Atomistry » Magnesium » PDB 7k16-7kee » 7k9m
Atomistry »
  Magnesium »
    PDB 7k16-7kee »
      7k9m »

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: Wed Oct 2 22:09:23 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy