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Magnesium in PDB 3twp: Crystal Structure of M. Tuberculosis Trpd in Complex with An Inhibitor

Enzymatic activity of Crystal Structure of M. Tuberculosis Trpd in Complex with An Inhibitor

All present enzymatic activity of Crystal Structure of M. Tuberculosis Trpd in Complex with An Inhibitor:
2.4.2.18;

Protein crystallography data

The structure of Crystal Structure of M. Tuberculosis Trpd in Complex with An Inhibitor, PDB code: 3twp was solved by A.Castell, F.L.Short, J.S.Lott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.12 / 1.83
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.689, 111.263, 81.118, 90.00, 90.06, 90.00
R / Rfree (%) 19.3 / 23.8

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 8 in 3twp

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Magnesium binding site 1 out of 8 in the Crystal Structure of M. Tuberculosis Trpd in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of M. Tuberculosis Trpd in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:20.1
occ:1.00
 OE1 A:GLU252 2.0 17.6 1.0
O3B A:PRP401 2.0 16.4 1.0
O1A A:PRP401 2.1 15.3 1.0
O A:HOH519 2.1 14.7 1.0
OG A:SER119 2.1 16.6 1.0
O A:HOH586 2.1 16.9 1.0
CD A:GLU252 3.0 19.0 1.0
CB A:SER119 3.1 15.1 1.0
PB A:PRP401 3.3 18.3 1.0
PA A:PRP401 3.3 19.6 1.0
OE2 A:GLU252 3.3 18.7 1.0
MG A:MG403 3.4 29.4 1.0
O3A A:PRP401 3.6 21.1 1.0
N A:GLY107 3.9 15.0 1.0
O A:HOH640 4.0 25.0 1.0
N A:SER119 4.0 15.7 1.0
OD2 A:ASP251 4.0 19.3 1.0
CA A:SER119 4.1 15.3 1.0
O A:ASP251 4.1 20.3 1.0
O A:HOH565 4.2 19.3 1.0
CA A:GLY107 4.3 14.9 1.0
O2A A:PRP401 4.3 26.2 1.0
O1B A:PRP401 4.3 16.8 1.0
O4 A:PRP401 4.4 27.7 1.0
CG A:GLU252 4.4 19.8 1.0
O2B A:PRP401 4.4 21.1 1.0
O1 A:PRP401 4.4 24.1 1.0
OD1 A:ASP251 4.4 21.3 1.0
CG A:ASP251 4.5 20.4 1.0
C A:VAL106 4.6 14.6 1.0
C1 A:PRP401 4.7 25.6 1.0
CA A:VAL106 4.8 13.8 1.0

Magnesium binding site 2 out of 8 in 3twp

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Magnesium binding site 2 out of 8 in the Crystal Structure of M. Tuberculosis Trpd in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of M. Tuberculosis Trpd in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:29.4
occ:1.00
 OE1 A:GLU252 2.3 17.6 1.0
O A:HOH586 2.4 16.9 1.0
OD1 A:ASP251 2.4 21.3 1.0
O A:HOH560 2.4 38.4 1.0
O A:HOH640 2.5 25.0 1.0
CD A:GLU252 3.2 19.0 1.0
CG A:ASP251 3.3 20.4 1.0
CG A:GLU252 3.4 19.8 1.0
MG A:MG402 3.4 20.1 1.0
O3B A:PRP401 3.5 16.4 1.0
OD2 A:ASP251 3.6 19.3 1.0
O A:HOH721 3.7 34.7 1.0
OD1 A:ASP111 4.0 25.9 1.0
O A:ASP251 4.3 20.3 1.0
O A:HOH519 4.3 14.7 1.0
O A:HOH558 4.4 32.3 1.0
OG1 A:THR115 4.4 26.4 1.0
OE2 A:GLU252 4.4 18.7 1.0
C A:ASP251 4.6 21.1 1.0
PB A:PRP401 4.6 18.3 1.0
O2B A:PRP401 4.7 21.1 1.0
CB A:ASP251 4.7 20.8 1.0
N A:ASP251 4.8 21.7 1.0
CG A:ASP111 4.8 27.7 1.0
O4 A:PRP401 4.8 27.7 1.0
CB A:GLU252 4.8 20.6 1.0
CA A:ASP251 4.9 20.9 1.0
O1A A:PRP401 4.9 15.3 1.0

