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Magnesium in PDB 3qqs: Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS172)

Enzymatic activity of Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS172)

All present enzymatic activity of Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS172):
2.4.2.18;

Protein crystallography data

The structure of Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS172), PDB code: 3qqs was solved by A.Castell, F.L.Short, 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) 88.75 / 1.97
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 94.929, 78.213, 101.702, 90.00, 111.01, 90.00
R / Rfree (%) 21.6 / 25.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS172) (pdb code 3qqs). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS172), PDB code: 3qqs:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 3qqs

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Magnesium binding site 1 out of 5 in the Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS172)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS172) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:19.6
occ:1.00
 O1A A:PRP401 2.0 17.7 1.0
O3B A:PRP401 2.0 17.3 1.0
OE1 A:GLU252 2.1 15.3 1.0
OG A:SER119 2.2 15.9 1.0
O A:HOH503 2.3 13.4 1.0
O A:HOH501 2.3 15.3 1.0
CD A:GLU252 3.0 15.6 1.0
CB A:SER119 3.0 14.6 1.0
PB A:PRP401 3.1 20.1 1.0
PA A:PRP401 3.1 20.2 1.0
MG A:MG403 3.2 27.1 1.0
OE2 A:GLU252 3.3 15.9 1.0
O3A A:PRP401 3.4 20.0 1.0
O1 A:PRP401 3.5 18.8 1.0
OD2 A:ASP251 3.9 14.9 1.0
N A:SER119 4.0 14.2 1.0
N A:GLY107 4.0 12.5 1.0
CA A:SER119 4.1 15.0 1.0
O A:HOH502 4.2 11.9 1.0
O2B A:PRP401 4.2 20.9 1.0
OD1 A:ASP251 4.2 15.1 1.0
O1B A:PRP401 4.2 15.7 1.0
O A:ASP251 4.3 13.9 1.0
CG A:ASP251 4.4 14.3 1.0
CG A:GLU252 4.4 14.5 1.0
O2A A:PRP401 4.5 24.1 1.0
CA A:GLY107 4.5 13.1 1.0
C A:VAL106 4.6 12.1 1.0
C1 A:PRP401 4.8 20.1 0.5
O4 A:PRP401 4.8 22.0 0.5
O A:HOH559 4.8 22.3 1.0
CA A:VAL106 4.9 12.0 1.0

Magnesium binding site 2 out of 5 in 3qqs

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Magnesium binding site 2 out of 5 in the Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS172)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS172) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:27.1
occ:1.00
 O A:HOH518 2.1 20.2 1.0
OE1 A:GLU252 2.2 15.3 1.0
O A:HOH503 2.2 13.4 1.0
OD1 A:ASP251 2.3 15.1 1.0
O A:HOH654 2.4 25.3 1.0
CD A:GLU252 3.2 15.6 1.0
MG A:MG402 3.2 19.6 1.0
CG A:ASP251 3.2 14.3 1.0
CG A:GLU252 3.4 14.5 1.0
O3B A:PRP401 3.4 17.3 1.0
OD2 A:ASP251 3.5 14.9 1.0
OD1 A:ASP111 4.0 25.9 1.0
OG1 A:THR115 4.2 27.5 1.0
O A:HOH501 4.3 15.3 1.0
OE2 A:GLU252 4.3 15.9 1.0
O A:ASP251 4.3 13.9 1.0
CB A:ASP251 4.6 14.1 1.0
PB A:PRP401 4.6 20.1 1.0
C A:ASP251 4.6 14.3 1.0
O2B A:PRP401 4.7 20.9 1.0
O1 A:PRP401 4.8 18.8 1.0
CG A:ASP111 4.8 27.9 1.0
O1A A:PRP401 4.8 17.7 1.0
C5 A:PRP401 4.8 18.3 0.5
N A:ASP251 4.8 14.4 1.0
O4 A:PRP401 4.9 22.0 0.5
CA A:ASP251 4.9 14.9 1.0
CB A:GLU252 4.9 13.4 1.0

Magnesium binding site 3 out of 5 in 3qqs

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Magnesium binding site 3 out of 5 in the Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS172)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS172) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:15.6
occ:1.00
 O1A B:PRP401 1.9 20.2 1.0
O1B B:PRP401 2.0 15.3 1.0
OG B:SER119 2.1 16.0 1.0
OE1 B:GLU252 2.2 9.6 1.0
O B:HOH505 2.2 21.6 1.0
O B:HOH550 2.2 14.2 1.0
CB B:SER119 3.0 14.1 1.0
CD B:GLU252 3.1 16.6 1.0
PA B:PRP401 3.2 19.9 1.0
PB B:PRP401 3.3 17.6 1.0
OE2 B:GLU252 3.3 16.4 1.0
MG B:MG403 3.3 22.7 1.0
O3A B:PRP401 3.6 21.2 1.0
O B:HOH525 3.6 27.9 1.0
O1 B:PRP401 3.8 22.9 1.0
N B:GLY107 3.9 14.2 1.0
N B:SER119 4.0 14.7 1.0
OD2 B:ASP251 4.0 17.1 1.0
CA B:SER119 4.0 14.9 1.0
O2B B:PRP401 4.3 17.8 1.0
CA B:GLY107 4.3 15.3 1.0
O B:ASP251 4.3 14.9 1.0
O3B B:PRP401 4.3 19.8 1.0
O B:HOH506 4.3 12.5 1.0
OD1 B:ASP251 4.4 20.4 1.0
O2A B:PRP401 4.4 22.3 1.0
CG B:ASP251 4.5 17.1 1.0
CG B:GLU252 4.5 13.3 1.0
C B:VAL106 4.5 13.4 1.0
CA B:VAL106 4.8 13.7 1.0
O B:HOH533 4.9 27.7 1.0
C1 B:PRP401 5.0 22.1 0.5

