Atomistry » Zinc » PDB 4r5a-4rkg » 4r7p
Atomistry »
  Zinc »
    PDB 4r5a-4rkg »
      4r7p »

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: Wed Dec 16 05:45:06 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy