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Zinc in PDB 1cdo: Alcohol Dehydrogenase (E.C.1.1.1.1) (Ee Isozyme) Complexed with Nicotinamide Adenine Dinucleotide (Nad), and Zinc

Enzymatic activity of Alcohol Dehydrogenase (E.C.1.1.1.1) (Ee Isozyme) Complexed with Nicotinamide Adenine Dinucleotide (Nad), and Zinc

All present enzymatic activity of Alcohol Dehydrogenase (E.C.1.1.1.1) (Ee Isozyme) Complexed with Nicotinamide Adenine Dinucleotide (Nad), and Zinc:
1.1.1.1;

Protein crystallography data

The structure of Alcohol Dehydrogenase (E.C.1.1.1.1) (Ee Isozyme) Complexed with Nicotinamide Adenine Dinucleotide (Nad), and Zinc, PDB code: 1cdo was solved by H.Eklund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.00 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 102.950, 47.600, 80.430, 90.00, 104.66, 90.00
R / Rfree (%) 17.7 / 24.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Alcohol Dehydrogenase (E.C.1.1.1.1) (Ee Isozyme) Complexed with Nicotinamide Adenine Dinucleotide (Nad), and Zinc (pdb code 1cdo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Alcohol Dehydrogenase (E.C.1.1.1.1) (Ee Isozyme) Complexed with Nicotinamide Adenine Dinucleotide (Nad), and Zinc, PDB code: 1cdo:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1cdo

Go back to Zinc Binding Sites List in 1cdo
Zinc binding site 1 out of 4 in the Alcohol Dehydrogenase (E.C.1.1.1.1) (Ee Isozyme) Complexed with Nicotinamide Adenine Dinucleotide (Nad), and Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Alcohol Dehydrogenase (E.C.1.1.1.1) (Ee Isozyme) Complexed with Nicotinamide Adenine Dinucleotide (Nad), and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn376

b:9.1
occ:1.00
 SG A:CYS175 2.2 6.1 1.0
NE2 A:HIS68 2.3 5.1 1.0
SG A:CYS46 2.3 8.5 1.0
O A:HOH1352 2.7 24.0 1.0
CD2 A:HIS68 3.2 5.4 1.0
CB A:CYS46 3.2 6.4 1.0
C5N A:NAD375 3.3 7.3 1.0
CE1 A:HIS68 3.3 3.5 1.0
CB A:CYS175 3.6 5.6 1.0
OG1 A:THR48 3.8 8.6 1.0
C6N A:NAD375 3.8 3.5 1.0
C4N A:NAD375 4.0 8.4 1.0
CB A:THR48 4.0 5.4 1.0
CG A:HIS68 4.4 5.8 1.0
ND1 A:HIS68 4.4 5.9 1.0
CA A:CYS46 4.7 5.8 1.0
OE1 A:GLU69 4.7 4.8 1.0
N A:GLY176 4.8 2.4 1.0
NH2 A:ARG369 4.8 6.9 1.0
N A:THR48 4.8 5.1 1.0
CA A:CYS175 4.9 4.7 1.0
N1N A:NAD375 4.9 6.9 1.0
CG2 A:THR48 5.0 8.0 1.0

Zinc binding site 2 out of 4 in 1cdo

Go back to Zinc Binding Sites List in 1cdo
Zinc binding site 2 out of 4 in the Alcohol Dehydrogenase (E.C.1.1.1.1) (Ee Isozyme) Complexed with Nicotinamide Adenine Dinucleotide (Nad), and Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Alcohol Dehydrogenase (E.C.1.1.1.1) (Ee Isozyme) Complexed with Nicotinamide Adenine Dinucleotide (Nad), and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn377

b:9.9
occ:1.00
 SG A:CYS104 2.3 2.8 1.0
SG A:CYS112 2.4 4.7 1.0
SG A:CYS98 2.5 7.8 1.0
SG A:CYS101 2.6 9.3 1.0
CB A:CYS112 3.3 4.5 1.0
N A:CYS98 3.4 7.4 1.0
CB A:CYS98 3.4 8.0 1.0
CB A:CYS104 3.5 3.4 1.0
CA A:CYS112 3.7 5.0 1.0
CB A:CYS101 3.7 6.3 1.0
CA A:CYS98 3.8 8.4 1.0
N A:VAL113 3.9 3.8 1.0
N A:GLY99 3.9 5.4 1.0
N A:CYS101 4.0 11.9 1.0
C A:CYS98 4.2 7.4 1.0
C A:CYS112 4.3 4.1 1.0
CA A:CYS101 4.4 9.4 1.0
N A:CYS104 4.4 8.8 1.0
C A:GLN97 4.4 8.8 1.0
CA A:CYS104 4.5 5.2 1.0
N A:GLU100 4.6 9.0 1.0
CA A:GLN97 4.7 8.1 1.0
O A:GLN111 4.7 7.8 1.0
CG2 A:VAL113 4.7 2.0 1.0
O A:HOH1281 4.8 17.6 1.0
CA A:GLY99 4.9 6.6 1.0
N A:CYS112 4.9 4.4 1.0
C A:CYS101 5.0 8.1 1.0

