Magnesium in PDB 6j7n: Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A Co-Expressed with Taka From Mycobacterium Tuberculosis

The structure of Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A Co-Expressed with Taka From Mycobacterium Tuberculosis, PDB code: 6j7n 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)	47.75 / 2.29
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	95.502, 95.502, 68.183, 90.00, 90.00, 120.00
R / Rfree (%)	21.1 / 26.7

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>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A Co-Expressed with Taka From Mycobacterium Tuberculosis (pdb code 6j7n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 14 binding sites of Magnesium where determined in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A Co-Expressed with Taka From Mycobacterium Tuberculosis, PDB code: 6j7n:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A Co-Expressed with Taka 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 D82A Co-Expressed with Taka From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:78.4 occ:0.00 H A:LEU224 1.7 88.5 1.0 OD1 A:ASP223 1.8 96.6 1.0 N A:LEU224 1.9 73.7 1.0 N A:MET225 2.0 64.8 1.0 CG A:ASP223 2.1 0.5 1.0 C A:ASP223 2.6 80.1 1.0 OD2 A:ASP223 2.6 0.9 1.0 C A:LEU224 2.7 60.2 1.0 CA A:LEU224 2.7 71.7 1.0 HA A:ASP223 2.9 97.8 1.0 CB A:ASP223 3.0 78.2 1.0 CA A:ASP223 3.0 81.5 1.0 CA A:MET225 3.1 74.9 1.0 HB2 A:LEU224 3.2 86.5 1.0 HB1 A:ALA290 3.3 0.6 1.0 CB A:MET225 3.3 73.2 1.0 HB3 A:ASP223 3.4 93.8 1.0 HA A:LEU224 3.5 86.1 1.0 HA A:MET225 3.5 89.9 1.0 CB A:LEU224 3.5 72.0 1.0 O A:ASP223 3.6 76.3 1.0 HD2 A:PRO226 3.7 79.5 1.0 HD3 A:PRO226 3.8 79.5 1.0 HB2 A:ASP223 3.8 93.8 1.0 CG A:MET225 3.8 94.2 1.0 HB2 A:ALA290 3.8 0.6 1.0 O A:LEU224 3.9 62.6 1.0 CB A:ALA290 4.0 84.6 1.0 HB3 A:LEU224 4.1 86.5 1.0 CD A:PRO226 4.1 66.2 1.0 C A:MET225 4.4 64.9 1.0 HD13 A:LEU224 4.5 79.5 1.0 N A:ASP223 4.5 88.2 1.0 HB3 A:ALA290 4.6 0.6 1.0 N A:PRO226 4.6 65.1 1.0 O A:THR291 4.8 0.2 1.0 CG A:LEU224 4.8 80.0 1.0 H A:ASP223 4.9 0.9 1.0 HA A:ALA290 4.9 0.6 1.0 CD1 A:LEU224 5.0 66.2 1.0 HD12 A:LEU224 5.0 79.5 1.0 HD23 A:LEU224 5.0 90.2 1.0

Magnesium binding site 2 out of 14 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A Co-Expressed with Taka 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 D82A Co-Expressed with Taka From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:0.7 occ:0.00 HH11 A:ARG138 2.4 0.1 1.0 HD2 A:ARG138 2.4 0.8 1.0 HB2 A:ASN11 3.1 0.8 1.0 H A:ARG13 3.1 0.1 1.0 H A:LEU12 3.1 97.9 1.0 NH1 A:ARG138 3.2 0.4 1.0 HB3 A:LEU12 3.2 0.1 1.0 HD3 A:ARG138 3.2 0.8 1.0 CD A:ARG138 3.2 0.0 1.0 HH12 A:ARG138 3.6 0.1 1.0 OD1 A:ASN11 3.6 0.9 1.0 HB2 A:ARG13 3.8 1.0 1.0 N A:LEU12 3.8 81.5 1.0 N A:ARG13 3.9 89.2 1.0 CB A:ASN11 3.9 0.7 1.0 CZ A:ARG138 4.0 0.8 1.0 NE A:ARG138 4.0 0.2 1.0 CB A:LEU12 4.1 83.4 1.0 CG A:ASN11 4.1 0.9 1.0 HH21 A:ARG13 4.3 0.2 1.0 HD23 A:LEU12 4.3 0.3 1.0 HB2 A:ARG138 4.3 0.4 1.0 CA A:LEU12 4.3 72.5 1.0 CG A:ARG138 4.4 0.5 1.0 HB3 A:ARG13 4.4 1.0 1.0 HB2 A:LEU12 4.4 0.1 1.0 NH2 A:ARG13 4.4 0.1 1.0 CB A:ARG13 4.5 0.1 1.0 HG2 A:ARG138 4.5 0.1 1.0 HB3 A:ASN11 4.5 0.8 1.0 C A:LEU12 4.6 91.7 1.0 HH22 A:ARG13 4.6 0.2 1.0 HB3 A:ARG138 4.7 0.4 1.0 C A:ASN11 4.7 81.1 1.0 CB A:ARG138 4.7 96.2 1.0 HE A:ARG138 4.8 0.7 1.0 CA A:ARG13 4.8 99.4 1.0 CA A:ASN11 4.8 98.0 1.0 CZ A:ARG13 4.9 0.9 1.0 HE A:ARG13 4.9 0.2 1.0 CD2 A:LEU12 5.0 86.9 1.0 HD22 A:LEU12 5.0 0.3 1.0

