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Magnesium in PDB 7ka0: Crystal Structure of the Complex of M. Tuberculosis Phers with Cognate Precursor Trna and Phenylalanine

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

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

Protein crystallography data

The structure of Crystal Structure of the Complex of M. Tuberculosis Phers with Cognate Precursor Trna and Phenylalanine, PDB code: 7ka0 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) 48.04 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 292.859, 109.98, 127.951, 90, 100.16, 90
R / Rfree (%) 17.7 / 21.5

Other elements in 7ka0:

The structure of Crystal Structure of the Complex of M. Tuberculosis Phers with Cognate Precursor Trna and Phenylalanine also contains other interesting chemical elements:

Potassium (K) 3 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the Complex of M. Tuberculosis Phers with Cognate Precursor Trna and Phenylalanine (pdb code 7ka0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Crystal Structure of the Complex of M. Tuberculosis Phers with Cognate Precursor Trna and Phenylalanine, PDB code: 7ka0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 7ka0

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Magnesium binding site 1 out of 12 in the Crystal Structure of the Complex of M. Tuberculosis Phers 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 Crystal Structure of the Complex of M. Tuberculosis Phers with Cognate Precursor Trna and Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg409

b:34.9
occ:1.00
 O B:HOH1085 2.0 35.6 1.0
O B:HOH1060 2.1 38.7 1.0
OE1 B:GLU476 2.1 48.2 1.0
OE2 A:GLU259 2.1 44.1 1.0
O A:HOH539 2.2 30.8 1.0
O B:HOH1097 2.4 28.2 1.0
CD A:GLU259 2.9 44.1 1.0
OE1 A:GLU259 3.0 39.1 1.0
CD B:GLU476 3.1 47.7 1.0
OD2 B:ASP172 3.8 44.0 1.0
OE2 B:GLU476 3.9 48.9 1.0
OD2 B:ASP467 3.9 52.3 1.0
OD1 B:ASP473 4.0 53.2 1.0
CG B:GLU476 4.1 42.4 1.0
O A:HOH534 4.2 39.6 1.0
CB B:GLU476 4.2 42.9 1.0
O B:HOH1278 4.3 35.6 1.0
CG A:GLU259 4.3 40.6 1.0
O B:ASP473 4.5 40.9 1.0
CA B:ASP473 4.5 34.5 1.0
NH1 B:ARG173 4.6 49.8 1.0
OE2 B:GLU477 4.6 39.1 1.0
O B:HOH1077 4.7 37.1 1.0
CB B:ASP473 4.7 39.8 1.0
MG A:MG410 4.7 59.9 1.0
CG B:ASP473 4.8 50.2 1.0
CG B:ASP172 4.9 44.7 1.0

Magnesium binding site 2 out of 12 in 7ka0

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Magnesium binding site 2 out of 12 in the Crystal Structure of the Complex of M. Tuberculosis Phers 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 Crystal Structure of the Complex of M. Tuberculosis Phers with Cognate Precursor Trna and Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg410

b:59.9
occ:1.00
 OD1 B:ASP473 2.6 53.2 1.0
O B:HOH1087 3.0 46.9 1.0
NE2 A:HIS287 3.0 30.6 1.0
O B:HOH1278 3.1 35.6 1.0
O A:HOH564 3.3 30.0 1.0
OE1 A:GLU259 3.3 39.1 1.0
O A:HOH588 3.3 37.4 1.0
O B:HOH1031 3.4 50.1 1.0
O A:HOH612 3.4 56.8 1.0
CD2 A:HIS287 3.5 27.3 1.0
O A:HOH539 3.7 30.8 1.0
CG B:ASP473 3.7 50.2 1.0
CD A:GLU259 3.7 44.1 1.0
O B:HOH1060 3.8 38.7 1.0
OD2 B:ASP473 4.1 50.9 1.0
CG A:GLU259 4.1 40.6 1.0
CE1 A:HIS287 4.1 26.9 1.0
CB A:GLU259 4.4 28.9 1.0
OE2 A:GLU259 4.4 44.1 1.0
O B:ASP467 4.7 50.4 1.0
MG A:MG409 4.7 34.9 1.0
ND2 A:ASN147 4.8 24.0 1.0
CG A:HIS287 4.8 33.6 1.0

