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Magnesium in PDB 4yb7: Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with Atp

Enzymatic activity of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with Atp

All present enzymatic activity of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with Atp:
2.4.2.17;

Protein crystallography data

The structure of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with Atp, PDB code: 4yb7 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) 50.00 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 91.667, 91.835, 154.903, 101.11, 95.21, 118.14
R / Rfree (%) 23.1 / 25.4

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with Atp (pdb code 4yb7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with Atp, PDB code: 4yb7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 4yb7

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Magnesium binding site 1 out of 12 in the Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with Atp


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 Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:39.0
occ:1.00
 O2B B:ATP303 1.9 42.5 1.0
OD1 B:ASP56 2.0 42.2 1.0
O1G B:ATP303 2.1 48.3 1.0
O B:HOH448 2.2 42.8 1.0
OD1 B:ASP55 2.3 29.4 1.0
CG B:ASP56 3.0 35.7 1.0
PB B:ATP303 3.1 47.6 1.0
PG B:ATP303 3.3 55.2 1.0
CG B:ASP55 3.3 30.2 1.0
OD2 B:ASP56 3.3 45.2 1.0
O3B B:ATP303 3.5 53.4 1.0
O B:HOH437 3.6 40.5 1.0
OD2 B:ASP55 3.7 33.6 1.0
NH2 B:ARG54 3.7 76.7 1.0
O2G B:ATP303 3.9 41.7 1.0
CZ B:ARG54 4.0 68.1 1.0
O3A B:ATP303 4.0 43.4 1.0
N B:ASP56 4.1 27.4 1.0
CB B:ASP56 4.2 33.8 1.0
O1B B:ATP303 4.3 49.6 1.0
NH1 B:ARG54 4.3 73.0 1.0
CG B:ARG54 4.5 48.2 1.0
O3G B:ATP303 4.5 51.2 1.0
CA B:ASP56 4.6 29.3 1.0
NE B:ARG54 4.6 63.3 1.0
CB B:ASP55 4.7 29.4 1.0
N B:ASP55 4.8 28.1 1.0
C B:ASP55 4.9 28.7 1.0
CA B:ASP55 5.0 28.0 1.0

Magnesium binding site 2 out of 12 in 4yb7

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Magnesium binding site 2 out of 12 in the Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with Atp


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 Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:45.1
occ:1.00
 O C:HOH437 1.9 37.6 1.0
OD1 C:ASP56 2.0 33.1 1.0
O2B C:ATP304 2.0 40.8 1.0
O C:HOH439 2.2 36.2 1.0
OD1 C:ASP55 2.3 28.2 1.0
O1G C:ATP304 2.3 50.5 1.0
CG C:ASP56 3.0 31.5 1.0
PB C:ATP304 3.2 42.1 1.0
PG C:ATP304 3.2 53.7 1.0
CG C:ASP55 3.3 29.2 1.0
OD2 C:ASP56 3.4 38.6 1.0
O3B C:ATP304 3.5 48.2 1.0
O3G C:ATP304 3.5 46.7 1.0
OD2 C:ASP55 3.7 32.7 1.0
O C:HOH436 3.8 38.0 1.0
NH1 C:ARG54 3.9 46.4 1.0
NE C:ARG54 4.1 42.1 1.0
O3A C:ATP304 4.1 40.5 1.0
N C:ASP56 4.1 25.9 1.0
CZ C:ARG54 4.1 49.4 1.0
CB C:ASP56 4.3 29.8 1.0
O1B C:ATP304 4.3 49.7 1.0
CG C:ARG54 4.4 38.8 1.0
CA C:ASP56 4.6 26.9 1.0
CB C:ASP55 4.6 29.0 1.0
O2G C:ATP304 4.7 52.6 1.0
N C:ASP55 4.7 25.9 1.0
CD C:ARG54 4.9 42.6 1.0
NH2 C:ARG54 4.9 59.3 1.0
C C:ASP55 4.9 28.6 1.0
CA C:ASP55 5.0 27.0 1.0

