Atomistry » Zinc » PDB 5u0d-5ubi » 5ubg
Atomistry »
  Zinc »
    PDB 5u0d-5ubi »
      5ubg »

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

Go back to Zinc Binding Sites List in 5ubg
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy