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
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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
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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
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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
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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
|