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Magnesium in PDB 7k98: Preaminoacylation Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine (F-Ams)

Enzymatic activity of Preaminoacylation Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine (F-Ams)

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

Protein crystallography data

The structure of Preaminoacylation Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine (F-Ams), PDB code: 7k98 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) 29.85 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 147.423, 65.302, 193.481, 90, 109.29, 90
R / Rfree (%) 17.8 / 22.4

Other elements in 7k98:

The structure of Preaminoacylation Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine (F-Ams) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the Preaminoacylation Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine (F-Ams) (pdb code 7k98). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the Preaminoacylation Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine (F-Ams), PDB code: 7k98:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in 7k98

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Magnesium binding site 1 out of 13 in the Preaminoacylation Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine (F-Ams)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Preaminoacylation Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine (F-Ams) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:48.5
occ:1.00
 O A:HOH517 2.0 46.7 1.0
O C:HOH213 2.1 47.2 1.0
OD1 A:ASP203 2.1 54.7 1.0
O C:HOH219 2.1 39.8 1.0
O C:HOH210 2.2 50.4 1.0
O A:HOH503 2.2 43.3 1.0
CG A:ASP203 3.2 56.5 1.0
OD2 A:ASP203 3.9 61.2 1.0
O2 C:C75 4.0 63.8 1.0
O2 C:C76 4.1 56.7 1.0
O A:THR202 4.1 50.0 1.0
OD2 A:ASP159 4.2 91.7 1.0
N3 C:C75 4.3 68.4 1.0
N1 C:A77 4.4 65.5 1.0
CB A:ASP203 4.4 48.3 1.0
CA A:ASP203 4.4 49.5 1.0
C A:THR202 4.5 53.7 1.0
CG A:ASP159 4.5 88.0 1.0
O A:HOH504 4.6 48.2 1.0
C2 C:C75 4.6 69.2 1.0
C2 C:C76 4.6 59.9 1.0
N A:ASP203 4.7 45.4 1.0
CA A:ASP159 4.7 67.8 1.0
O A:ASP159 4.7 49.7 1.0
C2 C:A77 4.7 59.6 1.0
CB A:ASP159 4.9 73.9 1.0
CB A:ARG201 4.9 46.2 1.0

Magnesium binding site 2 out of 13 in 7k98

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Magnesium binding site 2 out of 13 in the Preaminoacylation Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine (F-Ams)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Preaminoacylation Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine (F-Ams) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:40.8
occ:1.00
 OE1 B:GLU476 2.0 58.2 1.0
O B:HOH1014 2.1 38.8 1.0
O B:HOH1052 2.1 39.5 1.0
OE2 A:GLU259 2.1 50.1 1.0
O A:HOH506 2.2 41.0 1.0
O A:HOH528 2.2 42.1 1.0
CD B:GLU476 3.0 57.7 1.0
CD A:GLU259 3.0 46.7 1.0
OE1 A:GLU259 3.2 46.7 1.0
OD2 B:ASP172 3.5 55.5 1.0
OE2 B:GLU476 3.8 58.5 1.0
CG B:GLU476 3.9 39.0 1.0
OD2 B:ASP467 4.0 50.6 1.0
NH2 B:ARG173 4.0 38.2 1.0
CB B:GLU476 4.1 37.5 1.0
OE2 B:GLU477 4.2 43.6 1.0
OD2 B:ASP473 4.3 48.2 1.0
O B:HOH1213 4.4 50.5 1.0
O B:HOH1025 4.4 47.7 1.0
CG A:GLU259 4.5 48.9 1.0
O A:HOH501 4.5 44.2 1.0
O B:ASP473 4.6 43.4 1.0
CG B:ASP172 4.6 51.6 1.0
CA B:ASP473 4.7 37.8 1.0
CB B:ASP473 4.8 36.6 1.0
CZ B:ARG173 4.8 48.0 1.0

Magnesium binding site 3 out of 13 in 7k98

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Magnesium binding site 3 out of 13 in the Preaminoacylation Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine (F-Ams)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Preaminoacylation Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine (F-Ams) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:71.9
occ:1.00
 O A:HOH572 2.0 78.2 1.0
O C:HOH203 2.0 75.6 1.0
O C:HOH239 2.2 64.0 1.0
O A:HOH552 2.2 69.6 1.0
O C:HOH234 2.2 64.8 1.0
OE2 A:GLU204 3.4 74.0 1.0
O6 C:G71 4.2 76.2 1.0
O6 C:G70 4.3 72.4 1.0
CD A:GLU204 4.5 79.9 1.0
N7 C:G70 4.6 76.0 1.0
OE1 A:GLU204 4.8 88.2 1.0
C6 C:G70 5.0 73.6 1.0
N7 C:G71 5.0 84.1 1.0

