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Magnesium in PDB 3qs8: Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS174)

Enzymatic activity of Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS174)

All present enzymatic activity of Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS174):
2.4.2.18;

Protein crystallography data

The structure of Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS174), PDB code: 3qs8 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) 40.42 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.390, 80.823, 110.520, 90.00, 90.14, 90.00
R / Rfree (%) 18.8 / 24.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS174) (pdb code 3qs8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS174), PDB code: 3qs8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3qs8

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Magnesium binding site 1 out of 8 in the Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS174)


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 ACS174) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg500

b:16.4
occ:1.00
 O2B A:PRP400 2.0 14.6 1.0
O1A A:PRP400 2.1 19.3 1.0
O A:HOH409 2.1 15.2 1.0
O A:HOH392 2.1 13.5 1.0
OE2 A:GLU252 2.1 18.9 1.0
OG A:SER119 2.2 17.6 1.0
CD A:GLU252 3.0 19.4 1.0
CB A:SER119 3.2 12.6 1.0
PB A:PRP400 3.2 16.4 1.0
PA A:PRP400 3.3 19.4 1.0
MG A:MG501 3.3 34.4 1.0
OE1 A:GLU252 3.3 19.5 1.0
O3A A:PRP400 3.4 22.2 1.0
O A:HOH385 3.6 26.6 1.0
OD2 A:ASP251 3.9 20.2 1.0
N A:GLY107 3.9 16.9 1.0
N A:SER119 4.0 14.7 1.0
OD1 A:ASP251 4.1 19.7 1.0
O1B A:PRP400 4.1 22.6 1.0
O4 A:PRP400 4.2 21.8 1.0
O A:ASP251 4.2 16.7 1.0
CA A:SER119 4.2 14.7 1.0
O A:HOH451 4.2 21.5 1.0
O1 A:PRP400 4.3 19.4 1.0
CA A:GLY107 4.3 17.4 1.0
CG A:ASP251 4.3 18.8 1.0
O3B A:PRP400 4.3 17.3 1.0
O2A A:PRP400 4.3 23.3 1.0
CG A:GLU252 4.5 17.9 1.0
C1 A:PRP400 4.5 18.9 1.0
C A:VAL106 4.7 17.5 1.0
O A:HOH393 4.7 27.0 1.0
O A:HOH382 4.7 28.9 1.0
O A:HOH524 5.0 25.1 1.0
CA A:VAL106 5.0 17.2 1.0

Magnesium binding site 2 out of 8 in 3qs8

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Magnesium binding site 2 out of 8 in the Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS174)


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 ACS174) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:34.4
occ:1.00
 O A:HOH396 1.9 32.6 1.0
O A:HOH393 2.0 27.0 1.0
OD1 A:ASP251 2.2 19.7 1.0
OE2 A:GLU252 2.3 18.9 1.0
O A:HOH385 2.3 26.6 1.0
O A:HOH392 2.3 13.5 1.0
O A:HOH382 3.2 28.9 1.0
CD A:GLU252 3.2 19.4 1.0
CG A:ASP251 3.2 18.8 1.0
MG A:MG500 3.3 16.4 1.0
O2B A:PRP400 3.5 14.6 1.0
CG A:GLU252 3.5 17.9 1.0
OD2 A:ASP251 3.6 20.2 1.0
OD2 A:ASP111 3.7 27.8 1.0
O A:HOH380 4.0 36.4 1.0
OG1 A:THR115 4.2 26.9 1.0
O A:HOH409 4.3 15.2 1.0
O1B A:PRP400 4.3 22.6 1.0
OE1 A:GLU252 4.4 19.5 1.0
O A:ASP251 4.4 16.7 1.0
PB A:PRP400 4.6 16.4 1.0
O4 A:PRP400 4.6 21.8 1.0
CB A:ASP251 4.6 16.9 1.0
C A:ASP251 4.6 18.1 1.0
CG A:ASP111 4.6 25.5 1.0
N A:ASP251 4.7 17.7 1.0
O1A A:PRP400 4.9 19.3 1.0
CA A:ASP251 4.9 17.6 1.0

Magnesium binding site 3 out of 8 in 3qs8

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Magnesium binding site 3 out of 8 in the Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS174)


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 ACS174) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg500

