Zinc in PDB 5fb3: Structure of Glycerophosphate Dehydrogenase in Complex with Nadph
Enzymatic activity of Structure of Glycerophosphate Dehydrogenase in Complex with Nadph
All present enzymatic activity of Structure of Glycerophosphate Dehydrogenase in Complex with Nadph:
1.1.1.261;
Protein crystallography data
The structure of Structure of Glycerophosphate Dehydrogenase in Complex with Nadph, PDB code: 5fb3
was solved by
H.Sakuraba,
J.Hayashi,
K.Yamamoto,
K.Yoneda,
T.Ohshima,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
2.45
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
102.182,
123.335,
166.724,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.7 /
26
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Structure of Glycerophosphate Dehydrogenase in Complex with Nadph
(pdb code 5fb3). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
Structure of Glycerophosphate Dehydrogenase in Complex with Nadph, PDB code: 5fb3:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 5fb3
Go back to
Zinc Binding Sites List in 5fb3
Zinc binding site 1 out
of 6 in the Structure of Glycerophosphate Dehydrogenase in Complex with Nadph
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Structure of Glycerophosphate Dehydrogenase in Complex with Nadph within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2001
b:82.2
occ:1.00
|
OD2
|
A:ASP157
|
2.4
|
76.0
|
1.0
|
NE2
|
A:HIS256
|
2.5
|
60.4
|
1.0
|
NE2
|
A:HIS238
|
2.6
|
60.1
|
1.0
|
CD2
|
A:HIS238
|
3.0
|
57.2
|
1.0
|
CG
|
A:ASP157
|
3.0
|
66.0
|
1.0
|
OD1
|
A:ASP157
|
3.1
|
63.4
|
1.0
|
CD2
|
A:HIS256
|
3.2
|
57.9
|
1.0
|
CE1
|
A:HIS256
|
3.6
|
61.3
|
1.0
|
CE1
|
A:HIS238
|
3.8
|
63.2
|
1.0
|
OD2
|
A:ASP108
|
4.0
|
78.4
|
1.0
|
OD1
|
A:ASP108
|
4.1
|
76.5
|
1.0
|
CG2
|
A:VAL260
|
4.2
|
54.6
|
1.0
|
CG
|
A:ASP108
|
4.2
|
72.0
|
1.0
|
CG
|
A:HIS238
|
4.3
|
56.3
|
1.0
|
CB
|
A:ASP157
|
4.4
|
62.2
|
1.0
|
CG
|
A:HIS256
|
4.5
|
56.8
|
1.0
|
ND1
|
A:HIS256
|
4.6
|
58.8
|
1.0
|
ND1
|
A:HIS238
|
4.7
|
62.2
|
1.0
|
NZ
|
A:LYS161
|
4.8
|
61.5
|
1.0
|
N
|
A:ASP108
|
4.9
|
69.2
|
1.0
|
CA
|
A:ASP157
|
4.9
|
58.7
|
1.0
|
|
Zinc binding site 2 out
of 6 in 5fb3
Go back to
Zinc Binding Sites List in 5fb3
Zinc binding site 2 out
of 6 in the Structure of Glycerophosphate Dehydrogenase in Complex with Nadph
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Structure of Glycerophosphate Dehydrogenase in Complex with Nadph within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn2001
b:77.0
occ:1.00
|
OD1
|
B:ASP157
|
1.9
|
64.6
|
1.0
|
NE2
|
B:HIS238
|
2.4
|
58.4
|
1.0
|
NE2
|
B:HIS256
|
2.5
|
91.3
|
1.0
|
CG
|
B:ASP157
|
2.9
|
66.2
|
1.0
|
CE1
|
B:HIS238
|
3.0
|
54.6
|
1.0
|
CD2
|
B:HIS256
|
3.1
|
86.7
|
1.0
|
OD2
|
B:ASP157
|
3.3
|
75.6
|
1.0
|
CD2
|
B:HIS238
|
3.5
|
51.8
|
1.0
|
CE1
|
B:HIS256
|
