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Magnesium in PDB 4x5e: Anthranilate Phosphoribosyltransferase Variant R194A From Mycobacterium Tuberculosis with Pyrophosphate, MG2+ and Anthranilate Bound

Enzymatic activity of Anthranilate Phosphoribosyltransferase Variant R194A From Mycobacterium Tuberculosis with Pyrophosphate, MG2+ and Anthranilate Bound

All present enzymatic activity of Anthranilate Phosphoribosyltransferase Variant R194A From Mycobacterium Tuberculosis with Pyrophosphate, MG2+ and Anthranilate Bound:
2.4.2.18;

Protein crystallography data

The structure of Anthranilate Phosphoribosyltransferase Variant R194A From Mycobacterium Tuberculosis with Pyrophosphate, MG2+ and Anthranilate Bound, PDB code: 4x5e was solved by T.V.M.Cookson, G.L.Evans, 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) 95.10 / 1.77
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 94.938, 78.564, 101.318, 90.00, 110.18, 90.00
R / Rfree (%) 18.6 / 22.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Anthranilate Phosphoribosyltransferase Variant R194A From Mycobacterium Tuberculosis with Pyrophosphate, MG2+ and Anthranilate Bound (pdb code 4x5e). 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 R194A From Mycobacterium Tuberculosis with Pyrophosphate, MG2+ and Anthranilate Bound, PDB code: 4x5e:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4x5e

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Magnesium binding site 1 out of 4 in the Anthranilate Phosphoribosyltransferase Variant R194A From Mycobacterium Tuberculosis with Pyrophosphate, MG2+ and Anthranilate 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 R194A From Mycobacterium Tuberculosis with Pyrophosphate, MG2+ and Anthranilate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:17.4
occ:1.00
 O A:HOH586 2.1 20.2 1.0
O5 A:POP401 2.2 24.3 1.0
OE1 A:GLU252 2.2 21.9 1.0
O A:HOH594 2.2 28.8 1.0
O2 A:POP401 2.3 24.7 1.0
OG A:SER119 2.4 17.2 1.0
CD A:GLU252 3.0 22.4 1.0
OE2 A:GLU252 3.1 22.2 1.0
CB A:SER119 3.2 17.6 1.0
P2 A:POP401 3.3 25.7 1.0
MG A:MG403 3.3 25.4 1.0
P1 A:POP401 3.5 26.0 1.0
O A:POP401 3.6 26.1 1.0
O4 A:POP401 3.7 26.6 1.0
O A:HOH652 3.8 35.4 1.0
OD2 A:ASP251 3.9 18.6 1.0
N A:GLY107 4.0 17.5 1.0
O A:ASP251 4.1 18.1 1.0
N A:SER119 4.1 16.3 1.0
OD1 A:ASP251 4.2 20.7 1.0
O A:HOH616 4.2 23.3 1.0
CA A:SER119 4.2 16.9 1.0
CA A:GLY107 4.3 18.0 1.0
CG A:ASP251 4.3 19.4 1.0
CG A:GLU252 4.4 21.7 1.0
O1 A:POP401 4.4 27.0 1.0
O3 A:POP401 4.5 24.2 1.0
O6 A:POP401 4.6 24.2 1.0
C A:VAL106 4.6 18.0 1.0
O A:HOH665 4.6 29.6 1.0
CA A:VAL106 4.9 17.3 1.0
O A:HOH598 4.9 26.9 1.0

Magnesium binding site 2 out of 4 in 4x5e

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Magnesium binding site 2 out of 4 in the Anthranilate Phosphoribosyltransferase Variant R194A From Mycobacterium Tuberculosis with Pyrophosphate, MG2+ and Anthranilate 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 R194A From Mycobacterium Tuberculosis with Pyrophosphate, MG2+ and Anthranilate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:25.4
occ:1.00
 OE1 A:GLU252 2.1 21.9 1.0
O A:HOH652 2.1 35.4 1.0
O A:HOH612 2.2 22.8 1.0
OD1 A:ASP251 2.2 20.7 1.0
O A:HOH598 2.3 26.9 1.0
O A:HOH594 2.3 28.8 1.0
CD A:GLU252 3.1 22.4 1.0
CG A:ASP251 3.2 19.4 1.0
MG A:MG402 3.3 17.4 1.0
CG A:GLU252 3.4 21.7 1.0
OD2 A:ASP251 3.5 18.6 1.0
O2 A:POP401 3.7 24.7 1.0
OD2 A:ASP111 4.0 30.3 1.0
OG1 A:THR115 4.1 31.8 1.0
OE2 A:GLU252 4.2 22.2 1.0
O A:HOH756 4.3 52.6 1.0
O A:ASP251 4.3 18.1 1.0
O A:HOH586 4.3 20.2 1.0
OD1 A:ASP111 4.3 37.3 1.0
O A:HOH739 4.4 45.2 1.0
O A:HOH757 4.4 44.3 1.0
CG A:ASP111 4.5 33.2 1.0
C A:ASP251 4.5 19.9 1.0
CB A:ASP251 4.5 19.1 1.0
O1 A:POP401 4.7 27.0 1.0
N A:ASP251 4.8 19.6 1.0
O4 A:POP401 4.8 26.6 1.0
P1 A:POP401 4.8 26.0 1.0
CA A:ASP251 4.8 19.4 1.0
O5 A:POP401 4.9 24.3 1.0
CB A:GLU252 4.9 21.1 1.0

