Zinc in PDB 6fg0: Crystal Structure of R. Ruber Adh-A, Mutant Y54G, F43T, L119Y, F282W
Protein crystallography data
The structure of Crystal Structure of R. Ruber Adh-A, Mutant Y54G, F43T, L119Y, F282W, PDB code: 6fg0
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)
|
29.50 /
1.74
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
65.706,
105.463,
108.977,
90.00,
91.40,
90.00
|
R / Rfree (%)
|
16.3 /
18.1
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of R. Ruber Adh-A, Mutant Y54G, F43T, L119Y, F282W
(pdb code 6fg0). 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 Y54G, F43T, L119Y, F282W, PDB code: 6fg0:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 6fg0
Go back to
Zinc Binding Sites List in 6fg0
Zinc binding site 1 out
of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y54G, F43T, L119Y, F282W
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 Y54G, F43T, L119Y, F282W within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn501
b:22.4
occ:1.00
|
SG
|
A:CYS92
|
2.3
|
24.7
|
1.0
|
SG
|
A:CYS95
|
2.3
|
22.2
|
1.0
|
SG
|
A:CYS98
|
2.3
|
21.6
|
1.0
|
SG
|
A:CYS106
|
2.4
|
23.0
|
1.0
|
CB
|
A:CYS98
|
3.3
|
21.3
|
1.0
|
CB
|
A:CYS106
|
3.3
|
22.9
|
1.0
|
CB
|
A:CYS95
|
3.4
|
23.5
|
1.0
|
N
|
A:CYS92
|
3.4
|
22.8
|
1.0
|
CB
|
A:CYS92
|
3.5
|
24.7
|
1.0
|
CA
|
A:CYS106
|
3.8
|
23.0
|
1.0
|
N
|
A:CYS95
|
3.8
|
23.8
|
1.0
|
CA
|
A:CYS92
|
3.9
|
23.7
|
1.0
|
N
|
A:GLY93
|
3.9
|
23.1
|
1.0
|
CA
|
A:CYS95
|
4.2
|
24.0
|
1.0
|
N
|
A:THR107
|
4.3
|
27.7
|
1.0
|
C
|
A:CYS92
|
4.3
|
23.8
|
1.0
|
N
|
A:CYS98
|
4.3
|
19.7
|
1.0
|
N
|
A:ALA94
|
4.3
|
24.3
|
1.0
|
CA
|
A:CYS98
|
4.4
|
20.1
|
1.0
|
C
|
A:CYS106
|
4.4
|
25.3
|
1.0
|
C
|
A:GLY91
|
4.5
|
22.1
|
1.0
|
N
|
A:ARG108
|
4.6
|
32.3
|
1.0
|
CB
|
A:ARG108
|
4.6
|
36.1
|
1.0
|
CA
|
A:GLY91
|
4.7
|
21.4
|
1.0
|
C
|
A:CYS95
|
4.9
|
23.2
|
1.0
|
CA
|
A:GLY93
|
4.9
|
23.3
|
1.0
|
CG
|
A:ARG108
|
4.9
|
38.5
|
1.0
|
C
|
A:ALA94
|
4.9
|
24.6
|
1.0
|
O
|
A:CYS95
|
5.0
|
22.4
|
1.0
|
C
|
A:GLY93
|
5.0
|
24.3
|
1.0
|
|
Zinc binding site 2 out
of 8 in 6fg0
Go back to
Zinc Binding Sites List in 6fg0
Zinc binding site 2 out
