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

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

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

Protein crystallography data

The structure of Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Atp, PDB code: 5ubh 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) 39.95 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.166, 79.921, 92.245, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 25.7

Zinc Binding Sites:

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

Zinc binding site 1 out of 3 in 5ubh

Go back to Zinc Binding Sites List in 5ubh
Zinc binding site 1 out of 3 in the Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Atp


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 Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:42.1
occ:1.00
 ND1 A:HIS33 2.1 45.6 1.0
NE2 A:HIS35 2.2 36.2 1.0
CE1 A:HIS35 2.8 37.7 1.0
CG A:HIS33 3.1 40.4 1.0
CE1 A:HIS33 3.2 44.0 1.0
CB A:HIS33 3.3 36.4 1.0
CD2 A:HIS35 3.5 36.4 1.0
ND1 A:HIS35 4.1 37.9 1.0
CD2 A:HIS33 4.2 40.7 1.0
NE2 A:HIS33 4.3 42.1 1.0
CG A:HIS35 4.4 36.8 1.0
CA A:HIS33 4.8 34.0 1.0

Zinc binding site 2 out of 3 in 5ubh

Go back to Zinc Binding Sites List in 5ubh
Zinc binding site 2 out of 3 in the Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Atp


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 Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:50.0
occ:1.00
 O1B A:ATP303 2.0 49.1 1.0
OD1 A:ASP55 2.2 34.4 1.0
O2G A:ATP303 2.2 42.0 1.0
OD2 A:ASP56 2.3 43.6 1.0
O A:HOH440 2.4 32.7 1.0
O A:HOH410 2.6 30.0 1.0
CG A:ASP56 3.1 39.6 1.0
PB A:ATP303 3.2 51.3 1.0
CG A:ASP55 3.2 32.5 1.0
PG A:ATP303 3.2 46.1 1.0
O3B A:ATP303 3.3 49.4 1.0
OD1 A:ASP56 3.4 47.4 1.0
OD2 A:ASP55 3.5 39.7 1.0
O1G A:ATP303 4.0 36.1 1.0
O3A A:ATP303 4.1 52.7 1.0
N A:ASP56 4.2 27.9 1.0
NE A:ARG54 4.2 46.4 1.0
O2B A:ATP303 4.3 52.6 1.0
CG A:ARG54 4.4 38.8 1.0
CB A:ASP56 4.4 35.4 1.0
O3G A:ATP303 4.5 44.9 1.0
NH1 A:ARG54 4.5 50.7 1.0
CB A:ASP55 4.5 29.4 1.0
N A:ASP55 4.6 27.0 1.0
CZ A:ARG54 4.6 49.9 1.0
CA A:ASP56 4.8 30.3 1.0
CA A:ASP55 4.9 28.4 1.0
CD A:ARG54 4.9 43.0 1.0
C A:ASP55 5.0 27.3 1.0

Zinc binding site 3 out of 3 in 5ubh

Go back to Zinc Binding Sites List in 5ubh
Zinc binding site 3 out of 3 in the Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Atp


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 Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:51.2
occ:1.00
 O1G B:ATP302 2.2 49.5 1.0
OD1 B:ASP55 2.2 33.4 1.0
O2B B:ATP302 2.3 60.8 1.0
OD2 B:ASP56 2.5 49.8 1.0
O B:HOH458 2.6 48.3 1.0
O B:HOH409 2.9 45.5 1.0
PB B:ATP302 2.9 59.8 1.0
CG B:ASP56 3.2 44.0 1.0
PG B:ATP302 3.2 54.3 1.0
O3B B:ATP302 3.2 57.1 1.0
O1B B:ATP302 3.3 68.4 1.0
CG B:ASP55 3.3 31.7 1.0
OD1 B:ASP56 3.3 50.8 1.0
OD2 B:ASP55 3.7 38.0 1.0
O3G B:ATP302 4.0 39.5 1.0
N B:ASP56 4.2 25.5 1.0
CB B:ASP56 4.4 36.0 1.0
O3A B:ATP302 4.4 64.8 1.0
O2G B:ATP302 4.4 51.0 1.0
NE B:ARG54 4.5 54.0 1.0
CG B:ARG54 4.5 45.2 1.0
O B:HOH436 4.6 47.5 1.0
CB B:ASP55 4.6 30.0 1.0
NH1 B:ARG54 4.7 66.2 1.0
N B:ASP55 4.8 26.2 1.0
CZ B:ARG54 4.8 63.8 1.0
CA B:ASP56 4.9 30.1 1.0
O5' B:ATP302 5.0 55.9 1.0

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 09:19:36 2024

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