Zinc in PDB 5o9d: Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, H39Y
Protein crystallography data
The structure of Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, H39Y, PDB code: 5o9d
was solved by
D.Dobritzsch,
D.Maurer,
E.Hamnevik,
T.R.Enugala,
M.Widersten,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
28.30 /
1.79
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
65.492,
104.828,
109.009,
90.00,
91.13,
90.00
|
R / Rfree (%)
|
17 /
19.1
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, H39Y
(pdb code 5o9d). 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 R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, H39Y, PDB code: 5o9d:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 5o9d
Go back to
Zinc Binding Sites List in 5o9d
Zinc binding site 1 out
of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, H39Y
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 R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, H39Y within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn501
b:15.4
occ:1.00
|
SG
|
A:CYS106
|
2.3
|
17.6
|
1.0
|
SG
|
A:CYS92
|
2.3
|
17.7
|
1.0
|
SG
|
A:CYS95
|
2.3
|
16.4
|
1.0
|
SG
|
A:CYS98
|
2.4
|
15.2
|
1.0
|
CB
|
A:CYS106
|
3.3
|
17.7
|
1.0
|
CB
|
A:CYS98
|
3.3
|
15.0
|
1.0
|
CB
|
A:CYS95
|
3.4
|
17.9
|
1.0
|
N
|
A:CYS92
|
3.4
|
17.2
|
1.0
|
CB
|
A:CYS92
|
3.4
|
18.5
|
1.0
|
N
|
A:CYS95
|
3.8
|
17.9
|
1.0
|
N
|
A:GLY93
|
3.9
|
17.1
|
1.0
|
CA
|
A:CYS92
|
3.9
|
17.9
|
1.0
|
CA
|
A:CYS106
|
4.0
|
18.4
|
1.0
|
CA
|
A:CYS95
|
4.2
|
17.9
|
1.0
|
C
|
A:CYS92
|
4.2
|
17.8
|
1.0
|
N
|
A:CYS98
|
4.3
|
14.2
|
1.0
|
O
|
A:HOH604
|
4.3
|
35.6
|
1.0
|
N
|
A:ALA94
|
4.4
|
18.1
|
1.0
|
CA
|
A:CYS98
|
4.4
|
14.3
|
1.0
|
C
|
A:GLY91
|
4.5
|
16.8
|
1.0
|
CB
|
A:ARG108
|
4.5
|
31.8
|
1.0
|
CG
|
A:ARG108
|
4.6
|
34.1
|
1.0
|
CA
|
A:GLY91
|
4.7
|
16.3
|
1.0
|
C
|
A:CYS106
|
4.8
|
20.8
|
1.0
|
N
|
A:THR107
|
4.8
|
23.8
|
1.0
|
N
|
A:ARG108
|
4.8
|
28.2
|
1.0
|
C
|
A:CYS95
|
4.9
|
17.1
|
1.0
|
CA
|
A:GLY93
|
4.9
|
17.1
|
1.0
|
C
|
A:ALA94
|
5.0
|
18.6
|
1.0
|
O
|
A:CYS95
|
5.0
|
16.3
|
1.0
|
|
Zinc binding site 2 out
of 8 in 5o9d
Go back to
Zinc Binding Sites List in 5o9d
Zinc binding site 2 out
of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, H39Y
