Atomistry » Zinc » PDB 5cdg-5cup » 5cdt
Atomistry »
  Zinc »
    PDB 5cdg-5cup »
      5cdt »

Zinc in PDB 5cdt: I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol

Enzymatic activity of I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol

All present enzymatic activity of I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol:
1.1.1.1;

Protein crystallography data

The structure of I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol, PDB code: 5cdt was solved by B.V.Plapp, K.Shanmuganatham, 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
Cell size a, b, c (Å), α, β, γ (°) 44.300, 51.500, 92.350, 91.92, 103.09, 110.17
R / Rfree (%) 16.2 / 20.6

Other elements in 5cdt:

The structure of I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol also contains other interesting chemical elements:

Fluorine (F) 10 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol (pdb code 5cdt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol, PDB code: 5cdt:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5cdt

Go back to Zinc Binding Sites List in 5cdt
Zinc binding site 1 out of 4 in the I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:20.5
occ:1.00
 O1 A:PFB404 2.0 18.5 1.0
NE2 A:HIS67 2.1 16.7 1.0
SG A:CYS46 2.3 20.5 1.0
SG A:CYS174 2.3 18.3 1.0
C7 A:PFB404 2.9 21.4 1.0
CD2 A:HIS67 3.0 16.4 1.0
CE1 A:HIS67 3.1 16.8 1.0
CB A:CYS46 3.3 17.8 1.0
C5N A:NAJ403 3.4 16.1 1.0
CB A:CYS174 3.4 18.4 1.0
OG A:SER48 3.9 15.0 1.0
C4N A:NAJ403 4.0 16.3 1.0
C6N A:NAJ403 4.0 14.4 1.0
CB A:SER48 4.1 16.3 1.0
F6 A:PFB404 4.1 21.2 1.0
C1 A:PFB404 4.2 20.1 1.0
CG A:HIS67 4.2 15.9 1.0
ND1 A:HIS67 4.2 16.2 1.0
NH2 A:ARG369 4.6 22.7 1.0
C6 A:PFB404 4.6 20.6 1.0
CA A:CYS174 4.8 16.0 1.0
CA A:CYS46 4.8 18.2 1.0
CE2 A:PHE93 4.8 16.5 1.0
N A:SER48 4.9 18.1 1.0
N1N A:NAJ403 4.9 14.0 1.0
OE2 A:GLU68 4.9 21.6 1.0

Zinc binding site 2 out of 4 in 5cdt

Go back to Zinc Binding Sites List in 5cdt
Zinc binding site 2 out of 4 in the I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:18.8
occ:1.00
 SG A:CYS97 2.3 19.6 1.0
SG A:CYS100 2.3 18.0 1.0
SG A:CYS111 2.3 19.1 1.0
SG A:CYS103 2.4 19.4 1.0
CB A:CYS103 3.3 19.0 1.0
CB A:CYS111 3.3 17.9 1.0
CB A:CYS100 3.4 20.7 1.0
CB A:CYS97 3.4 19.8 1.0
N A:CYS97 3.5 16.8 1.0
CA A:CYS111 3.7 17.8 1.0
N A:CYS100 3.9 23.0 1.0
CA A:CYS97 3.9 20.7 1.0
N A:GLY98 3.9 20.3 1.0
N A:LEU112 4.0 18.4 1.0
N A:CYS103 4.1 19.6 1.0
CA A:CYS100 4.2 19.7 1.0
C A:CYS111 4.3 16.8 1.0
CA A:CYS103 4.3 18.5 1.0
C A:CYS97 4.3 20.8 1.0
N A:LYS99 4.5 22.9 1.0
C A:GLN96 4.6 17.3 1.0
O A:HOH872 4.8 34.2 1.0
N A:LYS113 4.8 14.6 1.0
C A:CYS100 4.8 18.6 1.0
CA A:GLN96 4.9 17.4 1.0
O A:CYS100 4.9 18.1 1.0
CG A:LYS113 4.9 24.3 1.0
CA A:GLY98 4.9 22.5 1.0

Zinc binding site 3 out of 4 in 5cdt

Go back to Zinc Binding Sites List in 5cdt
Zinc binding site 3 out of 4 in the I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:21.7
occ:1.00
 O1 B:PFB404 2.0 19.7 1.0
NE2 B:HIS67 2.2 18.2 1.0
SG B:CYS174 2.3 20.8 1.0
SG B:CYS46 2.3 21.0 1.0
C7 B:PFB404 3.0 19.9 1.0
CE1 B:HIS67 3.1 20.5 1.0
CD2 B:HIS67 3.1 18.8 1.0
CB B:CYS46 3.4 22.1 1.0
C5N B:NAJ403 3.4 17.3 1.0
CB B:CYS174 3.4 20.0 1.0
OG B:SER48 3.8 18.7 1.0
CB B:SER48 3.8 17.4 1.0
C4N B:NAJ403 3.9 19.6 1.0
C6N B:NAJ403 3.9 18.3 1.0
F6 B:PFB404 4.0 26.2 1.0
C1 B:PFB404 4.2 21.4 1.0
ND1 B:HIS67 4.2 19.9 1.0
CG B:HIS67 4.3 18.9 1.0
NH2 B:ARG369 4.6 24.5 1.0
C6 B:PFB404 4.6 22.3 1.0
CA B:CYS174 4.8 17.6 1.0
CA B:CYS46 4.8 21.6 1.0
N B:SER48 4.8 18.3 1.0
CE2 B:PHE93 4.9 19.6 1.0
OE2 B:GLU68 4.9 23.4 1.0
N1N B:NAJ403 4.9 15.6 1.0
CA B:SER48 5.0 17.4 1.0

Zinc binding site 4 out of 4 in 5cdt

Go back to Zinc Binding Sites List in 5cdt
Zinc binding site 4 out of 4 in the I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:20.3
occ:1.00
 SG B:CYS111 2.3 19.8 1.0
SG B:CYS103 2.3 19.3 1.0
SG B:CYS100 2.4 19.9 1.0
SG B:CYS97 2.4 22.5 1.0
CB B:CYS111 3.3 18.2 1.0
CB B:CYS103 3.3 18.5 1.0
CB B:CYS100 3.4 23.8 1.0
CB B:CYS97 3.4 22.6 1.0
N B:CYS97 3.5 21.3 1.0
CA B:CYS111 3.7 18.1 1.0
N B:CYS100 3.9 22.8 1.0
N B:GLY98 3.9 24.8 1.0
CA B:CYS97 3.9 23.9 1.0
N B:LEU112 4.0 19.3 1.0
N B:CYS103 4.2 18.4 1.0
CA B:CYS100 4.2 21.0 1.0
C B:CYS111 4.3 18.7 1.0
C B:CYS97 4.3 24.2 1.0
CA B:CYS103 4.3 19.1 1.0
N B:LYS99 4.5 25.5 1.0
C B:GLN96 4.6 19.3 1.0
N B:LYS113 4.8 20.5 1.0
CG B:LYS113 4.8 26.0 1.0
CA B:GLN96 4.8 19.9 1.0
C B:CYS100 4.8 21.1 1.0
CA B:GLY98 4.9 26.1 1.0
O B:HOH824 4.9 35.2 1.0

Reference:

K.K.Shanmuganatham, R.S.Wallace, A.T.Lee, B.V.Plapp. Contribution of Buried Distal Amino Acid Residues in Horse Liver Alcohol Dehydrogenase to Structure and Catalysis. Protein Sci. 2017.
ISSN: ESSN 1469-896X
PubMed: 29271062
DOI: 10.1002/PRO.3370
Page generated: Wed Dec 16 06:06:50 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy