Zinc in PDB 4r7p: Human Udp-Glucose Pyrophosphorylase Isoform 1 in Complex with Udp- Glucose
Enzymatic activity of Human Udp-Glucose Pyrophosphorylase Isoform 1 in Complex with Udp- Glucose
All present enzymatic activity of Human Udp-Glucose Pyrophosphorylase Isoform 1 in Complex with Udp- Glucose:
2.7.7.9;
Protein crystallography data
The structure of Human Udp-Glucose Pyrophosphorylase Isoform 1 in Complex with Udp- Glucose, PDB code: 4r7p
was solved by
J.Fuehring,
J.T.Cramer,
J.Schneider,
P.Baruch,
R.Gerardy-Schahn,
R.Fedorov,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.62 /
3.35
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
138.970,
138.970,
311.620,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
19.9 /
24.7
|
Zinc Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
11;
Binding sites:
The binding sites of Zinc atom in the Human Udp-Glucose Pyrophosphorylase Isoform 1 in Complex with Udp- Glucose
(pdb code 4r7p). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 11 binding sites of Zinc where determined in the
Human Udp-Glucose Pyrophosphorylase Isoform 1 in Complex with Udp- Glucose, PDB code: 4r7p:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Zinc binding site 1 out
of 11 in 4r7p
Go back to
Zinc Binding Sites List in 4r7p
Zinc binding site 1 out
of 11 in the Human Udp-Glucose Pyrophosphorylase Isoform 1 in Complex with Udp- Glucose
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Human Udp-Glucose Pyrophosphorylase Isoform 1 in Complex with Udp- Glucose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn614
b:0.0
occ:1.00
|
O
|
A:HOH730
|
2.2
|
0.5
|
1.0
|
OE2
|
A:GLU47
|
2.2
|
0.3
|
1.0
|
CD
|
A:GLU47
|
2.3
|
0.4
|
1.0
|
OE1
|
A:GLU47
|
2.8
|
1.0
|
1.0
|
CG
|
A:GLU47
|
3.0
|
0.7
|
1.0
|
CD2
|
A:HIS46
|
4.0
|
0.2
|
1.0
|
CB
|
A:GLU47
|
4.4
|
0.3
|
1.0
|
NE2
|
A:HIS46
|
4.7
|
0.3
|
1.0
|
CG
|
A:HIS46
|
4.8
|
0.0
|
1.0
|
|
Zinc binding site 2 out
of 11 in 4r7p
Go back to
Zinc Binding Sites List in 4r7p
Zinc binding site 2 out
of 11 in the Human Udp-Glucose Pyrophosphorylase Isoform 1 in Complex with Udp- Glucose
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Human Udp-Glucose Pyrophosphorylase Isoform 1 in Complex with Udp- Glucose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn615
b:0.4
occ:1.00
|
NE2
|
A:GLN440
|
2.1
|
0.4
|
1.0
|
O
|
A:HOH727
|
2.2
|
0.4
|
1.0
|
SG
|
A:CYS123
|
2.8
|
0.9
|
1.0
|
CD
|
A:GLN440
|
3.4
|
0.7
|
1.0
|
CB
|
A:CYS123
|
3.9
|
0.9
|
1.0
|
OE1
|
A:GLN440
|
4.1
|
0.7
|
1.0
|
CG
|
A:GLN440
|
4.4
|
0.6
|
1.0
|
CE
|
A:LYS124
|
4.6
|
0.9
|
1.0
|
CA
|
A:CYS123
|
4.6
|
0.5
|
1.0
|
CB
|
A:VAL439
|
5.0
|
72.5
|
1.0
|
|
Zinc binding site 3 out
of 11 in 4r7p
Go back to
Zinc Binding Sites List in 4r7p
Zinc binding site 3 out
of 11 in the Human Udp-Glucose Pyrophosphorylase Isoform 1 in Complex with Udp- Glucose
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Human Udp-Glucose Pyrophosphorylase Isoform 1 in Complex with Udp- Glucose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn608
b:0.1
occ:1.00
|
OD2
|
B:ASP170
|
2.0
|
0.0
|
1.0
|
OD1
|
B:ASP170
|
2.3
|
0.8
|
1.0
|
CG
|
B:ASP170
|
2.3
|
0.3
|
1.0
|
CB
|
B:ASP170
|
3.7
|
0.3
|
1.0
|
O
|
B:ASN166
|
4.4
|
0.2
|
1.0
|
CA
|
B:GLY125
|
4.8
|
0.7
|
1.0
|
CA
|
B:ASP170
|
4.8
|
0.3
|
1.0
|
CD
|
B:PRO126
|
4.9
|
0.5
|
1.0
|
|
Zinc binding site 4 out
of 11 in 4r7p
Go back to
Zinc Binding Sites List in 4r7p
Zinc binding site 4 out
of 11 in the Human Udp-Glucose Pyrophosphorylase Isoform 1 in Complex with Udp- Glucose
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Human Udp-Glucose Pyrophosphorylase Isoform 1 in Complex with Udp- Glucose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn609
b:1.0
occ:1.00
|
NE2
|
B:HIS180
|
2.0
|
0.2
|
1.0
|
OD1
|
B:ASN179
|
2.0
|
0.1
|
1.0
|
CD2
|
B:HIS180
|
2.6
|
0.3
|
1.0
|
CE1
|
B:HIS180
|
3.0
|
0.6
|
1.0
|
CG
|
B:ASN179
|
3.2
|
0.5
|
1.0
|
CG
|
B:HIS180
|
3.7
|
0.2
|
1.0
|
ND1
|
B:HIS180
|
3.8
|
0.1
|
1.0
|
ND2
|
B:ASN179
|
4.1
|
0.7
|
1.0
|
CB
|
B:ASN179
|
4.2
|
0.5
|
1.0
|
N
|
B:HIS180
|
4.8
|
0.7
|
1.0
|
C
|
B:ASN179
|
4.9
|
1.0
|
1.0
|
CB
|
B:HIS180
|
5.0
|
0.0
|
1.0
|
|
Zinc binding site 5 out
of 11 in 4r7p
Go back to
Zinc Binding Sites List in 4r7p
Zinc binding site 5 out
of 11 in the Human Udp-Glucose Pyrophosphorylase Isoform 1 in Complex with Udp- Glucose
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Human Udp-Glucose Pyrophosphorylase Isoform 1 in Complex with Udp- Glucose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn610
b:0.5
occ:0.51
|
ND1
|
B:HIS457
|
2.0
|
0.2
|
1.0
|
CE1
|
B:HIS457
|
2.8
|
0.4
|
1.0
|
CG
|
B:HIS457
|
3.1
|
0.3
|
1.0
|
CB
|
B:HIS457
|
3.6
|
83.6
|
1.0
|
NE2
|
B:HIS457
|
4.0
|
0.2
|
1.0
|
CD2
|
B:HIS457
|
4.2
|
0.6
|
1.0
|
|
Zinc binding site 6 out
of 11 in 4r7p
Go back to
Zinc Binding Sites List in 4r7p
Zinc binding site 6 out
of 11 in the Human Udp-Glucose Pyrophosphorylase Isoform 1 in Complex with Udp- Glucose
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Human Udp-Glucose Pyrophosphorylase Isoform 1 in Complex with Udp- Glucose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn606
b:0.7
occ:1.00
|
CE1
|
C:HIS223
|
2.8
|
0.0
|
1.0
|
ND1
|
C:HIS223
|
3.4
|
0.4
|
1.0
|
O
|
C:GLY222
|
3.6
|
0.8
|
1.0
|
NE2
|
C:HIS223
|
3.6
|
0.9
|
1.0
|
O
|
C:GLY115
|
4.3
|
0.8
|
1.0
|
CG
|
C:HIS223
|
4.4
|
0.4
|
1.0
|
CD2
|
C:HIS223
|
4.5
|
0.9
|
1.0
|
C
|
C:GLY115
|
4.7
|
0.8
|
1.0
|
C
|
C:GLY222
|
4.7
|
0.3
|
1.0
|
|
Zinc binding site 7 out
of 11 in 4r7p
Go back to
Zinc Binding Sites List in 4r7p
Zinc binding site 7 out
of 11 in the Human Udp-Glucose Pyrophosphorylase Isoform 1 in Complex with Udp- Glucose
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Human Udp-Glucose Pyrophosphorylase Isoform 1 in Complex with Udp- Glucose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn607
b:0.5
occ:1.00
|
OE1
|
C:GLU147
|
1.9
|
0.6
|
1.0
|
SG
|
C:CYS181
|
2.0
|
0.2
|
1.0
|
OE2
|
C:GLU147
|
2.1
|
0.4
|
1.0
|
CD
|
C:GLU147
|
2.3
|
0.1
|