Magnesium binding site 4 out of 13 in 7k98

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Magnesium binding site 4 out of 13 in the Preaminoacylation Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine (F-Ams)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Preaminoacylation Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine (F-Ams) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:69.1
occ:1.00
 NE2 A:HIS253 2.0 58.2 1.0
O A:HOH514 2.2 71.0 1.0
O C:HOH223 2.2 50.2 1.0
O C:HOH230 2.4 48.8 1.0
CE1 A:HIS253 3.0 53.1 1.0
O C:HOH229 3.0 51.0 1.0
CD2 A:HIS253 3.1 46.5 1.0
O C:HOH207 3.6 47.5 1.0
O A:HOH555 3.6 57.8 1.0
OE2 A:GLU263 3.9 78.0 1.0
ND1 A:HIS253 4.1 53.2 1.0
CG A:HIS253 4.2 49.3 1.0
O3' C:A77 4.2 56.0 1.0
CD A:GLU263 4.5 76.6 1.0
O A:PHE254 4.6 45.8 1.0
OP2 C:A77 4.6 70.4 1.0
CE1 A:PHE255 4.9 46.3 1.0
OE1 A:GLU263 4.9 82.9 1.0

Magnesium binding site 5 out of 13 in 7k98

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Magnesium binding site 5 out of 13 in the Preaminoacylation Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine (F-Ams)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Preaminoacylation Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine (F-Ams) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg901

b:54.9
occ:1.00
 O F:HOH203 2.1 49.1 1.0
OP1 F:A39 2.2 75.7 1.0
O B:HOH1035 2.2 46.1 1.0
OE2 B:GLU807 2.3 64.0 1.0
CD B:GLU807 3.3 61.9 1.0
P F:A39 3.6 58.8 1.0
O B:HOH1008 3.7 38.1 1.0
OP2 F:G27 3.7 55.4 1.0
OE1 B:GLU807 3.7 56.9 1.0
OP2 F:A39 4.2 60.7 1.0
OP1 F:G27 4.3 51.5 1.0
O5' F:A39 4.4 56.9 1.0
P F:G27 4.5 50.9 1.0
O3' F:A38 4.6 55.0 1.0
CG B:GLU807 4.7 51.5 1.0
C5' F:A39 4.8 54.4 1.0
O B:PHE743 5.0 53.8 1.0

Magnesium binding site 6 out of 13 in 7k98

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Magnesium binding site 6 out of 13 in the Preaminoacylation Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine (F-Ams)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Preaminoacylation Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine (F-Ams) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:47.0
occ:1.00
 OD2 D:ASP203 2.0 54.2 1.0
O D:HOH509 2.0 42.7 1.0
O F:HOH202 2.1 48.9 1.0
O F:HOH214 2.1 41.0 1.0
O D:HOH545 2.2 43.9 1.0
O F:HOH216 2.3 41.8 1.0
CG D:ASP203 3.1 50.8 1.0
OD1 D:ASP203 3.6 49.5 1.0
O2 F:C76 3.9 60.7 1.0
N1 F:A77 4.0 59.9 1.0
O F:HOH244 4.1 54.8 1.0
OD2 D:ASP159 4.2 67.7 1.0
O D:HOH574 4.2 52.8 1.0
O2 F:C75 4.3 57.3 1.0
CB D:ASP203 4.3 49.1 1.0
C2 F:A77 4.4 57.9 1.0
CA D:ASP203 4.5 55.6 1.0
O D:THR202 4.5 45.2 1.0
C2 F:C76 4.5 64.5 1.0
N3 F:C75 4.5 60.7 1.0
O D:HOH510 4.6 50.9 1.0
O D:ASP159 4.6 42.5 1.0
CB D:ARG201 4.6 40.4 1.0
CA D:ASP159 4.7 45.3 1.0
CG D:ASP159 4.7 70.9 1.0
C D:THR202 4.7 42.6 1.0
N D:ASP203 4.7 46.5 1.0
CB D:ASP159 4.7 58.6 1.0
O F:HOH215 4.8 50.7 1.0
CD D:ARG201 4.8 41.2 1.0
C2 F:C75 4.9 66.2 1.0
N3 F:C76 5.0 71.0 1.0

