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Magnesium in PDB 4yb6: Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with the Inhibitors Amp and Histidine

Enzymatic activity of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with the Inhibitors Amp and Histidine

All present enzymatic activity of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with the Inhibitors Amp and Histidine:
2.4.2.17;

Protein crystallography data

The structure of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with the Inhibitors Amp and Histidine, PDB code: 4yb6 was solved by G.Mittelstaedt, G.-J.Moggre, E.J.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.58 / 1.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.871, 124.906, 92.809, 90.00, 115.86, 90.00
R / Rfree (%) 19.5 / 21.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with the Inhibitors Amp and Histidine (pdb code 4yb6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with the Inhibitors Amp and Histidine, PDB code: 4yb6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4yb6

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Magnesium binding site 1 out of 9 in the Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with the Inhibitors Amp and Histidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with the Inhibitors Amp and Histidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:46.1
occ:1.00
 O A:HOH511 1.9 35.9 1.0
O A:HOH508 2.0 46.1 1.0
O A:HOH512 2.1 41.3 1.0
O A:HOH509 2.1 37.4 1.0
O A:HOH510 2.3 25.1 1.0
OD2 A:ASP56 2.3 24.2 1.0
CG A:ASP56 3.2 24.9 1.0
OD1 A:ASP56 3.4 25.1 1.0
O A:HOH443 3.7 24.8 1.0
OE2 A:GLU83 3.7 39.3 1.0
OD1 A:ASN80 3.8 14.6 1.0
O C:HOH438 4.3 21.6 1.0
CB A:ASP56 4.6 21.9 1.0
O A:HOH506 4.6 26.3 1.0
O A:ASP56 4.6 18.6 1.0
CG A:ASN80 4.8 14.7 1.0
CD A:GLU83 4.8 36.0 1.0
ND2 A:ASN80 5.0 13.6 1.0

Magnesium binding site 2 out of 9 in 4yb6

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Magnesium binding site 2 out of 9 in the Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with the Inhibitors Amp and Histidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with the Inhibitors Amp and Histidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:48.2
occ:1.00
 O B:HOH446 2.4 27.8 1.0
OD2 B:ASP56 2.4 27.6 1.0
O B:HOH497 2.4 35.6 1.0
CG B:ASP56 3.4 26.2 1.0
O B:HOH498 3.7 32.8 1.0
OD1 B:ASP56 3.7 27.6 1.0
OE2 B:GLU83 3.9 47.8 1.0
O B:HOH491 4.1 27.6 1.0
OD1 B:ASN80 4.3 24.8 1.0
CB B:ASP56 4.7 22.0 1.0
O B:ASP56 4.9 17.0 1.0
CD B:GLU83 4.9 43.7 1.0

Magnesium binding site 3 out of 9 in 4yb6

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Magnesium binding site 3 out of 9 in the Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with the Inhibitors Amp and Histidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with the Inhibitors Amp and Histidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg304

b:47.2
occ:1.00
 O C:HOH518 2.0 47.8 1.0
OD2 C:ASP56 2.1 24.4 1.0
O C:HOH516 2.2 49.6 1.0
O C:HOH515 2.3 38.9 1.0
O C:HOH517 2.4 40.9 1.0
CG C:ASP56 3.1 23.1 1.0
OD1 C:ASP56 3.3 23.6 1.0
OE2 C:GLU83 3.9 37.5 1.0
OD1 C:ASN80 3.9 22.1 1.0
CB C:ASP56 4.4 21.3 1.0
O C:ASP56 4.5 19.6 1.0
CG C:ASN80 4.9 20.3 1.0

Magnesium binding site 4 out of 9 in 4yb6

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Magnesium binding site 4 out of 9 in the Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with the Inhibitors Amp and Histidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with the Inhibitors Amp and Histidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg305

b:47.3
occ:1.00
 O C:HOH519 2.0 40.1 1.0
O C:HOH476 2.3 26.2 1.0
OE1 C:GLU156 4.3 23.6 1.0
N C:SER154 4.3 21.1 1.0
O3' C:AMP301 4.4 20.9 1.0
OG C:SER154 4.5 24.7 1.0
CA C:SER154 4.5 20.3 1.0
OE2 C:GLU156 4.5 23.4 1.0
O C:HOH446 4.7 20.0 1.0
CD C:GLU156 4.9 22.9 1.0

Magnesium binding site 5 out of 9 in 4yb6

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Magnesium binding site 5 out of 9 in the Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with the Inhibitors Amp and Histidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with the Inhibitors Amp and Histidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg304

b:42.1
occ:1.00
 O D:HOH530 2.0 40.5 1.0
O D:HOH522 2.2 32.4 1.0
OD2 D:ASP56 2.2 22.6 1.0
O D:HOH524 2.2 29.9 1.0
O D:HOH523 2.3 25.4 1.0
O D:HOH521 2.4 26.8 1.0
CG D:ASP56 3.2 20.2 1.0
OD1 D:ASP56 3.4 19.9 1.0
OE2 D:GLU83 3.9 44.4 1.0
O D:HOH493 3.9 30.7 1.0
OD1 D:ASN80 4.1 17.2 1.0
O F:HOH438 4.2 26.8 1.0
CB D:ASP56 4.5 19.6 1.0
O D:HOH449 4.6 24.8 1.0
O D:ASP56 4.7 17.4 1.0
CD D:GLU83 4.9 38.5 1.0