Magnesium binding site 3 out of 12 in 4yb7

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Magnesium binding site 3 out of 12 in the Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with Atp


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 Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:49.2
occ:1.00
 O2G D:ATP302 1.9 66.7 1.0
O2B D:ATP302 1.9 56.8 1.0
OD1 D:ASP56 2.1 48.2 1.0
OD1 D:ASP55 2.2 41.1 1.0
CG D:ASP56 3.1 46.9 1.0
PG D:ATP302 3.1 71.9 1.0
CG D:ASP55 3.2 41.3 1.0
PB D:ATP302 3.2 52.8 1.0
OD2 D:ASP56 3.4 57.5 1.0
OD2 D:ASP55 3.5 44.5 1.0
O3B D:ATP302 3.5 61.3 1.0
O1G D:ATP302 3.7 64.1 1.0
N D:ASP56 4.0 38.5 1.0
O3A D:ATP302 4.1 53.4 1.0
NH2 D:ARG54 4.3 62.9 1.0
O1B D:ATP302 4.3 60.4 1.0
CB D:ASP56 4.3 42.7 1.0
CZ D:ARG54 4.4 63.2 1.0
NE D:ARG54 4.4 56.6 1.0
O3G D:ATP302 4.4 68.8 1.0
O D:HOH421 4.5 33.9 1.0
CB D:ASP55 4.5 40.0 1.0
CG D:ARG54 4.6 50.5 1.0
CA D:ASP56 4.6 38.1 1.0
N D:ASP55 4.8 38.2 1.0
C D:ASP55 4.9 36.5 1.0
CA D:ASP55 4.9 38.8 1.0

Magnesium binding site 4 out of 12 in 4yb7

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Magnesium binding site 4 out of 12 in the Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with Atp


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 Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg301

b:59.9
occ:1.00
 O2B E:ATP303 1.9 58.0 1.0
O2G E:ATP303 2.0 65.9 1.0
OD1 E:ASP56 2.2 49.7 1.0
OD1 E:ASP55 2.4 52.1 1.0
CG E:ASP56 3.1 49.5 1.0
PG E:ATP303 3.2 74.6 1.0
PB E:ATP303 3.2 55.6 1.0
CG E:ASP55 3.3 47.0 1.0
O E:HOH408 3.3 43.1 1.0
OD2 E:ASP56 3.4 54.8 1.0
OD2 E:ASP55 3.5 47.8 1.0
O3B E:ATP303 3.6 70.4 1.0
O3G E:ATP303 3.8 62.5 1.0
NH2 E:ARG54 4.0 74.7 1.0
O3A E:ATP303 4.1 54.5 1.0
N E:ASP56 4.2 42.1 1.0
CZ E:ARG54 4.3 71.2 1.0
CB E:ASP56 4.4 46.0 1.0
O1B E:ATP303 4.4 62.7 1.0
O1G E:ATP303 4.5 72.6 1.0
NH1 E:ARG54 4.5 69.9 1.0
CA E:ASP56 4.7 42.2 1.0
O E:HOH409 4.7 45.6 1.0
CB E:ASP55 4.7 42.2 1.0
CG E:ARG54 4.8 62.8 1.0
NE E:ARG54 4.9 69.8 1.0
N E:ASP55 5.0 46.9 1.0

Magnesium binding site 5 out of 12 in 4yb7

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Magnesium binding site 5 out of 12 in the Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with Atp