Magnesium binding site 7 out of 13 in 7k98

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Magnesium binding site 7 out of 13 in the Preaminoacylation Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine (F-Ams)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Preaminoacylation Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine (F-Ams) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg403

b:41.5
occ:1.00
 O E:HOH1048 2.0 43.9 1.0
O E:HOH1090 2.0 36.7 1.0
OE1 E:GLU476 2.1 62.2 1.0
OE1 D:GLU259 2.2 42.5 1.0
O E:HOH1019 2.2 35.1 1.0
O E:HOH1039 2.3 39.1 1.0
CD E:GLU476 3.0 60.2 1.0
CD D:GLU259 3.1 43.5 1.0
OE2 D:GLU259 3.4 47.1 1.0
OD2 E:ASP172 3.6 46.5 1.0
OE2 E:GLU476 3.8 54.7 1.0
CG E:GLU476 3.9 47.7 1.0
OD2 E:ASP467 4.0 47.6 1.0
CB E:GLU476 4.2 36.4 1.0
OD2 E:ASP473 4.2 41.5 1.0
NH2 E:ARG173 4.2 37.5 1.0
O E:HOH1183 4.2 59.8 1.0
O E:ASP473 4.3 42.9 1.0
OE2 E:GLU477 4.3 44.1 1.0
O D:HOH505 4.3 44.7 1.0
CG D:GLU259 4.5 39.4 1.0
CA E:ASP473 4.5 34.9 1.0
O E:HOH1059 4.7 59.9 1.0
CB E:ASP473 4.8 38.2 1.0
CG E:ASP172 4.8 49.5 1.0
CZ E:ARG173 4.9 45.1 1.0
CD2 E:LEU468 4.9 38.9 1.0
C E:ASP473 4.9 37.4 1.0
NH1 E:ARG465 5.0 41.5 1.0
CG E:ASP473 5.0 46.4 1.0

Magnesium binding site 8 out of 13 in 7k98

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Magnesium binding site 8 out of 13 in the Preaminoacylation Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine (F-Ams)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Preaminoacylation Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine (F-Ams) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg404

b:61.2
occ:1.00
 NE2 D:HIS253 2.1 61.0 1.0
O D:HOH523 2.2 48.5 1.0
O D:HOH582 2.3 53.6 1.0
O F:HOH218 2.5 46.4 1.0
CE1 D:HIS253 3.0 46.0 1.0
CD2 D:HIS253 3.1 46.0 1.0
O D:HOH503 4.0 59.9 1.0
O3' F:A77 4.1 70.8 1.0
ND1 D:HIS253 4.1 49.4 1.0
OE1 D:GLU263 4.2 57.3 1.0
OP2 F:A77 4.2 78.0 1.0
CG D:HIS253 4.2 44.1 1.0
O D:PHE254 4.3 44.8 1.0
O5' F:A77 4.7 77.0 1.0
OE2 D:GLU263 4.8 54.5 1.0
CD D:GLU263 4.9 63.0 1.0
CE1 D:PHE255 4.9 34.9 1.0

Magnesium binding site 9 out of 13 in 7k98

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Magnesium binding site 9 out of 13 in the Preaminoacylation Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine (F-Ams)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Preaminoacylation Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine (F-Ams) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg101

b:65.9
occ:1.00
 O C:HOH216 2.1 56.1 1.0
O C:HOH221 2.1 57.4 1.0
O C:HOH202 2.2 51.5 1.0
O C:HOH222 2.5 56.3 1.0
OP1 C:U8 3.5 74.3 1.0
OP2 C:U8 3.7 59.4 1.0
OP2 C:A9 3.9 61.5 1.0
OP1 C:A9 3.9 63.6 1.0
P C:U8 4.0 63.5 1.0
OP2 C:U12 4.1 55.1 1.0
O C:HOH209 4.3 53.0 1.0
OP2 C:C11 4.3 70.0 1.0
P C:A9 4.4 61.0 1.0
O C:HOH233 4.7 74.2 1.0
O C:HOH231 4.9 63.5 1.0
O5' C:U8 4.9 67.2 1.0

Magnesium binding site 10 out of 13 in 7k98

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Magnesium binding site 10 out of 13 in the Preaminoacylation Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine (F-Ams)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Preaminoacylation Complex of M. Tuberculosis Phers with Cognate Precursor Trna and 5'-O-(N-Phenylalanyl)Sulfamoyl-Adenosine (F-Ams) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg102

b:64.1
occ:1.00
 OP1 C:A39 2.1 83.6 1.0
O C:HOH206 2.1 51.4 1.0
O E:HOH1029 2.3 38.0 1.0
OE1 E:GLU807 2.4 71.5 1.0
O E:HOH1004 3.3 37.3 1.0
CD E:GLU807 3.5 71.5 1.0
P C:A39 3.5 60.2 1.0
OP2 C:G27 3.6 54.4 1.0
OE2 E:GLU807 3.8 69.7 1.0
OP1 C:G27 4.1 52.9 1.0
OP2 C:A39 4.1 64.5 1.0
P C:G27 4.4 57.1 1.0
O3' C:A38 4.4 61.4 1.0
O5' C:A39 4.4 60.1 1.0
O E:PHE743 4.6 53.8 1.0
C5' C:A39 4.8 59.1 1.0
CG E:GLU807 4.8 64.2 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 22:09:24 2024

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