Magnesium binding site 3 out of 8 in 3twp

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Magnesium binding site 3 out of 8 in the Crystal Structure of M. Tuberculosis Trpd in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of M. Tuberculosis Trpd in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:12.7
occ:1.00
 O3B B:PRP401 2.0 10.4 1.0
OE1 B:GLU252 2.1 12.0 1.0
O1A B:PRP401 2.1 12.1 1.0
O B:HOH598 2.1 11.8 1.0
O B:HOH573 2.1 11.6 1.0
OG B:SER119 2.2 11.0 1.0
CD B:GLU252 3.0 12.9 1.0
CB B:SER119 3.1 8.6 1.0
PB B:PRP401 3.2 12.7 1.0
PA B:PRP401 3.2 12.9 1.0
OE2 B:GLU252 3.4 12.8 1.0
MG B:MG403 3.4 19.5 1.0
O3A B:PRP401 3.4 14.9 1.0
O B:HOH588 3.9 19.2 1.0
N B:GLY107 3.9 10.8 1.0
N B:SER119 4.0 9.0 1.0
OD2 B:ASP251 4.0 11.8 1.0
CA B:SER119 4.1 9.5 1.0
O4 B:PRP401 4.2 21.5 1.0
O2B B:PRP401 4.2 13.9 1.0
O B:ASP251 4.2 9.4 1.0
O1B B:PRP401 4.3 10.1 1.0
O1 B:PRP401 4.3 17.5 1.0
O B:HOH591 4.3 11.3 1.0
CA B:GLY107 4.3 10.1 1.0
O2A B:PRP401 4.3 21.3 1.0
OD1 B:ASP251 4.4 11.9 1.0
CG B:GLU252 4.4 10.8 1.0
CG B:ASP251 4.4 11.7 1.0
O B:HOH755 4.5 28.0 1.0
C1 B:PRP401 4.6 18.3 1.0
C B:VAL106 4.6 10.8 1.0
CA B:VAL106 4.9 10.9 1.0

Magnesium binding site 4 out of 8 in 3twp

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Magnesium binding site 4 out of 8 in the Crystal Structure of M. Tuberculosis Trpd in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of M. Tuberculosis Trpd in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:19.5
occ:1.00
 OE1 B:GLU252 2.3 12.0 1.0
OD1 B:ASP251 2.3 11.9 1.0
O B:HOH588 2.4 19.2 1.0
O B:HOH573 2.5 11.6 1.0
O B:HOH792 2.7 33.2 1.0
O B:HOH755 2.8 28.0 1.0
CD B:GLU252 3.2 12.9 1.0
CG B:ASP251 3.3 11.7 1.0
MG B:MG402 3.4 12.7 1.0
CG B:GLU252 3.4 10.8 1.0
O3B B:PRP401 3.5 10.4 1.0
O B:HOH530 3.6 20.3 1.0
OD2 B:ASP251 3.7 11.8 1.0
OD1 B:ASP111 3.9 18.6 1.0
O B:HOH593 4.1 27.1 1.0
OG1 B:THR115 4.3 18.1 1.0
O B:HOH598 4.3 11.8 1.0
O B:ASP251 4.4 9.4 1.0
OE2 B:GLU252 4.4 12.8 1.0
O2B B:PRP401 4.4 13.9 1.0
O B:HOH592 4.5 16.5 1.0
PB B:PRP401 4.5 12.7 1.0
C B:ASP251 4.6 11.1 1.0
CB B:ASP251 4.7 10.8 1.0
N B:ASP251 4.7 10.6 1.0
O4 B:PRP401 4.7 21.5 1.0
CG B:ASP111 4.8 18.2 1.0
CA B:ASP251 4.9 10.8 1.0
CB B:GLU252 4.9 11.1 1.0

