Zinc in PDB 2om0: Structure of Human Insulin in Presence of Urea at pH 6.5
Protein crystallography data
The structure of Structure of Human Insulin in Presence of Urea at pH 6.5, PDB code: 2om0
was solved by
M.Norrman,
G.Schluckebier,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
28.31 /
2.05
|
Space group
|
C 2 2 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
58.936,
219.318,
223.674,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.4 /
22.7
|
Other elements in 2om0:
The structure of Structure of Human Insulin in Presence of Urea at pH 6.5 also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Structure of Human Insulin in Presence of Urea at pH 6.5
(pdb code 2om0). 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 Human Insulin in Presence of Urea at pH 6.5, PDB code: 2om0:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 2om0
Go back to
Zinc Binding Sites List in 2om0
Zinc binding site 1 out
of 6 in the Structure of Human Insulin in Presence of Urea at pH 6.5
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Structure of Human Insulin in Presence of Urea at pH 6.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn801
b:22.4
occ:1.00
|
NE2
|
F:HIS10
|
1.9
|
25.5
|
1.0
|
NE2
|
B:HIS10
|
2.0
|
26.4
|
1.0
|
NE2
|
J:HIS10
|
2.1
|
20.1
|
1.0
|
CL
|
B:CL903
|
2.3
|
23.8
|
1.0
|
CE1
|
F:HIS10
|
2.7
|
26.1
|
1.0
|
CE1
|
B:HIS10
|
2.9
|
25.5
|
1.0
|
CD2
|
B:HIS10
|
3.0
|
18.1
|
1.0
|
CD2
|
J:HIS10
|
3.0
|
17.4
|
1.0
|
CE1
|
J:HIS10
|
3.0
|
21.2
|
1.0
|
CD2
|
F:HIS10
|
3.1
|
26.1
|
1.0
|
ND1
|
F:HIS10
|
3.9
|
25.2
|
1.0
|
ND1
|
B:HIS10
|
4.1
|
22.6
|
1.0
|
CG
|
F:HIS10
|
4.1
|
25.4
|
1.0
|
CG
|
B:HIS10
|
4.1
|
22.7
|
1.0
|
ND1
|
J:HIS10
|
4.1
|
20.0
|
1.0
|
CG
|
J:HIS10
|
4.2
|
20.1
|
1.0
|
O
|
F:LEU6
|
4.7
|
27.5
|
1.0
|
O
|
J:LEU6
|
4.7
|
23.4
|
1.0
|
CB
|
F:LEU6
|
4.8
|
26.2
|
1.0
|
CB
|
J:LEU6
|
4.8
|
25.2
|
1.0
|
O
|
B:LEU6
|
4.8
|
21.1
|
1.0
|
CB
|
B:LEU6
|
4.9
|
20.8
|
1.0
|
O
|
F:HOH42
|
4.9
|
37.3
|
1.0
|
O
|
B:HOH912
|
5.0
|
38.8
|
1.0
|
|
Zinc binding site 2 out
of 6 in 2om0
Go back to
Zinc Binding Sites List in 2om0
Zinc binding site 2 out
of 6 in the Structure of Human Insulin in Presence of Urea at pH 6.5
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Structure of Human Insulin in Presence of Urea at pH 6.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn802
b:18.0
occ:1.00
|
NE2
|
D:HIS10
|
1.9
|
16.4
|
1.0
|
NE2
|
L:HIS10
|
1.9
|
22.8
|
1.0
|
NE2
|
H:HIS10
|
2.1
|
21.0
|
1.0
|
CL
|
D:CL904
|
2.3
|
18.4
|
1.0
|
CE1
|
D:HIS10
|
2.9
|
19.5
|
1.0
|
CD2
|
L:HIS10
|
2.9
|
22.6
|
1.0
|
CE1
|
L:HIS10
|
3.0
|
26.5
|
1.0
|
CE1
|
H:HIS10
|
3.0
|
22.7
|
1.0
|
CD2
|
D:HIS10
|
3.0
|
15.6
|
1.0
|
CD2
|
H:HIS10
|
3.1
|
