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Magnesium in PDB 6j7q: Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant S78A From Mycobacterium Tuberculosis

Protein crystallography data

The structure of Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant S78A From Mycobacterium Tuberculosis, PDB code: 6j7q was solved by X.Yu, X.Gao, K.Zhu, J.A.Wojdyla, M.Wang, S.Cui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.08 / 1.85
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 95.413, 95.413, 68.129, 90.00, 90.00, 120.00
R / Rfree (%) 19.4 / 22

Other elements in 6j7q:

The structure of Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant S78A From Mycobacterium Tuberculosis also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant S78A From Mycobacterium Tuberculosis (pdb code 6j7q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant S78A From Mycobacterium Tuberculosis, PDB code: 6j7q:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 6j7q

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Magnesium binding site 1 out of 9 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant S78A From Mycobacterium Tuberculosis


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 Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant S78A From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:56.8
occ:1.00
 O A:HOH498 2.7 33.0 1.0
O A:HOH457 3.3 47.1 1.0
HD3 A:PRO56 3.3 42.6 1.0
O A:GLY54 3.3 36.1 1.0
HZ A:PHE158 3.4 36.1 1.0
HA A:ALA55 3.8 41.1 1.0
HG3 A:PRO56 4.1 41.0 1.0
CD A:PRO56 4.2 35.5 1.0
CZ A:PHE158 4.3 30.1 1.0
C A:GLY54 4.4 35.7 1.0
CG A:PRO56 4.6 34.2 1.0
CA A:ALA55 4.7 34.2 1.0
HE2 A:PHE158 4.8 39.1 1.0
HD2 A:PRO56 4.8 42.6 1.0
N A:PRO56 4.9 35.2 1.0
HG2 A:PRO56 5.0 41.0 1.0
N A:ALA55 5.0 36.2 1.0
CE2 A:PHE158 5.0 32.6 1.0

Magnesium binding site 2 out of 9 in 6j7q

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Magnesium binding site 2 out of 9 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant S78A From Mycobacterium Tuberculosis


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 Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant S78A From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:61.1
occ:1.00
 OD2 A:ASP204 2.7 37.1 1.0
CG A:ASP204 3.6 44.3 1.0
H A:VAL202 3.7 81.2 1.0
O A:VAL202 3.7 50.6 1.0
O A:HOH485 3.7 38.6 1.0
HB A:VAL202 3.8 80.2 1.0
OD1 A:ASP204 3.8 34.3 1.0
HG23 A:VAL202 4.0 0.1 1.0
O A:HOH429 4.2 46.1 1.0
HD3 A:LYS201 4.2 0.0 1.0
N A:VAL202 4.4 67.7 1.0
HE2 A:LYS201 4.5 0.6 1.0
CB A:VAL202 4.5 66.8 1.0
C A:VAL202 4.6 42.5 1.0
CG2 A:VAL202 4.6 85.1 1.0
HB2 A:ASP204 4.6 41.8 1.0
CA A:VAL202 4.7 56.9 1.0
CB A:ASP204 4.8 34.8 1.0
HG21 A:VAL202 4.8 0.1 1.0
HA A:LYS201 5.0 0.5 1.0

Magnesium binding site 3 out of 9 in 6j7q

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Magnesium binding site 3 out of 9 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant S78A From Mycobacterium Tuberculosis


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 Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant S78A From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:44.1
occ:1.00
 O A:HOH406 2.0 58.7 1.0
OE2 A:GLU262 2.8 37.9 1.0
O A:HOH510 2.8 45.4 1.0
O A:HOH407 3.0 58.0 1.0
O A:HOH555 3.2 51.2 1.0
OE1 A:GLU262 3.3 47.0 1.0
CD A:GLU262 3.3 41.2 1.0
HA A:GLU262 3.8 42.1 1.0
O A:HOH411 3.8 44.4 1.0
O A:HOH422 3.9 39.3 1.0
H A:GLY263 4.2 43.7 1.0
OD1 A:ASP265 4.4 47.2 1.0
OD2 A:ASP265 4.5 53.2 1.0
CG A:GLU262 4.6 37.5 1.0
CA A:GLU262 4.7 35.1 1.0
HG2 A:GLU262 4.8 45.0 1.0
O A:HOH574 4.8 60.9 1.0
CG A:ASP265 4.9 47.8 1.0
N A:GLY263 5.0 36.4 1.0

Magnesium binding site 4 out of 9 in 6j7q

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Magnesium binding site 4 out of 9 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant S78A From Mycobacterium Tuberculosis


