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

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

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:

Magnesium

(Mg)

9 atoms

The binding sites of Calcium 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 Calcium atom.
In total 6 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 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 Calcium with other atoms in the Ca 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:Ca310 b:52.8 occ:1.00 H A:GLY62 2.4 42.5 1.0 HE21 A:GLN185 2.8 36.3 1.0 HE2 A:LYS189 2.8 43.6 1.0 HA2 A:GLY62 3.1 33.9 1.0 N A:GLY62 3.2 35.4 1.0 HG2 A:GLN185 3.2 41.3 1.0 HB2 A:LYS61 3.3 42.7 1.0 HB3 A:GLN185 3.3 31.0 1.0 HA A:GLN185 3.4 33.2 1.0 HG3 A:LYS189 3.5 44.9 1.0 NE2 A:GLN185 3.6 30.2 1.0 CA A:GLY62 3.6 28.3 1.0 HD2 A:LYS61 3.7 61.5 1.0 HE2 A:MET180 3.7 37.5 1.0 CE A:LYS189 3.8 36.3 1.0 CB A:GLN185 3.9 25.9 1.0 CG A:GLN185 3.9 34.5 1.0 HE1 A:MET180 4.0 37.5 1.0 CA A:GLN185 4.0 27.7 1.0 CB A:LYS61 4.1 35.6 1.0 HG3 A:LYS61 4.2 44.2 1.0 HE22 A:GLN185 4.2 36.3 1.0 CD A:GLN185 4.3 46.4 1.0 CG A:LYS189 4.3 37.4 1.0 CE A:MET180 4.3 31.2 1.0 HE3 A:LYS189 4.3 43.6 1.0 O A:GLN185 4.3 26.4 1.0 HA3 A:GLY62 4.3 33.9 1.0 C A:LYS61 4.3 33.2 1.0 HD2 A:LYS189 4.3 41.3 1.0 HZ2 A:LYS189 4.4 45.3 1.0 CD A:LYS189 4.4 34.4 1.0 CG A:LYS61 4.5 36.9 1.0 CD A:LYS61 4.5 51.3 1.0 NZ A:LYS189 4.5 37.8 1.0 HB2 A:GLN188 4.5 42.9 1.0 HZ3 A:LYS189 4.5 45.3 1.0 HD11 A:LEU66 4.5 45.4 0.2 C A:GLY62 4.6 32.3 1.0 HG2 A:LYS189 4.6 44.9 1.0 HE3 A:MET180 4.6 37.5 1.0 HA A:LYS61 4.6 38.3 1.0 CA A:LYS61 4.6 31.9 1.0 C A:GLN185 4.7 23.5 1.0 HE3 A:LYS61 4.7 80.8 1.0 O A:GLY62 4.7 32.0 1.0 HG3 A:GLN185 4.8 41.3 1.0 HD13 A:LEU66 4.8 45.4 0.2 HB2 A:GLN185 4.8 31.0 1.0 HB3 A:LYS61 4.8 42.7 1.0 OE1 A:GLN188 4.9 42.0 1.0

Calcium binding site 2 out of 6 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 Calcium with other atoms in the Ca 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:Ca311 b:0.2 occ:1.00 HH11 A:ARG246 2.9 0.6 1.0 HH12 A:ARG246 3.0 0.6 1.0 NH1 A:ARG246 3.0 88.0 1.0 HD2 A:ARG246 3.8 95.4 1.0 CZ A:ARG246 3.9 89.8 1.0 NE A:ARG246 4.5 80.9 1.0 HH22 A:ARG246 4.5 0.2 1.0 CD A:ARG246 4.5 79.5 1.0 NH2 A:ARG246 4.6 86.9 1.0 HD3 A:ARG246 4.9 95.4 1.0

Calcium binding site 3 out of 6 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 Calcium with other atoms in the Ca 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:Ca312 b:95.3 occ:1.00 O A:HOH593 2.8 36.0 1.0 HD23 A:LEU255 3.6 36.8 1.0 HB3 A:PRO254 3.6 33.7 1.0 HB2 A:ALA258 3.7 36.5 1.0 O A:HOH499 3.7 35.7 1.0 O A:PRO254 4.1 26.7 1.0 HB2 A:PRO254 4.1 33.7 1.0 O A:HOH602 4.1 44.5 1.0 O A:HOH487 4.2 35.6 1.0 HA A:LEU255 4.2 33.5 1.0 CB A:PRO254 4.3 28.1 1.0 C A:PRO254 4.3 25.7 1.0 CD2 A:LEU255 4.5 30.7 1.0 HD21 A:LEU255 4.5 36.8 1.0 CB A:ALA258 4.6 30.4 1.0 HG A:LEU255 4.6 32.0 1.0 HB3 A:ALA258 4.7 36.5 1.0 N A:LEU255 4.7 26.5 1.0 CA A:PRO254 4.7 28.6 1.0 HA A:PRO254 4.8 34.3 1.0 HB1 A:ALA258 4.9 36.5 1.0 CA A:LEU255 5.0 27.9 1.0

