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

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

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

Protein crystallography data

The structure of Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Phosphoribosyl-Atp, PDB code: 5ubg 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) 34.55 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.458, 80.460, 92.728, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 22.9

Other elements in 5ubg:

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

Chlorine (Cl) 1 atom

Zinc Binding Sites:

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

Zinc binding site 1 out of 5 in 5ubg

Go back to Zinc Binding Sites List in 5ubg
Zinc binding site 1 out of 5 in the Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Phosphoribosyl-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 Phosphoribosyl-Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:28.2
occ:1.00
 ND1 A:HIS33 2.1 31.8 1.0
NE2 A:HIS35 2.1 31.5 1.0
CE1 A:HIS35 2.9 34.5 1.0
CE1 A:HIS33 3.0 32.2 1.0
CG A:HIS33 3.0 30.3 1.0
CD2 A:HIS35 3.3 32.5 1.0
CB A:HIS33 3.4 25.3 1.0
O A:HOH497 3.9 26.2 1.0
NE2 A:HIS33 4.1 32.8 1.0
O A:HOH482 4.1 28.7 1.0
CD2 A:HIS33 4.1 30.8 1.0
ND1 A:HIS35 4.1 38.7 1.0
CG A:HIS35 4.3 33.3 1.0
CA A:HIS33 4.9 24.9 1.0

Zinc binding site 2 out of 5 in 5ubg

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Zinc binding site 2 out of 5 in the Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Phosphoribosyl-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 Phosphoribosyl-Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:29.4
occ:1.00
 O3G A:PRT302 2.1 35.6 1.0
O2B A:PRT302 2.1 29.1 1.0
OD2 A:ASP56 2.2 27.4 1.0
OD1 A:ASP55 2.2 22.8 1.0
O A:HOH423 2.3 32.2 1.0
O A:HOH434 2.3 29.1 1.0
CG A:ASP56 3.0 25.2 1.0
PB A:PRT302 3.1 32.7 1.0
PG A:PRT302 3.1 35.0 1.0
CG A:ASP55 3.3 18.8 1.0
O3B A:PRT302 3.3 36.5 1.0
OD1 A:ASP56 3.3 32.4 1.0
O A:HOH414 3.6 23.0 1.0
OD2 A:ASP55 3.7 23.6 1.0
O3A A:PRT302 3.9 27.0 1.0
O1G A:PRT302 4.1 25.9 1.0
N A:ASP56 4.1 15.9 1.0
O A:HOH485 4.2 43.4 1.0
NE A:ARG54 4.3 42.7 1.0
CB A:ASP56 4.3 21.3 1.0
O1B A:PRT302 4.3 39.6 1.0
NH1 A:ARG54 4.3 60.2 1.0
O2G A:PRT302 4.4 38.2 1.0
CZ A:ARG54 4.4 52.1 1.0
CG A:ARG54 4.4 29.4 1.0
CB A:ASP55 4.6 17.9 1.0
N A:ASP55 4.6 18.2 1.0
O A:HOH488 4.7 43.2 1.0
CA A:ASP56 4.7 17.4 1.0
C A:ASP55 4.9 16.7 1.0
CA A:ASP55 4.9 16.9 1.0
CD A:ARG54 5.0 35.3 1.0

Zinc binding site 3 out of 5 in 5ubg

Go back to Zinc Binding Sites List in 5ubg
Zinc binding site 3 out of 5 in the Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Phosphoribosyl-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 Phosphoribosyl-Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:84.6
occ:1.00
 NE2 B:HIS35 2.1 74.5 0.5
NE2 B:HIS33 2.3 68.4 1.0
CD2 B:HIS35 2.3 71.5 0.5
CE1 B:HIS33 2.5 63.2 1.0
CL B:CL305 2.5 68.3 1.0
CE1 B:HIS35 3.3 69.6 0.5
CG B:HIS35 3.5 68.5 0.5
CD2 B:HIS33 3.6 65.6 1.0
ND1 B:HIS33 3.8 56.9 1.0
ND1 B:HIS35 3.9 69.8 0.5
CG B:HIS33 4.4 59.8 1.0
ND1 B:HIS35 4.6 63.1 0.5
CB B:HIS35 4.7 65.0 0.5
CB B:HIS35 4.7 59.1 0.5

Zinc binding site 4 out of 5 in 5ubg

Go back to Zinc Binding Sites List in 5ubg
Zinc binding site 4 out of 5 in the Catalytic Core Domain of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni with Bound Phosphoribosyl-Atp


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

b:93.4
occ:1.00
 NE2 B:HIS35 2.6 63.3 0.5
CE1 B:HIS35 2.9 64.4 0.5
CD2 B:HIS35 3.7 62.3 0.5
ND1 B:HIS35 4.1 63.1 0.5
CG B:HIS35 4.5 63.5 0.5

Zinc binding site 5 out of 5 in 5ubg

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


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 Phosphoribosyl-Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:38.9
occ:1.00
 O2G B:PRT303 2.0 50.0 1.0
O2B B:PRT303 2.3 42.9 1.0
OD2 B:ASP56 2.3 29.0 1.0
OD1 B:ASP55 2.3 25.3 1.0
O B:HOH402 2.4 32.7 1.0
O B:HOH451 2.4 37.9 1.0
CG B:ASP56 3.1 34.4 1.0
PB B:PRT303 3.1 46.8 1.0
PG B:PRT303 3.1 61.1 1.0
O3B B:PRT303 3.3 61.9 1.0
CG B:ASP55 3.3 25.7 1.0
OD1 B:ASP56 3.3 42.6 1.0
O B:HOH411 3.4 35.0 1.0
OD2 B:ASP55 3.6 32.6 1.0
O3A B:PRT303 3.7 44.6 1.0
O3G B:PRT303 3.7 37.8 1.0
N B:ASP56 4.2 20.8 1.0
CB B:ASP56 4.3 24.6 1.0
O1G B:PRT303 4.4 60.5 1.0
NE B:ARG54 4.4 54.3 1.0
NH1 B:ARG54 4.5 67.0 1.0
O1B B:PRT303 4.5 54.3 1.0
CZ B:ARG54 4.5 62.5 1.0
CG B:ARG54 4.6 38.6 1.0
CB B:ASP55 4.6 23.5 1.0
CA B:ASP56 4.8 23.1 1.0
N B:ASP55 4.8 22.0 1.0
C B:ASP55 5.0 22.9 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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