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 Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant S78A From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:52.6
occ:1.00
 CB A:ALA78 2.6 75.6 1.0
O A:ASP80 2.7 37.7 1.0
HA3 A:GLY63 2.9 36.8 1.0
HG A:SER64 2.9 42.9 1.0
H A:SER64 3.0 42.4 1.0
H A:ASP80 3.1 54.5 1.0
N A:SER64 3.2 35.3 1.0
C A:ALA78 3.4 60.9 1.0
OD1 A:ASP80 3.4 73.7 1.0
C A:GLY63 3.5 28.7 1.0
CA A:GLY63 3.5 30.7 1.0
OG A:SER64 3.5 35.7 1.0
H A:GLY63 3.5 35.2 1.0
N A:ASP80 3.5 45.4 1.0
N A:LYS79 3.6 48.3 1.0
CA A:ALA78 3.6 65.2 1.0
H A:LYS79 3.6 58.0 1.0
O A:HOH453 3.6 41.3 1.0
O A:HOH464 3.7 31.4 1.0
O A:ALA78 3.7 58.7 1.0
C A:ASP80 3.8 52.4 1.0
O A:HOH522 3.8 42.6 1.0
N A:GLY63 3.9 29.4 1.0
HA A:SER64 4.0 37.1 1.0
CA A:SER64 4.1 30.9 1.0
C A:LYS79 4.1 53.5 1.0
HA A:ALA78 4.2 78.3 1.0
CA A:ASP80 4.2 42.6 1.0
O A:GLY63 4.3 31.8 1.0
CA A:CA313 4.3 88.2 1.0
H A:ALA78 4.4 67.9 1.0
CB A:SER64 4.4 34.9 1.0
HA2 A:GLY63 4.4 36.8 1.0
CA A:LYS79 4.4 49.3 1.0
CG A:ASP80 4.5 66.3 1.0
N A:ALA78 4.5 56.6 1.0
O A:HOH514 4.6 43.0 1.0
O A:HOH409 4.8 48.9 1.0
HB2 A:SER64 4.8 41.9 1.0
HA A:LYS79 4.8 59.2 1.0
HA A:PHE81 4.9 44.8 1.0
O A:LYS79 4.9 55.3 1.0
N A:PHE81 5.0 43.3 1.0
HA A:ASP80 5.0 51.1 1.0

Magnesium binding site 5 out of 9 in 6j7q

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Magnesium binding site 5 out of 9 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant S78A From Mycobacterium Tuberculosis


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 Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant S78A From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:82.5
occ:1.00
 MG A:MG308 1.9 0.1 1.0
OE1 A:GLN157 2.6 86.2 1.0
O A:HOH518 2.7 51.8 1.0
O A:HOH573 3.3 58.0 1.0
HB3 A:GLN157 3.5 51.3 1.0
CD A:GLN157 3.5 83.8 1.0
HG21 A:THR181 3.6 39.4 1.0
OD1 A:ASP159 4.1 35.7 1.0
CB A:GLN157 4.2 42.8 1.0
CG A:GLN157 4.3 54.2 1.0
HG22 A:THR181 4.3 39.4 1.0
NE2 A:GLN157 4.4 74.1 1.0
HE22 A:GLN157 4.4 89.0 1.0
CG2 A:THR181 4.4 32.8 1.0
HG2 A:GLN157 4.4 65.1 1.0
HB2 A:GLN157 4.5 51.3 1.0
O A:PHE158 4.6 31.5 1.0
H A:PHE158 4.9 37.2 1.0
HG23 A:THR181 5.0 39.4 1.0
HB A:THR181 5.0 36.1 1.0

Magnesium binding site 6 out of 9 in 6j7q

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Magnesium binding site 6 out of 9 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant S78A From Mycobacterium Tuberculosis


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 Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant S78A From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg306

b:65.8
occ:1.00
 HD3 A:PRO73 3.0 56.3 1.0
HG2 A:PRO73 3.1 48.3 1.0
HG3 A:PRO73 3.1 48.3 1.0
HE21 A:GLN26 3.2 70.5 1.0
CG A:PRO73 3.3 40.3 1.0
NE2 A:GLN26 3.4 58.7 1.0
CD A:PRO73 3.5 46.9 1.0
HB2 A:GLN26 3.6 81.2 1.0
HE22 A:GLN26 3.6 70.5 1.0
HD2 A:PRO73 3.7 56.3 1.0
O A:HOH513 3.9 65.3 1.0
HG3 A:GLN26 3.9 64.9 1.0
CD A:GLN26 3.9 67.8 1.0
O A:HOH504 4.1 44.0 1.0
HB A:ILE72 4.1 50.7 1.0
HG21 A:VAL28 4.2 75.3 1.0
CG A:GLN26 4.2 54.1 1.0
CB A:GLN26 4.3 67.6 1.0
HG23 A:VAL28 4.3 75.3 1.0
O A:GLN26 4.5 51.1 1.0
OE1 A:GLN26 4.6 66.6 1.0
H A:ILE72 4.7 37.0 1.0
HB3 A:GLN26 4.7 81.2 1.0
CG2 A:VAL28 4.7 62.7 1.0
CB A:PRO73 4.9 38.8 1.0
N A:PRO73 4.9 43.6 1.0
HB A:VAL28 4.9 59.1 1.0
MG A:MG307 5.0 62.5 1.0

Magnesium binding site 7 out of 9 in 6j7q

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Magnesium binding site 7 out of 9 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant S78A From Mycobacterium Tuberculosis


