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Magnesium in PDB 5xet: Crystal Structure of Mycobacterium Tuberculosis Methionyl-Trna Synthetase Bound By Methionyl-Adenylate (Met-Amp)

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Methionyl-Trna Synthetase Bound By Methionyl-Adenylate (Met-Amp)

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Methionyl-Trna Synthetase Bound By Methionyl-Adenylate (Met-Amp):
6.1.1.10;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Methionyl-Trna Synthetase Bound By Methionyl-Adenylate (Met-Amp), PDB code: 5xet was solved by W.Wang, B.Qin, J.A.Wojdyla, M.Wang, X.Gao, S.Cui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.42 / 2.38
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 198.017, 198.017, 39.161, 90.00, 90.00, 120.00
R / Rfree (%) 20.1 / 25.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Methionyl-Trna Synthetase Bound By Methionyl-Adenylate (Met-Amp) (pdb code 5xet). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Mycobacterium Tuberculosis Methionyl-Trna Synthetase Bound By Methionyl-Adenylate (Met-Amp), PDB code: 5xet:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5xet

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Magnesium binding site 1 out of 5 in the Crystal Structure of Mycobacterium Tuberculosis Methionyl-Trna Synthetase Bound By Methionyl-Adenylate (Met-Amp)


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 Mycobacterium Tuberculosis Methionyl-Trna Synthetase Bound By Methionyl-Adenylate (Met-Amp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:47.4
occ:1.00
 OG C:SER301 1.8 56.8 1.0
HG22 C:VAL19 2.8 42.9 1.0
CB C:SER301 3.0 64.1 1.0
HG21 C:VAL19 3.4 42.9 1.0
CG2 C:VAL19 3.4 35.7 1.0
HG23 C:VAL19 3.5 42.9 1.0
HB2 C:ASN295 3.6 63.4 1.0
CG2 C:VAL308 3.6 36.0 1.0
N C:VAL308 3.7 47.3 1.0
HB2 C:HIS18 3.8 38.1 1.0
CB C:VAL308 3.8 36.2 1.0
CA C:SER301 4.2 70.2 1.0
O C:ASN306 4.2 53.4 1.0
H C:VAL19 4.2 39.2 1.0
CA C:VAL308 4.3 43.0 1.0
O C:HOH708 4.4 38.3 1.0
O C:LEU293 4.4 34.9 1.0
C C:ILE307 4.5 49.6 1.0
CB C:ASN295 4.6 52.9 1.0
CA C:ILE307 4.6 51.4 1.0
H C:GLY20 4.6 37.6 1.0
CB C:HIS18 4.7 31.8 1.0
HB3 C:ASN295 4.8 63.4 1.0
HD22 C:ASN295 4.8 62.8 1.0
CB C:VAL19 4.8 39.1 1.0
O C:VAL308 4.8 46.0 1.0
N C:SER301 4.9 71.5 1.0
N C:VAL19 4.9 32.6 1.0
HG13 C:VAL19 5.0 53.9 1.0
CG C:HIS18 5.0 39.0 1.0

Magnesium binding site 2 out of 5 in 5xet

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Magnesium binding site 2 out of 5 in the Crystal Structure of Mycobacterium Tuberculosis Methionyl-Trna Synthetase Bound By Methionyl-Adenylate (Met-Amp)


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 Mycobacterium Tuberculosis Methionyl-Trna Synthetase Bound By Methionyl-Adenylate (Met-Amp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg604

b:27.7
occ:1.00
 O C:HOH788 1.9 38.3 1.0
HE C:ARG397 2.7 53.2 1.0
HE2 C:HIS401 3.0 22.2 1.0
O C:HOH863 3.1 38.3 1.0
NE C:ARG397 3.5 44.4 1.0
HD2 C:ARG397 3.5 54.1 1.0
O C:HOH866 3.7 38.3 1.0
NE2 C:HIS401 3.7 18.5 1.0
HB3 C:ARG397 3.8 45.1 1.0
HE1 C:HIS401 3.9 23.2 1.0
HH21 C:ARG397 3.9 48.6 1.0
CD C:ARG397 4.0 45.1 1.0
CE1 C:HIS401 4.1 19.3 1.0
CZ C:ARG397 4.4 46.6 1.0
NH2 C:ARG397 4.5 40.5 1.0
HD3 C:ARG397 4.7 54.1 1.0
CB C:ARG397 4.7 37.6 1.0
HB2 C:ALA413 4.8 32.3 1.0
CD2 C:HIS401 4.9 18.4 1.0

Magnesium binding site 3 out of 5 in 5xet

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Magnesium binding site 3 out of 5 in the Crystal Structure of Mycobacterium Tuberculosis Methionyl-Trna Synthetase Bound By Methionyl-Adenylate (Met-Amp)


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 Mycobacterium Tuberculosis Methionyl-Trna Synthetase Bound By Methionyl-Adenylate (Met-Amp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg605