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 R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, H39Y within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn502
b:18.0
occ:1.00
|
OD2
|
A:ASP153
|
1.9
|
20.0
|
1.0
|
NE2
|
A:HIS62
|
2.0
|
16.8
|
1.0
|
O9
|
A:9ON504
|
2.1
|
23.8
|
1.0
|
SG
|
A:CYS38
|
2.3
|
16.4
|
1.0
|
C1
|
A:9ON504
|
3.0
|
28.6
|
1.0
|
CD2
|
A:HIS62
|
3.0
|
17.1
|
1.0
|
CE1
|
A:HIS62
|
3.1
|
17.2
|
1.0
|
CB
|
A:CYS38
|
3.1
|
15.9
|
1.0
|
CG
|
A:ASP153
|
3.1
|
18.3
|
1.0
|
O8
|
A:9ON504
|
3.2
|
25.1
|
1.0
|
C5N
|
A:NAD503
|
3.5
|
13.6
|
1.0
|
OG
|
A:SER40
|
3.8
|
17.3
|
1.0
|
CB
|
A:SER40
|
3.8
|
16.6
|
1.0
|
OD1
|
A:ASP153
|
3.8
|
19.9
|
1.0
|
O
|
A:HOH601
|
4.0
|
21.4
|
1.0
|
C6N
|
A:NAD503
|
4.1
|
13.6
|
1.0
|
CB
|
A:ASP153
|
4.1
|
16.6
|
1.0
|
CG
|
A:HIS62
|
4.1
|
17.1
|
1.0
|
ND1
|
A:HIS62
|
4.1
|
17.0
|
1.0
|
C4N
|
A:NAD503
|
4.3
|
13.9
|
1.0
|
C2
|
A:9ON504
|
4.4
|
32.1
|
1.0
|
CA
|
A:CYS38
|
4.6
|
16.2
|
1.0
|
NH2
|
A:ARG340
|
4.7
|
15.3
|
1.0
|
N
|
A:SER40
|
4.8
|
16.4
|
1.0
|
CA
|
A:SER40
|
4.9
|
16.9
|
1.0
|
|
Zinc binding site 3 out
of 8 in 5o9d
Go back to
Zinc Binding Sites List in 5o9d
Zinc binding site 3 out
of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, H39Y
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 R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, H39Y within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn501
b:16.1
occ:1.00
|
SG
|
B:CYS106
|
2.3
|
18.1
|
1.0
|
SG
|
B:CYS92
|
2.3
|
18.1
|
1.0
|
SG
|
B:CYS95
|
2.3
|
17.1
|
1.0
|
SG
|
B:CYS98
|
2.4
|
15.4
|
1.0
|
CB
|
B:CYS106
|
3.2
|
17.7
|
1.0
|
CB
|
B:CYS98
|
3.3
|
15.4
|
1.0
|
CB
|
B:CYS95
|
3.4
|
18.6
|
1.0
|
N
|
B:CYS92
|
3.4
|
17.3
|
1.0
|
CB
|
B:CYS92
|
3.5
|
18.8
|
1.0
|
N
|
B:CYS95
|
3.8
|
18.6
|
1.0
|
CA
|
B:CYS92
|
3.9
|
18.1
|
1.0
|
N
|
B:GLY93
|
3.9
|
17.0
|
1.0
|
CA
|
B:CYS106
|
3.9
|
18.4
|
1.0
|
CA
|
B:CYS95
|
4.2
|
18.7
|
1.0
|
N
|
B:CYS98
|
4.2
|
14.9
|
1.0
|
O
|
B:HOH619
|
4.3
|
35.9
|
1.0
|
C
|
B:CYS92
|
4.3
|
17.8
|
1.0
|
CA
|
B:CYS98
|
4.3
|
14.8
|
1.0
|
N
|
B:ALA94
|
4.4
|
18.6
|
1.0
|
C
|
B:GLY91
|
4.5
|
16.9
|
1.0
|
CB
|
B:ARG108
|
4.5
|
31.2
|
1.0
|
CG
|
B:ARG108
|
4.6
|
33.2
|
1.0
|
CA
|
B:GLY91
|
4.7
|
16.2
|
1.0
|
C
|
B:CYS106
|
4.8
|
20.9
|
1.0
|
N
|
B:ARG108
|
4.8
|
28.5
|
1.0
|
N
|
B:THR107
|
4.8
|
23.8
|
1.0
|
C
|
B:CYS95
|
4.8
|
17.8
|
1.0
|
CA
|
B:GLY93
|
4.9
|
17.1
