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Magnesium in PDB 4gkm: Bianthranilate-Like Analogue Bound in the Outer Site of Anthranilate Phosphoribosyltransferase (Anprt; Trpd)

Enzymatic activity of Bianthranilate-Like Analogue Bound in the Outer Site of Anthranilate Phosphoribosyltransferase (Anprt; Trpd)

All present enzymatic activity of Bianthranilate-Like Analogue Bound in the Outer Site of Anthranilate Phosphoribosyltransferase (Anprt; Trpd):
2.4.2.18;

Protein crystallography data

The structure of Bianthranilate-Like Analogue Bound in the Outer Site of Anthranilate Phosphoribosyltransferase (Anprt; Trpd), PDB code: 4gkm was solved by G.L.Evans, E.N.Baker, J.S.Lott, Tb Structural Genomics Consortium(Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.47 / 1.67
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 111.167, 81.342, 78.468, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 22.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Bianthranilate-Like Analogue Bound in the Outer Site of Anthranilate Phosphoribosyltransferase (Anprt; Trpd) (pdb code 4gkm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Bianthranilate-Like Analogue Bound in the Outer Site of Anthranilate Phosphoribosyltransferase (Anprt; Trpd), PDB code: 4gkm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4gkm

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Magnesium binding site 1 out of 4 in the Bianthranilate-Like Analogue Bound in the Outer Site of Anthranilate Phosphoribosyltransferase (Anprt; Trpd)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bianthranilate-Like Analogue Bound in the Outer Site of Anthranilate Phosphoribosyltransferase (Anprt; Trpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:16.1
occ:1.00
 O3B A:PRP401 2.0 17.0 1.0
O2A A:PRP401 2.0 18.2 1.0
O A:HOH677 2.1 17.8 1.0
OE2 A:GLU252 2.1 18.6 1.0
O A:HOH679 2.1 17.8 1.0
OG A:SER119 2.1 17.5 1.0
CD A:GLU252 3.0 17.4 1.0
CB A:SER119 3.1 15.3 1.0
OE1 A:GLU252 3.2 19.5 1.0
MG A:MG403 3.3 23.3 1.0
PA A:PRP401 3.4 20.4 1.0
PB A:PRP401 3.4 19.2 1.0
O A:HOH681 3.6 26.1 1.0
O3A A:PRP401 3.7 20.4 1.0
N A:GLY107 3.9 14.6 1.0
OD2 A:ASP251 3.9 17.1 1.0
N A:SER119 4.1 14.2 1.0
O A:HOH678 4.1 18.2 1.0
O4 A:PRP401 4.1 29.6 0.8
OD1 A:ASP251 4.2 20.7 1.0
O A:ASP251 4.2 17.2 1.0
CA A:SER119 4.2 13.9 1.0
CA A:GLY107 4.3 14.1 1.0
O1B A:PRP401 4.3 22.6 1.0
CG A:ASP251 4.3 19.5 1.0
O2B A:PRP401 4.4 17.3 1.0
O1 A:PRP401 4.4 31.8 1.0
CG A:GLU252 4.4 20.8 1.0
C1 A:PRP401 4.5 24.9 0.8
O1A A:PRP401 4.5 28.0 1.0
C A:VAL106 4.6 15.1 1.0
O A:HOH680 4.8 27.9 1.0
O A:HOH695 4.9 25.2 1.0
CA A:VAL106 4.9 13.2 1.0

Magnesium binding site 2 out of 4 in 4gkm

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Magnesium binding site 2 out of 4 in the Bianthranilate-Like Analogue Bound in the Outer Site of Anthranilate Phosphoribosyltransferase (Anprt; Trpd)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Bianthranilate-Like Analogue Bound in the Outer Site of Anthranilate Phosphoribosyltransferase (Anprt; Trpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:23.3
occ:1.00
 O A:HOH682 2.0 27.5 1.0
O A:HOH680 2.1 27.9 1.0
O A:HOH679 2.1 17.8 1.0
O A:HOH681 2.1 26.1 1.0
OE2 A:GLU252 2.2 18.6 1.0
OD1 A:ASP251 2.2 20.7 1.0
CG A:ASP251 3.2 19.5 1.0
CD A:GLU252 3.2 17.4 1.0
MG A:MG402 3.3 16.1 1.0
OD2 A:ASP251 3.5 17.1 1.0
CG A:GLU252 3.6 20.8 1.0
O3B A:PRP401 3.7 17.0 1.0
OD2 A:ASP111 3.9 26.9 1.0
O A:HOH697 4.0 34.1 1.0
O A:HOH705 4.0 33.3 1.0
O A:HOH702 4.2 35.1 1.0
O4 A:PRP401 4.2 29.6 0.8
OG1 A:THR115 4.2 28.1 1.0
O A:HOH677 4.3 17.8 1.0
OE1 A:GLU252 4.3 19.5 1.0
O A:ASP251 4.4 17.2 1.0
CB A:ASP251 4.6 20.0 1.0
O1B A:PRP401 4.6 22.6 1.0
C A:ASP251 4.6 21.0 1.0
O2A A:PRP401 4.7 18.2 1.0
CG A:ASP111 4.7 29.6 1.0
PB A:PRP401 4.7 19.2 1.0
N A:ASP251 4.8 18.8 1.0
CA A:ASP251 4.9 17.9 1.0
OD1 A:ASP111 4.9 32.5 1.0
C5 A:PRP401 5.0 28.7 0.8

