Magnesium in PDB 7k9m: Crystal Structure of the Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine

Enzymatic activity of Crystal Structure of the Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine

All present enzymatic activity of Crystal Structure of the Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine:
6.1.1.20;

Protein crystallography data

The structure of Crystal Structure of the Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine, PDB code: 7k9m was solved by K.Michalska, C.Chang, R.Jedrzejczak, J.Wower, B.Baragana, B.Forte, I.H.Gilbert, A.Joachimiak, Center For Structural Genomics Ofinfectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.92 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 128.432, 110.753, 147.897, 90, 103.59, 90
R / Rfree (%) 17.9 / 21.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine (pdb code 7k9m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine, PDB code: 7k9m:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7k9m

Go back to Magnesium Binding Sites List in 7k9m
Magnesium binding site 1 out of 3 in the Crystal Structure of the Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine


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 the Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:51.2
occ:1.00
 OE1 A:GLU263 2.2 70.8 1.0
OE1 B:GLU36 2.7 77.5 1.0
CD A:GLU263 2.8 65.6 1.0
OE2 A:GLU263 2.9 75.1 1.0
CD B:GLU36 3.7 71.5 1.0
CE1 A:HIS253 3.7 28.4 1.0
NH2 A:ARG251 3.8 36.9 1.0
NH1 A:ARG251 3.9 40.8 1.0
NE2 A:HIS253 4.0 29.0 1.0
ND1 A:HIS253 4.2 28.9 1.0
OE2 B:GLU36 4.3 70.3 1.0
CG A:GLU263 4.3 48.1 1.0
CZ A:ARG251 4.3 37.8 1.0
CD2 A:HIS253 4.6 29.9 1.0
O A:HOH628 4.6 41.9 1.0
CG B:GLU36 4.6 64.6 1.0
CG A:HIS253 4.7 28.2 1.0
CB B:GLU36 4.9 45.0 1.0
CB A:GLU263 4.9 30.2 1.0
C3 A:GOL506 5.0 73.7 1.0

Magnesium binding site 2 out of 3 in 7k9m

Go back to Magnesium Binding Sites List in 7k9m
Magnesium binding site 2 out of 3 in the Crystal Structure of the Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine


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 the Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:48.6
occ:1.00
 O A:GLY156 2.4 48.3 1.0
O A:HOH684 2.5 51.6 1.0
O A:GLN158 2.6 46.6 1.0
O A:HOH655 2.7 39.7 1.0
O A:HOH641 2.9 29.4 1.0
C A:GLY156 3.5 51.2 1.0
C A:GLN158 3.7 44.3 1.0
N A:GLN158 4.0 51.5 1.0
CA A:GLY156 4.1 35.0 1.0
CE2 A:TYR162 4.2 30.0 1.0
OH A:TYR162 4.4 31.9 1.0
CA A:GLN158 4.4 52.3 1.0
O A:ARG155 4.4 44.0 1.0
C A:GLU157 4.4 56.2 1.0
N A:THR160 4.5 26.6 1.0
N A:GLU157 4.5 55.8 1.0
OG1 A:THR160 4.6 28.0 1.0
CB A:THR160 4.6 29.3 1.0
CA A:GLU157 4.7 62.9 1.0
CB A:GLN158 4.8 52.8 1.0
N A:ASP159 4.8 33.4 1.0
CZ A:TYR162 4.8 37.8 1.0
O A:GLU157 5.0 59.6 1.0

Magnesium binding site 3 out of 3 in 7k9m

Go back to Magnesium Binding Sites List in 7k9m
Magnesium binding site 3 out of 3 in the Crystal Structure of the Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine


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 the Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg508

b:21.8
occ:1.00
 OE1 B:GLU476 2.0 31.2 1.0
OE2 A:GLU259 2.0 32.4 1.0
O B:HOH1057 2.1 26.2 1.0
O B:HOH1061 2.2 23.1 1.0
O B:HOH1089 2.2 29.6 1.0
O B:HOH1055 2.2 31.4 1.0
CD A:GLU259 3.0 31.9 1.0
CD B:GLU476 3.0 37.5 1.0
OE1 A:GLU259 3.4 36.4 1.0
OE2 B:GLU476 3.8 40.6 1.0
OD2 B:ASP467 3.8 36.0 1.0
OD2 B:ASP172 3.9 32.4 1.0
OD1 B:ASP473 3.9 37.5 1.0
CB B:GLU476 3.9 31.6 1.0
CG B:GLU476 4.0 37.7 1.0
O B:ASP473 4.3 33.5 1.0
CG A:GLU259 4.4 23.9 1.0
NH1 B:ARG173 4.4 27.1 1.0
CA B:ASP473 4.4 25.2 1.0
O B:HOH1020 4.5 23.3 1.0
O B:HOH1192 4.5 25.0 1.0
CB B:ASP473 4.6 25.7 1.0
OE2 B:GLU477 4.6 27.6 1.0
CG B:ASP473 4.7 36.1 1.0
C B:ASP473 4.9 31.0 1.0
CG B:ASP467 4.9 38.4 1.0
CD2 B:LEU468 5.0 29.8 1.0
O A:HOH652 5.0 36.9 1.0

Reference:

K.Michalska, R.Jedrzejczak, J.Wower, C.Chang, B.Baragana, I.H.Gilbert, B.Forte, A.Joachimiak. Mycobacterium Tuberculosis Phe-Trna Synthetase: Structural Insights Into Trna Recognition and Aminoacylation. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 33885823
DOI: 10.1093/NAR/GKAB272
Page generated: Sun Jul 11 17:41:48 2021

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