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Magnesium in PDB 7kab: M. Tuberculosis Phers Complex with Cognate Precursor Trna and Phenylalanine

Enzymatic activity of M. Tuberculosis Phers Complex with Cognate Precursor Trna and Phenylalanine

All present enzymatic activity of M. Tuberculosis Phers Complex with Cognate Precursor Trna and Phenylalanine:
6.1.1.20;

Protein crystallography data

The structure of M. Tuberculosis Phers Complex with Cognate Precursor Trna and Phenylalanine, PDB code: 7kab was solved by C.Chang, K.Michalska, R.Jedrzejczak, J.Wower, A.Joachimiak, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.69 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 127.597, 110.452, 148.413, 90, 105.07, 90
R / Rfree (%) 18.6 / 21.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the M. Tuberculosis Phers Complex with Cognate Precursor Trna and Phenylalanine (pdb code 7kab). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the M. Tuberculosis Phers Complex with Cognate Precursor Trna and Phenylalanine, PDB code: 7kab:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 7kab

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Magnesium binding site 1 out of 10 in the M. Tuberculosis Phers Complex with Cognate Precursor Trna and Phenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of M. Tuberculosis Phers Complex with Cognate Precursor Trna and Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:61.8
occ:1.00
 O A:HOH623 2.1 59.0 1.0
O A:HOH632 2.1 64.9 1.0
O A:GLN158 2.4 61.2 1.0
O A:HOH627 2.5 66.3 1.0
O A:GLY156 2.5 72.0 1.0
C A:GLY156 3.5 61.4 1.0
C A:GLN158 3.6 62.4 1.0
N A:GLN158 4.0 58.9 1.0
O A:HOH633 4.1 60.6 1.0
CE2 A:TYR162 4.1 50.2 1.0
O A:HOH651 4.2 75.9 1.0
N A:THR160 4.2 47.5 1.0
C A:GLU157 4.3 64.0 1.0
OH A:TYR162 4.3 62.7 1.0
OG1 A:THR160 4.4 60.2 1.0
N A:GLU157 4.4 53.6 1.0
CA A:GLU157 4.4 52.3 1.0
CA A:GLN158 4.4 64.1 1.0
CA A:GLY156 4.4 53.2 1.0
CB A:THR160 4.5 52.0 1.0
O A:ARG155 4.6 62.8 1.0
N A:ASP159 4.7 58.5 1.0
CZ A:TYR162 4.7 60.9 1.0
CA A:ASP159 4.8 59.3 1.0
CA A:THR160 5.0 42.8 1.0
O A:THR160 5.0 46.4 1.0
CB A:GLN158 5.0 63.3 1.0

Magnesium binding site 2 out of 10 in 7kab

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Magnesium binding site 2 out of 10 in the M. Tuberculosis Phers Complex with Cognate Precursor Trna and Phenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of M. Tuberculosis Phers Complex with Cognate Precursor Trna and Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg507

b:59.5
occ:1.00
 O B:HOH1047 2.0 67.6 1.0
OE1 B:GLU476 2.0 81.8 1.0
O B:HOH1028 2.1 57.6 1.0
OE2 A:GLU259 2.1 69.3 1.0
O B:HOH1024 2.2 56.5 1.0
O B:HOH1033 2.3 50.2 1.0
CD A:GLU259 2.9 56.3 1.0
CD B:GLU476 3.0 83.7 1.0
OE1 A:GLU259 3.1 65.1 1.0
OE2 B:GLU476 3.7 81.7 1.0
OD2 B:ASP172 3.7 79.7 1.0
OD1 B:ASP473 3.9 81.5 1.0
OD2 B:ASP467 4.0 75.4 1.0
CG B:GLU476 4.1 70.4 1.0
CB B:GLU476 4.1 57.2 1.0
O B:HOH1008 4.2 53.6 1.0
O B:HOH1094 4.3 53.2 1.0
CG A:GLU259 4.3 45.2 1.0
CA B:ASP473 4.5 58.7 1.0
O B:ASP473 4.5 58.0 1.0
CB B:ASP473 4.6 68.9 1.0
OE2 B:GLU477 4.6 63.3 1.0
NH1 B:ARG173 4.7 66.0 1.0
CG B:ASP473 4.7 71.2 1.0
CG B:ASP172 4.9 74.5 1.0

