Zinc in PDB 8goa: Crystal Structure of Glycerol Dehydrogenase in the Absence of Nad+
Enzymatic activity of Crystal Structure of Glycerol Dehydrogenase in the Absence of Nad+
All present enzymatic activity of Crystal Structure of Glycerol Dehydrogenase in the Absence of Nad+:
1.1.1.6;
Protein crystallography data
The structure of Crystal Structure of Glycerol Dehydrogenase in the Absence of Nad+, PDB code: 8goa
was solved by
T.Park,
H.N.Hoang,
J.Y.Kang,
J.Park,
S.A.Mun,
M.Jin,
J.Yang,
C.-H.Jung,
S.H.Eom,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.24 /
2.90
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
161.47,
161.47,
291.907,
90,
90,
90
|
R / Rfree (%)
|
19.2 /
22
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Glycerol Dehydrogenase in the Absence of Nad+
(pdb code 8goa). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystal Structure of Glycerol Dehydrogenase in the Absence of Nad+, PDB code: 8goa:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 8goa
Go back to
Zinc Binding Sites List in 8goa
Zinc binding site 1 out
of 4 in the Crystal Structure of Glycerol Dehydrogenase in the Absence of Nad+
![](/pictures/ZN/pdb/go/8goa-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/go/8goa-ZN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of Glycerol Dehydrogenase in the Absence of Nad+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn401
b:49.3
occ:1.00
|
NE2
|
A:HIS254
|
2.2
|
53.3
|
1.0
|
OD1
|
A:ASP171
|
2.3
|
51.1
|
1.0
|
NE2
|
A:HIS271
|
2.3
|
54.9
|
1.0
|
O1
|
A:TRS402
|
2.3
|
75.7
|
0.7
|
C3
|
A:TRS402
|
2.8
|
74.8
|
0.7
|
OD2
|
A:ASP171
|
2.8
|
49.9
|
1.0
|
CG
|
A:ASP171
|
2.8
|
50.1
|
1.0
|
CD2
|
A:HIS254
|
3.0
|
56.9
|
1.0
|
CD2
|
A:HIS271
|
3.1
|
54.6
|
1.0
|
C1
|
A:TRS402
|
3.3
|
75.6
|
0.7
|
O3
|
A:TRS402
|
3.3
|
82.0
|
0.7
|
CE1
|
A:HIS271
|
3.3
|
58.4
|
1.0
|
CE1
|
A:HIS254
|
3.4
|
58.2
|
1.0
|
OD1
|
A:ASP121
|
3.4
|
58.8
|
1.0
|
C
|
A:TRS402
|
3.4
|
75.5
|
0.7
|
OD2
|
A:ASP121
|
3.4
|
56.4
|
1.0
|
C2
|
A:TRS402
|
3.6
|
82.6
|
0.7
|
CG
|
A:ASP121
|
3.7
|
57.3
|
1.0
|
CG
|
A:HIS254
|
4.2
|
56.7
|
1.0
|
CG2
|
A:VAL275
|
4.3
|
50.4
|
1.0
|
CG
|
A:HIS271
|
4.3
|
56.7
|
1.0
|
CB
|
A:ASP171
|
4.3
|
47.0
|
1.0
|
ND1
|
A:HIS254
|
4.4
|
59.7
|
1.0
|
ND1
|
A:HIS271
|
4.4
|
61.0
|
1.0
|
O2
|
A:TRS402
|
4.5
|
88.4
|
0.7
|
OG1
|
A:THR120
|
4.7
|
65.8
|
1.0
|