|
1.0
|
O
|
B:CYS95
|
5.0
|
16.8
|
1.0
|
C
|
B:ALA94
|
5.0
|
19.3
|
1.0
|
|
Zinc binding site 4 out
of 8 in 5o9d
Go back to
Zinc Binding Sites List in 5o9d
Zinc binding site 4 out
of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, H39Y
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 R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, H39Y within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn502
b:16.4
occ:1.00
|
OD2
|
B:ASP153
|
1.9
|
18.2
|
1.0
|
O8
|
B:9ON504
|
2.0
|
21.7
|
1.0
|
NE2
|
B:HIS62
|
2.1
|
16.7
|
1.0
|
SG
|
B:CYS38
|
2.3
|
16.2
|
1.0
|
C1
|
B:9ON504
|
2.9
|
27.4
|
1.0
|
CD2
|
B:HIS62
|
3.0
|
16.3
|
1.0
|
CG
|
B:ASP153
|
3.1
|
17.1
|
1.0
|
CE1
|
B:HIS62
|
3.1
|
16.6
|
1.0
|
CB
|
B:CYS38
|
3.1
|
15.6
|
1.0
|
O9
|
B:9ON504
|
3.2
|
24.4
|
1.0
|
C5N
|
B:NAD503
|
3.4
|
12.7
|
1.0
|
OD1
|
B:ASP153
|
3.8
|
19.1
|
1.0
|
CB
|
B:SER40
|
3.8
|
16.2
|
1.0
|
OG
|
B:SER40
|
3.8
|
16.9
|
1.0
|
C6N
|
B:NAD503
|
4.0
|
12.4
|
1.0
|
O
|
B:HOH707
|
4.0
|
4.9
|
0.5
|
CB
|
B:ASP153
|
4.1
|
16.0
|
1.0
|
CG
|
B:HIS62
|
4.2
|
16.4
|
1.0
|
ND1
|
B:HIS62
|
4.2
|
16.0
|
1.0
|
C4N
|
B:NAD503
|
4.2
|
12.8
|
1.0
|
C2
|
B:9ON504
|
4.3
|
30.6
|
1.0
|
CA
|
B:CYS38
|
4.6
|
15.8
|
1.0
|
NH2
|
B:ARG340
|
4.7
|
15.6
|
1.0
|
N
|
B:SER40
|
4.8
|
16.0
|
1.0
|
CA
|
B:SER40
|
4.9
|
16.4
|
1.0
|
|
Zinc binding site 5 out
of 8 in 5o9d
Go back to
Zinc Binding Sites List in 5o9d
Zinc binding site 5 out
of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, H39Y
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 R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, H39Y within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn501
b:14.8
occ:1.00
|
SG
|
C:CYS95
|
2.3
|
15.8
|
1.0
|
SG
|
C:CYS92
|
2.3
|
17.1
|
1.0
|
SG
|
C:CYS106
|
2.3
|
17.5
|
1.0
|
SG
|
C:CYS98
|
2.3
|
14.4
|
1.0
|
CB
|
C:CYS106
|
3.3
|
17.8
|
1.0
|
CB
|
C:CYS98
|
3.3
|
14.2
|
1.0
|
CB
|
C:CYS95
|
3.4
|
16.7
|
1.0
|
N
|
C:CYS92
|
3.5
|
16.8
|
1.0
|
CB
|
C:CYS92
|
3.5
|
17.9
|
1.0
|
N
|
C:CYS95
|
3.8
|
16.7
|
1.0
|
N
|
C:GLY93
|
3.9
|
16.2
|
1.0
|
CA
|
C:CYS92
|
3.9
|
17.4
|
1.0
|
CA
|
C:CYS106
|
3.9
|
18.2
|
1.0
|
CA
|
C:CYS95
|
4.2
|
16.7
|
1.0
|
N
|
C:CYS98
|
4.2
|
13.4
|
1.0
|
O
|
C:HOH646
|
4.3
|
34.8
|
1.0
|
C
|
C:CYS92
|
4.3
|
17.1
|
1.0
|
CA
|
C:CYS98
|
4.3
|
13.5
|
1.0
|
N
|
C:ALA94
|
4.4
|
