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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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