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Magnesium in PDB 9drs: Crystal Structure of M. Tuberculosis Phers-Trna Complex Bound to Inhibitor D-116

Enzymatic activity of Crystal Structure of M. Tuberculosis Phers-Trna Complex Bound to Inhibitor D-116

All present enzymatic activity of Crystal Structure of M. Tuberculosis Phers-Trna Complex Bound to Inhibitor D-116:
6.1.1.20;

Protein crystallography data

The structure of Crystal Structure of M. Tuberculosis Phers-Trna Complex Bound to Inhibitor D-116, PDB code: 9drs was solved by P.Gade, C.Chang, B.Forte, J.Wower, I.H.Gilbert, B.Baragana, K.Michalska, A.Joachimiak, Center For Structural Biology Of Infectious Diseases(Csbid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.77 / 2.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 146.676, 64.106, 188.334, 90, 111.21, 90
R / Rfree (%) 20.1 / 25

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of M. Tuberculosis Phers-Trna Complex Bound to Inhibitor D-116 (pdb code 9drs). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of M. Tuberculosis Phers-Trna Complex Bound to Inhibitor D-116, PDB code: 9drs:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 9drs

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Magnesium binding site 1 out of 7 in the Crystal Structure of M. Tuberculosis Phers-Trna Complex Bound to Inhibitor D-116


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 Phers-Trna Complex Bound to Inhibitor D-116 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:20.4
occ:1.00
 OE1 B:GLU476 1.9 31.8 1.0
O B:HOH1059 2.1 22.8 1.0
O B:HOH1097 2.1 30.2 1.0
O A:HOH517 2.1 30.0 1.0
OE2 A:GLU259 2.2 35.8 1.0
O B:HOH1159 2.4 21.0 1.0
CD B:GLU476 3.0 31.1 1.0
CD A:GLU259 3.1 37.1 1.0
OE1 A:GLU259 3.2 39.1 1.0
OD2 B:ASP172 3.5 31.9 1.0
OE2 B:GLU476 3.6 34.9 1.0
CG B:GLU476 4.0 27.6 1.0
CB B:GLU476 4.2 22.1 1.0
OD1 B:ASP473 4.2 33.8 1.0
NH2 B:ARG173 4.2 26.7 1.0
OD2 B:ASP467 4.3 29.4 1.0
CG A:GLU259 4.5 30.1 1.0
CG B:ASP172 4.6 23.7 1.0
O B:ASP473 4.7 25.0 1.0
OE2 B:GLU477 4.7 26.6 1.0
CA B:ASP473 4.7 22.5 1.0
CB B:ASP473 4.9 28.0 1.0
O B:HOH1283 4.9 43.3 1.0
CZ B:ARG173 4.9 28.4 1.0
O B:HOH1054 4.9 33.8 1.0

Magnesium binding site 2 out of 7 in 9drs

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Magnesium binding site 2 out of 7 in the Crystal Structure of M. Tuberculosis Phers-Trna Complex Bound to Inhibitor D-116


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 Phers-Trna Complex Bound to Inhibitor D-116 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg103

b:47.5
occ:1.00
 O C:HOH214 2.0 28.0 1.0
O C:HOH211 2.2 26.4 1.0
O C:HOH233 2.3 38.9 1.0
O C:HOH219 2.4 24.9 1.0
O C:HOH216 2.4 32.4 1.0
OP1 C:U8 3.7 51.5 1.0
OP2 C:U8 3.9 46.3 1.0
OP1 C:A9 3.9 37.0 1.0
OP2 C:U12 4.0 25.2 1.0
OP2 C:A9 4.0 35.7 1.0
OP2 C:C11 4.2 22.1 1.0
P C:U8 4.3 40.2 1.0
O C:HOH213 4.3 18.9 1.0
P C:A9 4.5 35.3 1.0
O C:HOH209 4.5 27.7 1.0
C5 C:U12 4.9 20.2 1.0
O C:HOH242 5.0 38.2 1.0
O5' C:C11 5.0 20.9 1.0

Magnesium binding site 3 out of 7 in 9drs

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Magnesium binding site 3 out of 7 in the Crystal Structure of M. Tuberculosis Phers-Trna Complex Bound to Inhibitor D-116


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 Phers-Trna Complex Bound to Inhibitor D-116 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg104

b:47.5
occ:1.00
 O C:HOH245 2.5 54.1 1.0
O C:HOH246 2.5 45.1 1.0
O C:HOH241 2.6 39.5 1.0
O6 C:G46 2.7 32.5 1.0
O C:HOH244 3.5 36.2 1.0
C6 C:G46 3.8 27.1 1.0
N7 C:A45 4.5 28.8 1.0
N7 C:G46 4.5 37.0 1.0
C5 C:G46 4.5 33.4 1.0
OP1 C:G23 4.5 82.8 1.0
OP2 C:A45 4.9 39.6 1.0
N1 C:G46 4.9 30.6 1.0
N6 C:A45 5.0 30.9 1.0

Magnesium binding site 4 out of 7 in 9drs

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Magnesium binding site 4 out of 7 in the Crystal Structure of M. Tuberculosis Phers-Trna Complex Bound to Inhibitor D-116


