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Magnesium in PDB 4x5c: Anthranilate Phosphoribosyltransferase Variant R193L From Mycobacterium Tuberculosis with Pyrophosphate/Prpp and MG2+ Bound

Enzymatic activity of Anthranilate Phosphoribosyltransferase Variant R193L From Mycobacterium Tuberculosis with Pyrophosphate/Prpp and MG2+ Bound

All present enzymatic activity of Anthranilate Phosphoribosyltransferase Variant R193L From Mycobacterium Tuberculosis with Pyrophosphate/Prpp and MG2+ Bound:
2.4.2.18;

Protein crystallography data

The structure of Anthranilate Phosphoribosyltransferase Variant R193L From Mycobacterium Tuberculosis with Pyrophosphate/Prpp and MG2+ Bound, PDB code: 4x5c was solved by T.V.M.Cookson, E.J.Parker, J.S.Lott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 94.12 / 2.33
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 94.485, 78.106, 100.550, 90.00, 110.60, 90.00
R / Rfree (%) 19.7 / 25.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Anthranilate Phosphoribosyltransferase Variant R193L From Mycobacterium Tuberculosis with Pyrophosphate/Prpp and MG2+ Bound (pdb code 4x5c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Anthranilate Phosphoribosyltransferase Variant R193L From Mycobacterium Tuberculosis with Pyrophosphate/Prpp and MG2+ Bound, PDB code: 4x5c:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4x5c

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Magnesium binding site 1 out of 4 in the Anthranilate Phosphoribosyltransferase Variant R193L From Mycobacterium Tuberculosis with Pyrophosphate/Prpp and MG2+ Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Anthranilate Phosphoribosyltransferase Variant R193L From Mycobacterium Tuberculosis with Pyrophosphate/Prpp and MG2+ Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:48.0
occ:1.00
 O A:HOH532 2.0 48.4 1.0
O A:HOH533 2.3 46.5 1.0
OD1 A:ASP251 2.3 32.1 1.0
O A:HOH530 2.3 25.9 1.0
OE1 A:GLU252 2.7 33.7 1.0
O A:HOH534 3.1 50.5 1.0
CG A:ASP251 3.3 31.1 1.0
OD2 A:ASP111 3.5 45.4 1.0
OD2 A:ASP251 3.6 31.2 1.0
CD A:GLU252 3.7 33.2 1.0
MG A:MG403 3.7 32.9 1.0
O3B A:PRP401 3.7 47.9 1.0
CG A:GLU252 3.8 32.7 1.0
OG1 A:THR115 3.9 49.0 1.0
CG A:ASP111 4.3 46.4 1.0
O A:HOH531 4.6 38.3 1.0
O3A A:PRP401 4.6 45.6 1.0
OD1 A:ASP111 4.6 50.6 1.0
O4 A:PRP401 4.6 44.0 1.0
CB A:ASP251 4.7 31.6 1.0
PB A:PRP401 4.8 45.1 1.0
O A:ASP251 4.8 30.9 1.0
N A:ASP251 4.8 32.6 1.0
OE2 A:GLU252 4.9 32.6 1.0
C A:ASP251 4.9 31.0 1.0
O1B A:PRP401 4.9 47.5 1.0

Magnesium binding site 2 out of 4 in 4x5c

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Magnesium binding site 2 out of 4 in the Anthranilate Phosphoribosyltransferase Variant R193L From Mycobacterium Tuberculosis with Pyrophosphate/Prpp and MG2+ Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Anthranilate Phosphoribosyltransferase Variant R193L From Mycobacterium Tuberculosis with Pyrophosphate/Prpp and MG2+ Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:32.9
occ:1.00
 OG A:SER119 1.9 26.4 1.0
O A:HOH531 2.1 38.3 1.0
OE1 A:GLU252 2.3 33.7 1.0
O A:HOH530 2.3 25.9 1.0
O3A A:PRP401 2.5 45.6 1.0
O3B A:PRP401 2.6 47.9 1.0
O2A A:PRP401 2.6 50.9 1.0
PA A:PRP401 3.1 40.0 1.0
CB A:SER119 3.2 25.7 1.0
CD A:GLU252 3.2 33.2 1.0
PB A:PRP401 3.2 45.1 1.0
OE2 A:GLU252 3.5 32.6 1.0
MG A:MG402 3.7 48.0 1.0
N A:GLY107 3.8 31.9 1.0
OD2 A:ASP251 3.9 31.2 1.0
O A:HOH532 4.0 48.4 1.0
OD1 A:ASP251 4.0 32.1 1.0
O4 A:PRP401 4.1 44.0 1.0
O2B A:PRP401 4.1 43.2 1.0
O1 A:PRP401 4.1 43.2 1.0
N A:SER119 4.2 26.5 1.0
CA A:GLY107 4.2 32.6 1.0
O A:HOH535 4.2 41.1 1.0
CG A:ASP251 4.2 31.1 1.0
CA A:SER119 4.3 25.8 1.0
C1 A:PRP401 4.3 43.2 1.0
O1A A:PRP401 4.3 55.0 1.0
O A:ASP251 4.4 30.9 1.0
O1B A:PRP401 4.4 47.5 1.0
CG A:GLU252 4.6 32.7 1.0
C A:VAL106 4.6 29.6 1.0
CA A:VAL106 4.9 27.4 1.0
C A:GLY107 5.0 32.3 1.0