Magnesium binding site 3 out of 4 in 4x5e

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Magnesium binding site 3 out of 4 in the Anthranilate Phosphoribosyltransferase Variant R194A From Mycobacterium Tuberculosis with Pyrophosphate, MG2+ and Anthranilate 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 R194A From Mycobacterium Tuberculosis with Pyrophosphate, MG2+ and Anthranilate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:37.2
occ:1.00
 O5 B:POP401 2.0 27.6 0.5
O2 B:POP401 2.1 24.1 0.5
O B:HOH586 2.2 39.8 1.0
OE2 B:GLU252 2.3 46.4 1.0
O B:HOH682 2.5 52.2 1.0
OG B:SER119 2.6 34.8 1.0
CB B:SER119 3.2 33.0 1.0
P1 B:POP401 3.2 26.7 0.5
P2 B:POP401 3.2 29.1 0.5
O B:POP401 3.5 28.1 0.5
CD B:GLU252 3.5 46.1 1.0
MG B:MG403 3.7 61.9 1.0
N B:GLY107 3.7 35.0 1.0
O3 B:POP401 3.7 26.3 0.5
CA B:GLY107 4.0 35.7 1.0
OD2 B:ASP251 4.0 35.6 1.0
O B:HOH622 4.1 56.7 1.0
O4 B:POP401 4.1 29.2 0.5
CG B:GLU252 4.3 42.2 1.0
O6 B:POP401 4.3 29.2 0.5
C B:VAL106 4.3 32.7 1.0
OE1 B:GLU252 4.3 53.7 1.0
O B:ASP251 4.4 30.4 1.0
CA B:SER119 4.4 31.8 1.0
N B:SER119 4.4 29.9 1.0
O1 B:POP401 4.5 27.0 0.5
CG B:ASP251 4.5 34.9 1.0
OD1 B:ASP251 4.5 33.7 1.0
CA B:VAL106 4.7 30.7 1.0
C B:GLY107 4.9 36.2 1.0
O B:VAL106 5.0 32.6 1.0

Magnesium binding site 4 out of 4 in 4x5e

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Magnesium binding site 4 out of 4 in the Anthranilate Phosphoribosyltransferase Variant R194A From Mycobacterium Tuberculosis with Pyrophosphate, MG2+ and Anthranilate 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 R194A From Mycobacterium Tuberculosis with Pyrophosphate, MG2+ and Anthranilate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:61.9
occ:1.00
 O B:HOH622 2.0 56.7 1.0
O B:HOH682 2.6 52.2 1.0
OD1 B:ASP251 2.7 33.7 1.0
OE2 B:GLU252 2.8 46.4 1.0
OE1 B:GLU252 2.9 53.7 1.0
CD B:GLU252 3.2 46.1 1.0
O5 B:POP401 3.4 27.6 0.5
OG1 B:THR115 3.5 57.6 1.0
CG B:ASP251 3.6 34.9 1.0
MG B:MG402 3.7 37.2 1.0
OD2 B:ASP251 3.7 35.6 1.0
OD2 B:ASP111 3.9 59.9 1.0
O6 B:POP401 4.5 29.2 0.5
P2 B:POP401 4.6 29.1 0.5
CG B:GLU252 4.8 42.2 1.0
CG B:ASP111 4.8 61.2 1.0
O B:HOH586 4.8 39.8 1.0
O B:ASP251 4.8 30.4 1.0
CB B:THR115 4.9 58.3 1.0
OD1 B:ASP111 4.9 67.0 1.0
CB B:ASP251 5.0 34.2 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 14:05:01 2024

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