Zinc in PDB 8h2b: Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans
Protein crystallography data
The structure of Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans, PDB code: 8h2b
was solved by
S.Brott,
U.T.Bornscheuer,
K.H.Nam,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.58 /
2.10
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
90.569,
92.67,
154.118,
90,
90,
90
|
R / Rfree (%)
|
16.1 /
20.5
|
Other elements in 8h2b:
The structure of Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans
(pdb code 8h2b). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans, PDB code: 8h2b:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 8h2b
Go back to
Zinc Binding Sites List in 8h2b
Zinc binding site 1 out
of 8 in the Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:38.4
occ:1.00
|
NE2
|
A:HIS58
|
2.3
|
36.5
|
1.0
|
SG
|
A:CYS170
|
2.3
|
33.2
|
1.0
|
SG
|
A:CYS41
|
2.3
|
39.1
|
1.0
|
O
|
A:HOH605
|
2.5
|
23.6
|
1.0
|
CD2
|
A:HIS58
|
3.2
|
29.8
|
1.0
|
CB
|
A:CYS41
|
3.2
|
38.7
|
1.0
|
CE1
|
A:HIS58
|
3.2
|
36.9
|
1.0
|
CB
|
A:CYS170
|
3.4
|
30.4
|
1.0
|
C5N
|
A:NAD401
|
3.6
|
28.1
|
1.0
|
OG1
|
A:THR43
|
3.8
|
39.1
|
1.0
|
CB
|
A:THR43
|
4.1
|
36.3
|
1.0
|
C6N
|
A:NAD401
|
4.2
|
26.7
|
1.0
|
C4N
|
A:NAD401
|
4.3
|
28.6
|
1.0
|
ND1
|
A:HIS58
|
4.4
|
33.3
|
1.0
|
CG
|
A:HIS58
|
4.4
|
31.7
|
1.0
|
NE1
|
A:TRP84
|
4.7
|
22.6
|
1.0
|
CA
|
A:CYS41
|
4.7
|
39.1
|
1.0
|
CA
|
A:CYS170
|
4.8
|
26.7
|
1.0
|
OE2
|
A:GLU59
|
4.9
|
41.9
|
1.0
|
N
|
A:THR43
|
5.0
|
34.8
|
1.0
|
|
Zinc binding site 2 out
of 8 in 8h2b
Go back to
Zinc Binding Sites List in 8h2b
Zinc binding site 2 out
of 8 in the Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn403
b:24.7
occ:1.00
|
SG
|
A:CYS94
|
2.3
|
26.6
|
1.0
|
SG
|
A:CYS102
|
2.3
|
21.2
|
1.0
|
SG
|
A:CYS91
|
2.3
|
19.2
|
1.0
|
SG
|
A:CYS88
|
2.4
|
23.0
|
1.0
|
CB
|
A:CYS102
|
3.2
|
24.0
|
1.0
|
CB
|
A:CYS91
|
3.3
|
24.2
|
1.0
|
CB
|
A:CYS94
|
3.4
|
25.1
|
1.0
|
CB
|
A:CYS88
|
3.4
|
26.7
|
1.0
|
N
|
A:CYS88
|
3.6
|
25.6
|
1.0
|
CA
|
A:CYS102
|
3.7
|
22.2
|
1.0
|
N
|
A:CYS91
|
3.7
|
23.4
|
1.0
|
N
|
A:MET89
|
3.8
|
25.6
|
1.0
|
CA
|
A:CYS88
|
3.9
|
29.4
|
1.0
|
N
|
A:GLU103
|
4.0
|
22.5
|
1.0
|
CA
|
A:CYS91
|
4.1
|
24.0
|
1.0
|
N
|
A:CYS94
|
4.2
|
19.5
|
1.0
|
C
|
A:CYS102
|
4.2
|
20.1
|
1.0
|
C
|
A:CYS88