b:47.9
occ:1.00
 OH C:TYR23 2.4 28.6 1.0
HD1 C:PHE332 2.5 32.5 1.0
O C:VAL330 2.6 30.6 1.0
HB C:VAL330 2.8 30.8 1.0
O C:LEU326 2.9 21.9 1.0
HA C:LEU327 3.0 25.6 1.0
HA C:PHE332 3.1 32.2 1.0
CE1 C:TYR23 3.1 19.4 1.0
CZ C:TYR23 3.2 22.3 1.0
O C:HOH795 3.2 21.5 1.0
HB2 C:PHE332 3.3 31.4 1.0
CD1 C:PHE332 3.4 27.1 1.0
C C:VAL330 3.6 30.9 1.0
HD23 C:LEU327 3.7 28.1 1.0
CB C:VAL330 3.7 25.6 1.0
CA C:PHE332 3.7 26.8 1.0
H C:VAL330 3.8 30.9 1.0
CB C:PHE332 3.8 26.2 1.0
N C:PHE332 3.9 28.1 1.0
CA C:LEU327 3.9 21.4 1.0
HG12 C:VAL330 3.9 26.1 1.0
C C:LEU326 4.0 21.6 1.0
H C:PHE332 4.0 33.7 1.0
CA C:VAL330 4.1 27.4 1.0
CG C:PHE332 4.1 29.5 1.0
C C:LEU327 4.2 26.8 1.0
O C:LEU327 4.2 26.5 1.0
CG1 C:VAL330 4.3 21.8 1.0
C C:PRO331 4.3 33.0 1.0
N C:VAL330 4.3 25.7 1.0
HB3 C:HIS408 4.4 25.6 1.0
HG11 C:VAL330 4.4 26.1 1.0
HE1 C:PHE332 4.4 31.9 1.0
CD1 C:TYR23 4.4 22.3 1.0
N C:LEU327 4.4 18.2 1.0
CE1 C:PHE332 4.4 26.5 1.0
CE2 C:TYR23 4.5 23.1 1.0
HD22 C:LEU327 4.5 28.1 1.0
CD2 C:LEU327 4.5 23.4 1.0
O C:PRO331 4.6 34.9 1.0
N C:PRO331 4.7 33.2 1.0
HB3 C:PHE332 4.7 31.4 1.0
CG2 C:VAL330 4.8 27.4 1.0
HG23 C:VAL330 4.8 32.9 1.0
O C:HOH742 4.8 12.2 1.0
HG21 C:VAL330 4.9 32.9 1.0
HE2 C:MET407 4.9 35.0 1.0
N C:ARG328 4.9 31.0 1.0
CA C:PRO331 4.9 40.3 1.0
HB3 C:LEU327 5.0 25.8 1.0
CB C:LEU327 5.0 21.5 1.0
HA C:PRO331 5.0 48.3 1.0

Magnesium binding site 4 out of 5 in 5xet

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Magnesium binding site 4 out of 5 in the Crystal Structure of Mycobacterium Tuberculosis Methionyl-Trna Synthetase Bound By Methionyl-Adenylate (Met-Amp)


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 Mycobacterium Tuberculosis Methionyl-Trna Synthetase Bound By Methionyl-Adenylate (Met-Amp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg606

b:42.3
occ:1.00
 O C:HOH855 2.1 38.3 1.0
O C:HOH751 2.1 38.3 1.0
HH12 C:ARG328 2.8 46.5 1.0
HH22 C:ARG328 2.9 51.3 1.0
HH22 C:ARG346 3.3 40.5 1.0
NH1 C:ARG328 3.6 38.8 1.0
NH2 C:ARG328 3.7 42.7 1.0
CZ C:ARG328 4.1 41.0 1.0
NH2 C:ARG346 4.1 33.7 1.0
HH11 C:ARG328 4.3 46.5 1.0
HH21 C:ARG328 4.3 51.3 1.0
HH21 C:ARG346 4.4 40.5 1.0
HH12 C:ARG346 4.6 35.6 1.0

Magnesium binding site 5 out of 5 in 5xet

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Magnesium binding site 5 out of 5 in the Crystal Structure of Mycobacterium Tuberculosis Methionyl-Trna Synthetase Bound By Methionyl-Adenylate (Met-Amp)


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 Mycobacterium Tuberculosis Methionyl-Trna Synthetase Bound By Methionyl-Adenylate (Met-Amp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg607

b:43.0
occ:1.00
 HD3 C:ARG446 2.3 79.1 1.0
HG2 C:ARG446 3.0 70.1 1.0
HG3 C:ARG446 3.0 70.1 1.0
HB3 C:GLN442 3.0 72.5 1.0
CD C:ARG446 3.0 65.9 1.0
CG C:ARG446 3.2 58.4 1.0
NE C:ARG446 3.6 71.7 1.0
HD21 C:LEU370 3.7 61.4 1.0
HD2 C:ARG446 3.8 79.1 1.0
HE C:ARG446 3.9 86.1 1.0
OE1 C:GLN442 3.9 74.5 1.0
HD2 C:PHE445 3.9 42.6 1.0
CB C:GLN442 3.9 60.4 1.0
HD23 C:LEU370 4.1 61.4 1.0
CD2 C:LEU370 4.2 51.2 1.0
HG2 C:GLN442 4.2 81.3 1.0
HD22 C:LEU370 4.2 61.4 1.0
O C:GLN442 4.2 46.5 1.0
HH11 C:ARG446 4.3 90.8 1.0
CZ C:ARG446 4.4 74.5 1.0
CG C:GLN442 4.5 67.7 1.0
HB2 C:GLN442 4.5 72.5 1.0
C C:GLN442 4.5 45.5 1.0
HA C:GLN442 4.5 60.8 1.0
NH1 C:ARG446 4.6 75.6 1.0
CA C:GLN442 4.6 50.7 1.0
CD C:GLN442 4.6 72.4 1.0
CB C:ARG446 4.7 49.1 1.0
HE2 C:PHE445 4.8 43.1 1.0
CD2 C:PHE445 4.8 35.5 1.0
O C:HOH840 4.9 38.3 1.0

Reference:

W.Wang, B.Qin, J.A.Wojdyla, M.Wang, X.Gao, S.Cui. Structural Characterization of Free-State and Product-Statemycobacterium Tuberculosismethionyl-Trna Synthetase Reveals An Induced-Fit Ligand-Recognition Mechanism. Iucrj V. 5 478 2018.
ISSN: ESSN 2052-2525
PubMed: 30002848
DOI: 10.1107/S2052252518008217
Page generated: Mon Sep 30 09:19:59 2024

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