Atomistry » Cadmium » PDB 1gyn-1jre » 1heu
Atomistry »
  Cadmium »
    PDB 1gyn-1jre »
      1heu »

Cadmium in PDB 1heu: Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing Cadmium and A Hydroxide Adduct to Nadh

Enzymatic activity of Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing Cadmium and A Hydroxide Adduct to Nadh

All present enzymatic activity of Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing Cadmium and A Hydroxide Adduct to Nadh:
1.1.1.1;

Protein crystallography data

The structure of Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing Cadmium and A Hydroxide Adduct to Nadh, PDB code: 1heu was solved by R.Meijers, R.J.Morris, H.W.Adolph, A.Merli, V.S.Lamzin, E.S.Cedergen-Zeppezauer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.15
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 51.180, 44.570, 94.100, 104.30, 101.07, 70.67
R / Rfree (%) 11.8 / 14.9

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing Cadmium and A Hydroxide Adduct to Nadh (pdb code 1heu). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing Cadmium and A Hydroxide Adduct to Nadh, PDB code: 1heu:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 1heu

Go back to Cadmium Binding Sites List in 1heu
Cadmium binding site 1 out of 4 in the Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing Cadmium and A Hydroxide Adduct to Nadh


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing Cadmium and A Hydroxide Adduct to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd400

b:10.4
occ:0.90
 NE2 A:HIS67 2.3 8.8 1.0
O A:HOH2178 2.3 8.7 0.2
SG A:CYS174 2.4 6.8 1.0
SG A:CYS46 2.4 6.9 1.0
O A:HOH2177 2.7 14.2 0.8
OE2 A:GLU68 3.0 7.5 0.2
CE1 A:HIS67 3.3 7.9 1.0
CD2 A:HIS67 3.3 8.6 1.0
CB A:CYS174 3.4 7.5 1.0
CB A:CYS46 3.4 7.6 1.0
C5N A:NAD402 3.5 7.8 1.0
C6N A:NAD402 3.8 7.8 1.0
CD A:GLU68 3.9 7.8 0.2
C4N A:NAD402 4.0 6.7 1.0
CG A:GLU68 4.0 8.0 0.2
OG A:SER48 4.3 7.6 1.0
CB A:SER48 4.3 6.8 1.0
NH2 A:ARG369 4.3 9.4 1.0
OE1 A:GLU68 4.4 9.5 0.8
ND1 A:HIS67 4.4 6.8 1.0
CG A:HIS67 4.5 7.1 1.0
CM A:MRD403 4.5 15.4 1.0
CA A:CYS174 4.7 6.5 1.0
N A:GLY175 4.8 6.5 1.0
CA A:CYS46 4.9 7.5 1.0
N1N A:NAD402 4.9 6.8 1.0
C A:CYS174 4.9 6.4 1.0

Cadmium binding site 2 out of 4 in 1heu

Go back to Cadmium Binding Sites List in 1heu
Cadmium binding site 2 out of 4 in the Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing Cadmium and A Hydroxide Adduct to Nadh


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing Cadmium and A Hydroxide Adduct to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd401

b:8.9
occ:1.00
 SG A:CYS100 2.5 8.4 1.0
SG A:CYS111 2.6 7.2 1.0
SG A:CYS97 2.6 9.3 1.0
SG A:CYS103 2.6 7.8 1.0
CB A:CYS111 3.5 7.6 1.0
CB A:CYS100 3.5 11.4 1.0
CB A:CYS97 3.5 10.2 1.0
CB A:CYS103 3.6 9.0 1.0
N A:CYS97 3.6 8.0 1.0
CA A:CYS111 3.8 7.1 1.0
N A:CYS100 3.9 12.4 1.0
CA A:CYS97 4.0 9.3 1.0
N A:LEU112 4.0 8.2 1.0
N A:GLY98 4.0 9.8 1.0
CA A:CYS100 4.3 11.9 1.0
N A:CYS103 4.3 8.6 1.0
C A:CYS111 4.4 7.3 1.0
C A:CYS97 4.4 9.7 1.0
N A:LYS99 4.5 13.1 1.0
CA A:CYS103 4.5 9.2 1.0
C A:GLN96 4.7 8.1 1.0
CG A:LYS113 4.8 10.4 0.6
N A:LYS113 4.9 8.8 1.0
C A:CYS100 4.9 10.8 1.0