|
4.2
|
26.8
|
1.0
|
CA
|
A:CYS94
|
4.3
|
24.2
|
1.0
|
N
|
A:HIS90
|
4.4
|
27.1
|
1.0
|
N
|
A:ASN104
|
4.6
|
19.3
|
1.0
|
C
|
A:CYS91
|
4.7
|
21.3
|
1.0
|
C
|
A:PRO87
|
4.7
|
27.8
|
1.0
|
ND2
|
A:ASN104
|
4.8
|
21.1
|
1.0
|
CA
|
A:MET89
|
4.8
|
24.9
|
1.0
|
O
|
A:CYS91
|
4.8
|
24.3
|
1.0
|
C
|
A:HIS90
|
4.9
|
28.1
|
1.0
|
N
|
A:CYS102
|
5.0
|
17.7
|
1.0
|
|
Zinc binding site 3 out
of 8 in 8h2b
Go back to
Zinc Binding Sites List in 8h2b
Zinc binding site 3 out
of 8 in the Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn402
b:43.3
occ:1.00
|
NE2
|
B:HIS58
|
2.3
|
36.4
|
1.0
|
SG
|
B:CYS170
|
2.3
|
37.6
|
1.0
|
SG
|
B:CYS41
|
2.4
|
36.2
|
1.0
|
O
|
B:HOH579
|
2.5
|
25.2
|
1.0
|
CD2
|
B:HIS58
|
3.1
|
31.8
|
1.0
|
CB
|
B:CYS41
|
3.2
|
37.6
|
1.0
|
CE1
|
B:HIS58
|
3.3
|
36.6
|
1.0
|
CB
|
B:CYS170
|
3.4
|
30.8
|
1.0
|
C5N
|
B:NAD401
|
3.5
|
29.6
|
1.0
|
OG1
|
B:THR43
|
4.0
|
41.1
|
1.0
|
CB
|
B:THR43
|
4.1
|
39.0
|
1.0
|
C6N
|
B:NAD401
|
4.2
|
28.3
|
1.0
|
C4N
|
B:NAD401
|
4.2
|
26.8
|
1.0
|
CG
|
B:HIS58
|
4.3
|
33.5
|
1.0
|
ND1
|
B:HIS58
|
4.4
|
36.0
|
1.0
|
NE1
|
B:TRP84
|
4.7
|
27.2
|
1.0
|
CA
|
B:CYS41
|
4.7
|
39.6
|
1.0
|
CA
|
B:CYS170
|
4.8
|
32.1
|
1.0
|
CG2
|
B:THR43
|
4.9
|
37.8
|
1.0
|
|
Zinc binding site 4 out
of 8 in 8h2b
Go back to
Zinc Binding Sites List in 8h2b
Zinc binding site 4 out
of 8 in the Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn403
b:26.8
occ:1.00
|
SG
|
B:CYS102
|
2.3
|
22.4
|
1.0
|
SG
|
B:CYS94
|
2.3
|
23.1
|
1.0
|
SG
|
B:CYS91
|
2.3
|
23.5
|
1.0
|
SG
|
B:CYS88
|
2.4
|
24.2
|
1.0
|
CB
|
B:CYS102
|
3.3
|
22.2
|
1.0
|
CB
|
B:CYS94
|
3.4
|
23.4
|
1.0
|
CB
|
B:CYS88
|
3.4
|
22.9
|
1.0
|
CB
|
B:CYS91
|
3.5
|
24.3
|
1.0
|
N
|
B:CYS88
|
3.5
|
24.6
|
1.0
|
CA
|
B:CYS102
|
3.7
|
21.5
|
1.0
|
N
|
B:MET89
|
3.7
|
29.4
|
1.0
|
N
|
B:CYS91
|
3.8
|
21.7
|
1.0
|
CA
|
B:CYS88
|
3.9
|
28.9
|
1.0
|
N
|
B:GLU103
|
4.1
|
23.2
|
1.0
|
C
|
B:CYS88
|
4.1
|
30.0
|
1.0
|
CA
|
B:CYS91
|
4.2
|
23.5
|
1.0
|
N
|
B:CYS94
|
4.2
|
18.6
|
1.0
|
C
|
B:CYS102
|
4.2
|
22.8
|
1.0
|
N
|
B:HIS90
|
4.3
|
24.9
|
1.0
|
CA
|
B:CYS94
|
4.4
|
23.3
|
1.0
|
N
|
B:ASN104
|
4.6
|
23.1
|
1.0
|
C
|
B:PRO87
|
4.7
|
24.5
|
1.0
|
CA
|
B:MET89
|
4.7
|
26.3
|
1.0
|
C
|
B:CYS91
|
4.8
|
19.5
|
1.0
|
O
|
B:CYS91
|
4.8
|
27.4
|
1.0
|
C
|
B:HIS90
|
4.9
|
28.5
|
1.0
|
ND2
|
B:ASN104