1.0
|
CB
|
C:CYS181
|
2.3
|
0.7
|
1.0
|
CA
|
C:CYS181
|
3.1
|
0.4
|
1.0
|
CG
|
C:GLU147
|
3.7
|
0.3
|
1.0
|
C
|
C:CYS181
|
4.2
|
0.7
|
1.0
|
N
|
C:CYS181
|
4.2
|
0.8
|
1.0
|
N
|
C:ARG182
|
4.4
|
0.5
|
1.0
|
CB
|
C:GLU147
|
4.5
|
0.3
|
1.0
|
CG1
|
C:VAL143
|
4.9
|
86.7
|
1.0
|
|
Zinc binding site 8 out
of 11 in 4r7p
Go back to
Zinc Binding Sites List in 4r7p
Zinc binding site 8 out
of 11 in the Human Udp-Glucose Pyrophosphorylase Isoform 1 in Complex with Udp- Glucose
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Human Udp-Glucose Pyrophosphorylase Isoform 1 in Complex with Udp- Glucose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn608
b:0.8
occ:1.00
|
OD2
|
C:ASP441
|
2.0
|
84.2
|
1.0
|
OD1
|
C:ASP441
|
2.0
|
0.6
|
1.0
|
O
|
C:HOH722
|
2.1
|
0.0
|
1.0
|
CG
|
C:ASP441
|
2.2
|
95.7
|
1.0
|
CB
|
C:ASP441
|
3.6
|
83.7
|
1.0
|
CD
|
C:LYS438
|
3.8
|
0.9
|
1.0
|
NH2
|
C:ARG444
|
4.0
|
0.0
|
1.0
|
CA
|
C:ASP441
|
4.4
|
78.6
|
1.0
|
N
|
C:ASP441
|
4.6
|
85.7
|
1.0
|
CB
|
C:LYS438
|
4.7
|
0.1
|
1.0
|
CE
|
C:LYS438
|
4.8
|
0.3
|
1.0
|
CG
|
C:LYS438
|
4.8
|
0.4
|
1.0
|
|
Zinc binding site 9 out
of 11 in 4r7p
Go back to
Zinc Binding Sites List in 4r7p
Zinc binding site 9 out
of 11 in the Human Udp-Glucose Pyrophosphorylase Isoform 1 in Complex with Udp- Glucose
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 9 of Human Udp-Glucose Pyrophosphorylase Isoform 1 in Complex with Udp- Glucose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn609
b:0.2
occ:1.00
|
NE2
|
C:GLN87
|
1.7
|
0.3
|
1.0
|
NE2
|
C:HIS266
|
1.8
|
0.6
|
1.0
|
CE1
|
C:HIS266
|
2.3
|
0.8
|
1.0
|
CD
|
C:GLN87
|
2.4
|
0.0
|
1.0
|
CD2
|
C:HIS266
|
2.4
|
0.9
|
1.0
|
OE1
|
C:GLN87
|
2.5
|
0.1
|
1.0
|
ND1
|
C:HIS266
|
3.0
|
0.3
|
1.0
|
CG
|
C:HIS266
|
3.0
|
0.1
|
1.0
|
CG1
|
C:ILE92
|
3.7
|
0.8
|
1.0
|
CG
|
C:GLN87
|
3.7
|
0.4
|
1.0
|
CD1
|
C:ILE92
|
3.9
|
0.9
|
1.0
|
CB
|
C:GLN87
|
4.1
|
0.8
|
1.0
|
CB
|
C:HIS266
|
4.3
|
0.1
|
1.0
|
CD2
|
C:LEU383
|
4.5
|
0.8
|
1.0
|
|
Zinc binding site 10 out
of 11 in 4r7p
Go back to
Zinc Binding Sites List in 4r7p
Zinc binding site 10 out
of 11 in the Human Udp-Glucose Pyrophosphorylase Isoform 1 in Complex with Udp- Glucose
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 10 of Human Udp-Glucose Pyrophosphorylase Isoform 1 in Complex with Udp- Glucose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn607
b:0.5
occ:1.00
|
O
|
D:HOH721
|
2.4
|
0.9
|
1.0
|
OD2
|
D:ASP507
|
4.4
|
0.5
|
1.0
|
OE2
|
D:GLU447
|
4.4
|
0.2
|
1.0
|
OE1
|
D:GLU447
|
4.5
|
0.1
|
1.0
|
CD
|
D:GLU447
|
4.5
|
0.7
|
1.0
|
OD1
|
D:ASP507
|
4.7
|
0.6
|
1.0
|
CG
|
D:ASP507
|
4.9
|
0.9
|
1.0
|
|
Reference:
J.I.Fuhring,
J.T.Cramer,
J.Schneider,
P.Baruch,
R.Gerardy-Schahn,
R.Fedorov.
A Quaternary Mechanism Enables the Complex Biological Functions of Octameric Human Udp-Glucose Pyrophosphorylase, A Key Enzyme in Cell Metabolism. Sci Rep V. 5 9618.
ISSN: ESSN 2045-2322
PubMed: 25860585
DOI: 10.1038/SREP09618
Page generated: Sun Oct 27 06:54:37 2024
|