Magnesium binding site 3 out of 14 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A Co-Expressed with Taka 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 D82A Co-Expressed with Taka From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:59.4 occ:0.00 H A:PHE158 2.2 71.2 1.0 HB3 A:GLN157 2.7 71.8 1.0 N A:PHE158 3.1 59.3 1.0 HA A:GLN157 3.1 65.7 1.0 O A:PHE158 3.1 61.5 1.0 CB A:GLN157 3.5 59.8 1.0 CA A:GLN157 3.6 54.7 1.0 C A:GLN157 3.8 58.9 1.0 CD1 A:PHE158 3.9 69.0 1.0 HD1 A:PHE158 3.9 82.8 1.0 C A:PHE158 4.0 51.9 1.0 CA A:PHE158 4.1 57.8 1.0 HG3 A:GLN157 4.1 91.5 1.0 CE1 A:PHE158 4.2 50.6 1.0 HB2 A:GLN157 4.2 71.8 1.0 CG A:GLN157 4.2 76.2 1.0 HG2 A:GLN157 4.3 91.5 1.0 CG A:PHE158 4.3 61.5 1.0 HE1 A:PHE158 4.4 60.7 1.0 CB A:PHE158 4.8 58.2 1.0 CZ A:PHE158 4.8 57.4 1.0 CD2 A:PHE158 4.9 60.8 1.0 HA A:PHE158 4.9 69.4 1.0 N A:GLN157 5.0 74.8 1.0

Magnesium binding site 4 out of 14 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A Co-Expressed with Taka 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 D82A Co-Expressed with Taka From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:68.8 occ:0.00 HD3 A:ARG286 1.9 78.7 1.0 HH11 A:ARG286 2.1 96.0 1.0 HA A:PHE283 2.8 66.1 1.0 CD A:ARG286 2.8 65.6 1.0 HD2 A:ARG286 2.8 78.7 1.0 OE2 A:GLU216 2.9 93.9 1.0 NH1 A:ARG286 3.0 80.0 1.0 HB2 A:ARG286 3.2 83.4 1.0 HD1 A:PHE283 3.3 74.4 1.0 HH12 A:ARG286 3.5 96.0 1.0 CA A:PHE283 3.6 55.0 1.0 NE A:ARG286 3.7 84.4 1.0 CG A:ARG286 3.8 68.2 1.0 CZ A:ARG286 3.8 64.0 1.0 O A:ARG282 3.8 59.1 1.0 CB A:ARG286 3.8 69.5 1.0 N A:PHE283 3.8 55.1 1.0 HB2 A:PHE283 3.9 71.1 1.0 CD A:GLU216 3.9 91.1 1.0 HG3 A:ARG286 4.0 81.9 1.0 C A:ARG282 4.0 56.2 1.0 HB3 A:ARG286 4.0 83.4 1.0 CD1 A:PHE283 4.1 62.0 1.0 HB3 A:ARG282 4.1 56.7 1.0 CB A:PHE283 4.2 59.2 1.0 OE1 A:GLU216 4.2 97.0 1.0 H A:PHE283 4.2 66.2 1.0 HE A:ARG286 4.5 0.3 1.0 CG A:PHE283 4.6 51.4 1.0 HB2 A:ARG282 4.6 56.7 1.0 HG2 A:ARG286 4.6 81.9 1.0 CB A:ARG282 4.7 47.2 1.0 C A:PHE283 4.8 50.1 1.0 H A:ARG286 4.8 73.6 1.0 O A:PHE283 4.9 49.4 1.0

Magnesium binding site 5 out of 14 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A Co-Expressed with Taka 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 D82A Co-Expressed with Taka From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg305 b:77.6 occ:0.00 HH11 A:ARG246 1.8 0.4 1.0 HH12 A:ARG246 2.1 0.4 1.0 NH1 A:ARG246 2.1 92.0 1.0 HD2 A:ARG246 3.1 0.3 1.0 CZ A:ARG246 3.2 0.1 1.0 CD A:ARG246 3.9 85.2 1.0 NE A:ARG246 3.9 0.3 1.0 HH22 A:ARG246 4.1 99.5 1.0 NH2 A:ARG246 4.1 82.9 1.0 HD3 A:ARG246 4.2 0.3 1.0 HE A:ARG246 4.7 0.4 1.0 HH21 A:ARG246 4.9 99.5 1.0

Magnesium binding site 6 out of 14 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A Co-Expressed with Taka 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 D82A Co-Expressed with Taka From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg306 b:82.8 occ:0.00 HG1 A:THR112 1.8 85.0 1.0 OG1 A:THR112 2.5 70.8 1.0 O A:ALA113 2.6 93.4 1.0 HA A:PHE129 2.7 90.6 1.0 HB A:THR112 3.0 0.2 1.0 CB A:THR112 3.3 84.3 1.0 H A:ALA113 3.4 0.3 1.0 HB3 A:PHE129 3.4 88.4 1.0 HB2 A:PHE129 3.4 88.4 1.0 N A:ALA113 3.5 90.2 1.0 CA A:PHE129 3.5 75.5 1.0 C A:ALA113 3.6 76.5 1.0 CB A:PHE129 3.6 73.7 1.0 C A:THR112 3.7 93.1 1.0 H A:THR130 3.8 96.8 1.0 O A:ARG128 4.0 84.6 1.0 CA A:THR112 4.1 81.4 1.0 CA A:ALA113 4.1 92.0 1.0 O A:THR112 4.3 94.1 1.0 N A:THR130 4.3 80.6 1.0 C A:PHE129 4.4 71.2 1.0 HA A:PRO114 4.4 0.2 1.0 HB2 A:GLU115 4.5 0.3 1.0 CG2 A:THR112 4.5 74.2 1.0 HG21 A:THR112 4.5 89.1 1.0 HB3 A:ALA113 4.5 0.7 1.0 N A:PHE129 4.5 69.5 1.0 C A:ARG128 4.7 72.0 1.0 N A:PRO114 4.7 93.7 1.0 H A:GLU115 4.7 0.6 1.0 HA A:THR112 4.7 97.7 1.0 HG23 A:THR112 4.8 89.1 1.0 HB A:THR130 4.8 0.5 1.0 HA A:ALA113 4.9 0.4 1.0 CB A:ALA113 4.9 0.6 1.0 CA A:PRO114 4.9 99.4 1.0

Magnesium binding site 7 out of 14 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A Co-Expressed with Taka 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 D82A Co-Expressed with Taka From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg307 b:70.6 occ:0.00 HH2 A:TRP184 2.7 58.4 1.0 H A:GLY153 2.8 79.2 1.0 HB1 A:ALA152 2.8 80.0 1.0 HZ2 A:TRP184 3.3 68.4 1.0 N A:GLY153 3.3 66.0 1.0 HA3 A:GLY153 3.4 85.8 1.0 CH2 A:TRP184 3.5 48.6 1.0 CB A:ALA152 3.7 66.7 1.0 CZ2 A:TRP184 3.8 57.0 1.0 HB2 A:ALA233 3.8 74.6 1.0 HB1 A:ALA233 3.8 74.6 1.0 CA A:GLY153 3.9 71.5 1.0 HB3 A:ALA152 4.0 80.0 1.0 CB A:ALA233 4.1 62.1 1.0 C A:ALA152 4.2 62.7 1.0 HB3 A:ALA233 4.2 74.6 1.0 HB2 A:ALA152 4.3 80.0 1.0 CA A:ALA152 4.3 55.0 1.0 HA A:ALA152 4.4 66.1 1.0 HA2 A:GLY153 4.5 85.8 1.0 CZ3 A:TRP184 4.7 61.7 1.0 HZ3 A:TRP184 4.9 74.1 1.0 C A:GLY153 5.0 65.3 1.0

Magnesium binding site 8 out of 14 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A Co-Expressed with Taka 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 D82A Co-Expressed with Taka From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg308 b:61.1 occ:0.00 HB1 A:ALA258 3.4 55.0 1.0 HB2 A:ALA258 3.6 55.0 1.0 CB A:ALA258 4.0 45.8 1.0 O A:ARG271 4.4 64.9 1.0 HA A:ALA258 4.5 71.3 1.0 MG A:MG312 4.6 59.5 0.0 HB3 A:ALA258 4.7 55.0 1.0 CA A:ALA258 4.9 59.4 1.0