N
|
A:TRS402
|
4.8
|
95.1
|
0.7
|
O
|
A:HOH509
|
4.9
|
50.6
|
1.0
|
CA
|
A:ASP171
|
4.9
|
45.0
|
1.0
|
|
Zinc binding site 2 out
of 4 in 8goa
Go back to
Zinc Binding Sites List in 8goa
Zinc binding site 2 out
of 4 in the Crystal Structure of Glycerol Dehydrogenase in the Absence of Nad+
![](/pictures/ZN/pdb/go/8goa-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/go/8goa-ZN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of Glycerol Dehydrogenase in the Absence of Nad+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn401
b:44.7
occ:1.00
|
OD1
|
B:ASP171
|
2.1
|
51.8
|
1.0
|
NE2
|
B:HIS254
|
2.2
|
51.7
|
1.0
|
NE2
|
B:HIS271
|
2.3
|
59.3
|
1.0
|
O3
|
B:TRS402
|
2.4
|
88.9
|
0.9
|
N
|
B:TRS402
|
2.4
|
91.5
|
0.9
|
OD2
|
B:ASP171
|
2.8
|
49.5
|
1.0
|
CG
|
B:ASP171
|
2.8
|
49.8
|
1.0
|
CD2
|
B:HIS254
|
3.0
|
51.4
|
1.0
|
CD2
|
B:HIS271
|
3.1
|
57.6
|
1.0
|
C3
|
B:TRS402
|
3.2
|
87.9
|
0.9
|
C
|
B:TRS402
|
3.2
|
89.5
|
0.9
|
CE1
|
B:HIS271
|
3.3
|
65.3
|
1.0
|
CE1
|
B:HIS254
|
3.3
|
56.4
|
1.0
|
OD1
|
B:ASP121
|
3.5
|
61.3
|
1.0
|
C1
|
B:TRS402
|
3.5
|
89.2
|
0.9
|
OD2
|
B:ASP121
|
3.5
|
65.7
|
1.0
|
O1
|
B:TRS402
|
3.7
|
88.7
|
0.9
|
CG
|
B:ASP121
|
3.9
|
64.4
|
1.0
|
CG2
|
B:VAL275
|
4.2
|
53.0
|
1.0
|
CG
|
B:HIS271
|
4.2
|
55.0
|
1.0
|
CG
|
B:HIS254
|
4.2
|
49.2
|
1.0
|
ND1
|
B:HIS271
|
4.3
|
62.2
|
1.0
|
CB
|
B:ASP171
|
4.3
|
47.3
|
1.0
|
ND1
|
B:HIS254
|
4.4
|
53.4
|
1.0
|
C2
|
B:TRS402
|
4.6
|
119.9
|
0.9
|
O
|
B:HOH510
|
4.8
|
52.1
|
1.0
|
O
|
B:ASP171
|
4.9
|
42.4
|
1.0
|
CA
|
B:ASP171
|
4.9
|
46.0
|
1.0
|
|
Zinc binding site 3 out
of 4 in 8goa
Go back to
Zinc Binding Sites List in 8goa
Zinc binding site 3 out
of 4 in the Crystal Structure of Glycerol Dehydrogenase in the Absence of Nad+
![](/pictures/ZN/pdb/go/8goa-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/go/8goa-ZN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of Glycerol Dehydrogenase in the Absence of Nad+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn401
b:53.2
occ:1.00
|
OD1
|
C:ASP171
|
2.1
|
51.0
|
1.0
|
NE2
|
C:HIS254
|
2.2
|
49.5
|
1.0
|
NE2
|
C:HIS271
|
2.3
|
64.1
|
1.0
|
C2
|
C:TRS402
|
2.5
|
59.5
|
0.8
|
O2
|
C:TRS402
|
2.6
|
52.9
|
0.8
|
CG
|
C:ASP171
|
2.8
|
52.2
|
1.0
|
OD2
|
C:ASP171
|
2.8
|
48.8
|
1.0
|
CD2
|
C:HIS271
|
3.0
|
60.9
|
1.0
|
CE1
|
C:HIS254
|
3.1
|
51.7
|
1.0
|
CD2
|
C:HIS254