3.6
|
91.1
|
1.0
|
OD2
|
B:ASP108
|
3.7
|
83.3
|
1.0
|
CB
|
B:ASP108
|
3.7
|
80.2
|
1.0
|
CB
|
B:ASP157
|
4.2
|
63.4
|
1.0
|
CG
|
B:ASP108
|
4.2
|
79.5
|
1.0
|
ND1
|
B:HIS238
|
4.2
|
54.4
|
1.0
|
CG2
|
B:VAL260
|
4.2
|
56.4
|
1.0
|
N
|
B:ASP108
|
4.3
|
77.4
|
1.0
|
CG
|
B:HIS256
|
4.4
|
86.2
|
1.0
|
CG
|
B:HIS238
|
4.5
|
51.8
|
1.0
|
ND1
|
B:HIS256
|
4.6
|
85.4
|
1.0
|
CA
|
B:ASP108
|
4.7
|
76.7
|
1.0
|
NZ
|
B:LYS161
|
4.9
|
59.3
|
1.0
|
CA
|
B:ASP157
|
5.0
|
62.6
|
1.0
|
|
Zinc binding site 3 out
of 6 in 5fb3
Go back to
Zinc Binding Sites List in 5fb3
Zinc binding site 3 out
of 6 in the Structure of Glycerophosphate Dehydrogenase in Complex with Nadph
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Structure of Glycerophosphate Dehydrogenase in Complex with Nadph within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn2001
b:96.2
occ:1.00
|
OD2
|
C:ASP157
|
1.9
|
68.7
|
1.0
|
NE2
|
C:HIS256
|
2.4
|
68.6
|
1.0
|
NE2
|
C:HIS238
|
2.4
|
59.7
|
1.0
|
CD2
|
C:HIS238
|
3.1
|
56.4
|
1.0
|
CG
|
C:ASP157
|
3.1
|
65.2
|
1.0
|
CD2
|
C:HIS256
|
3.2
|
67.7
|
1.0
|
CE1
|
C:HIS256
|
3.4
|
69.2
|
1.0
|
OD2
|
C:ASP108
|
3.5
|
76.4
|
1.0
|
CE1
|
C:HIS238
|
3.6
|
59.7
|
1.0
|
OD1
|
C:ASP157
|
3.6
|
71.0
|
1.0
|
OD1
|
C:ASP108
|
3.8
|
70.3
|
1.0
|
CG
|
C:ASP108
|
3.9
|
67.0
|
1.0
|
CB
|
C:ASP157
|
4.3
|
61.7
|
1.0
|
CG
|
C:HIS238
|
4.3
|
53.4
|
1.0
|
CG
|
C:HIS256
|
4.4
|
68.8
|
1.0
|
ND1
|
C:HIS256
|
4.4
|
69.0
|
1.0
|
ND1
|
C:HIS238
|
4.6
|
56.4
|
1.0
|
CG2
|
C:VAL260
|
4.6
|
57.2
|
1.0
|
N
|
C:ASP108
|
4.6
|
68.4
|
1.0
|
CA
|
C:HIS107
|
4.8
|
81.3
|
1.0
|
|
Zinc binding site 4 out
of 6 in 5fb3
Go back to
Zinc Binding Sites List in 5fb3
Zinc binding site 4 out
of 6 in the Structure of Glycerophosphate Dehydrogenase in Complex with Nadph
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Structure of Glycerophosphate Dehydrogenase in Complex with Nadph within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn1002
b:47.2
occ:1.00
|
OD1
|
D:ASP157
|
2.1
|
34.6
|
1.0
|
NE2
|
D:HIS256
|
2.2
|
38.7
|
1.0
|
NE2
|
D:HIS238
|
2.2
|
34.9
|
1.0
|
CD2
|
D:HIS256
|
2.9
|
35.8
|
1.0
|
CG
|
D:ASP157
|
3.1
|
35.9
|
1.0
|
CD2
|
D:HIS238
|
3.1
|
36.5
|
1.0
|
CE1
|
D:HIS238
|
3.2
|
36.2
|
1.0
|
OD2
|
D:ASP157
|
3.3
|
38.5
|
1.0
|
CE1
|
D:HIS256
|
3.4
|
37.4
|
1.0
|
OD1
|
D:ASP108
|
3.6
|
56.5
|
1.0
|
CG
|
D:HIS256
|
4.1
|
37.4
|
1.0
|
CG2
|
D:VAL260
|
4.2
|
36.9
|
1.0
|
ND1
|
D:HIS238
|
4.2
|
38.3
|
1.0
|
CG
|
D:HIS238
|
4.2
|
36.2
|
1.0
|
CG
|
D:ASP108
|
4.3
|
49.2
|
1.0
|
ND1
|
D:HIS256
|
4.3
|
37.3
|
1.0
|
NZ
|
D:LYS161
|
4.4
|
46.3
|
1.0
|
OD2
|
D:ASP108
|
4.4
|
48.7
|
1.0
|
CB
|
D:ASP157
|
4.4
|
35.4
|
1.0
|
C4N
|
D:NDP1001
|
4.6
|
47.8
|
1.0
|
CB
|
D:HIS107
|
4.6
|
46.3
|
1.0
|
O7N
|
D:NDP1001
|
4.6
|
56.8
|
1.0
|
O
|
D:CYS233
|
4.9
|
57.5
|
1.0
|
|