Magnesium binding site 9 out of 14 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A Co-Expressed with Taka 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 D82A Co-Expressed with Taka From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg309 b:95.2 occ:0.00 HH12 A:ARG25 1.7 0.5 1.0 HG23 A:VAL22 2.0 0.4 1.0 OH A:TYR5 2.0 0.9 1.0 NH1 A:ARG25 2.5 0.9 1.0 HB2 A:GLN21 2.6 0.0 1.0 CG2 A:VAL22 2.8 94.5 1.0 HG22 A:VAL22 2.9 0.4 1.0 HH22 A:ARG25 2.9 0.1 1.0 HH11 A:ARG25 2.9 0.5 1.0 O A:ARG18 3.0 76.1 1.0 HE1 A:TYR5 3.1 0.4 1.0 HB3 A:GLN21 3.1 0.0 1.0 CZ A:TYR5 3.1 0.5 1.0 H A:VAL22 3.2 98.0 1.0 N A:VAL22 3.2 81.7 1.0 CB A:GLN21 3.3 95.0 1.0 CZ A:ARG25 3.3 0.1 1.0 HG21 A:VAL22 3.4 0.4 1.0 NH2 A:ARG25 3.4 0.9 1.0 CE1 A:TYR5 3.5 0.6 1.0 C A:GLN21 3.5 82.2 1.0 HA A:VAL22 3.6 91.0 1.0 HA A:ARG18 3.7 0.9 1.0 CA A:VAL22 3.8 75.8 1.0 CB A:VAL22 3.8 84.0 1.0 CA A:GLN21 3.9 84.9 1.0 HB3 A:ARG18 3.9 0.9 1.0 C A:ARG18 4.0 82.7 1.0 O A:GLN21 4.1 91.6 1.0 HB A:VAL22 4.2 0.8 1.0 HH21 A:ARG25 4.2 0.1 1.0 CA A:ARG18 4.2 97.4 1.0 OE1 A:GLN21 4.3 0.0 1.0 CE2 A:TYR5 4.3 0.7 1.0 H A:GLN21 4.4 0.3 1.0 HG12 A:VAL169 4.4 0.0 1.0 CG A:GLN21 4.5 0.7 1.0 CB A:ARG18 4.5 92.4 1.0 N A:GLN21 4.5 86.9 1.0 HE2 A:TYR5 4.6 0.9 1.0 NE A:ARG25 4.6 1.0 1.0 HG2 A:ARG18 4.6 0.9 1.0 HD2 A:ARG25 4.7 0.4 1.0 CD A:GLN21 4.7 0.8 1.0 HA A:GLN21 4.8 0.9 1.0 CD1 A:TYR5 4.8 90.7 1.0 HG3 A:GLN21 5.0 0.9 1.0

Magnesium binding site 10 out of 14 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A Co-Expressed with Taka From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A Co-Expressed with Taka From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg310 b:67.6 occ:0.00 HB3 A:GLN188 3.0 70.7 1.0 HA A:LYS189 3.3 64.7 1.0 O A:GLN188 3.4 52.4 1.0 HB2 A:ALA192 3.5 67.6 1.0 HG3 A:LYS189 3.5 75.5 1.0 C A:GLN188 3.6 52.1 1.0 HG2 A:LYS189 3.7 75.5 1.0 CB A:GLN188 3.8 58.9 1.0 HB3 A:ALA192 3.8 67.6 1.0 N A:LYS189 3.9 48.2 1.0 HB2 A:GLN188 4.0 70.7 1.0 CA A:LYS189 4.0 53.9 1.0 HZ3 A:LYS189 4.0 0.0 1.0 CG A:LYS189 4.0 62.9 1.0 CB A:ALA192 4.1 56.3 1.0 CA A:GLN188 4.3 57.2 1.0 H A:LYS189 4.4 57.9 1.0 OE1 A:GLN188 4.4 0.3 1.0 HB1 A:ALA192 4.4 67.6 1.0 CB A:LYS189 4.7 58.7 1.0 HA A:GLN188 4.7 68.7 1.0 H A:ALA192 4.8 53.2 1.0 OD2 A:ASP208 4.9 84.7 1.0 NZ A:LYS189 4.9 85.0 1.0 HZ1 A:LYS61 4.9 1.0 1.0 HH12 A:ARG238 4.9 0.7 1.0 CG A:GLN188 5.0 90.4 1.0 HH22 A:ARG238 5.0 0.2 1.0

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