain Aldehyde Dehydrogenase J.Mol.Biol. V. 343 29 2004.
ISSN: ISSN 0022-2836
PubMed: 15381418
DOI: 10.1016/J.JMB.2004.08.030
Page generated: Fri Jul 12 07:13:34 2024

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