Magnesium binding site 3 out of 12 in 7ka0

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Magnesium binding site 3 out of 12 in the Crystal Structure of the Complex of M. Tuberculosis Phers 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 Crystal Structure of the Complex of M. Tuberculosis Phers with Cognate Precursor Trna and Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg907

b:68.1
occ:1.00
 OP1 C:A39 2.7 43.0 1.0
O B:PHE743 2.7 32.9 1.0
O B:HOH1197 3.3 44.7 1.0
OE1 B:GLU807 3.5 91.3 1.0
C B:PHE743 3.8 32.5 1.0
OE2 B:GLU807 3.8 93.1 1.0
CG B:GLN744 3.8 34.9 1.0
P C:A39 3.9 47.2 1.0
O3' C:A38 4.0 42.5 1.0
C5' C:A39 4.0 47.8 1.0
CD B:GLU807 4.1 87.4 1.0
CG1 B:VAL742 4.2 25.5 1.0
N B:PHE743 4.4 29.3 1.0
MG C:MG101 4.4 93.1 1.0
O5' C:A39 4.4 50.0 1.0
NE2 B:GLN744 4.5 37.4 1.0
CA B:PHE743 4.7 27.6 1.0
CD B:GLN744 4.7 42.3 1.0
N B:GLN744 4.7 31.7 1.0
CA B:GLN744 4.8 28.2 1.0
CB B:GLN744 4.9 29.0 1.0

Magnesium binding site 4 out of 12 in 7ka0

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Magnesium binding site 4 out of 12 in the Crystal Structure of the Complex of M. Tuberculosis Phers 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 Crystal Structure of the Complex of M. Tuberculosis Phers with Cognate Precursor Trna and Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg101

b:93.1
occ:1.00
 OP1 C:G27 2.9 102.3 1.0
OP1 C:A39 3.0 43.0 1.0
P C:A39 4.0 47.2 1.0
P C:G27 4.1 105.6 1.0
OP2 C:A39 4.1 52.4 1.0
OP2 C:U28 4.2 111.6 1.0
O5' C:G27 4.4 103.9 1.0
MG B:MG907 4.4 68.1 1.0
C5' C:G27 4.5 101.3 1.0
OP2 C:G27 4.9 101.8 1.0
O B:HOH1197 5.0 44.7 1.0
P C:U28 5.0 111.2 1.0

Magnesium binding site 5 out of 12 in 7ka0

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Magnesium binding site 5 out of 12 in the Crystal Structure of the Complex of M. Tuberculosis Phers 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 Crystal Structure of the Complex of M. Tuberculosis Phers with Cognate Precursor Trna and Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg102

b:86.4
occ:1.00
 OP2 C:A45 2.6 140.0 1.0
C5' C:A44 3.1 134.0 1.0
P C:A45 3.1 138.0 1.0
O3' C:A44 3.1 135.6 1.0
O5' C:A44 3.3 134.8 1.0
OP1 C:A45 3.3 142.2 1.0
C3' C:A44 3.5 133.2 1.0
OP1 C:A44 3.5 139.4 1.0
C4' C:A44 3.8 132.6 1.0
P C:A44 4.0 136.3 1.0
O5' C:A45 4.7 134.7 1.0
OP2 C:A44 4.8 137.2 1.0
C2' C:A44 5.0 129.7 1.0
O4' C:A44 5.0 129.1 1.0

Magnesium binding site 6 out of 12 in 7ka0

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Magnesium binding site 6 out of 12 in the Crystal Structure of the Complex of M. Tuberculosis Phers 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 Crystal Structure of the Complex of M. Tuberculosis Phers with Cognate Precursor Trna and Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg103