Magnesium binding site 6 out of 9 in 4yb6

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Magnesium binding site 6 out of 9 in the Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with the Inhibitors Amp and Histidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with the Inhibitors Amp and Histidine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg304

b:42.4
occ:1.00
 O E:HOH496 1.9 46.3 1.0
O E:HOH495 2.2 28.1 1.0
O E:HOH497 2.3 27.7 1.0
O E:HOH494 2.3 38.1 1.0
O E:HOH498 2.3 37.0 1.0
OD2 E:ASP56 2.4 26.3 1.0
CG E:ASP56 3.3 23.6 1.0
OD1 E:ASP56 3.5 23.4 1.0
OE2 E:GLU83 3.7 43.9 1.0
OD1 E:ASN80 4.0 20.2 1.0
O B:HOH504 4.5 35.5 1.0
O E:HOH491 4.6 27.1 1.0
CB E:ASP56 4.7 21.7 1.0
CD E:GLU83 4.7 41.2 1.0
O E:ASP56 4.8 20.5 1.0
CG E:ASN80 4.9 21.6 1.0
OE1 E:GLU83 5.0 51.9 1.0

Magnesium binding site 7 out of 9 in 4yb6

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Magnesium binding site 7 out of 9 in the Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with the Inhibitors Amp and Histidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with the Inhibitors Amp and Histidine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg305

b:33.7
occ:1.00
 O E:HOH499 2.3 17.6 1.0
O E:SER226 2.6 14.1 1.0
O E:HOH481 2.9 29.4 1.0
O E:HOH427 2.9 19.4 1.0
O E:ALA223 3.1 17.5 1.0
O E:ILE294 3.5 14.4 1.0
N E:SER226 3.6 19.7 1.0
N E:GLU225 3.7 23.7 1.0
C E:SER226 3.7 15.6 1.0
CE E:LYS227 3.7 13.5 1.0
NZ E:LYS227 3.8 13.7 1.0
CD E:LYS227 4.1 13.7 1.0
C E:ALA223 4.2 20.2 1.0
C E:GLU225 4.2 22.3 1.0
CA E:GLU225 4.2 26.0 1.0
CA E:SER226 4.3 18.3 1.0
N E:ILE294 4.4 13.0 1.0
C E:ARG224 4.4 22.3 1.0
CA E:ARG224 4.5 23.2 1.0
C E:ILE294 4.5 13.6 1.0
O E:HOH455 4.7 23.7 1.0
N E:LYS227 4.8 14.1 1.0
N E:ARG224 4.8 20.1 1.0
CA E:ILE294 4.9 13.3 1.0
CG E:LYS227 4.9 13.8 1.0
CB E:ILE294 4.9 13.0 1.0
O E:HOH446 5.0 31.2 1.0

Magnesium binding site 8 out of 9 in 4yb6

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Magnesium binding site 8 out of 9 in the Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with the Inhibitors Amp and Histidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with the Inhibitors Amp and Histidine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg306

b:47.4
occ:1.00
 O E:HOH506 2.0 42.9 1.0
O E:HOH456 2.0 30.5 1.0
O E:HOH502 2.0 26.7 1.0
O E:HOH505 2.2 42.4 1.0
O E:HOH439 3.8 22.1 1.0
O3' E:AMP301 3.9 22.6 1.0
N E:SER154 4.1 24.6 1.0
OE2 E:GLU156 4.5 20.8 1.0
CA E:SER154 4.6 23.6 1.0
OE1 E:GLU156 4.9 23.3 1.0
O E:HOH492 4.9 26.2 1.0

Magnesium binding site 9 out of 9 in 4yb6

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Magnesium binding site 9 out of 9 in the Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with the Inhibitors Amp and Histidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with the Inhibitors Amp and Histidine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg304

b:41.4
occ:1.00
 O F:HOH508 1.9 37.8 1.0
O F:HOH509 2.0 33.0 1.0
O F:HOH510 2.0 38.9 1.0
OD2 F:ASP56 2.1 19.6 1.0
CG F:ASP56 3.1 19.2 1.0
OD1 F:ASP56 3.4 20.1 1.0
OE2 F:GLU83 4.0 43.5 1.0
OD1 F:ASN80 4.1 18.5 1.0
CB F:ASP56 4.4 18.0 1.0
O F:ASP56 4.6 14.7 1.0

Reference:

G.Mittelstadt, G.J.Moggre, S.Panjikar, A.R.Nazmi, E.J.Parker. Campylobacter Jejuni Adenosine Triphosphate Phosphoribosyltransferase Is An Active Hexamer That Is Allosterically Controlled By the Twisting of A Regulatory Tail. Protein Sci. V. 25 1492 2016.
ISSN: ESSN 1469-896X
PubMed: 27191057
DOI: 10.1002/PRO.2948
Page generated: Sat Sep 28 23:11:37 2024

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