of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y54G, F43T, L119Y, F282W
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 Y54G, F43T, L119Y, F282W within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn502
b:24.3
occ:1.00
|
OD2
|
A:ASP153
|
1.9
|
20.0
|
1.0
|
NE2
|
A:HIS62
|
2.1
|
21.4
|
1.0
|
SG
|
A:CYS38
|
2.3
|
22.2
|
1.0
|
CD2
|
A:HIS62
|
3.0
|
21.4
|
1.0
|
CB
|
A:CYS38
|
3.1
|
22.3
|
1.0
|
CE1
|
A:HIS62
|
3.1
|
22.2
|
1.0
|
CG
|
A:ASP153
|
3.1
|
19.6
|
1.0
|
C5N
|
A:NAD503
|
3.4
|
19.8
|
1.0
|
OD1
|
A:ASP153
|
3.7
|
19.9
|
1.0
|
OG
|
A:SER40
|
3.8
|
22.8
|
1.0
|
CB
|
A:SER40
|
3.8
|
22.7
|
1.0
|
C6N
|
A:NAD503
|
4.0
|
19.9
|
1.0
|
CG
|
A:HIS62
|
4.1
|
21.6
|
1.0
|
ND1
|
A:HIS62
|
4.2
|
22.1
|
1.0
|
CB
|
A:ASP153
|
4.2
|
18.8
|
1.0
|
C4N
|
A:NAD503
|
4.3
|
19.5
|
1.0
|
NH2
|
A:ARG340
|
4.4
|
20.6
|
1.0
|
CA
|
A:CYS38
|
4.6
|
22.6
|
1.0
|
N
|
A:SER40
|
4.8
|
22.5
|
1.0
|
CA
|
A:SER40
|
4.9
|
23.2
|
1.0
|
|
Zinc binding site 3 out
of 8 in 6fg0
Go back to
Zinc Binding Sites List in 6fg0
Zinc binding site 3 out
of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y54G, F43T, L119Y, F282W
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 Y54G, F43T, L119Y, F282W within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn501
b:22.0
occ:1.00
|
SG
|
B:CYS92
|
2.3
|
23.7
|
1.0
|
SG
|
B:CYS98
|
2.3
|
21.2
|
1.0
|
SG
|
B:CYS95
|
2.3
|
21.5
|
1.0
|
SG
|
B:CYS106
|
2.4
|
22.7
|
1.0
|
CB
|
B:CYS106
|
3.3
|
21.8
|
1.0
|
CB
|
B:CYS98
|
3.3
|
21.0
|
1.0
|
CB
|
B:CYS95
|
3.4
|
22.5
|
1.0
|
N
|
B:CYS92
|
3.4
|
22.2
|
1.0
|
CB
|
B:CYS92
|
3.5
|
24.2
|
1.0
|
CA
|
B:CYS106
|
3.8
|
22.1
|
1.0
|
N
|
B:CYS95
|
3.8
|
23.1
|
1.0
|
CA
|
B:CYS92
|
3.9
|
23.1
|
1.0
|
N
|
B:GLY93
|
3.9
|
22.3
|
1.0
|
CA
|
B:CYS95
|
4.2
|
22.9
|
1.0
|
C
|
B:CYS92
|
4.3
|
23.1
|
1.0
|
N
|
B:THR107
|
4.3
|
27.1
|
1.0
|
N
|
B:CYS98
|
4.3
|
19.6
|
1.0
|
N
|
B:ALA94
|
4.4
|
23.6
|
1.0
|
CA
|
B:CYS98
|
4.4
|
19.9
|
1.0
|
C
|
B:CYS106
|
4.4
|
24.3
|
1.0
|
C
|
B:GLY91
|
4.5
|
21.8
|
1.0
|
N
|
B:ARG108
|
4.6
|
31.4
|
1.0
|
CB
|
B:ARG108
|
4.7
|
33.9
|
1.0
|
CA
|
B:GLY91
|
4.7
|
21.1
|
1.0
|
C
|
B:CYS95
|
4.9
|
22.0
|
1.0
|
CA
|
B:GLY93
|
4.9
|
22.7
|
1.0
|
C
|
B:ALA94
|
4.9
|
24.0
|
1.0
|
CG
|
B:ARG108
|
5.0
|
35.5
|
1.0
|
O
|
B:CYS95
|
5.0
|
21.9
|
1.0
|
|
Zinc binding site 4 out
of 8 in 6fg0
Go back to
Zinc Binding Sites List in 6fg0
Zinc binding site 4 out
of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y54G, F43T, L119Y, F282W
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 Y54G, F43T, L119Y, F282W within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn502
b:24.1
occ:1.00
|
OD2
|
B:ASP153
|
1.9
|
19.9
|
1.0
|
NE2
|
B:HIS62
|
2.1
|
20.7
|
1.0
|
SG
|
B:CYS38
|
2.3
|
20.5
|
1.0
|
CD2
|
B:HIS62
|
3.0
|
20.6
|
1.0
|
CB
|
B:CYS38
|
3.1
|
21.2
|
1.0
|
CE1
|
B:HIS62
|
3.1
|
21.3
|
1.0
|
CG
|
B:ASP153
|
3.1
|
19.9
|
1.0
|
C5N
|
B:NAD503
|
3.4
|
18.9
|
1.0
|
OD1
|
B:ASP153
|
3.7
|
20.6
|
1.0
|
OG
|
B:SER40
|
3.8
|
21.1
|
1.0
|
CB
|
B:SER40
|
3.8
|
21.8
|
1.0
|
C6N
|
B:NAD503
|
4.0
|
19.3
|
1.0
|
CG
|
B:HIS62
|
4.1
|
20.6
|
1.0
|
ND1
|
B:HIS62
|
4.2
|
21.2
|
1.0
|
CB
|
B:ASP153
|
4.2
|
18.7
|
1.0
|
C4N
|
B:NAD503
|
4.3
|
18.9
|
1.0
|
NH2
|
B:ARG340
|
4.4
|
18.7
|
1.0
|
CA
|
B:CYS38
|
4.6
|
21.1
|
1.0
|
N
|
B:SER40
|
4.8
|
21.1
|
1.0
|
CA
|
B:SER40
|
5.0
|
22.2
|
1.0
|
|
Zinc binding site 5 out
of 8 in 6fg0
Go back to
Zinc Binding Sites List in 6fg0
Zinc binding site 5 out
of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y54G, F43T, L119Y, F282W
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 Y54G, F43T, L119Y, F282W within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn501
b:21.8
occ:1.00
|
SG
|
C:CYS95
|
2.3
|
21.8
|
1.0
|
SG
|
C:CYS92
|
2.3
|
24.5
|
1.0
|
SG
|
C:CYS98
|
2.4
|
22.1
|
1.0
|
SG
|
C:CYS106
|
2.4
|
23.3
|
1.0
|
CB
|
C:CYS106
|
3.3
|
23.9
|
1.0
|
CB
|
C:CYS98
|
3.3
|
21.6
|
1.0
|
CB
|
C:CYS95
|
3.4
|
21.9
|
1.0
|
N
|
C:CYS92
|
3.5
|
24.1
|
1.0
|
CB
|
C:CYS92
|
3.5
|
24.9
|
1.0
|
N
|
C:CYS95
|
3.8
|
22.7
|
1.0
|
CA
|
C:CYS106
|
3.8
|
23.8
|
1.0
|
CA
|
C:CYS92
|
3.9
|
24.8
|
1.0
|
N
|
C:GLY93
|
3.9
|
23.6
|
1.0
|
CA
|
C:CYS95
|
4.1
|
22.2
|
1.0
|
N
|
C:CYS98
|
4.3
|
19.7
|
1.0
|
N
|
C:THR107
|
4.3
|
28.5
|
1.0
|
C
|
C:CYS92
|
4.3
|
24.6
|
1.0
|
CA
|
C:CYS98
|
4.4
|
20.5
|
1.0
|
N
|
C:ALA94
|
4.4
|
23.7
|
1.0
|
C
|
C:CYS106
|
4.4
|
26.5
|
1.0
|
C
|
C:GLY91
|
4.5
|
24.3
|
1.0
|
N
|
C:ARG108
|
4.5
|
33.4
|
1.0
|
CB
|
C:ARG108
|
4.6
|
36.4
|
1.0
|
CA
|
C:GLY91
|
4.7
|
23.5
|
1.0
|
C
|
C:CYS95
|
4.8
|
21.2
|
1.0
|
CA
|
C:GLY93
|
4.9
|
23.7
|
1.0
|
CG
|
C:ARG108
|
4.9
|
38.0
|
1.0
|
C
|
C:ALA94
|
4.9
|
23.6
|
1.0
|
O
|
C:CYS95
|
5.0
|
20.9
|
1.0
|
|
Zinc binding site 6 out
of 8 in 6fg0
Go back to
Zinc Binding Sites List in 6fg0
Zinc binding site 6 out
of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y54G, F43T, L119Y, F282W
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 Y54G, F43T, L119Y, F282W within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn502
b:30.0
occ:1.00
|
OD2
|
C:ASP153
|
1.9
|
27.9
|
1.0
|
NE2
|
C:HIS62
|
2.1
|
28.1
|
1.0
|
SG
|
C:CYS38
|
2.3
|
28.4
|
1.0
|
CD2
|
C:HIS62
|
3.0
|
28.2
|
1.0
|
CB
|
C:CYS38
|
3.1
|
28.6
|
1.0
|
CG
|
C:ASP153
|
3.1
|
26.1
|
1.0
|
CE1
|
C:HIS62
|
3.1
|
29.6
|
1.0
|
C5N
|
C:NAD503
|
3.4
|
24.8
|
1.0
|
OD1
|
C:ASP153
|
3.7
|
27.4
|
1.0
|
OG
|
C:SER40
|
3.8
|
28.7
|
1.0
|
CB
|
C:SER40
|
3.9
|
29.4
|
1.0
|
C6N
|
C:NAD503
|
3.9
|
25.1
|
1.0
|
CG
|
C:HIS62
|
4.2
|
28.9
|
1.0
|
ND1
|
C:HIS62
|
4.2
|
30.0
|
1.0
|
CB
|
C:ASP153
|
4.2
|
25.3
|
1.0
|
C4N
|
C:NAD503
|
4.2
|
24.6
|
1.0
|
NH2
|
C:ARG340
|
4.4
|
26.6
|
1.0
|
CA
|
C:CYS38
|
4.6
|
29.8
|
1.0
|
N
|
C:SER40
|
4.9
|
29.8
|
1.0
|
CA
|
C:SER40
|
5.0
|
30.3
|
1.0
|
|
Zinc binding site 7 out
of 8 in 6fg0
Go back to
Zinc Binding Sites List in 6fg0
Zinc binding site 7 out
of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y54G, F43T, L119Y, F282W
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 Y54G, F43T, L119Y, F282W within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn501
b:21.8
occ:1.00
|
SG
|
D:CYS98
|
2.3
|
22.0
|
1.0
|
SG
|
D:CYS92
|
2.3
|
24.4
|
1.0
|
SG
|
D:CYS95
|
2.3
|
21.5
|
1.0
|
SG
|
D:CYS106
|
2.4
|
23.5
|
1.0
|
CB
|
D:CYS98
|
3.3
|
21.4
|
1.0
|
CB
|
D:CYS106
|
3.3
|
23.9
|
1.0
|
CB
|
D:CYS95
|
3.4
|
21.9
|
1.0
|
N
|
D:CYS92
|
3.5
|
24.1
|
1.0
|
CB
|
D:CYS92
|
3.5
|
25.2
|
1.0
|
N
|
D:CYS95
|
3.8
|
22.8
|
1.0
|
CA
|
D:CYS106
|
3.8
|
24.4
|
1.0
|
N
|