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 Phers-Trna Complex Bound to Inhibitor D-116 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg105

b:50.4
occ:1.00
 O C:HOH204 2.4 33.0 1.0
O C:HOH212 2.5 35.8 1.0
O C:HOH260 2.6 37.4 1.0
O C:HOH220 2.6 38.6 1.0
O C:HOH255 3.6 33.4 1.0
OP1 C:A38 3.8 37.6 1.0
O C:HOH215 3.9 35.7 1.0
OP2 C:A38 4.1 27.5 1.0
O C:HOH231 4.3 30.2 1.0
P C:A38 4.3 32.9 1.0
N4 C:C30 4.4 33.0 1.0
O C:HOH263 4.4 37.7 1.0
C5 C:C30 4.6 32.7 1.0
OP2 C:A39 4.8 21.2 1.0
O6 C:G31 4.8 29.0 1.0
C4 C:C30 4.8 31.8 1.0
O5' C:A38 4.9 38.4 1.0

Magnesium binding site 5 out of 7 in 9drs

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Magnesium binding site 5 out of 7 in the Crystal Structure of M. Tuberculosis Phers-Trna Complex Bound to Inhibitor D-116


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 Phers-Trna Complex Bound to Inhibitor D-116 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg106

b:52.1
occ:1.00
 O C:HOH263 2.3 37.7 1.0
O6 C:G42 2.5 36.9 1.0
O C:HOH253 2.8 35.5 1.0
O6 C:G43 3.2 30.1 1.0
C6 C:G42 3.6 36.5 1.0
N4 C:C30 3.9 33.0 1.0
C6 C:G43 4.0 32.1 1.0
N4 C:C41 4.1 33.9 1.0
N4 C:C29 4.1 31.4 1.0
N7 C:G43 4.1 32.5 1.0
O C:HOH235 4.2 34.6 1.0
C5 C:G43 4.3 33.5 1.0
C5 C:G42 4.4 41.4 1.0
N7 C:G42 4.5 43.0 1.0
O C:HOH248 4.6 33.8 1.0
O C:HOH225 4.6 41.6 1.0
N1 C:G42 4.7 34.1 1.0
O C:HOH277 4.8 42.5 1.0
O C:HOH212 4.9 35.8 1.0

Magnesium binding site 6 out of 7 in 9drs

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Magnesium binding site 6 out of 7 in the Crystal Structure of M. Tuberculosis Phers-Trna Complex Bound to Inhibitor D-116


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 Phers-Trna Complex Bound to Inhibitor D-116 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:33.6
occ:1.00
 O E:HOH1066 2.0 30.1 1.0
OE2 D:GLU259 2.1 35.5 1.0
O E:HOH1013 2.1 33.1 1.0
O D:HOH516 2.1 33.7 1.0
OE1 E:GLU476 2.3 32.8 1.0
O E:HOH1009 2.3 31.7 1.0
CD D:GLU259 3.1 36.8 1.0
CD E:GLU476 3.1 42.9 1.0
OE1 D:GLU259 3.4 34.2 1.0
OE2 E:GLU476 3.7 44.7 1.0
OD2 E:ASP172 3.8 38.3 1.0
OD2 E:ASP467 3.9 32.9 1.0
CG E:GLU476 4.1 31.0 1.0
CB E:GLU476 4.1 25.3 1.0
OD1 E:ASP473 4.1 31.9 1.0
O E:ASP473 4.4 24.7 1.0
O D:HOH502 4.4 34.8 1.0
CG D:GLU259 4.4 29.8 1.0
CA E:ASP473 4.5 31.7 1.0
OE2 E:GLU477 4.5 29.7 1.0
NH2 E:ARG173 4.6 34.3 1.0
CB E:ASP473 4.7 29.2 1.0
NH1 E:ARG173 4.7 38.0 1.0
CD2 E:LEU468 4.8 31.7 1.0
CG E:ASP172 4.8 39.6 1.0
CG E:ASP473 4.9 37.4 1.0
C E:ASP473 4.9 31.5 1.0
CZ E:ARG173 5.0 40.7 1.0

Magnesium binding site 7 out of 7 in 9drs

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Magnesium binding site 7 out of 7 in the Crystal Structure of M. Tuberculosis Phers-Trna Complex Bound to Inhibitor D-116


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 Phers-Trna Complex Bound to Inhibitor D-116 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg101

b:56.4
occ:1.00
 O F:HOH216 2.4 42.7 1.0
O F:HOH210 2.7 43.0 1.0
O F:HOH214 2.9 31.6 1.0
O6 F:G31 3.8 62.4 1.0
N4 F:C30 4.1 50.4 1.0
N7 F:G31 4.4 52.1 1.0
OP2 F:A38 4.4 28.3 1.0
N4 F:C32 4.5 47.5 1.0
C4 F:C30 4.5 48.3 1.0
C5 F:C30 4.6 53.0 1.0
OP1 F:A38 4.6 35.7 1.0
C6 F:G31 4.7 55.8 1.0
O6 F:G40 5.0 44.5 1.0
C5 F:G31 5.0 54.7 1.0
OP2 F:A39 5.0 19.3 1.0

Reference:

P.Gade, C.Chang, D.S.Pryde, D.Fletcher, S.Niven, L.G.Magalhaes, D.Robinson, J.Saini, P.E.Ibrahim, B.Forte, J.Wower, M.J.Bodkin, B.Baragana, I.H.Gilbert, K.Michalska, A.Joachimiak. Different Chemical Scaffolds Bind to L-Phe Site in Mycobacterium Tuberculosis Phe-Trna Synthetase Eur.J.Med.Chem. 17335 2025.
ISSN: ISSN 0223-5234
DOI: 10.1016/J.EJMECH.2025.117335
Page generated: Tue Feb 25 11:17:35 2025

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