Magnesium binding site 5 out of 8 in 3twp

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Magnesium binding site 5 out of 8 in the Crystal Structure of M. Tuberculosis Trpd in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of M. Tuberculosis Trpd in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:12.8
occ:1.00
 O1B C:PRP401 2.0 10.0 1.0
OE1 C:GLU252 2.0 9.9 1.0
O1A C:PRP401 2.1 9.6 1.0
O C:HOH606 2.1 10.7 1.0
O C:HOH604 2.1 10.4 1.0
OG C:SER119 2.2 12.2 1.0
CD C:GLU252 3.0 11.6 1.0
CB C:SER119 3.1 9.2 1.0
PB C:PRP401 3.2 13.1 1.0
PA C:PRP401 3.3 13.4 1.0
OE2 C:GLU252 3.3 13.0 1.0
O3A C:PRP401 3.4 14.6 1.0
MG C:MG403 3.4 18.1 1.0
N C:GLY107 3.9 10.1 1.0
O C:HOH768 4.0 18.5 1.0
N C:SER119 4.0 9.7 1.0
OD2 C:ASP251 4.0 11.4 1.0
CA C:SER119 4.1 10.5 1.0
O3B C:PRP401 4.2 14.5 1.0
O C:ASP251 4.2 10.4 1.0
O4 C:PRP401 4.2 21.6 1.0
O2B C:PRP401 4.2 10.5 1.0
O C:HOH623 4.2 11.8 1.0
O1 C:PRP401 4.3 19.0 1.0
O2A C:PRP401 4.3 21.8 1.0
CA C:GLY107 4.3 10.2 1.0
CG C:GLU252 4.4 12.0 1.0
OD1 C:ASP251 4.4 12.7 1.0
CG C:ASP251 4.4 12.5 1.0
O C:HOH607 4.5 26.6 1.0
C1 C:PRP401 4.6 18.2 1.0
C C:VAL106 4.6 11.2 1.0
CA C:VAL106 4.9 10.8 1.0

Magnesium binding site 6 out of 8 in 3twp

Go back to Magnesium Binding Sites List in 3twp
Magnesium binding site 6 out of 8 in the Crystal Structure of M. Tuberculosis Trpd in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of M. Tuberculosis Trpd in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:18.1
occ:1.00
 OD1 C:ASP251 2.4 12.7 1.0
OE1 C:GLU252 2.4 9.9 1.0
O C:HOH768 2.4 18.5 1.0
O C:HOH606 2.5 10.7 1.0
O C:HOH574 2.7 29.9 1.0
O C:HOH607 2.7 26.6 1.0
CD C:GLU252 3.3 11.6 1.0
CG C:ASP251 3.4 12.5 1.0
MG C:MG402 3.4 12.8 1.0
CG C:GLU252 3.4 12.0 1.0
O1B C:PRP401 3.5 10.0 1.0
O C:HOH603 3.6 20.5 1.0
OD2 C:ASP251 3.7 11.4 1.0
OD1 C:ASP111 3.9 17.6 1.0
OG1 C:THR115 4.3 17.4 1.0
O C:ASP251 4.4 10.4 1.0
O C:HOH604 4.4 10.4 1.0
O C:HOH767 4.4 17.0 1.0
O3B C:PRP401 4.4 14.5 1.0
OE2 C:GLU252 4.5 13.0 1.0
PB C:PRP401 4.6 13.1 1.0
C C:ASP251 4.6 11.4 1.0
CB C:ASP251 4.7 11.2 1.0
N C:ASP251 4.7 10.9 1.0
CG C:ASP111 4.7 18.4 1.0
O4 C:PRP401 4.8 21.6 1.0
CA C:ASP251 4.9 11.2 1.0
CB C:GLU252 4.9 10.9 1.0
O C:HOH609 5.0 30.3 1.0

Magnesium binding site 7 out of 8 in 3twp

Go back to Magnesium Binding Sites List in 3twp
Magnesium binding site 7 out of 8 in the Crystal Structure of M. Tuberculosis Trpd in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of M. Tuberculosis Trpd in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:20.0
occ:1.00
 O1A D:PRP401 2.0 17.4 1.0
O1B D:PRP401 2.0 16.6 1.0
OE1 D:GLU252 2.1 18.1 1.0
O D:HOH524 2.1 13.9 1.0
OG D:SER119 2.1 16.9 1.0
O D:HOH554 2.2 19.0 1.0
CD D:GLU252 3.0 18.0 1.0
CB D:SER119 3.1 16.1 1.0
PA D:PRP401 3.3 18.4 1.0
PB D:PRP401 3.3 17.7 1.0
OE2 D:GLU252 3.3 18.9 1.0
MG D:MG403 3.4 27.5 1.0
O3A D:PRP401 3.6 21.4 1.0
OD2 D:ASP251 3.9 18.2 1.0
N D:GLY107 3.9 14.0 1.0
O D:HOH575 4.0 23.3 1.0
N D:SER119 4.0 16.5 1.0
CA D:SER119 4.1 15.6 1.0
O D:ASP251 4.2 20.5 1.0
O D:HOH576 4.2 18.2 1.0
O2B D:PRP401 4.3 17.2 1.0
CA D:GLY107 4.3 14.3 1.0
O3B D:PRP401 4.3 22.1 1.0
O2A D:PRP401 4.4 27.4 1.0
CG D:GLU252 4.4 19.8 1.0
O1 D:PRP401 4.4 23.8 1.0
O4 D:PRP401 4.4 26.9 1.0
OD1 D:ASP251 4.4 20.8 1.0
CG D:ASP251 4.4 19.6 1.0
C D:VAL106 4.6 14.1 1.0
C1 D:PRP401 4.7 24.7 1.0
CA D:VAL106 4.9 13.5 1.0

Magnesium binding site 8 out of 8 in 3twp

Go back to Magnesium Binding Sites List in 3twp
Magnesium binding site 8 out of 8 in the Crystal Structure of M. Tuberculosis Trpd in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of M. Tuberculosis Trpd in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg403

b:27.5
occ:1.00
 OD1 D:ASP251 2.3 20.8 1.0
OE1 D:GLU252 2.3 18.1 1.0
O D:HOH554 2.4 19.0 1.0
O D:HOH575 2.6 23.3 1.0
CD D:GLU252 3.2 18.0 1.0
CG D:ASP251 3.3 19.6 1.0
CG D:GLU252 3.4 19.8 1.0
MG D:MG402 3.4 20.0 1.0
OD2 D:ASP251 3.6 18.2 1.0
O1B D:PRP401 3.6 16.6 1.0
OD1 D:ASP111 4.0 26.7 1.0
O D:ASP251 4.2 20.5 1.0
O D:HOH524 4.3 13.9 1.0
OG1 D:THR115 4.3 25.6 1.0
OE2 D:GLU252 4.4 18.9 1.0
C D:ASP251 4.5 21.1 1.0
CB D:ASP251 4.6 20.5 1.0
O3B D:PRP401 4.7 22.1 1.0
PB D:PRP401 4.7 17.7 1.0
CG D:ASP111 4.7 27.4 1.0
N D:ASP251 4.7 22.4 1.0
CA D:ASP251 4.8 21.0 1.0
CB D:GLU252 4.9 20.7 1.0
O4 D:PRP401 4.9 26.9 1.0
O1A D:PRP401 4.9 17.4 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 12:16:58 2024

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