Zinc binding site 3 out of 4 in 1cdo

Go back to Zinc Binding Sites List in 1cdo
Zinc binding site 3 out of 4 in the Alcohol Dehydrogenase (E.C.1.1.1.1) (Ee Isozyme) Complexed with Nicotinamide Adenine Dinucleotide (Nad), and Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Alcohol Dehydrogenase (E.C.1.1.1.1) (Ee Isozyme) Complexed with Nicotinamide Adenine Dinucleotide (Nad), and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn376

b:19.4
occ:1.00
 NE2 B:HIS68 2.0 9.3 1.0
SG B:CYS175 2.2 8.6 1.0
O B:HOH1253 2.2 12.9 1.0
SG B:CYS46 2.4 9.4 1.0
CD2 B:HIS68 3.0 5.1 1.0
CE1 B:HIS68 3.1 8.5 1.0
CB B:CYS46 3.4 6.4 1.0
CB B:CYS175 3.4 4.7 1.0
C5N B:NAD375 3.7 29.5 1.0
OG1 B:THR48 3.9 5.8 1.0
CB B:THR48 3.9 6.0 1.0
CG B:HIS68 4.2 5.9 1.0
ND1 B:HIS68 4.2 6.3 1.0
C4N B:NAD375 4.4 30.1 1.0
OE2 B:GLU69 4.5 20.5 1.0
C6N B:NAD375 4.7 28.3 1.0
N B:THR48 4.8 5.8 1.0
CG2 B:THR48 4.8 9.3 1.0
CA B:CYS175 4.8 7.8 1.0
N B:GLY176 4.8 5.3 1.0
CA B:CYS46 4.9 7.0 1.0
CA B:THR48 5.0 5.2 1.0

Zinc binding site 4 out of 4 in 1cdo

Go back to Zinc Binding Sites List in 1cdo
Zinc binding site 4 out of 4 in the Alcohol Dehydrogenase (E.C.1.1.1.1) (Ee Isozyme) Complexed with Nicotinamide Adenine Dinucleotide (Nad), and Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Alcohol Dehydrogenase (E.C.1.1.1.1) (Ee Isozyme) Complexed with Nicotinamide Adenine Dinucleotide (Nad), and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn377

b:7.3
occ:1.00
 SG B:CYS104 2.2 2.0 1.0
SG B:CYS112 2.3 5.9 1.0
SG B:CYS101 2.4 5.8 1.0
SG B:CYS98 2.4 7.4 1.0
CB B:CYS104 3.3 7.2 1.0
CB B:CYS112 3.4 6.3 1.0
CB B:CYS98 3.5 9.3 1.0
N B:CYS98 3.5 10.7 1.0
CB B:CYS101 3.5 3.0 1.0
CA B:CYS112 3.8 4.6 1.0
N B:GLY99 3.8 6.7 1.0
N B:CYS101 3.8 2.1 1.0
CA B:CYS98 3.9 7.8 1.0
N B:VAL113 4.0 5.3 1.0
N B:CYS104 4.2 6.8 1.0
CA B:CYS101 4.2 4.6 1.0
C B:CYS98 4.3 9.0 1.0
N B:GLU100 4.3 6.5 1.0
CA B:CYS104 4.3 6.3 1.0
C B:CYS112 4.5 4.7 1.0
C B:GLN97 4.5 4.6 1.0
O B:GLN111 4.7 2.0 1.0
CA B:GLY99 4.7 7.8 1.0
CG2 B:VAL113 4.7 2.0 1.0
O B:HOH1135 4.8 16.7 1.0
CA B:GLN97 4.8 3.1 1.0
C B:GLU100 4.9 7.8 1.0
C B:CYS101 4.9 4.2 1.0
C B:GLY99 5.0 9.2 1.0

Reference:

S.Ramaswamy, M.El Ahmad, O.Danielsson, H.Jornvall, H.Eklund. Crystal Structure of Cod Liver Class I Alcohol Dehydrogenase: Substrate Pocket and Structurally Variable Segments. Protein Sci. V. 5 663 1996.
ISSN: ISSN 0961-8368
PubMed: 8845755
Page generated: Sat Oct 12 23:03:29 2024

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