Cadmium binding site 3 out of 4 in 1heu

Go back to Cadmium Binding Sites List in 1heu
Cadmium binding site 3 out of 4 in the Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing Cadmium and A Hydroxide Adduct to Nadh


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing Cadmium and A Hydroxide Adduct to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd400

b:10.8
occ:0.90
 NE2 B:HIS67 2.3 10.2 1.0
SG B:CYS174 2.4 8.8 1.0
O B:HOH2614 2.4 12.4 0.7
SG B:CYS46 2.5 8.8 1.0
O B:HOH2616 2.8 13.4 0.3
CE1 B:HIS67 3.2 9.2 1.0
CD2 B:HIS67 3.3 10.5 1.0
CB B:CYS174 3.4 8.6 1.0
CB B:CYS46 3.4 10.2 1.0
C5N B:NAD402 3.6 10.6 1.0
C6N B:NAD402 3.9 10.0 1.0
C4N B:NAD402 4.0 9.7 1.0
OG B:SER48 4.3 9.6 1.0
CB B:SER48 4.3 8.9 1.0
NH2 B:ARG369 4.3 10.2 1.0
ND1 B:HIS67 4.4 9.5 1.0
CG B:HIS67 4.4 9.6 1.0
O2 B:MRD403 4.4 16.8 0.7
OE2 B:GLU68 4.5 13.5 1.0
CA B:CYS174 4.8 8.3 1.0
N B:GLY175 4.9 8.2 1.0
CA B:CYS46 4.9 10.3 1.0
N1N B:NAD402 4.9 8.0 1.0

Cadmium binding site 4 out of 4 in 1heu

Go back to Cadmium Binding Sites List in 1heu
Cadmium binding site 4 out of 4 in the Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing Cadmium and A Hydroxide Adduct to Nadh


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing Cadmium and A Hydroxide Adduct to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd401

b:11.4
occ:1.00
 SG B:CYS100 2.5 10.5 1.0
SG B:CYS111 2.6 9.6 1.0
SG B:CYS97 2.6 12.3 1.0
SG B:CYS103 2.6 9.6 1.0
CB B:CYS111 3.5 10.4 1.0
CB B:CYS100 3.5 13.3 1.0
CB B:CYS97 3.5 13.8 1.0
CB B:CYS103 3.6 10.7 1.0
N B:CYS97 3.6 10.7 1.0
CA B:CYS111 3.9 9.4 1.0
N B:CYS100 3.9 13.8 1.0
CA B:CYS97 4.0 12.5 1.0
N B:LEU112 4.0 10.4 1.0
N B:GLY98 4.1 12.8 1.0
CA B:CYS100 4.3 12.8 1.0
N B:CYS103 4.3 10.3 1.0
C B:CYS111 4.4 10.3 1.0
C B:CYS97 4.4 13.0 1.0
CA B:CYS103 4.5 10.6 1.0
N B:LYS99 4.6 14.1 1.0
C B:GLN96 4.7 10.4 1.0
CG B:LYS113 4.8 18.5 1.0
C B:CYS100 4.9 12.6 1.0
N B:LYS113 4.9 11.2 1.0
CA B:GLN96 5.0 9.4 1.0

Reference:

R.Meijers, R.J.Morris, H.W.Adolph, A.Merli, V.S.Lamzin, E.S.Cedergen-Zeppezauer. On the Enzymatic Activation of Nadh J.Biol.Chem. V. 276 9316 2001.
ISSN: ISSN 0021-9258
PubMed: 11134046
DOI: 10.1074/JBC.M010870200
Page generated: Fri Jul 19 13:28:07 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy