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Zinc in PDB 5cdg: I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol

Enzymatic activity of I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol

All present enzymatic activity of I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol:
1.1.1.1;

Protein crystallography data

The structure of I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol, PDB code: 5cdg 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 / 1.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.260, 51.380, 92.390, 91.75, 103.10, 109.36
R / Rfree (%) 14.2 / 18.7

Other elements in 5cdg:

The structure of I220F 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 I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol (pdb code 5cdg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol, PDB code: 5cdg:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5cdg

Go back to Zinc Binding Sites List in 5cdg
Zinc binding site 1 out of 4 in the I220F 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 I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:17.5
occ:1.00
 O1 A:PFB404 1.9 16.0 1.0
NE2 A:HIS67 2.1 14.7 1.0
SG A:CYS174 2.3 16.4 1.0
SG A:CYS46 2.3 17.4 1.0
C7 A:PFB404 2.9 17.9 1.0
CD2 A:HIS67 3.1 14.8 1.0
CE1 A:HIS67 3.1 16.9 1.0
CB A:CYS46 3.3 15.9 1.0
C5N A:NAJ403 3.4 14.3 1.0
CB A:CYS174 3.4 14.2 1.0
OG A:SER48 3.8 14.7 1.0
C6N A:NAJ403 3.9 12.8 1.0
C4N A:NAJ403 3.9 15.4 1.0
CB A:SER48 4.0 16.1 1.0
F6 A:PFB404 4.1 19.6 1.0
ND1 A:HIS67 4.2 16.4 1.0
C1 A:PFB404 4.2 18.5 1.0
CG A:HIS67 4.2 14.2 1.0
NH2 A:ARG369 4.6 18.4 1.0
C6 A:PFB404 4.6 19.1 1.0
CA A:CYS174 4.7 13.2 1.0
CA A:CYS46 4.8 15.9 1.0
N A:SER48 4.8 15.2 1.0
CE2 A:PHE93 4.9 17.1 1.0
N1N A:NAJ403 4.9 12.6 1.0
OE2 A:GLU68 4.9 18.1 1.0

Zinc binding site 2 out of 4 in 5cdg

Go back to Zinc Binding Sites List in 5cdg
Zinc binding site 2 out of 4 in the I220F 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 I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:17.4
occ:1.00
 SG A:CYS111 2.3 16.7 1.0
SG A:CYS100 2.3 17.9 1.0
SG A:CYS103 2.4 17.1 1.0
SG A:CYS97 2.4 19.3 1.0
CB A:CYS111 3.3 16.1 1.0
CB A:CYS103 3.4 17.4 1.0
CB A:CYS97 3.4 17.4 1.0
CB A:CYS100 3.5 16.8 1.0
N A:CYS97 3.6 16.4 1.0
CA A:CYS111 3.8 15.1 1.0
N A:CYS100 3.9 21.1 1.0
CA A:CYS97 3.9 17.7 1.0
N A:GLY98 3.9 19.9 1.0
N A:LEU112 3.9 15.7 1.0
N A:CYS103 4.2 16.0 1.0
CA A:CYS100 4.2 19.5 1.0
C A:CYS111 4.3 17.2 1.0
C A:CYS97 4.3 19.5 1.0
CA A:CYS103 4.4 16.4 1.0
N A:LYS99 4.5 20.6 1.0
C A:GLN96 4.6 15.8 1.0
N A:LYS113 4.9 16.6 1.0
C A:CYS100 4.9 16.9 1.0
O A:CYS100 4.9 19.0 1.0
CA A:GLN96 4.9 17.0 1.0
CA A:GLY98 5.0 21.0 1.0
CG A:LYS113 5.0 21.3 1.0

Zinc binding site 3 out of 4 in 5cdg

Go back to Zinc Binding Sites List in 5cdg
Zinc binding site 3 out of 4 in the I220F 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 I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:20.1
occ:1.00
 O1 B:PFB404 2.0 18.1 1.0
NE2 B:HIS67 2.1 17.2 1.0
SG B:CYS174 2.3 18.6 1.0
SG B:CYS46 2.3 18.9 1.0
C7 B:PFB404 2.9 18.8 1.0
CE1 B:HIS67 3.1 17.1 1.0
CD2 B:HIS67 3.1 17.6 1.0
C5N B:NAJ403 3.3 17.3 1.0
CB B:CYS46 3.4 17.9 1.0
CB B:CYS174 3.4 18.7 1.0
OG B:SER48 3.8 17.3 1.0
C4N B:NAJ403 3.9 17.6 1.0
C6N B:NAJ403 3.9 15.8 1.0
CB B:SER48 4.0 17.3 1.0
F6 B:PFB404 4.0 22.1 1.0
C1 B:PFB404 4.2 19.6 1.0
ND1 B:HIS67 4.2 19.1 1.0
CG B:HIS67 4.2 17.1 1.0
NH2 B:ARG369 4.5 22.2 1.0
C6 B:PFB404 4.6 20.0 1.0
CA B:CYS174 4.7 17.0 1.0
CA B:CYS46 4.8 19.4 1.0
N B:SER48 4.8 17.8 1.0
CE2 B:PHE93 4.9 16.8 1.0
OE2 B:GLU68 4.9 21.0 1.0
N1N B:NAJ403 5.0 16.0 1.0

Zinc binding site 4 out of 4 in 5cdg

Go back to Zinc Binding Sites List in 5cdg
Zinc binding site 4 out of 4 in the I220F 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 I220F 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 20.5 1.0
SG B:CYS100 2.3 20.7 1.0
SG B:CYS103 2.3 19.1 1.0
SG B:CYS97 2.3 22.5 1.0
CB B:CYS111 3.3 19.2 1.0
CB B:CYS103 3.4 19.7 1.0
CB B:CYS100 3.4 21.6 1.0
CB B:CYS97 3.5 17.0 1.0
N B:CYS97 3.5 20.6 1.0
CA B:CYS111 3.7 18.5 1.0
N B:CYS100 3.9 21.8 1.0
CA B:CYS97 3.9 19.2 1.0
N B:GLY98 3.9 21.7 1.0
N B:LEU112 4.0 19.5 1.0
N B:CYS103 4.1 19.2 1.0
CA B:CYS100 4.2 21.2 1.0
C B:CYS111 4.3 18.2 1.0
CA B:CYS103 4.3 20.2 1.0
C B:CYS97 4.4 22.3 1.0
N B:LYS99 4.5 21.6 1.0
C B:GLN96 4.6 17.4 1.0
N B:LYS113 4.8 22.0 1.0
CG B:LYS113 4.9 25.3 1.0
C B:CYS100 4.9 19.2 1.0
CA B:GLN96 4.9 17.4 1.0
O B:HOH836 4.9 35.1 1.0
O B:CYS100 5.0 21.5 1.0
CA B:GLY98 5.0 24.2 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: Sun Oct 27 14:17:02 2024

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