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 Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant S78A From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg307

b:62.5
occ:1.00
 O A:HOH513 2.2 65.3 1.0
HE22 A:GLN26 2.5 70.5 1.0
OD1 A:ASP164 2.7 51.7 1.0
NE2 A:GLN26 3.4 58.7 1.0
HD11 A:LEU168 3.4 59.2 1.0
HA A:ALA165 3.4 42.1 1.0
HD12 A:LEU168 3.4 59.2 1.0
HB2 A:ALA165 3.6 47.6 1.0
HE21 A:GLN26 3.8 70.5 1.0
CG A:ASP164 3.9 44.8 1.0
CD1 A:LEU168 3.9 49.3 1.0
O A:HOH503 3.9 46.0 1.0
HG A:SER163 4.0 46.1 1.0
N A:ALA165 4.0 37.4 1.0
CA A:ALA165 4.0 35.1 1.0
O A:HOH504 4.1 44.0 1.0
H A:ALA165 4.1 44.8 1.0
H A:ASP164 4.1 43.7 1.0
CB A:ALA165 4.2 39.6 1.0
CD A:GLN26 4.3 67.8 1.0
OD2 A:ASP164 4.4 58.6 1.0
OE1 A:GLN26 4.4 66.6 1.0
C A:ASP164 4.4 40.2 1.0
HD13 A:LEU168 4.5 59.2 1.0
HB1 A:ALA165 4.5 47.6 1.0
HD11 A:LEU33 4.5 44.9 1.0
OG A:SER163 4.6 38.4 1.0
HG A:LEU168 4.7 62.8 1.0
N A:ASP164 4.7 36.5 1.0
O A:ASP164 4.9 43.4 1.0
CG A:LEU168 4.9 52.4 1.0
CA A:ASP164 5.0 34.8 1.0
MG A:MG306 5.0 65.8 1.0

Magnesium binding site 8 out of 9 in 6j7q

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Magnesium binding site 8 out of 9 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant S78A From Mycobacterium Tuberculosis


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 Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant S78A From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg308

b:0.1
occ:1.00
 O A:HOH518 1.9 51.8 1.0
MG A:MG305 1.9 82.5 1.0
OD1 A:ASP159 2.1 35.7 1.0
O A:HOH573 2.7 58.0 1.0
HG21 A:THR181 3.1 39.4 1.0
HG22 A:THR181 3.2 39.4 1.0
CG A:ASP159 3.3 34.8 1.0
CG2 A:THR181 3.6 32.8 1.0
O A:HOH548 3.7 53.5 1.0
HA A:ASP159 3.9 36.1 1.0
O A:PHE158 3.9 31.5 1.0
OD2 A:ASP159 4.0 35.2 1.0
HB A:THR181 4.1 36.1 1.0
OE1 A:GLN157 4.1 86.2 1.0
C A:PHE158 4.2 34.7 1.0
HB3 A:GLN157 4.2 51.3 1.0
O A:HOH415 4.2 30.6 1.0
N A:ASP159 4.3 30.0 1.0
CA A:ASP159 4.4 30.1 1.0
HG23 A:THR181 4.4 39.4 1.0
CB A:ASP159 4.4 27.2 1.0
CB A:THR181 4.5 30.1 1.0
H A:ASP159 4.6 36.0 1.0
HB3 A:ASP159 4.8 32.6 1.0
H A:PHE158 4.9 37.2 1.0

Magnesium binding site 9 out of 9 in 6j7q

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Magnesium binding site 9 out of 9 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant S78A From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant S78A From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg309

b:0.2
occ:1.00
 O A:HOH496 1.9 56.7 1.0
OE2 A:GLU268 2.2 82.9 1.0
O A:HOH454 2.8 40.7 1.0
CD A:GLU268 3.0 74.4 1.0
HA A:GLU268 3.0 52.3 1.0
O A:LEU267 3.3 41.4 1.0
OE1 A:GLU268 3.6 80.0 1.0
HG3 A:GLU268 3.8 92.5 1.0
CA A:GLU268 3.9 43.6 1.0
CG A:GLU268 4.0 77.1 1.0
C A:LEU267 4.0 38.5 1.0
N A:GLU268 4.2 38.9 1.0
H A:LEU269 4.3 38.0 1.0
HH21 A:ARG271 4.3 54.6 1.0
HE A:ARG271 4.4 67.1 1.0
O A:ASP265 4.4 38.3 1.0
CB A:GLU268 4.5 48.7 1.0
HG2 A:GLU268 4.8 92.5 1.0
N A:LEU269 4.9 31.7 1.0
H A:GLU268 4.9 46.6 1.0
C A:GLU268 5.0 47.4 1.0
HB2 A:GLU268 5.0 58.4 1.0
NH2 A:ARG271 5.0 45.5 1.0

Reference:

X.Yu, X.Gao, K.Zhu, H.Yin, X.Mao, J.A.Wojdyla, B.Qin, H.Huang, M.Wang, Y.Sun, S.Cui. Characterization of A Toxin-Antitoxin System in Mycobacterium Tuberculosis Suggests Neutralization By Phosphorylation As the Antitoxicity Mechanism Commun Biol 2020.
ISSN: ESSN 2399-3642
Page generated: Tue Oct 1 04:43:31 2024

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