Zinc in PDB 6sch: Nadh-Dependent Variant of Cbadh
Enzymatic activity of Nadh-Dependent Variant of Cbadh
All present enzymatic activity of Nadh-Dependent Variant of Cbadh:
1.1.1.80;
Protein crystallography data
The structure of Nadh-Dependent Variant of Cbadh, PDB code: 6sch
was solved by
L.Selles Vidal,
J.W.Murray,
J.T.Heap,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
69.01 /
2.20
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
75.812,
99.570,
114.089,
90.00,
102.77,
90.00
|
R / Rfree (%)
|
16.4 /
20.8
|
Other elements in 6sch:
The structure of Nadh-Dependent Variant of Cbadh also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Nadh-Dependent Variant of Cbadh
(pdb code 6sch). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Nadh-Dependent Variant of Cbadh, PDB code: 6sch:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 6sch
Go back to
Zinc Binding Sites List in 6sch
Zinc binding site 1 out
of 4 in the Nadh-Dependent Variant of Cbadh
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Nadh-Dependent Variant of Cbadh within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn405
b:40.1
occ:1.00
|
OD2
|
A:ASP150
|
2.0
|
47.7
|
1.0
|
NE2
|
A:HIS59
|
2.0
|
41.8
|
1.0
|
SG
|
A:CYS37
|
2.4
|
38.9
|
1.0
|
N7N
|
A:NAD401
|
2.6
|
45.1
|
0.8
|
CE1
|
A:HIS59
|
3.0
|
38.1
|
1.0
|
C4N
|
A:NAD401
|
3.0
|
88.1
|
0.8
|
CG
|
A:ASP150
|
3.1
|
37.7
|
1.0
|
CD2
|
A:HIS59
|
3.1
|
36.6
|
1.0
|
CB
|
A:CYS37
|
3.2
|
36.9
|
1.0
|
C3N
|
A:NAD401
|
3.3
|
82.5
|
0.8
|
C7N
|
A:NAD401
|
3.4
|
62.8
|
0.8
|
OG
|
A:SER39
|
3.4
|
50.0
|
1.0
|
OD1
|
A:ASP150
|
3.5
|
40.3
|
1.0
|
C5N
|
A:NAD401
|
3.7
|
87.5
|
0.8
|
ND1
|
A:HIS59
|
4.1
|
38.1
|
1.0
|
OE2
|
A:GLU60
|
4.1
|
45.5
|
1.0
|
CG
|
A:HIS59
|
4.2
|
34.5
|
1.0
|
CB
|
A:SER39
|
4.3
|
45.2
|
1.0
|
CB
|
A:ASP150
|
4.3
|
31.1
|
1.0
|
C2N
|
A:NAD401
|
4.3
|
84.6
|
0.8
|
CE
|
A:MET151
|
4.5
|
32.5
|
1.0
|
O7N
|
A:NAD401
|
4.5
|
65.3
|
0.8
|
CD
|
A:GLU60
|
4.6
|
46.7
|
1.0
|
C6N
|
A:NAD401
|
4.6
|
86.7
|
0.8
|
CA
|
A:CYS37
|
4.7
|
32.0
|
1.0
|
CG
|
A:GLU60
|
4.8
|
37.5
|
1.0
|
N1N
|
A:NAD401
|
4.8
|
86.2
|
0.8
|
|
Zinc binding site 2 out
of 4 in 6sch
Go back to
Zinc Binding Sites List in 6sch
Zinc binding site 2 out
of 4 in the Nadh-Dependent Variant of Cbadh
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Nadh-Dependent Variant of Cbadh within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn404
b:45.6
occ:1.00
|
OD2
|
B:ASP150
|
2.0
|
47.4
|
1.0
|
NE2
|
B:HIS59
|
2.1
|
45.9
|
1.0
|
SG
|
B:CYS37
|
2.4
|
42.5
|
1.0
|
O7N
|
B:NAD401
|
2.5
|
67.5
|
0.8
|
CE1
|
B:HIS59
|
2.8
|
41.9
|
1.0
|
CG
|
B:ASP150
|
3.0
|
34.8
|
1.0
|
CD2
|
B:HIS59
|
3.2
|
39.4
|
1.0
|
CB
|
B:CYS37
|
3.2
|
40.5
|
1.0
|
C7N
|
B:NAD401
|
3.3
|
71.3
|
0.8
|
OD1
|
B:ASP150
|
3.3
|
36.5
|
1.0
|
C3N
|
B:NAD401
|
3.4
|
92.0
|
0.8
|
C4N
|
B:NAD401
|
3.4
|
98.0
|
0.8
|
OG
|
B:SER39
|
3.5
|
46.2
|
1.0
|
OE2
|
B:GLU60
|
4.0
|
57.4
|
1.0
|
ND1
|
B:HIS59
|
4.0
|
39.8
|
1.0
|
C2N
|
B:NAD401
|
4.2
|
0.0
|
0.8
|
CG
|
B:HIS59
|
4.2
|
40.5
|
1.0
|
C5N
|