D:GLY93
|
3.9
|
24.1
|
1.0
|
CA
|
D:CYS92
|
3.9
|
25.2
|
1.0
|
CA
|
D:CYS95
|
4.2
|
22.2
|
1.0
|
N
|
D:CYS98
|
4.2
|
19.3
|
1.0
|
C
|
D:CYS92
|
4.3
|
25.0
|
1.0
|
N
|
D:THR107
|
4.3
|
30.8
|
1.0
|
CA
|
D:CYS98
|
4.3
|
20.5
|
1.0
|
N
|
D:ALA94
|
4.4
|
24.1
|
1.0
|
C
|
D:CYS106
|
4.5
|
26.9
|
1.0
|
C
|
D:GLY91
|
4.5
|
24.4
|
1.0
|
N
|
D:ARG108
|
4.6
|
36.1
|
1.0
|
CB
|
D:ARG108
|
4.7
|
39.5
|
1.0
|
CA
|
D:GLY91
|
4.7
|
23.8
|
1.0
|
C
|
D:CYS95
|
4.8
|
21.1
|
1.0
|
CA
|
D:GLY93
|
4.9
|
24.3
|
1.0
|
C
|
D:ALA94
|
4.9
|
23.7
|
1.0
|
CG
|
D:ARG108
|
5.0
|
41.0
|
1.0
|
O
|
D:CYS95
|
5.0
|
20.5
|
1.0
|
|
Zinc binding site 8 out
of 8 in 6fg0
Go back to
Zinc Binding Sites List in 6fg0
Zinc binding site 8 out
of 8 in the Crystal Structure of R. Ruber Adh-A, Mutant Y54G, F43T, L119Y, F282W
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 Y54G, F43T, L119Y, F282W within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn502
b:34.8
occ:1.00
|
OD2
|
D:ASP153
|
1.9
|
31.3
|
1.0
|
NE2
|
D:HIS62
|
2.1
|
34.5
|
1.0
|
SG
|
D:CYS38
|
2.3
|
33.3
|
1.0
|
CD2
|
D:HIS62
|
3.0
|
34.5
|
1.0
|
CG
|
D:ASP153
|
3.1
|
29.1
|
1.0
|
CB
|
D:CYS38
|
3.1
|
34.1
|
1.0
|
CE1
|
D:HIS62
|
3.1
|
36.3
|
1.0
|
C5N
|
D:NAD503
|
3.3
|
26.0
|
1.0
|
OD1
|
D:ASP153
|
3.6
|
29.9
|
1.0
|
OG
|
D:SER40
|
3.8
|
35.4
|
1.0
|
CB
|
D:SER40
|
3.8
|
36.5
|
1.0
|
C6N
|
D:NAD503
|
3.9
|
26.2
|
1.0
|
CG
|
D:HIS62
|
4.2
|
35.3
|
1.0
|
ND1
|
D:HIS62
|
4.2
|
36.1
|
1.0
|
C4N
|
D:NAD503
|
4.2
|
25.9
|
1.0
|
CB
|
D:ASP153
|
4.2
|
28.0
|
1.0
|
NH2
|
D:ARG340
|
4.5
|
31.2
|
1.0
|
CA
|
D:CYS38
|
4.6
|
35.1
|
1.0
|
N
|
D:SER40
|
4.8
|
36.3
|
1.0
|
CA
|
D:SER40
|
5.0
|
37.3
|
1.0
|
|
Reference:
D.Maurer,
T.R.Enugala,
E.Hamnevik,
P.Bauer,
M.Luking,
H.Hillier,
S.C.L.Kamerlin,
D.Dobritzsch,
M.Widersten.
Stereo- and Regioselectivity in Catalyzed Transformation of A 1,2-Disubstituted Vicinal Diol and the Corresponding Diketone By Wild Type and Laboratory Evolved Alcohol Dehydrogenases Acs Catalysis V. 8 7526 2018.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.8B01762
Page generated: Mon Oct 28 20:59:05 2024
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