Calcium binding site 4 out of 6 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 Calcium with other atoms in the Ca 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:Ca313 b:88.2 occ:1.00 O A:HOH522 2.1 42.6 1.0 OE1 A:GLU67 3.2 42.2 1.0 O A:HOH476 3.4 46.9 1.0 O A:ALA78 3.4 58.7 1.0 O A:HOH409 3.6 48.9 1.0 CD A:GLU67 3.6 53.9 1.0 HE2 A:MET39 3.7 62.3 1.0 OE2 A:GLU67 3.7 34.5 1.0 HA A:SER64 3.7 37.1 1.0 HG3 A:MET39 3.8 47.7 1.0 HB2 A:MET39 3.9 50.0 1.0 HA A:HIS36 3.9 41.5 1.0 H A:ALA78 4.1 67.9 1.0 HG2 A:ARG35 4.1 65.2 1.0 MG A:MG304 4.3 52.6 1.0 HB3 A:MET39 4.3 50.0 1.0 OG A:SER64 4.3 35.7 1.0 HB3 A:GLU67 4.4 36.7 1.0 C A:ALA78 4.4 60.9 1.0 HE3 A:MET39 4.4 62.3 1.0 CB A:MET39 4.4 41.6 1.0 CE A:MET39 4.5 51.9 1.0 HB2 A:GLU67 4.5 36.7 1.0 O A:HOH426 4.5 48.0 1.0 CG A:MET39 4.5 39.8 1.0 CA A:SER64 4.6 30.9 1.0 HG A:SER64 4.6 42.9 1.0 HD1 A:HIS36 4.7 43.3 1.0 HB3 A:ARG35 4.7 50.8 1.0 O A:ARG35 4.7 38.0 1.0 CB A:GLU67 4.8 30.6 1.0 CA A:HIS36 4.8 34.5 1.0 CG A:GLU67 4.8 36.3 1.0 N A:ALA78 4.8 56.6 1.0 CB A:SER64 4.9 34.9 1.0 HE A:ARG35 4.9 80.8 1.0 HB3 A:SER64 4.9 41.9 1.0 N A:HIS36 5.0 33.4 1.0 C A:ARG35 5.0 40.2 1.0 CG A:ARG35 5.0 54.3 1.0

Calcium binding site 5 out of 6 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 Calcium with other atoms in the Ca 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:Ca314 b:79.2 occ:1.00 HH22 A:ARG286 2.4 43.8 1.0 O A:GLU216 2.7 31.1 1.0 O A:LEU220 2.7 42.4 1.0 NH2 A:ARG286 3.2 36.5 1.0 HG2 A:GLU216 3.2 38.3 1.0 HG3 A:GLU216 3.4 38.3 1.0 H A:LEU220 3.5 52.3 1.0 HB2 A:LEU219 3.5 39.9 1.0 HH21 A:ARG286 3.6 43.8 1.0 O A:HOH475 3.6 47.8 1.0 N A:LEU220 3.6 43.6 1.0 C A:LEU220 3.7 49.7 1.0 CG A:GLU216 3.7 31.9 1.0 C A:GLU216 3.7 33.7 1.0 HH12 A:ARG286 3.8 49.6 1.0 HA A:LEU220 3.9 56.4 1.0 CA A:LEU220 4.0 47.0 1.0 HB3 A:LEU219 4.1 39.9 1.0 HA2 A:GLY217 4.1 41.9 1.0 C A:LEU219 4.1 40.7 1.0 CB A:LEU219 4.2 33.3 1.0 CZ A:ARG286 4.2 47.7 1.0 NH1 A:ARG286 4.3 41.3 1.0 HA A:GLU216 4.3 35.7 1.0 H A:LEU219 4.4 41.8 1.0 CA A:GLU216 4.5 29.8 1.0 CA A:LEU219 4.6 35.5 1.0 N A:GLY217 4.6 29.1 1.0 OE2 A:GLU216 4.6 37.0 1.0 CA A:GLY217 4.7 34.9 1.0 O A:HOH493 4.7 53.7 1.0 CD A:GLU216 4.8 40.1 1.0 CB A:GLU216 4.8 31.2 1.0 O A:LEU219 4.8 39.6 1.0 N A:LEU219 4.8 34.8 1.0 HD11 A:LEU224 4.8 54.6 1.0 HD13 A:LEU219 4.8 50.7 1.0 HA A:ASP221 4.9 65.4 1.0 HE1 A:PHE283 4.9 44.0 1.0 N A:ASP221 5.0 57.1 1.0 C A:GLY217 5.0 37.3 1.0

Calcium binding site 6 out of 6 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 Calcium with other atoms in the Ca 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:Ca315 b:92.4 occ:1.00 HH2 A:TRP184 2.7 47.9 1.0 H A:GLY153 2.7 46.7 1.0 HA3 A:GLY153 3.1 60.0 1.0 HZ2 A:TRP184 3.1 46.6 1.0 HB1 A:ALA152 3.1 43.6 1.0 O A:HOH586 3.2 55.2 1.0 N A:GLY153 3.3 38.9 1.0 CH2 A:TRP184 3.4 39.9 1.0 CZ2 A:TRP184 3.6 38.8 1.0 CA A:GLY153 3.7 50.0 1.0 HB2 A:ALA233 4.0 43.5 1.0 HB1 A:ALA233 4.0 43.5 1.0 CB A:ALA152 4.0 36.3 1.0 HB3 A:ALA152 4.2 43.6 1.0 C A:ALA152 4.2 42.8 1.0 CB A:ALA233 4.3 36.2 1.0 HA2 A:GLY153 4.3 60.0 1.0 HB3 A:ALA233 4.4 43.5 1.0 CA A:ALA152 4.6 38.9 1.0 CZ3 A:TRP184 4.6 35.0 1.0 HB2 A:ALA152 4.7 43.6 1.0 C A:GLY153 4.7 36.0 1.0 HA A:ALA152 4.8 46.6 1.0 HZ3 A:TRP184 4.9 42.0 1.0 OD2 A:ASP156 5.0 46.1 1.0 CE2 A:TRP184 5.0 34.0 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