17.1
|
1.0
|
C
|
C:GLY91
|
4.5
|
16.6
|
1.0
|
CB
|
C:ARG108
|
4.5
|
31.3
|
1.0
|
CG
|
C:ARG108
|
4.6
|
33.1
|
1.0
|
CA
|
C:GLY91
|
4.7
|
16.2
|
1.0
|
C
|
C:CYS106
|
4.8
|
20.7
|
1.0
|
N
|
C:THR107
|
4.8
|
23.7
|
1.0
|
C
|
C:CYS95
|
4.8
|
15.8
|
1.0
|
N
|
C:ARG108
|
4.8
|
28.6
|
1.0
|
CA
|
C:GLY93
|
4.9
|
16.2
|
1.0
|
O
|
C:CYS95
|
4.9
|
15.0
|
1.0
|
C
|
C:ALA94
|
5.0
|
17.4
|
1.0
|
|
Zinc binding site 6 out
of 8 in 5o9d
Go back to
Zinc Binding Sites List in 5o9d
Zinc binding site 6 out
of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, H39Y
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 R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, H39Y within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn502
b:20.9
occ:1.00
|
OD2
|
C:ASP153
|
1.9
|
22.4
|
1.0
|
O9
|
C:9ON504
|
2.0
|
28.4
|
1.0
|
NE2
|
C:HIS62
|
2.0
|
20.7
|
1.0
|
SG
|
C:CYS38
|
2.3
|
20.1
|
1.0
|
C1
|
C:9ON504
|
3.0
|
32.8
|
1.0
|
CD2
|
C:HIS62
|
3.0
|
20.8
|
1.0
|
CE1
|
C:HIS62
|
3.0
|
21.0
|
1.0
|
CB
|
C:CYS38
|
3.1
|
19.3
|
1.0
|
CG
|
C:ASP153
|
3.1
|
20.5
|
1.0
|
O8
|
C:9ON504
|
3.3
|
30.8
|
1.0
|
C5N
|
C:NAD503
|
3.4
|
14.5
|
1.0
|
CB
|
C:SER40
|
3.8
|
20.4
|
1.0
|
OG
|
C:SER40
|
3.8
|
20.5
|
1.0
|
OD1
|
C:ASP153
|
3.8
|
21.7
|
1.0
|
C6N
|
C:NAD503
|
4.0
|
14.5
|
1.0
|
O
|
C:HOH604
|
4.0
|
8.2
|
0.5
|
CB
|
C:ASP153
|
4.1
|
19.3
|
1.0
|
ND1
|
C:HIS62
|
4.1
|
20.9
|
1.0
|
CG
|
C:HIS62
|
4.1
|
20.5
|
1.0
|
C4N
|
C:NAD503
|
4.2
|
14.5
|
1.0
|
C2
|
C:9ON504
|
4.3
|
36.9
|
1.0
|
CA
|
C:CYS38
|
4.6
|
19.7
|
1.0
|
NH2
|
C:ARG340
|
4.7
|
18.6
|
1.0
|
N
|
C:SER40
|
4.8
|
20.4
|
1.0
|
CA
|
C:SER40
|
4.9
|
20.8
|
1.0
|
|
Zinc binding site 7 out
of 8 in 5o9d
Go back to
Zinc Binding Sites List in 5o9d
Zinc binding site 7 out
of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, H39Y
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 R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, H39Y within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn501
b:15.0
occ:1.00
|
SG
|
D:CYS95
|
2.3
|
16.5
|
1.0
|
SG
|
D:CYS92
|
2.3
|
17.2
|
1.0
|
SG
|
D:CYS106
|
2.3
|
17.6
|
1.0
|
SG
|
D:CYS98
|
2.3
|
15.2
|
1.0
|
CB
|
D:CYS106
|
3.3
|
17.4
|
1.0
|
CB
|
D:CYS98
|
3.3
|
15.3
|
1.0
|
CB
|
D:CYS95
|
3.4
|
17.4
|
1.0
|
N
|
D:CYS92
|
3.5
|
17.3
|
1.0
|
CB
|
D:CYS92
|
3.5
|
18.2
|
1.0
|
N
|
D:CYS95
|
3.8