|
4.9
|
27.2
|
1.0
|
C
|
B:MET89
|
4.9
|
24.9
|
1.0
|
CA
|
B:PRO87
|
5.0
|
28.2
|
1.0
|
N
|
B:CYS102
|
5.0
|
26.9
|
1.0
|
|
Zinc binding site 5 out
of 8 in 8h2b
Go back to
Zinc Binding Sites List in 8h2b
Zinc binding site 5 out
of 8 in the Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn402
b:30.4
occ:1.00
|
NE2
|
C:HIS58
|
2.2
|
28.8
|
1.0
|
SG
|
C:CYS41
|
2.3
|
31.0
|
1.0
|
SG
|
C:CYS170
|
2.3
|
23.4
|
1.0
|
O
|
C:HOH575
|
2.4
|
16.5
|
1.0
|
CD2
|
C:HIS58
|
3.1
|
24.9
|
1.0
|
CB
|
C:CYS41
|
3.2
|
25.9
|
1.0
|
CE1
|
C:HIS58
|
3.3
|
26.0
|
1.0
|
CB
|
C:CYS170
|
3.5
|
26.6
|
1.0
|
C5N
|
C:NAD401
|
3.5
|
22.3
|
1.0
|
OG1
|
C:THR43
|
3.9
|
25.2
|
1.0
|
CB
|
C:THR43
|
4.1
|
29.5
|
1.0
|
C4N
|
C:NAD401
|
4.2
|
23.3
|
1.0
|
C6N
|
C:NAD401
|
4.2
|
23.8
|
1.0
|
CG
|
C:HIS58
|
4.3
|
23.8
|
1.0
|
ND1
|
C:HIS58
|
4.3
|
25.4
|
1.0
|
NE1
|
C:TRP84
|
4.7
|
22.8
|
1.0
|
CA
|
C:CYS41
|
4.7
|
28.6
|
1.0
|
O
|
C:HOH592
|
4.7
|
34.9
|
1.0
|
CA
|
C:CYS170
|
4.8
|
27.9
|
1.0
|
CG2
|
C:THR43
|
4.9
|
27.8
|
1.0
|
|
Zinc binding site 6 out
of 8 in 8h2b
Go back to
Zinc Binding Sites List in 8h2b
Zinc binding site 6 out
of 8 in the Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn403
b:23.2
occ:1.00
|
SG
|
C:CYS94
|
2.3
|
20.9
|
1.0
|
SG
|
C:CYS91
|
2.3
|
20.8
|
1.0
|
SG
|
C:CYS88
|
2.3
|
22.1
|
1.0
|
SG
|
C:CYS102
|
2.3
|
20.4
|
1.0
|
CB
|
C:CYS91
|
3.3
|
19.2
|
1.0
|
CB
|
C:CYS102
|
3.3
|
16.5
|
1.0
|
CB
|
C:CYS94
|
3.4
|
20.5
|
1.0
|
CB
|
C:CYS88
|
3.4
|
23.9
|
1.0
|
N
|
C:CYS88
|
3.5
|
23.5
|
1.0
|
N
|
C:CYS91
|
3.7
|
19.8
|
1.0
|
N
|
C:MET89
|
3.8
|
21.9
|
1.0
|
CA
|
C:CYS102
|
3.8
|
20.6
|
1.0
|
CA
|
C:CYS88
|
3.9
|
23.3
|
1.0
|
CA
|
C:CYS91
|
4.1
|
22.4
|
1.0
|
N
|
C:GLU103
|
4.1
|
20.9
|
1.0
|
C
|
C:CYS88
|
4.2
|
28.3
|
1.0
|
N
|
C:CYS94
|
4.2
|
20.8
|
1.0
|
C
|
C:CYS102
|
4.3
|
20.8
|
1.0
|
N
|
C:HIS90
|
4.3
|
23.6
|
1.0
|
CA
|
C:CYS94
|
4.4
|
19.0
|
1.0
|
ND2
|
C:ASN104
|
4.5
|
22.6
|
1.0
|
N
|
C:ASN104
|
4.6
|
20.2
|
1.0
|
C
|
C:PRO87
|
4.6
|
23.6
|
1.0
|
CA
|
C:MET89
|
4.7
|
24.8
|
1.0
|
C
|
C:CYS91
|
4.7
|
23.5
|
1.0
|
CB
|
C:ASN104
|
4.8
|
21.4
|
1.0
|
C
|
C:HIS90
|
4.9
|
24.7
|
1.0
|
CA
|
C:PRO87
|
4.9
|
21.5
|
1.0
|
C
|
C:MET89
|
4.9
|
23.9
|
1.0
|
O
|
C:CYS91
|
4.9
|
19.2
|
1.0
|
|
Zinc binding site 7 out
of 8 in 8h2b
Go back to
Zinc Binding Sites List in 8h2b