Magnesium binding site 3 out of 10 in 7kab

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Magnesium binding site 3 out of 10 in the M. Tuberculosis Phers Complex with Cognate Precursor Trna and Phenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of M. Tuberculosis Phers Complex with Cognate Precursor Trna and Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg508

b:80.4
occ:1.00
 O B:HOH1064 2.3 72.7 1.0
OE2 A:GLU263 2.4 81.0 1.0
OE2 A:GLU279 2.9 112.1 1.0
CD A:GLU263 3.1 76.5 1.0
OE1 A:GLU263 3.2 85.4 1.0
OE1 B:GLU36 3.4 100.2 1.0
CD A:GLU279 3.8 111.6 1.0
OE1 A:GLU279 4.0 120.2 1.0
CD B:GLU36 4.0 96.1 1.0
OE2 B:GLU36 4.1 96.8 1.0
CE1 A:HIS253 4.4 53.4 1.0
NE2 A:HIS253 4.5 55.8 1.0
CG A:GLU263 4.6 63.6 1.0

Magnesium binding site 4 out of 10 in 7kab

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Magnesium binding site 4 out of 10 in the M. Tuberculosis Phers Complex with Cognate Precursor Trna and Phenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of M. Tuberculosis Phers Complex with Cognate Precursor Trna and Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg905

b:87.9
occ:1.00
 O B:PHE743 2.8 57.4 1.0
OP1 C:A39 2.8 94.8 1.0
OE2 B:GLU807 2.9 119.2 1.0
MG C:MG101 3.1 105.9 1.0
OE1 B:GLU807 3.4 121.9 1.0
CD B:GLU807 3.5 115.1 1.0
C B:PHE743 3.9 44.9 1.0
P C:A39 4.0 91.1 1.0
CG B:GLN744 4.0 55.1 1.0
C5' C:A39 4.1 104.2 1.0
O3' C:A38 4.1 90.5 1.0
CG1 B:VAL742 4.2 45.1 1.0
N B:PHE743 4.5 55.3 1.0
O5' C:A39 4.5 97.6 1.0
NE2 B:GLN744 4.7 73.7 1.0
CA B:PHE743 4.8 42.1 1.0
N B:GLN744 4.9 47.6 1.0
CD B:GLN744 5.0 73.9 1.0
CA B:GLN744 5.0 48.9 1.0

Magnesium binding site 5 out of 10 in 7kab

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Magnesium binding site 5 out of 10 in the M. Tuberculosis Phers Complex with Cognate Precursor Trna and Phenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of M. Tuberculosis Phers Complex with Cognate Precursor Trna and Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg101

b:105.9
occ:1.00
 OP1 C:A39 2.4 94.8 1.0
OP1 C:G27 2.6 207.1 1.0
MG B:MG905 3.1 87.9 1.0
P C:A39 3.7 91.1 1.0
P C:G27 3.9 208.5 1.0
OE2 B:GLU807 4.0 119.2 1.0
OP2 C:A39 4.4 88.9 1.0
OP2 C:G27 4.5 208.2 1.0
O5' C:A39 4.5 97.6 1.0
O5' C:G27 4.7 205.7 1.0
C5' C:A39 4.8 104.2 1.0
O3' C:A38 4.8 90.5 1.0
CD B:GLU807 4.9 115.1 1.0
OP2 C:G40 4.9 160.5 1.0

Magnesium binding site 6 out of 10 in 7kab

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Magnesium binding site 6 out of 10 in the M. Tuberculosis Phers Complex with Cognate Precursor Trna and Phenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of M. Tuberculosis Phers Complex with Cognate Precursor Trna and Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg102

b:104.7
occ:1.00
 O6 C:G46 2.8 198.0 1.0
MG C:MG103 3.1 113.4 1.0
C6 C:G46 3.9 195.8 1.0
OP2 C:A24 4.0 220.6 1.0
N1 C:G46 4.3 189.1 1.0
O5' C:A24 4.4 221.3 1.0
C5' C:G23 4.9 226.3 1.0
P C:A24 4.9 221.6 1.0