b:21.4
occ:1.00
 O2B B:PRP400 1.9 17.6 1.0
OE2 B:GLU252 2.0 22.8 1.0
O B:HOH383 2.1 25.3 1.0
O1A B:PRP400 2.1 18.9 1.0
O B:HOH390 2.1 21.5 1.0
OG B:SER119 2.2 18.2 1.0
CD B:GLU252 3.0 25.4 1.0
CB B:SER119 3.1 18.2 1.0
OE1 B:GLU252 3.2 27.4 1.0
PB B:PRP400 3.3 21.9 1.0
PA B:PRP400 3.4 23.1 1.0
MG B:MG501 3.4 38.3 1.0
O3A B:PRP400 3.6 24.8 1.0
O B:HOH392 3.8 39.6 1.0
N B:SER119 4.0 18.9 1.0
N B:GLY107 4.0 18.8 1.0
O B:HOH388 4.0 24.4 1.0
OD2 B:ASP251 4.0 27.6 1.0
O B:ASP251 4.1 26.8 1.0
CA B:SER119 4.1 19.1 1.0
O4 B:PRP400 4.2 31.6 1.0
O1B B:PRP400 4.3 23.7 1.0
OD1 B:ASP251 4.3 27.4 1.0
CA B:GLY107 4.3 18.6 1.0
CG B:GLU252 4.3 24.0 1.0
O3B B:PRP400 4.3 20.5 1.0
O1 B:PRP400 4.4 26.4 1.0
O2A B:PRP400 4.4 28.8 1.0
CG B:ASP251 4.4 26.7 1.0
C1 B:PRP400 4.6 27.7 1.0
O B:HOH391 4.6 43.4 1.0
C B:VAL106 4.6 18.7 1.0
CA B:VAL106 5.0 19.1 1.0

Magnesium binding site 4 out of 8 in 3qs8

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Magnesium binding site 4 out of 8 in the Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS174)


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 ACS174) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:38.3
occ:1.00
 O B:HOH822 2.0 38.8 1.0
O B:HOH391 2.1 43.4 1.0
OE2 B:GLU252 2.4 22.8 1.0
O B:HOH390 2.4 21.5 1.0
O B:HOH392 2.4 39.6 1.0
OD1 B:ASP251 2.4 27.4 1.0
CD B:GLU252 3.3 25.4 1.0
CG B:ASP251 3.4 26.7 1.0
MG B:MG500 3.4 21.4 1.0
CG B:GLU252 3.5 24.0 1.0
O B:HOH384 3.5 40.7 1.0
O2B B:PRP400 3.6 17.6 1.0
OD2 B:ASP111 3.7 35.0 1.0
OD2 B:ASP251 3.8 27.6 1.0
O B:HOH511 4.1 40.4 1.0
OG1 B:THR115 4.1 37.3 1.0
O B:ASP251 4.3 26.8 1.0
O B:HOH383 4.4 25.3 1.0
OE1 B:GLU252 4.4 27.4 1.0
O1B B:PRP400 4.5 23.7 1.0
CG B:ASP111 4.6 32.8 1.0
O4 B:PRP400 4.6 31.6 1.0
C B:ASP251 4.6 26.8 1.0
N B:ASP251 4.7 26.3 1.0
PB B:PRP400 4.7 21.9 1.0
CB B:ASP251 4.7 26.4 1.0
CA B:ASP251 4.9 26.2 1.0
OD1 B:ASP111 5.0 34.5 1.0
CB B:GLU252 5.0 26.1 1.0

Magnesium binding site 5 out of 8 in 3qs8

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Magnesium binding site 5 out of 8 in the Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS174)


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 ACS174) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg500

b:17.3
occ:1.00
 O2B C:PRP400 2.0 15.9 1.0
O C:HOH407 2.1 15.9 1.0
OE2 C:GLU252 2.1 18.4 1.0
O1A C:PRP400 2.1 19.3 1.0
O C:HOH380 2.2 13.7 1.0
OG C:SER119 2.2 16.8 1.0
CD C:GLU252 3.0 19.8 1.0
CB C:SER119 3.1 15.0 1.0
OE1 C:GLU252 3.3 21.5 1.0
PA C:PRP400 3.3 18.7 1.0
PB C:PRP400 3.3 17.3 1.0
MG C:MG501 3.4 31.9 1.0
O3A C:PRP400 3.5 23.2 1.0
O C:HOH385 3.6 27.1 1.0
OD2 C:ASP251 3.9 18.2 1.0
N C:GLY107 3.9 16.5 1.0
N C:SER119 4.0 16.5 1.0
O C:ASP251 4.1 17.9 1.0
O C:HOH823 4.1 22.0 1.0
CA C:SER119 4.2 16.2 1.0
O4 C:PRP400 4.2 19.6 1.0
OD1 C:ASP251 4.2 16.9 1.0
CA C:GLY107 4.2 16.7 1.0
O1B C:PRP400 4.2 21.4 1.0
O1 C:PRP400 4.3 20.1 1.0
CG C:ASP251 4.3 16.8 1.0
O2A C:PRP400 4.4 23.5 1.0
O3B C:PRP400 4.4 15.8 1.0
CG C:GLU252 4.4 16.7 1.0
C1 C:PRP400 4.5 17.2 1.0
O C:HOH421 4.6 30.2 1.0
C C:VAL106 4.6 16.3 1.0
O C:HOH388 4.8 32.4 1.0
CA C:VAL106 4.9 16.0 1.0