B:NAD401
|
4.2
|
99.6
|
0.8
|
CB
|
B:SER39
|
4.3
|
39.7
|
1.0
|
CB
|
B:ASP150
|
4.3
|
30.3
|
1.0
|
CE
|
B:MET151
|
4.4
|
39.4
|
1.0
|
CD
|
B:GLU60
|
4.5
|
52.2
|
1.0
|
N7N
|
B:NAD401
|
4.5
|
62.4
|
0.8
|
CA
|
B:CYS37
|
4.7
|
42.4
|
1.0
|
CG
|
B:GLU60
|
4.8
|
40.0
|
1.0
|
N1N
|
B:NAD401
|
4.9
|
0.4
|
0.8
|
C6N
|
B:NAD401
|
4.9
|
99.8
|
0.8
|
O
|
B:HOH536
|
5.0
|
39.4
|
1.0
|
|
Zinc binding site 3 out
of 4 in 6sch
Go back to
Zinc Binding Sites List in 6sch
Zinc binding site 3 out
of 4 in the Nadh-Dependent Variant of Cbadh
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Nadh-Dependent Variant of Cbadh within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn403
b:48.8
occ:1.00
|
OD2
|
C:ASP150
|
1.9
|
50.4
|
1.0
|
NE2
|
C:HIS59
|
2.0
|
48.7
|
1.0
|
SG
|
C:CYS37
|
2.5
|
44.3
|
1.0
|
CE1
|
C:HIS59
|
2.9
|
45.6
|
1.0
|
CG
|
C:ASP150
|
3.0
|
39.1
|
1.0
|
CD2
|
C:HIS59
|
3.1
|
33.4
|
1.0
|
CB
|
C:CYS37
|
3.1
|
35.5
|
1.0
|
OD1
|
C:ASP150
|
3.4
|
36.5
|
1.0
|
C4N
|
C:NAD401
|
3.4
|
88.1
|
0.8
|
C7N
|
C:NAD401
|
3.7
|
63.5
|
0.8
|
C3N
|
C:NAD401
|
3.7
|
84.9
|
0.8
|
O7N
|
C:NAD401
|
3.8
|
58.7
|
0.8
|
OG
|
C:SER39
|
3.8
|
51.1
|
1.0
|
OE2
|
C:GLU60
|
3.9
|
55.1
|
1.0
|
ND1
|
C:HIS59
|
4.1
|
41.1
|
1.0
|
CG
|
C:HIS59
|
4.2
|
34.5
|
1.0
|
C5N
|
C:NAD401
|
4.2
|
88.2
|
0.8
|
N7N
|
C:NAD401
|
4.2
|
51.5
|
0.8
|
CB
|
C:ASP150
|
4.2
|
30.8
|
1.0
|
CD
|
C:GLU60
|
4.5
|
45.4
|
1.0
|
CE
|
C:MET151
|
4.5
|
31.3
|
1.0
|
C2N
|
C:NAD401
|
4.6
|
89.6
|
0.8
|
CA
|
C:CYS37
|
4.6
|
37.8
|
1.0
|
CB
|
C:SER39
|
4.7
|
49.2
|
1.0
|
CG
|
C:GLU60
|
4.8
|
38.2
|
1.0
|
C6N
|
C:NAD401
|
5.0
|
89.4
|
0.8
|
|
Zinc binding site 4 out
of 4 in 6sch
Go back to
Zinc Binding Sites List in 6sch
Zinc binding site 4 out
of 4 in the Nadh-Dependent Variant of Cbadh
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Nadh-Dependent Variant of Cbadh within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn404
b:44.3
occ:1.00
|
OD2
|
D:ASP150
|
1.9
|
45.2
|
1.0
|
NE2
|
D:HIS59
|
2.0
|
46.6
|
1.0
|
SG
|
D:CYS37
|
2.4
|
39.5
|
1.0
|
CE1
|
D:HIS59
|
2.9
|
40.2
|
1.0
|
CG
|
D:ASP150
|
3.0
|
34.8
|
1.0
|
CD2
|
D:HIS59
|
3.1
|
39.2
|
1.0
|
O7N
|
D:NAD401
|
3.2
|
57.0
|
0.8
|
CB
|
D:CYS37
|
3.2
|
30.9
|
1.0
|
C4N
|
D:NAD401
|
3.3
|
85.6
|
0.8
|
OD1
|
D:ASP150
|
3.4
|
41.7
|
1.0
|
C3N
|
D:NAD401
|
3.5
|
82.1
|
0.8
|
OG
|
D:SER39
|
3.5
|
49.3
|
1.0
|
C7N
|
D:NAD401
|
3.5
|
64.4
|
0.8
|
C5N
|
D:NAD401
|
4.0
|
87.3
|
0.8
|
ND1
|
D:HIS59
|
4.1
|
40.9
|
1.0
|
OE2
|
D:GLU60
|
4.1
|
51.8
|
1.0
|
CG
|
D:HIS59
|
4.2
|
39.3
|
1.0
|
CB
|
D:ASP150
|
4.2
|
31.6
|
1.0
|
C2N
|
D:NAD401
|
4.3
|
87.2
|
0.8
|
CB
|
D:SER39
|
4.3
|
43.6
|
1.0
|
CE
|
D:MET151
|
4.4
|
48.2
|
1.0
|
N7N
|
D:NAD401
|
4.5
|
61.3
|
0.8
|
CD
|
D:GLU60
|
4.6
|
47.4
|
1.0
|
CA
|
D:CYS37
|
4.7
|
35.2
|
1.0
|
C6N
|
D:NAD401
|
4.7
|
85.6
|
0.8
|
CG
|
D:GLU60
|
4.7
|
38.2
|
1.0
|
N1N
|
D:NAD401
|
4.8
|
83.9
|
0.8
|
|
Reference:
L.Selles Vidal,
J.W.Murray,
J.T.Heap.
Nadh-Dependent Variant of Cbadh To Be Published.
Page generated: Tue Oct 29 07:10:14 2024
|