Zinc binding site 5 out
of 6 in 5fb3
Go back to
Zinc Binding Sites List in 5fb3
Zinc binding site 5 out
of 6 in the Structure of Glycerophosphate Dehydrogenase in Complex with Nadph
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Structure of Glycerophosphate Dehydrogenase in Complex with Nadph within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn1002
b:57.0
occ:1.00
|
OD1
|
E:ASP157
|
2.0
|
51.0
|
1.0
|
NE2
|
E:HIS238
|
2.2
|
37.1
|
1.0
|
NE2
|
E:HIS256
|
2.2
|
48.9
|
1.0
|
CG
|
E:ASP157
|
2.9
|
49.3
|
1.0
|
CD2
|
E:HIS238
|
2.9
|
37.8
|
1.0
|
CD2
|
E:HIS256
|
3.1
|
49.2
|
1.0
|
OD2
|
E:ASP157
|
3.1
|
48.9
|
1.0
|
CE1
|
E:HIS256
|
3.2
|
50.7
|
1.0
|
CE1
|
E:HIS238
|
3.3
|
39.2
|
1.0
|
OD2
|
E:ASP108
|
4.0
|
54.9
|
1.0
|
O7N
|
E:NDP1001
|
4.1
|
58.9
|
1.0
|
CG
|
E:HIS238
|
4.2
|
38.8
|
1.0
|
ND1
|
E:HIS256
|
4.3
|
50.0
|
1.0
|
CG
|
E:HIS256
|
4.3
|
49.8
|
1.0
|
OD1
|
E:ASP108
|
4.3
|
53.9
|
1.0
|
CB
|
E:ASP157
|
4.3
|
48.1
|
1.0
|
ND1
|
E:HIS238
|
4.3
|
37.9
|
1.0
|
CG2
|
E:VAL260
|
4.3
|
55.4
|
1.0
|
CG
|
E:ASP108
|
4.4
|
52.8
|
1.0
|
CB
|
E:HIS107
|
4.4
|
49.9
|
1.0
|
NZ
|
E:LYS161
|
4.6
|
52.2
|
1.0
|
C4N
|
E:NDP1001
|
4.6
|
54.7
|
1.0
|
N
|
E:ASP108
|
4.9
|
48.5
|
1.0
|
CA
|
E:ASP157
|
5.0
|
49.1
|
1.0
|
|
Zinc binding site 6 out
of 6 in 5fb3
Go back to
Zinc Binding Sites List in 5fb3
Zinc binding site 6 out
of 6 in the Structure of Glycerophosphate Dehydrogenase in Complex with Nadph
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Structure of Glycerophosphate Dehydrogenase in Complex with Nadph within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn403
b:40.9
occ:1.00
|
OD1
|
F:ASP157
|
2.0
|
36.1
|
1.0
|
NE2
|
F:HIS238
|
2.1
|
33.8
|
1.0
|
NE2
|
F:HIS256
|
2.2
|
28.0
|
1.0
|
O
|
F:HOH527
|
3.0
|
45.8
|
1.0
|
CG
|
F:ASP157
|
3.0
|
35.1
|
1.0
|
CE1
|
F:HIS238
|
3.0
|
35.6
|
1.0
|
CD2
|
F:HIS256
|
3.0
|
29.3
|
1.0
|
CD2
|
F:HIS238
|
3.1
|
35.4
|
1.0
|
OD2
|
F:ASP157
|
3.3
|
37.0
|
1.0
|
CE1
|
F:HIS256
|
3.3
|
28.6
|
1.0
|
OD1
|
F:ASP108
|
4.1
|
35.1
|
1.0
|
OD2
|
F:ASP108
|
4.1
|
41.8
|
1.0
|
CG2
|
F:VAL260
|
4.1
|
37.0
|
1.0
|
ND1
|
F:HIS238
|
4.1
|
36.9
|
1.0
|
CG
|
F:HIS238
|
4.2
|
34.7
|
1.0
|
CG
|
F:HIS256
|
4.3
|
30.7
|
1.0
|
CB
|
F:ASP157
|
4.3
|
35.6
|
1.0
|
ND1
|
F:HIS256
|
4.4
|
29.8
|
1.0
|
CG
|
F:ASP108
|
4.4
|
36.9
|
1.0
|
CB
|
F:HIS107
|
4.4
|
35.4
|
1.0
|
NZ
|
F:LYS161
|
4.6
|
43.3
|
1.0
|
C4N
|
F:NDP402
|
4.8
|
36.5
|
1.0
|
O7N
|
F:NDP402
|
4.8
|
37.8
|
1.0
|
CA
|
F:ASP157
|
5.0
|
37.3
|
1.0
|
|
Reference:
J.Hayashi,
K.Yamamoto,
K.Yoneda,
T.Ohshima,
H.Sakuraba.
Unique Coenzyme Binding Mode of Hyperthermophilic Archaeal Sn-Glycerol-1-Phosphate Dehydrogenase From Pyrobaculum Calidifontis Proteins V. 84 1786 2016.
ISSN: ESSN 1097-0134
PubMed: 27616573
DOI: 10.1002/PROT.25161
Page generated: Sun Oct 27 15:54:57 2024
|