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 Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:44.0
occ:1.00
 O2B I:ATP303 1.7 46.1 1.0
OD1 I:ASP56 2.0 34.6 1.0
O3G I:ATP303 2.1 55.1 1.0
OD1 I:ASP55 2.2 35.2 1.0
PB I:ATP303 3.0 48.6 1.0
CG I:ASP56 3.0 34.4 1.0
PG I:ATP303 3.1 64.2 1.0
CG I:ASP55 3.3 35.7 1.0
O3B I:ATP303 3.3 59.2 1.0
O2G I:ATP303 3.4 53.4 1.0
OD2 I:ASP56 3.5 36.1 1.0
OD2 I:ASP55 3.7 35.7 1.0
O3A I:ATP303 4.0 47.0 1.0
N I:ASP56 4.1 33.4 1.0
NH2 I:ARG54 4.1 63.5 1.0
NE I:ARG54 4.1 57.8 1.0
O1B I:ATP303 4.2 56.6 1.0
CZ I:ARG54 4.2 62.2 1.0
CB I:ASP56 4.3 34.5 1.0
CG I:ARG54 4.4 46.3 1.0
O1G I:ATP303 4.5 64.7 1.0
CB I:ASP55 4.6 31.6 1.0
CA I:ASP56 4.6 34.0 1.0
N I:ASP55 4.7 31.6 1.0
NH1 I:ARG54 4.9 68.9 1.0
CD I:ARG54 4.9 52.1 1.0
C I:ASP55 4.9 34.0 1.0
CA I:ASP55 5.0 33.7 1.0

Magnesium binding site 6 out of 12 in 4yb7

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Magnesium binding site 6 out of 12 in the Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with Atp


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 Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:70.3
occ:1.00
 O2B K:ATP302 2.1 55.8 1.0
OD1 K:ASP56 2.3 46.7 1.0
O2G K:ATP302 2.4 59.3 1.0
OD1 K:ASP55 2.7 48.7 1.0
CG K:ASP56 3.0 47.3 1.0
OD2 K:ASP56 3.2 55.3 1.0
O K:HOH409 3.2 37.3 1.0
PB K:ATP302 3.5 59.4 1.0
CG K:ASP55 3.5 46.1 1.0
OD2 K:ASP55 3.6 45.3 1.0
PG K:ATP302 3.7 68.0 1.0
O3B K:ATP302 3.9 66.5 1.0
O1G K:ATP302 4.2 61.9 1.0
N K:ASP56 4.3 42.5 1.0
CB K:ASP56 4.4 45.4 1.0
O1B K:ATP302 4.5 67.2 1.0
O3A K:ATP302 4.5 57.3 1.0
CA K:ASP56 4.7 43.7 1.0
NH1 K:ARG54 4.7 70.7 1.0
NE K:ARG54 4.8 69.2 1.0
O3G K:ATP302 4.9 66.5 1.0
CB K:ASP55 5.0 42.3 1.0

Magnesium binding site 7 out of 12 in 4yb7

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Magnesium binding site 7 out of 12 in the Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with Atp


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 Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:44.9
occ:1.00
 O2B A:ATP302 1.8 48.0 1.0
OD1 A:ASP56 2.1 37.1 1.0
O2G A:ATP302 2.1 57.6 1.0
OD1 A:ASP55 2.2 24.1 1.0
O A:HOH461 2.3 38.4 1.0
PG A:ATP302 3.0 62.6 1.0
PB A:ATP302 3.0 45.5 1.0
CG A:ASP56 3.1 35.1 1.0
CG A:ASP55 3.2 26.7 1.0
O3B A:ATP302 3.3 55.3 1.0
O1G A:ATP302 3.4 49.5 1.0
O A:HOH460 3.5 27.1 1.0
OD2 A:ASP56 3.5 40.4 1.0
OD2 A:ASP55 3.5 31.0 1.0
O3A A:ATP302 3.9 41.0 1.0
N A:ASP56 4.1 26.1 1.0
O1B A:ATP302 4.2 54.3 1.0
CB A:ASP56 4.4 32.0 1.0
O3G A:ATP302 4.4 61.8 1.0
NE A:ARG54 4.4 57.7 1.0
CG A:ARG54 4.5 48.7 1.0
CB A:ASP55 4.6 26.0 1.0
CA A:ASP56 4.7 27.3 1.0
N A:ASP55 4.7 26.0 1.0
C A:ASP55 4.9 26.7 1.0
CA A:ASP55 5.0 26.4 1.0

Magnesium binding site 8 out of 12 in 4yb7

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Magnesium binding site 8 out of 12 in the Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with Atp


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 Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg301

b:39.1
occ:1.00
 O2B F:ATP302 1.8 38.8 1.0
O3G F:ATP302 1.9 51.0 1.0
OD1 F:ASP55 2.2 31.3 1.0
O F:HOH425 2.2 43.4 1.0
OD1 F:ASP56 2.3 28.3 1.0
PB F:ATP302 2.9 42.1 1.0
PG F:ATP302 2.9 57.1 1.0
O3B F:ATP302 3.1 54.2 1.0
CG F:ASP55 3.2 27.7 1.0
CG F:ASP56 3.3 26.7 1.0
O2G F:ATP302 3.4 46.9 1.0
OD2 F:ASP55 3.4 32.0 1.0
O3A F:ATP302 3.7 41.6 1.0
OD2 F:ASP56 3.7 32.4 1.0
O1B F:ATP302 4.2 51.5 1.0
N F:ASP56 4.2 24.2 1.0
O1G F:ATP302 4.3 54.2 1.0
NE F:ARG54 4.4 45.1 1.0
CB F:ASP55 4.5 25.9 1.0
CB F:ASP56 4.6 25.9 1.0
CG F:ARG54 4.6 38.5 1.0
NH2 F:ARG54 4.7 50.5 1.0
N F:ASP55 4.8 24.5 1.0
CA F:ASP56 4.8 24.7 1.0
CZ F:ARG54 4.9 52.7 1.0
CA F:ASP55 5.0 24.5 1.0
C F:ASP55 5.0 25.0 1.0

Magnesium binding site 9 out of 12 in 4yb7

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Magnesium binding site 9 out of 12 in the Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with Atp


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 Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:51.4
occ:1.00
 O2B G:ATP302 1.9 56.0 1.0
O2G G:ATP302 1.9 54.2 1.0
OD1 G:ASP56 2.3 42.1 1.0
OD1 G:ASP55 2.4 42.3 1.0
PB G:ATP302 3.0 54.4 1.0
PG G:ATP302 3.1 63.2 1.0
O3B G:ATP302 3.2 58.8 1.0
CG G:ASP56 3.3 39.7 1.0
CG G:ASP55 3.4 39.7 1.0
OD2 G:ASP56 3.6 47.1 1.0
OD2 G:ASP55 3.6 41.0 1.0
O3A G:ATP302 3.8 49.6 1.0
O1G G:ATP302 3.9 49.0 1.0
O3G G:ATP302 4.2 59.5 1.0
O1B G:ATP302 4.3 59.9 1.0
N G:ASP56 4.4 34.9 1.0
CB G:ASP56 4.6 37.9 1.0
CB G:ASP55 4.7 36.5 1.0
CA G:ASP56 4.9 33.8 1.0
N G:ASP55 5.0 33.7 1.0

Magnesium binding site 10 out of 12 in 4yb7

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Magnesium binding site 10 out of 12 in the Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Adenosine Triphosphate Phosphoribosyltransferase From Campylobacter Jejuni in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:55.7
occ:1.00
 O2B H:ATP302 1.7 52.1 1.0
OD1 H:ASP56 2.0 42.9 1.0
O3G H:ATP302 2.3 68.9 1.0
OD1 H:ASP55 2.5 43.2 1.0
CG H:ASP56 2.9 41.6 1.0
PB H:ATP302 3.1 56.1 1.0
OD2 H:ASP56 3.2 51.7 1.0
PG H:ATP302 3.4 70.1 1.0
CG H:ASP55 3.5 42.2 1.0
O3B H:ATP302 3.6 66.1 1.0
O2G H:ATP302 3.8 61.2 1.0
OD2 H:ASP55 3.8 44.5 1.0
O1B H:ATP302 4.1 59.5 1.0
O3A H:ATP302 4.2 54.0 1.0
N H:ASP56 4.2 41.3 1.0
CB H:ASP56 4.3 41.7 1.0
CA H:ASP56 4.7 40.5 1.0
O1G H:ATP302 4.7 65.5 1.0
CB H:ASP55 4.9 40.4 1.0
N H:ASP55 5.0 38.2 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 23:11:47 2024

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