Magnesium binding site 7 out of 10 in 7kab

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Magnesium binding site 7 out of 10 in the M. Tuberculosis Phers Complex with Cognate Precursor Trna and Phenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of M. Tuberculosis Phers Complex with Cognate Precursor Trna and Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg103

b:113.4
occ:1.00
 MG C:MG102 3.1 104.7 1.0
N6 C:A9 3.2 187.0 1.0
O5' C:A24 3.3 221.3 1.0
C3' C:G23 3.8 218.5 1.0
C8 C:G23 3.8 214.6 1.0
N1 C:A9 3.9 185.9 1.0
C5' C:G23 3.9 226.3 1.0
C6 C:A9 4.0 188.6 1.0
C8 C:A24 4.1 208.5 1.0
N7 C:G23 4.1 214.5 1.0
OP2 C:A24 4.1 220.6 1.0
O6 C:G46 4.1 198.0 1.0
C5' C:A24 4.2 218.9 1.0
N9 C:G23 4.2 215.5 1.0
P C:A24 4.3 221.6 1.0
C4' C:G23 4.3 220.9 1.0
N1 C:G46 4.4 189.1 1.0
O3' C:G23 4.5 219.7 1.0
O4' C:G23 4.5 218.3 1.0
C2' C:G23 4.6 216.2 1.0
N7 C:A24 4.6 208.6 1.0
O4' C:A24 4.6 213.2 1.0
C5 C:G23 4.7 214.5 1.0
C6 C:G46 4.7 195.8 1.0
C1' C:G23 4.7 216.7 1.0
C4 C:G23 4.8 215.6 1.0
O5' C:G23 4.9 233.8 1.0

Magnesium binding site 8 out of 10 in 7kab

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Magnesium binding site 8 out of 10 in the M. Tuberculosis Phers Complex with Cognate Precursor Trna and Phenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of M. Tuberculosis Phers Complex with Cognate Precursor Trna and Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg104

b:111.4
occ:1.00
 OP2 C:U16 3.2 191.8 1.0
OP1 C:U16 3.4 191.0 1.0
P C:U16 3.6 193.9 1.0
OP1 C:G15 3.8 198.3 1.0
C5' C:G15 3.9 201.4 1.0
O3' C:G15 4.0 197.3 1.0
O5' C:G15 4.0 200.7 1.0
C3' C:G15 4.6 199.8 1.0
P C:G15 4.6 197.9 1.0
C4' C:G15 4.7 201.7 1.0

Magnesium binding site 9 out of 10 in 7kab

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Magnesium binding site 9 out of 10 in the M. Tuberculosis Phers Complex with Cognate Precursor Trna and Phenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of M. Tuberculosis Phers Complex with Cognate Precursor Trna and Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg105

b:94.3
occ:1.00
 O2 C:C29 2.2 250.5 1.0
N2 C:G43 2.8 165.6 1.0
C1' C:C30 3.1 181.8 1.0
O4' C:C30 3.3 180.8 1.0
C2 C:C29 3.3 226.8 1.0
N3 C:A44 3.5 196.2 1.0
N1 C:C30 3.7 178.3 1.0
O2 C:C30 3.8 175.6 1.0
N3 C:C29 3.9 218.7 1.0
C2 C:C30 3.9 174.2 1.0
C2 C:G43 4.1 170.2 1.0
C2 C:A44 4.1 192.8 1.0
C1' C:A44 4.2 209.7 1.0
C4 C:A44 4.2 200.5 1.0
N1 C:C29 4.4 214.5 1.0
C2' C:C29 4.4 200.8 1.0
C2' C:C30 4.4 184.4 1.0
O2' C:C30 4.5 186.2 1.0
O2' C:C29 4.5 194.3 1.0
C6 C:C30 4.5 176.6 1.0
C1' C:C29 4.5 203.6 1.0
C4' C:C30 4.5 179.5 1.0
O2' C:A44 4.6 212.7 1.0
N9 C:A44 4.6 204.1 1.0
N3 C:G43 4.7 170.6 1.0
C2' C:A44 4.9 213.9 1.0
N3 C:C30 4.9 169.3 1.0

Magnesium binding site 10 out of 10 in 7kab

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Magnesium binding site 10 out of 10 in the M. Tuberculosis Phers Complex with Cognate Precursor Trna and Phenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of M. Tuberculosis Phers Complex with Cognate Precursor Trna and Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg106

b:91.7
occ:1.00
 OP1 C:G10 3.1 216.7 1.0
OP1 C:G47 3.1 225.4 1.0
O3' C:G46 3.6 225.4 1.0
P C:G47 3.9 226.6 1.0
P C:G10 4.5 217.7 1.0
O2' C:G46 4.7 206.6 1.0
OP2 C:G47 4.8 232.8 1.0
C3' C:G46 4.9 217.6 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 22:10:23 2024

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