Magnesium binding site 6 out of 8 in 3qs8

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Magnesium binding site 6 out of 8 in the Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS174)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS174) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:31.9
occ:1.00
 O C:HOH379 1.9 27.9 1.0
O C:HOH421 2.1 30.2 1.0
OE2 C:GLU252 2.2 18.4 1.0
OD1 C:ASP251 2.2 16.9 1.0
O C:HOH385 2.3 27.1 1.0
O C:HOH380 2.6 13.7 1.0
CD C:GLU252 3.1 19.8 1.0
CG C:GLU252 3.3 16.7 1.0
CG C:ASP251 3.3 16.8 1.0
MG C:MG500 3.4 17.3 1.0
O2B C:PRP400 3.6 15.9 1.0
O C:HOH388 3.6 32.4 1.0
OD2 C:ASP111 3.6 28.0 1.0
OD2 C:ASP251 3.6 18.2 1.0
O C:HOH394 4.1 37.5 1.0
O C:ASP251 4.1 17.9 1.0
OG1 C:THR115 4.2 25.6 1.0
OE1 C:GLU252 4.3 21.5 1.0
O C:HOH407 4.3 15.9 1.0
C C:ASP251 4.4 18.4 1.0
CB C:ASP251 4.6 17.2 1.0
N C:ASP251 4.6 17.8 1.0
CG C:ASP111 4.6 26.1 1.0
O1B C:PRP400 4.6 21.4 1.0
CB C:GLU252 4.8 16.9 1.0
CA C:ASP251 4.8 17.4 1.0
PB C:PRP400 4.8 17.3 1.0
O4 C:PRP400 4.8 19.6 1.0

Magnesium binding site 7 out of 8 in 3qs8

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Magnesium binding site 7 out of 8 in the Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS174)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS174) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg500

b:21.2
occ:1.00
 O D:HOH404 2.0 23.6 1.0
OE2 D:GLU252 2.0 21.8 1.0
O2B D:PRP400 2.1 16.8 1.0
OG D:SER119 2.1 20.3 1.0
O1A D:PRP400 2.2 20.5 1.0
O D:HOH383 2.2 22.6 1.0
CD D:GLU252 3.0 23.7 1.0
CB D:SER119 3.0 19.4 1.0
OE1 D:GLU252 3.2 23.9 1.0
PA D:PRP400 3.3 22.8 1.0
PB D:PRP400 3.4 23.9 1.0
MG D:MG501 3.4 39.1 1.0
O3A D:PRP400 3.6 25.8 1.0
O D:HOH768 3.8 37.2 1.0
OD2 D:ASP251 4.0 26.2 1.0
N D:GLY107 4.0 19.1 1.0
N D:SER119 4.0 20.9 1.0
O D:HOH384 4.0 23.7 1.0
CA D:SER119 4.1 20.2 1.0
O D:ASP251 4.1 24.9 1.0
O4 D:PRP400 4.2 31.1 1.0
CA D:GLY107 4.3 19.5 1.0
O1B D:PRP400 4.3 23.9 1.0
OD1 D:ASP251 4.3 26.8 1.0
CG D:GLU252 4.3 21.6 1.0
O1 D:PRP400 4.4 26.0 1.0
O2A D:PRP400 4.4 27.0 1.0
O3B D:PRP400 4.4 20.6 1.0
CG D:ASP251 4.4 25.2 1.0
C1 D:PRP400 4.5 26.7 1.0
C D:VAL106 4.6 18.8 1.0
O D:HOH381 4.7 30.1 1.0
O D:HOH707 4.8 39.1 1.0
CA D:VAL106 4.9 18.8 1.0

Magnesium binding site 8 out of 8 in 3qs8

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Magnesium binding site 8 out of 8 in the Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS174)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Anthranilate Phosphoribosyltransferase (Trpd) From Mycobacterium Tuberculosis (Complex with Inhibitor ACS174) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:39.1
occ:1.00
 O D:HOH824 2.0 35.5 1.0
O D:HOH381 2.1 30.1 1.0
OE2 D:GLU252 2.2 21.8 1.0
OD1 D:ASP251 2.4 26.8 1.0
O D:HOH383 2.4 22.6 1.0
O D:HOH768 2.5 37.2 1.0
CD D:GLU252 3.1 23.7 1.0
CG D:GLU252 3.4 21.6 1.0
CG D:ASP251 3.4 25.2 1.0
MG D:MG500 3.4 21.2 1.0
O2B D:PRP400 3.6 16.8 1.0
OD2 D:ASP251 3.7 26.2 1.0
OD2 D:ASP111 3.9 36.3 1.0
OG1 D:THR115 4.2 35.5 1.0
O D:HOH404 4.3 23.6 1.0
O D:ASP251 4.3 24.9 1.0
OE1 D:GLU252 4.3 23.9 1.0
O D:HOH386 4.3 42.7 1.0
C D:ASP251 4.6 25.1 1.0
O1B D:PRP400 4.6 23.9 1.0
O4 D:PRP400 4.6 31.1 1.0
CG D:ASP111 4.6 34.1 1.0
CB D:ASP251 4.7 24.2 1.0
N D:ASP251 4.7 24.3 1.0
PB D:PRP400 4.8 23.9 1.0
CB D:GLU252 4.9 24.3 1.0
CA D:ASP251 4.9 24.7 1.0
OD1 D:ASP111 4.9 35.5 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 10:08:39 2024

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