Zinc binding site 7 out
of 8 in the Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn402
b:47.6
occ:1.00
|
OE2
|
D:GLU59
|
2.2
|
38.9
|
1.0
|
NE2
|
D:HIS58
|
2.3
|
38.2
|
1.0
|
SG
|
D:CYS41
|
2.3
|
36.8
|
1.0
|
SG
|
D:CYS170
|
2.4
|
44.0
|
1.0
|
O
|
D:HOH557
|
2.9
|
38.3
|
1.0
|
CE1
|
D:HIS58
|
3.0
|
34.7
|
1.0
|
CB
|
D:CYS170
|
3.1
|
32.1
|
1.0
|
CD
|
D:GLU59
|
3.1
|
36.6
|
1.0
|
CD2
|
D:HIS58
|
3.2
|
31.1
|
1.0
|
CB
|
D:CYS41
|
3.4
|
36.6
|
1.0
|
CG
|
D:GLU59
|
3.5
|
28.6
|
1.0
|
ND1
|
D:HIS58
|
4.0
|
35.2
|
1.0
|
CG
|
D:HIS58
|
4.2
|
30.6
|
1.0
|
OE1
|
D:GLU59
|
4.3
|
30.2
|
1.0
|
CA
|
D:CYS41
|
4.5
|
32.3
|
1.0
|
N
|
D:CYS41
|
4.5
|
30.1
|
1.0
|
O
|
D:HOH580
|
4.6
|
39.4
|
1.0
|
CA
|
D:CYS170
|
4.6
|
33.4
|
1.0
|
NZ
|
D:LYS366
|
4.7
|
36.3
|
1.0
|
N
|
D:GLY171
|
4.8
|
30.0
|
1.0
|
CB
|
D:GLU59
|
5.0
|
29.6
|
1.0
|
CB
|
D:THR43
|
5.0
|
38.9
|
1.0
|
|
Zinc binding site 8 out
of 8 in 8h2b
Go back to
Zinc Binding Sites List in 8h2b
Zinc binding site 8 out
of 8 in the Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn403
b:26.7
occ:1.00
|
SG
|
D:CYS88
|
2.3
|
23.6
|
1.0
|
SG
|
D:CYS94
|
2.3
|
21.4
|
1.0
|
SG
|
D:CYS91
|
2.3
|
21.5
|
1.0
|
SG
|
D:CYS102
|
2.4
|
24.6
|
1.0
|
CB
|
D:CYS102
|
3.2
|
25.1
|
1.0
|
CB
|
D:CYS94
|
3.4
|
20.6
|
1.0
|
CB
|
D:CYS91
|
3.4
|
17.3
|
1.0
|
CB
|
D:CYS88
|
3.5
|
24.8
|
1.0
|
N
|
D:CYS88
|
3.5
|
25.8
|
1.0
|
CA
|
D:CYS102
|
3.7
|
22.0
|
1.0
|
N
|
D:CYS91
|
3.8
|
22.6
|
1.0
|
N
|
D:MET89
|
3.8
|
26.6
|
1.0
|
CA
|
D:CYS88
|
3.9
|
22.0
|
1.0
|
N
|
D:GLU103
|
4.1
|
23.1
|
1.0
|
CA
|
D:CYS91
|
4.1
|
22.6
|
1.0
|
C
|
D:CYS102
|
4.2
|
24.6
|
1.0
|
C
|
D:CYS88
|
4.2
|
32.5
|
1.0
|
N
|
D:CYS94
|
4.2
|
18.7
|
1.0
|
N
|
D:HIS90
|
4.3
|
23.2
|
1.0
|
CA
|
D:CYS94
|
4.4
|
24.1
|
1.0
|
N
|
D:ASN104
|
4.5
|
24.8
|
1.0
|
C
|
D:PRO87
|
4.7
|
27.8
|
1.0
|
ND2
|
D:ASN104
|
4.7
|
26.7
|
1.0
|
CA
|
D:MET89
|
4.8
|
24.9
|
1.0
|
C
|
D:CYS91
|
4.8
|
23.8
|
1.0
|
C
|
D:HIS90
|
4.9
|
28.2
|
1.0
|
CB
|
D:ASN104
|
4.9
|
29.2
|
1.0
|
C
|
D:MET89
|
4.9
|
28.5
|
1.0
|
CA
|
D:PRO87
|
4.9
|
29.0
|
1.0
|
O
|
D:CYS91
|
4.9
|
22.2
|
1.0
|
N
|
D:CYS102
|
5.0
|
28.1
|
1.0
|
|
Reference:
S.Brott,
U.T.Bornscheuer,
K.H.Nam.
Crystal Structure of Alcohol Dehydrogenase From Zobellia Galactanivorans To Be Published.
Page generated: Thu Oct 31 06:55:05 2024
|