|
17.8
|
1.0
|
N
|
D:GLY93
|
3.9
|
17.3
|
1.0
|
CA
|
D:CYS92
|
3.9
|
18.1
|
1.0
|
CA
|
D:CYS106
|
4.0
|
17.6
|
1.0
|
CA
|
D:CYS95
|
4.2
|
17.5
|
1.0
|
N
|
D:CYS98
|
4.2
|
14.2
|
1.0
|
C
|
D:CYS92
|
4.3
|
18.0
|
1.0
|
O
|
D:HOH656
|
4.3
|
25.8
|
1.0
|
CA
|
D:CYS98
|
4.4
|
14.5
|
1.0
|
N
|
D:ALA94
|
4.4
|
18.1
|
1.0
|
C
|
D:GLY91
|
4.5
|
17.5
|
1.0
|
CB
|
D:ARG108
|
4.5
|
29.4
|
1.0
|
CG
|
D:ARG108
|
4.6
|
30.9
|
1.0
|
CA
|
D:GLY91
|
4.7
|
17.0
|
1.0
|
C
|
D:CYS106
|
4.8
|
19.6
|
1.0
|
C
|
D:CYS95
|
4.9
|
16.6
|
1.0
|
N
|
D:ARG108
|
4.9
|
26.1
|
1.0
|
N
|
D:THR107
|
4.9
|
21.7
|
1.0
|
CA
|
D:GLY93
|
4.9
|
17.5
|
1.0
|
O
|
D:CYS95
|
5.0
|
16.0
|
1.0
|
C
|
D:ALA94
|
5.0
|
18.5
|
1.0
|
|
Zinc binding site 8 out
of 8 in 5o9d
Go back to
Zinc Binding Sites List in 5o9d
Zinc binding site 8 out
of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, H39Y
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 R. Ruber Adh-A, Mutant Y294F, W295A, Y54F, F43H, H39Y within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn502
b:26.5
occ:1.00
|
OD2
|
D:ASP153
|
1.9
|
26.0
|
1.0
|
O8
|
D:9ON504
|
2.0
|
38.3
|
1.0
|
NE2
|
D:HIS62
|
2.1
|
28.9
|
1.0
|
SG
|
D:CYS38
|
2.3
|
25.8
|
1.0
|
CD2
|
D:HIS62
|
3.0
|
28.7
|
1.0
|
C1
|
D:9ON504
|
3.1
|
43.8
|
1.0
|
CE1
|
D:HIS62
|
3.1
|
29.3
|
1.0
|
CG
|
D:ASP153
|
3.1
|
23.8
|
1.0
|
CB
|
D:CYS38
|
3.2
|
25.7
|
1.0
|
C5N
|
D:NAD503
|
3.4
|
15.8
|
1.0
|
O9
|
D:9ON504
|
3.4
|
40.4
|
1.0
|
CB
|
D:SER40
|
3.7
|
27.0
|
1.0
|
OG
|
D:SER40
|
3.8
|
27.0
|
1.0
|
OD1
|
D:ASP153
|
3.8
|
24.5
|
1.0
|
C6N
|
D:NAD503
|
4.0
|
15.8
|
1.0
|
O
|
D:HOH603
|
4.0
|
24.9
|
1.0
|
CB
|
D:ASP153
|
4.1
|
22.9
|
1.0
|
CG
|
D:HIS62
|
4.2
|
28.9
|
1.0
|
ND1
|
D:HIS62
|
4.2
|
29.3
|
1.0
|
C4N
|
D:NAD503
|
4.2
|
16.1
|
1.0
|
C2
|
D:9ON504
|
4.4
|
47.7
|
1.0
|
CA
|
D:CYS38
|
4.6
|
26.2
|
1.0
|
NH2
|
D:ARG340
|
4.7
|
26.3
|
1.0
|
N
|
D:SER40
|
4.8
|
27.2
|
1.0
|
CA
|
D:SER40
|
4.9
|
27.5
|
1.0
|
|
Reference:
E.Hamnevik,
T.R.Enugala,
D.Maurer,
S.Ntuku,
A.Oliveira,
D.Dobritzsch,
M.Widersten.
Relaxation of Nonproductive Binding and Increased Rate of Coenzyme Release in An Alcohol Dehydrogenase Increases Turnover with A Nonpreferred Alcohol Enantiomer. Febs J. V. 284 3895 2017.
ISSN: ISSN 1742-4658
PubMed: 28963762
DOI: 10.1111/FEBS.14279
Page generated: Sun Oct 27 23:20:58 2024
|