22.0
|
1.0
|
ND1
|
D:HIS10
|
4.0
|
19.4
|
1.0
|
ND1
|
L:HIS10
|
4.1
|
25.1
|
1.0
|
CG
|
L:HIS10
|
4.1
|
23.8
|
1.0
|
CG
|
D:HIS10
|
4.1
|
19.3
|
1.0
|
ND1
|
H:HIS10
|
4.1
|
23.0
|
1.0
|
CG
|
H:HIS10
|
4.2
|
24.1
|
1.0
|
O
|
D:LEU6
|
4.7
|
20.7
|
1.0
|
O
|
L:LEU6
|
4.7
|
22.9
|
1.0
|
O
|
H:LEU6
|
4.7
|
23.1
|
1.0
|
O
|
D:HOH1023
|
4.8
|
35.0
|
1.0
|
CB
|
H:LEU6
|
4.8
|
22.3
|
1.0
|
CB
|
D:LEU6
|
4.9
|
20.2
|
1.0
|
CB
|
L:LEU6
|
4.9
|
24.6
|
1.0
|
|
Zinc binding site 3 out
of 6 in 2om0
Go back to
Zinc Binding Sites List in 2om0
Zinc binding site 3 out
of 6 in the Structure of Human Insulin in Presence of Urea at pH 6.5
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Structure of Human Insulin in Presence of Urea at pH 6.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
R:Zn803
b:20.5
occ:1.00
|
NE2
|
V:HIS10
|
1.9
|
19.9
|
1.0
|
NE2
|
T:HIS10
|
2.0
|
19.0
|
1.0
|
NE2
|
R:HIS10
|
2.1
|
28.1
|
1.0
|
CL
|
R:CL905
|
2.1
|
23.8
|
1.0
|
CE1
|
V:HIS10
|
2.9
|
25.6
|
1.0
|
CE1
|
T:HIS10
|
2.9
|
25.1
|
1.0
|
CD2
|
V:HIS10
|
3.0
|
18.1
|
1.0
|
CD2
|
R:HIS10
|
3.0
|
24.5
|
1.0
|
CE1
|
R:HIS10
|
3.1
|
27.2
|
1.0
|
CD2
|
T:HIS10
|
3.1
|
19.0
|
1.0
|
ND1
|
V:HIS10
|
4.0
|
23.6
|
1.0
|
CG
|
V:HIS10
|
4.1
|
22.0
|
1.0
|
ND1
|
T:HIS10
|
4.1
|
22.2
|
1.0
|
ND1
|
R:HIS10
|
4.2
|
26.6
|
1.0
|
CG
|
R:HIS10
|
4.2
|
27.4
|
1.0
|
CG
|
T:HIS10
|
4.2
|
23.6
|
1.0
|
O
|
V:LEU6
|
4.7
|
24.8
|
1.0
|
O
|
R:LEU6
|
4.8
|
24.1
|
1.0
|
CG
|
R:LEU6
|
4.8
|
27.1
|
1.0
|
CB
|
R:LEU6
|
4.8
|
25.9
|
1.0
|
O
|
T:LEU6
|
4.8
|
24.6
|
1.0
|
CB
|
T:LEU6
|
4.8
|
24.1
|
1.0
|
CB
|
V:LEU6
|
4.9
|
24.7
|
1.0
|
|
Zinc binding site 4 out
of 6 in 2om0
Go back to
Zinc Binding Sites List in 2om0
Zinc binding site 4 out
of 6 in the Structure of Human Insulin in Presence of Urea at pH 6.5
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Structure of Human Insulin in Presence of Urea at pH 6.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Y:Zn804
b:21.6
occ:1.00
|
NE2
|
2:HIS10
|
2.0
|
24.4
|
1.0
|
NE2
|
Y:HIS10
|
2.0
|
27.6
|
1.0
|
NE2
|
4:HIS10
|
2.0
|
27.0
|
1.0
|
CL
|
Y:CL906
|
2.2
|
23.4
|
1.0
|
CE1
|
Y:HIS10
|
2.9
|
28.1
|
1.0
|
CE1
|
2:HIS10
|
2.9
|
25.8
|
1.0
|
CD2
|
4:HIS10
|
3.0
|
23.0
|
1.0
|
CE1
|
4:HIS10
|
3.0
|
29.1
|
1.0
|
CD2
|
2:HIS10
|
3.0
|
21.1
|
1.0
|
CD2
|
Y:HIS10
|
3.1
|
21.9
|
1.0
|
ND1
|
Y:HIS10
|
4.0
|
26.5
|
1.0
|
ND1
|
2:HIS10
|
4.0
|
25.0
|
1.0
|
CG
|
2:HIS10
|
4.1
|
23.7
|
1.0
|
ND1
|
4:HIS10
|
4.1
|
24.9
|
1.0
|
CG
|
Y:HIS10
|
4.2
|
25.5
|
1.0
|
CG
|
4:HIS10
|
4.2
|
25.5
|
1.0
|
O
|
2:LEU6
|
4.6
|
24.1
|
1.0
|
O
|
Y:LEU6
|
4.7
|
26.9
|
1.0
|
O
|
4:LEU6
|
4.7
|
26.3
|
1.0
|
CB
|
2:LEU6
|
4.8
|
23.9
|
1.0
|
CB
|
4:LEU6
|
4.9
|
26.7
|
1.0
|
CG
|
Y:LEU6
|
5.0
|
25.7
|