Magnesium binding site 3 out of 4 in 4gkm

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Magnesium binding site 3 out of 4 in the Bianthranilate-Like Analogue Bound in the Outer Site of Anthranilate Phosphoribosyltransferase (Anprt; Trpd)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Bianthranilate-Like Analogue Bound in the Outer Site of Anthranilate Phosphoribosyltransferase (Anprt; Trpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:12.0
occ:1.00
 O2B B:PRP401 2.0 15.7 1.0
OE2 B:GLU252 2.0 12.3 1.0
O B:HOH703 2.1 14.5 1.0
OG B:SER119 2.1 13.5 1.0
O2A B:PRP401 2.1 14.5 1.0
O B:HOH702 2.1 13.7 1.0
CD B:GLU252 3.0 13.7 1.0
CB B:SER119 3.1 11.0 1.0
OE1 B:GLU252 3.2 14.4 1.0
MG B:MG403 3.2 18.8 1.0
PB B:PRP401 3.3 15.0 1.0
PA B:PRP401 3.3 16.6 1.0
O B:HOH706 3.6 22.7 1.0
O3A B:PRP401 3.7 17.9 1.0
OD2 B:ASP251 3.9 13.4 1.0
N B:GLY107 4.0 13.4 1.0
N B:SER119 4.0 11.3 1.0
O4 B:PRP401 4.1 22.5 0.7
CA B:SER119 4.2 10.1 1.0
OD1 B:ASP251 4.2 15.4 1.0
O B:ASP251 4.2 12.9 1.0
O B:HOH715 4.2 13.4 1.0
O1B B:PRP401 4.3 20.3 1.0
O3B B:PRP401 4.3 12.9 1.0
CA B:GLY107 4.3 12.6 1.0
CG B:ASP251 4.3 14.2 1.0
CG B:GLU252 4.4 14.8 1.0
O1 B:PRP401 4.4 25.6 1.0
O1A B:PRP401 4.5 28.7 1.0
C1 B:PRP401 4.5 19.3 0.7
C B:VAL106 4.6 11.6 1.0
O B:HOH705 4.7 22.1 1.0
CA B:VAL106 5.0 11.8 1.0

Magnesium binding site 4 out of 4 in 4gkm

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Magnesium binding site 4 out of 4 in the Bianthranilate-Like Analogue Bound in the Outer Site of Anthranilate Phosphoribosyltransferase (Anprt; Trpd)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Bianthranilate-Like Analogue Bound in the Outer Site of Anthranilate Phosphoribosyltransferase (Anprt; Trpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:18.8
occ:1.00
 O B:HOH704 2.0 22.8 1.0
O B:HOH705 2.1 22.1 1.0
O B:HOH706 2.1 22.7 1.0
O B:HOH702 2.1 13.7 1.0
OE2 B:GLU252 2.2 12.3 1.0
OD1 B:ASP251 2.2 15.4 1.0
CG B:ASP251 3.1 14.2 1.0
CD B:GLU252 3.2 13.7 1.0
MG B:MG402 3.2 12.0 1.0
OD2 B:ASP251 3.4 13.4 1.0
CG B:GLU252 3.5 14.8 1.0
O B:HOH707 3.6 30.4 1.0
O2B B:PRP401 3.6 15.7 1.0
OD2 B:ASP111 3.9 19.9 1.0
O B:HOH745 4.1 29.5 1.0
O B:HOH703 4.2 14.5 1.0
O4 B:PRP401 4.2 22.5 0.7
OG1 B:THR115 4.3 20.8 1.0
OE1 B:GLU252 4.3 14.4 1.0
O B:ASP251 4.3 12.9 1.0
O B:HOH708 4.3 31.7 1.0
O1B B:PRP401 4.5 20.3 1.0
CB B:ASP251 4.5 13.8 1.0
C B:ASP251 4.6 14.3 1.0
PB B:PRP401 4.6 15.0 1.0
O2A B:PRP401 4.7 14.5 1.0
CG B:ASP111 4.7 24.8 1.0
N B:ASP251 4.8 13.1 1.0
CA B:ASP251 4.9 14.1 1.0
C5 B:PRP401 4.9 20.8 0.7
C4 B:PRP401 5.0 17.9 0.7
CB B:GLU252 5.0 12.3 1.0

Reference:

G.L.Evans, S.A.Gamage, E.M.Bulloch, E.N.Baker, W.A.Denny, J.S.Lott. Repurposing the Chemical Scaffold of the Anti-Arthritic Drug Lobenzarit to Target Tryptophan Biosynthesis in Mycobacterium Tuberculosis. Chembiochem V. 15 852 2014.
ISSN: ISSN 1439-4227
PubMed: 24623674
DOI: 10.1002/CBIC.201300628
Page generated: Fri Aug 16 15:32:58 2024

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