Magnesium binding site 4 out of 5 in 3qqs

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Magnesium binding site 4 out of 5 in the Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS172)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS172) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:22.7
occ:1.00
 O B:HOH525 2.0 27.9 1.0
O B:HOH620 2.1 22.8 1.0
OE1 B:GLU252 2.1 9.6 1.0
OD1 B:ASP251 2.2 20.4 1.0
O B:HOH550 2.3 14.2 1.0
CD B:GLU252 3.0 16.6 1.0
CG B:ASP251 3.2 17.1 1.0
CG B:GLU252 3.3 13.3 1.0
MG B:MG402 3.3 15.6 1.0
OD2 B:ASP251 3.4 17.1 1.0
O1B B:PRP401 3.5 15.3 1.0
OD2 B:ASP111 3.9 24.1 1.0
O B:HOH553 4.0 38.1 1.0
O B:HOH505 4.2 21.6 1.0
O B:ASP251 4.2 14.9 1.0
OE2 B:GLU252 4.2 16.4 1.0
OG1 B:THR115 4.3 27.9 1.0
C B:ASP251 4.5 15.1 1.0
CB B:ASP251 4.5 15.5 1.0
N B:ASP251 4.7 14.9 1.0
CG B:ASP111 4.7 26.5 1.0
O3B B:PRP401 4.7 19.8 1.0
CB B:GLU252 4.8 15.1 1.0
PB B:PRP401 4.8 17.6 1.0
CA B:ASP251 4.8 15.3 1.0
O1A B:PRP401 4.8 20.2 1.0
OD1 B:ASP111 4.9 28.2 1.0
OG B:SER119 4.9 16.0 1.0

Magnesium binding site 5 out of 5 in 3qqs

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Magnesium binding site 5 out of 5 in the Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS172)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS172) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:17.1
occ:0.50
 O2B C:PRP401 1.7 32.5 0.5
O C:HOH508 2.0 34.5 1.0
O C:HOH611 2.2 36.0 1.0
O1A C:PRP401 2.4 32.5 0.5
OE2 C:GLU252 2.4 39.6 1.0
OG C:SER119 2.6 35.7 1.0
PB C:PRP401 3.2 32.1 0.5
CB C:SER119 3.3 35.2 1.0
CD C:GLU252 3.4 40.6 1.0
PA C:PRP401 3.6 33.5 0.5
OE1 C:GLU252 3.7 40.8 1.0
O3A C:PRP401 3.8 33.2 0.5
N C:GLY107 3.8 36.7 1.0
O C:HOH509 3.9 39.5 1.0
CA C:GLY107 4.0 38.6 1.0
O3B C:PRP401 4.0 32.4 0.5
O1 C:PRP401 4.1 35.4 0.5
OD2 C:ASP251 4.1 38.7 1.0
O1B C:PRP401 4.2 31.2 0.5
OD1 C:ASP251 4.3 38.8 1.0
N C:SER119 4.4 37.4 1.0
CA C:SER119 4.4 35.3 1.0
C C:VAL106 4.4 34.9 1.0
O C:ASP251 4.5 38.3 1.0
CG C:ASP251 4.5 38.5 1.0
C1 C:PRP401 4.7 36.4 0.5
O4 C:PRP401 4.7 36.7 0.5
CG C:GLU252 4.7 39.9 1.0
CA C:VAL106 4.8 33.0 1.0
O2A C:PRP401 4.9 34.6 0.5
C C:GLY107 4.9 40.2 1.0

Reference:

A.Castell, F.L.Short, G.L.Evans, T.V.Cookson, E.M.Bulloch, D.D.Joseph, C.E.Lee, E.J.Parker, E.N.Baker, J.S.Lott. The Substrate Capture Mechanism of Mycobacterium Tuberculosis Anthranilate Phosphoribosyltransferase Provides A Mode For Inhibition. Biochemistry V. 52 1776 2013.
ISSN: ISSN 0006-2960
PubMed: 23363292
DOI: 10.1021/BI301387M
Page generated: Thu Aug 15 10:08:06 2024

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