1.0
|
CB
|
Y:LEU6
|
5.0
|
24.2
|
1.0
|
O
|
Y:HOH919
|
5.0
|
38.1
|
1.0
|
O
|
2:HOH38
|
5.0
|
35.3
|
1.0
|
|
Zinc binding site 5 out
of 6 in 2om0
Go back to
Zinc Binding Sites List in 2om0
Zinc binding site 5 out
of 6 in the Structure of Human Insulin in Presence of Urea at pH 6.5
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Structure of Human Insulin in Presence of Urea at pH 6.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
b:Zn806
b:23.2
occ:1.00
|
NE2
|
d:HIS10
|
2.0
|
24.9
|
1.0
|
NE2
|
b:HIS10
|
2.0
|
26.2
|
1.0
|
CL
|
b:CL902
|
2.0
|
26.4
|
1.0
|
NE2
|
f:HIS10
|
2.1
|
28.2
|
1.0
|
CE1
|
b:HIS10
|
2.9
|
28.6
|
1.0
|
CD2
|
d:HIS10
|
2.9
|
22.4
|
1.0
|
CE1
|
d:HIS10
|
3.0
|
24.6
|
1.0
|
CD2
|
f:HIS10
|
3.1
|
23.0
|
1.0
|
CE1
|
f:HIS10
|
3.1
|
28.4
|
1.0
|
CD2
|
b:HIS10
|
3.1
|
22.1
|
1.0
|
ND1
|
b:HIS10
|
4.0
|
28.7
|
1.0
|
ND1
|
d:HIS10
|
4.1
|
23.7
|
1.0
|
CG
|
d:HIS10
|
4.1
|
25.7
|
1.0
|
CG
|
b:HIS10
|
4.2
|
28.4
|
1.0
|
ND1
|
f:HIS10
|
4.2
|
26.7
|
1.0
|
CG
|
f:HIS10
|
4.2
|
25.1
|
1.0
|
O
|
f:LEU6
|
4.7
|
27.8
|
1.0
|
O
|
b:LEU6
|
4.7
|
29.3
|
1.0
|
O
|
d:LEU6
|
4.7
|
27.9
|
1.0
|
CB
|
d:LEU6
|
4.8
|
28.4
|
1.0
|
CB
|
f:LEU6
|
4.8
|
27.5
|
1.0
|
CB
|
b:LEU6
|
4.9
|
29.9
|
1.0
|
CG
|
b:LEU6
|
5.0
|
31.6
|
1.0
|
|
Zinc binding site 6 out
of 6 in 2om0
Go back to
Zinc Binding Sites List in 2om0
Zinc binding site 6 out
of 6 in the Structure of Human Insulin in Presence of Urea at pH 6.5
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Structure of Human Insulin in Presence of Urea at pH 6.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
h:Zn805
b:26.2
occ:1.00
|
NE2
|
l:HIS10
|
2.0
|
35.7
|
1.0
|
NE2
|
h:HIS10
|
2.0
|
24.5
|
1.0
|
NE2
|
j:HIS10
|
2.0
|
33.2
|
1.0
|
CL
|
h:CL901
|
2.1
|
26.8
|
1.0
|
CE1
|
l:HIS10
|
2.9
|
35.2
|
1.0
|
CE1
|
j:HIS10
|
3.0
|
30.7
|
1.0
|
CD2
|
h:HIS10
|
3.0
|
24.4
|
1.0
|
CE1
|
h:HIS10
|
3.0
|
27.4
|
1.0
|
CD2
|
l:HIS10
|
3.0
|
34.0
|
1.0
|
CD2
|
j:HIS10
|
3.1
|
29.2
|
1.0
|
ND1
|
l:HIS10
|
4.1
|
34.8
|
1.0
|
ND1
|
j:HIS10
|
4.1
|
30.5
|
1.0
|
ND1
|
h:HIS10
|
4.1
|
24.4
|
1.0
|
CG
|
h:HIS10
|
4.1
|
26.9
|
1.0
|
CG
|
l:HIS10
|
4.1
|
35.4
|
1.0
|
CG
|
j:HIS10
|
4.2
|
32.5
|
1.0
|
O
|
j:LEU6
|
4.7
|
33.4
|
1.0
|
O
|
l:LEU6
|
4.7
|
37.8
|
1.0
|
O
|
h:LEU6
|
4.7
|
28.2
|
1.0
|
CB
|
l:LEU6
|
4.8
|
36.3
|
1.0
|
CB
|
h:LEU6
|
4.8
|
27.2
|
1.0
|
CB
|
j:LEU6
|
4.9
|
33.9
|
1.0
|
O
|
h:HOH922
|
4.9
|
44.8
|
1.0
|
|
Reference:
M.Norrman,
G.Schluckebier.
Crystallographic Characterization of Two Novel Crystal Forms of Human Insulin Induced By Chaotropic Agents and A Shift in pH. Bmc Struct.Biol. V. 7 83 2007.
ISSN: ESSN 1472-6807
PubMed: 18093308
DOI: 10.1186/1472-6807-7-83
Page generated: Thu Oct 17 02:40:25 2024
|