|
3.2
|
54.0
|
1.0
|
O1
|
C:TRS402
|
3.2
|
73.8
|
0.8
|
OD1
|
C:ASP121
|
3.4
|
55.8
|
1.0
|
CE1
|
C:HIS271
|
3.4
|
70.8
|
1.0
|
OD2
|
C:ASP121
|
3.7
|
63.4
|
1.0
|
C
|
C:TRS402
|
3.8
|
74.7
|
0.8
|
CG
|
C:ASP121
|
4.0
|
57.5
|
1.0
|
C1
|
C:TRS402
|
4.0
|
73.7
|
0.8
|
ND1
|
C:HIS254
|
4.2
|
51.8
|
1.0
|
CG
|
C:HIS271
|
4.2
|
63.9
|
1.0
|
CG2
|
C:VAL275
|
4.2
|
53.4
|
1.0
|
CG
|
C:HIS254
|
4.3
|
49.8
|
1.0
|
CB
|
C:ASP171
|
4.3
|
50.5
|
1.0
|
ND1
|
C:HIS271
|
4.4
|
70.1
|
1.0
|
C3
|
C:TRS402
|
4.6
|
83.2
|
0.8
|
N
|
C:TRS402
|
4.8
|
69.2
|
0.8
|
CA
|
C:ASP171
|
4.9
|
48.4
|
1.0
|
O
|
C:HOH542
|
5.0
|
52.7
|
1.0
|
|
Zinc binding site 4 out
of 4 in 8goa
Go back to
Zinc Binding Sites List in 8goa
Zinc binding site 4 out
of 4 in the Crystal Structure of Glycerol Dehydrogenase in the Absence of Nad+
![](/pictures/ZN/pdb/go/8goa-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/go/8goa-ZN-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of Glycerol Dehydrogenase in the Absence of Nad+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn401
b:57.5
occ:1.00
|
O2
|
D:TRS402
|
2.1
|
130.2
|
0.9
|
OD1
|
D:ASP171
|
2.2
|
59.5
|
1.0
|
NE2
|
D:HIS254
|
2.2
|
66.7
|
1.0
|
NE2
|
D:HIS271
|
2.3
|
63.0
|
1.0
|
O3
|
D:TRS402
|
2.5
|
86.7
|
0.9
|
OD2
|
D:ASP171
|
2.6
|
60.9
|
1.0
|
CG
|
D:ASP171
|
2.7
|
60.5
|
1.0
|
CD2
|
D:HIS254
|
3.1
|
67.1
|
1.0
|
CE1
|
D:HIS271
|
3.2
|
70.5
|
1.0
|
C3
|
D:TRS402
|
3.2
|
91.1
|
0.9
|
CD2
|
D:HIS271
|
3.2
|
62.0
|
1.0
|
CE1
|
D:HIS254
|
3.3
|
64.0
|
1.0
|
C2
|
D:TRS402
|
3.3
|
94.5
|
0.9
|
O1
|
D:TRS402
|
3.4
|
90.3
|
0.9
|
OD1
|
D:ASP121
|
3.6
|
68.1
|
1.0
|
C
|
D:TRS402
|
3.7
|
91.4
|
0.9
|
C1
|
D:TRS402
|
3.8
|
94.7
|
0.9
|
OD2
|
D:ASP121
|
4.0
|
70.9
|
1.0
|
CB
|
D:ASP171
|
4.2
|
57.4
|
1.0
|
CG
|
D:ASP121
|
4.2
|
69.8
|
1.0
|
CG
|
D:HIS254
|
4.3
|
62.2
|
1.0
|
ND1
|
D:HIS271
|
4.3
|
70.4
|
1.0
|
CG2
|
D:VAL275
|
4.3
|
61.6
|
1.0
|
CG
|
D:HIS271
|
4.3
|
64.3
|
1.0
|
ND1
|
D:HIS254
|
4.4
|
62.6
|
1.0
|
CA
|
D:ASP171
|
4.9
|
55.1
|
1.0
|
CG1
|
D:VAL275
|
4.9
|
60.7
|
1.0
|
|
Reference:
T.Park,
H.N.Hoang,
J.Y.Kang,
J.Park,
S.A.Mun,
M.Jin,
J.Yang,
C.H.Jung,
S.H.Eom.
Structural and Functional Insights Into the Flexible Beta-Hairpin of Glycerol Dehydrogenase. Febs J. 2023.
ISSN: ISSN 1742-464X
PubMed: 37165682
DOI: 10.1111/FEBS.16813
Page generated: Fri Jul 28 06:59:49 2023
|