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Zinc in PDB 5ubi: Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Prpp

Enzymatic activity of Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Prpp

All present enzymatic activity of Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Prpp:
2.4.2.17;

Protein crystallography data

The structure of Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Prpp, PDB code: 5ubi was solved by G.Mittelstaedt, W.Jiao, E.K.Livingstone, E.J.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.56 / 2.14
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.003, 79.690, 91.119, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 28.3

Other elements in 5ubi:

The structure of Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Prpp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Prpp (pdb code 5ubi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Prpp, PDB code: 5ubi:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5ubi

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Zinc binding site 1 out of 6 in the Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Prpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Prpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:26.9
occ:0.70
 ZN A:ZN302 1.9 34.6 0.3
ND1 A:HIS33 2.2 37.1 1.0
NE2 A:HIS35 2.4 32.1 1.0
CG A:HIS33 3.1 34.0 1.0
CE1 A:HIS33 3.2 37.3 1.0
CD2 A:HIS35 3.3 31.1 1.0
CB A:HIS33 3.4 27.9 1.0
CE1 A:HIS35 3.4 31.3 1.0
CD2 A:HIS33 4.2 36.5 1.0
NE2 A:HIS33 4.2 37.9 1.0
ND1 A:HIS35 4.5 34.5 1.0
CG A:HIS35 4.5 35.2 1.0
O A:HOH487 4.5 46.7 1.0
CA A:HIS33 4.9 26.1 1.0

Zinc binding site 2 out of 6 in 5ubi

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Zinc binding site 2 out of 6 in the Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Prpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Prpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:34.6
occ:0.30
 ZN A:ZN301 1.9 26.9 0.7
ND1 A:HIS33 2.5 37.1 1.0
NE2 A:HIS35 2.5 32.1 1.0
CD2 A:HIS35 2.6 31.1 1.0
O A:HOH487 2.7 46.7 1.0
CG A:HIS33 2.9 34.0 1.0
CB A:HIS33 3.1 27.9 1.0
CE1 A:HIS33 3.3 37.3 1.0
CD2 A:HIS33 3.8 36.5 1.0
CE1 A:HIS35 3.8 31.3 1.0
CG A:HIS35 3.9 35.2 1.0
NE2 A:HIS33 4.0 37.9 1.0
CA A:HIS33 4.3 26.1 1.0
ND1 A:HIS35 4.5 34.5 1.0
C A:HIS33 5.0 26.6 1.0

Zinc binding site 3 out of 6 in 5ubi

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Zinc binding site 3 out of 6 in the Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Prpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Prpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:90.7
occ:1.00
 OD1 A:ASP55 2.4 22.4 1.0
OD2 A:ASP56 2.5 22.1 0.5
O2B A:PRP306 2.9 73.3 1.0
O A:HOH476 3.1 43.1 1.0
CG A:ASP56 3.1 19.6 0.5
OD1 A:ASP56 3.2 15.8 0.5
CG A:ASP55 3.2 23.1 1.0
OD2 A:ASP55 3.3 28.7 1.0
PB A:PRP306 4.1 0.1 1.0
O3B A:PRP306 4.2 0.9 1.0
NH1 A:ARG54 4.2 54.4 1.0
O A:HOH430 4.3 23.9 1.0
O A:HOH464 4.4 36.4 1.0
NE A:ARG54 4.4 34.5 1.0
CB A:ASP56 4.5 18.3 0.5
N A:ASP56 4.5 19.1 0.5
N A:ASP56 4.5 19.0 0.5
CZ A:ARG54 4.5 41.6 1.0
CB A:ASP56 4.5 19.2 0.5
CB A:ASP55 4.6 24.0 1.0
CG A:ARG54 4.7 25.2 1.0
O A:HOH429 4.7 44.9 1.0
N A:ASP55 4.9 17.4 1.0

Zinc binding site 4 out of 6 in 5ubi

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Zinc binding site 4 out of 6 in the Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Prpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Prpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:0.9
occ:0.80
 NE2 B:HIS35 1.9 62.6 0.5
CE1 B:HIS35 2.4 60.5 0.5
NE2 B:HIS33 2.5 56.1 1.0
CE1 B:HIS33 2.7 56.4 1.0
CD2 B:HIS35 3.0 53.8 0.5
ND1 B:HIS35 3.5 58.0 0.5
CD2 B:HIS33 3.9 51.3 1.0
CG B:HIS35 3.9 55.8 0.5
ND1 B:HIS33 4.0 57.0 1.0
ND1 B:HIS35 4.1 49.0 0.5
CG B:HIS33 4.6 52.2 1.0
CE1 B:HIS35 4.9 52.0 0.5

Zinc binding site 5 out of 6 in 5ubi

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Zinc binding site 5 out of 6 in the Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Prpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Prpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:72.2
occ:1.00
 OD1 B:ASP55 2.3 26.2 1.0
OD2 B:ASP56 2.6 34.5 1.0
O B:HOH496 2.7 35.8 1.0
O1B B:PRP305 3.0 78.2 1.0
CG B:ASP55 3.1 24.5 1.0
PB B:PRP305 3.2 82.2 1.0
OD2 B:ASP55 3.2 31.9 1.0
O3B B:PRP305 3.2 82.8 1.0
CG B:ASP56 3.3 25.6 1.0
OD1 B:ASP56 3.3 27.9 1.0
O2B B:PRP305 3.4 70.9 1.0
O B:HOH479 3.7 44.6 1.0
O B:HOH468 4.0 26.6 1.0
O B:HOH503 4.0 41.2 1.0
N B:ASP56 4.3 20.6 1.0
NE B:ARG54 4.4 39.0 1.0
CG B:ARG54 4.5 27.3 1.0
CB B:ASP55 4.5 20.2 1.0
CB B:ASP56 4.6 21.4 1.0
N B:ASP55 4.7 17.9 1.0
O3A B:PRP305 4.8 72.8 1.0
NE2 B:GLN12 5.0 30.0 1.0
CA B:ASP55 5.0 18.3 1.0

Zinc binding site 6 out of 6 in 5ubi

Go back to Zinc Binding Sites List in 5ubi
Zinc binding site 6 out of 6 in the Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Prpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Prpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:86.6
occ:0.70
 OD2 B:ASP100 2.1 27.9 0.5
CG B:ASP100 2.8 29.4 0.5
OE2 B:GLU225 2.9 52.4 1.0
OD1 B:ASP100 3.0 25.3 0.5
O B:HOH408 3.6 30.7 1.0
CD B:GLU225 3.9 55.5 1.0
CB B:ASP100 4.2 28.9 0.5
CG B:GLU225 4.2 46.3 1.0
CE B:MET221 4.7 33.0 1.0
CB B:ASP100 4.9 29.7 0.5

Reference:

G.Mittelstadt, W.Jiao, E.K.Livingstone, G.J.Moggre, A.R.Nazmi, E.J.Parker. A Dimeric Catalytic Core Relates the Short and Long Forms of Atp-Phosphoribosyltransferase. Biochem. J. V. 475 247 2018.
ISSN: ESSN 1470-8728
PubMed: 29208762
DOI: 10.1042/BCJ20170762
Page generated: Mon Oct 28 09:20:01 2024

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