Magnesium binding site 3 out of 4 in 4x5c

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Magnesium binding site 3 out of 4 in the Anthranilate Phosphoribosyltransferase Variant R193L From Mycobacterium Tuberculosis with Pyrophosphate/Prpp and MG2+ Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Anthranilate Phosphoribosyltransferase Variant R193L From Mycobacterium Tuberculosis with Pyrophosphate/Prpp and MG2+ Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:53.0
occ:1.00
 O3 B:POP401 1.7 73.7 1.0
O6 B:POP401 2.2 71.8 1.0
O B:HOH523 2.3 48.5 1.0
O B:HOH521 2.3 54.6 1.0
OG B:SER119 2.5 40.5 1.0
OE2 B:GLU252 2.6 46.7 1.0
P1 B:POP401 3.1 69.5 1.0
MG B:MG403 3.2 54.7 1.0
CB B:SER119 3.2 38.1 1.0
N B:GLY107 3.3 51.3 1.0
P2 B:POP401 3.4 76.5 1.0
O B:POP401 3.4 76.3 1.0
CA B:GLY107 3.6 53.3 1.0
CD B:GLU252 3.7 44.1 1.0
OD2 B:ASP251 3.8 39.9 1.0
O2 B:POP401 4.0 67.4 1.0
O1 B:POP401 4.0 67.2 1.0
C B:VAL106 4.1 44.9 1.0
O4 B:POP401 4.1 72.8 1.0
O B:HOH520 4.2 40.5 1.0
OE1 B:GLU252 4.3 44.8 1.0
CG B:ASP251 4.4 38.4 1.0
CA B:SER119 4.5 38.1 1.0
OD1 B:ASP251 4.5 37.2 1.0
N B:SER119 4.5 37.4 1.0
C B:GLY107 4.5 51.3 1.0
CA B:VAL106 4.6 40.6 1.0
O5 B:POP401 4.6 66.2 1.0
O B:ASP251 4.6 38.4 1.0
O B:HOH522 4.6 58.5 1.0
O B:GLY107 4.7 49.7 1.0
O B:VAL106 4.8 40.9 1.0
CG B:GLU252 4.8 42.1 1.0
O B:HOH524 4.9 67.8 1.0

Magnesium binding site 4 out of 4 in 4x5c

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Magnesium binding site 4 out of 4 in the Anthranilate Phosphoribosyltransferase Variant R193L From Mycobacterium Tuberculosis with Pyrophosphate/Prpp and MG2+ Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Anthranilate Phosphoribosyltransferase Variant R193L From Mycobacterium Tuberculosis with Pyrophosphate/Prpp and MG2+ Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:54.7
occ:1.00
 O B:HOH524 1.9 67.8 1.0
O B:HOH522 2.2 58.5 1.0
O B:HOH520 2.3 40.5 1.0
O B:HOH521 2.5 54.6 1.0
OD1 B:ASP251 2.6 37.2 1.0
OE2 B:GLU252 2.7 46.7 1.0
O6 B:POP401 3.1 71.8 1.0
MG B:MG402 3.2 53.0 1.0
CG B:ASP251 3.4 38.4 1.0
CD B:GLU252 3.5 44.1 1.0
OD2 B:ASP251 3.5 39.9 1.0
CG B:GLU252 3.6 42.1 1.0
CG2 B:THR115 4.1 68.3 1.0
O B:HOH523 4.2 48.5 1.0
OG1 B:THR115 4.4 61.3 1.0
CB B:THR115 4.4 66.9 1.0
P2 B:POP401 4.4 76.5 1.0
O B:ASP251 4.6 38.4 1.0
O3 B:POP401 4.6 73.7 1.0
O5 B:POP401 4.7 66.2 1.0
O B:VAL116 4.7 57.8 1.0
OE1 B:GLU252 4.8 44.8 1.0
C B:ASP251 4.8 38.5 1.0
CB B:ASP251 4.8 39.3 1.0
OG B:SER119 4.9 40.5 1.0

Reference:

T.V.Cookson, G.L.Evans, A.Castell, E.N.Baker, J.S.Lott, E.J.Parker. Structures of Mycobacterium Tuberculosis Anthranilate Phosphoribosyltransferase Variants Reveal the Conformational Changes That Facilitate Delivery of the Substrate to the Active Site. Biochemistry V. 54 6082 2015.
ISSN: ISSN 0006-2960
PubMed: 26356348
DOI: 10.1021/ACS.BIOCHEM.5B00612
Page generated: Tue Aug 20 14:04:51 2024

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