b:63.4
occ:1.00
 OP2 C:A36 2.1 77.9 1.0
OP2 C:G35 2.7 63.1 1.0
O5' C:G35 3.0 57.9 1.0
C3' C:U34 3.1 60.7 1.0
P C:A36 3.2 60.4 1.0
C5' C:G35 3.3 56.9 1.0
P C:G35 3.3 58.2 1.0
C6 C:U34 3.4 55.8 1.0
O5' C:U34 3.5 76.2 1.0
O3' C:G35 3.6 53.7 1.0
O3' C:U34 3.7 58.0 1.0
C2' C:U34 3.7 54.2 1.0
C3' C:G35 3.9 51.1 1.0
C5 C:U34 3.9 57.7 1.0
N1 C:U34 3.9 57.3 1.0
OP2 C:U34 3.9 77.0 1.0
OP1 C:A36 4.0 61.9 1.0
C4' C:G35 4.1 51.5 1.0
C4' C:U34 4.2 64.8 1.0
C1' C:U34 4.3 57.2 1.0
P C:U34 4.3 79.6 1.0
C5' C:U34 4.4 70.8 1.0
O5' C:A36 4.5 63.2 1.0
O4' C:U34 4.5 63.4 1.0
C4 C:U34 4.7 60.2 1.0
C2 C:U34 4.7 59.5 1.0
OP1 C:G35 4.7 59.2 1.0
N3 C:U34 4.9 57.8 1.0
O2' C:U34 5.0 52.4 1.0

Magnesium binding site 7 out of 12 in 7ka0

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Magnesium binding site 7 out of 12 in the Crystal Structure of the Complex of M. Tuberculosis Phers 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 Crystal Structure of the Complex of M. Tuberculosis Phers with Cognate Precursor Trna and Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:41.4
occ:1.00
 O D:HOH543 2.5 19.1 1.0
O D:HOH620 2.7 27.0 1.0
O B:HOH1280 2.8 30.1 1.0
O B:HOH1131 3.1 24.0 1.0
CD1 D:ILE95 3.9 21.9 1.0
CD1 D:LEU99 3.9 31.6 1.0
O D:HOH579 4.1 37.5 1.0
CB B:ALA653 4.3 11.8 1.0
CB D:ILE95 4.4 24.1 1.0
OE1 B:GLU651 4.4 31.2 0.5
O B:HOH1255 4.5 35.0 1.0
O D:HOH505 4.5 34.6 1.0
CG2 D:ILE95 4.6 16.5 1.0
O D:ASP96 4.6 27.3 1.0
CG1 D:ILE95 4.6 19.7 1.0
O D:HOH583 4.8 30.9 1.0
N B:ALA653 4.9 26.1 1.0
CB D:LEU99 4.9 25.2 1.0

Magnesium binding site 8 out of 12 in 7ka0

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Magnesium binding site 8 out of 12 in the Crystal Structure of the Complex of M. Tuberculosis Phers 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 Crystal Structure of the Complex of M. Tuberculosis Phers with Cognate Precursor Trna and Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg410

b:31.2
occ:1.00
 OE1 E:GLU476 1.9 45.6 1.0
O D:HOH560 2.1 26.7 1.0
O D:HOH558 2.1 31.9 1.0
OE2 D:GLU259 2.1 43.4 1.0
O E:HOH1058 2.3 30.4 1.0
O E:HOH1066 2.3 24.4 1.0
CD D:GLU259 3.0 40.6 1.0
CD E:GLU476 3.0 42.4 1.0
OE1 D:GLU259 3.1 42.6 1.0
OD2 E:ASP172 3.5 47.0 1.0
OE2 E:GLU476 3.7 39.6 1.0
CG E:GLU476 4.0 33.9 1.0
O D:HOH510 4.1 37.0 1.0
OD2 E:ASP467 4.1 35.7 1.0
OD1 E:ASP473 4.2 42.0 1.0
O E:HOH1296 4.2 40.8 1.0
CB E:GLU476 4.2 32.8 1.0
NH1 E:ARG173 4.3 34.4 1.0
CG D:GLU259 4.4 30.4 1.0
CG E:ASP172 4.7 43.2 1.0
OE2 E:GLU477 4.7 38.9 1.0
O E:HOH1009 4.8 37.1 1.0
O E:ASP473 4.8 32.6 1.0
CA E:ASP473 4.9 36.0 1.0

Magnesium binding site 9 out of 12 in 7ka0

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Magnesium binding site 9 out of 12 in the Crystal Structure of the Complex of M. Tuberculosis Phers 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 Crystal Structure of the Complex of M. Tuberculosis Phers with Cognate Precursor Trna and Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg902

b:71.7
occ:1.00
 O E:HOH1011 2.6 44.4 1.0
O E:PHE743 2.7 30.1 1.0
OP1 F:A39 2.9 49.3 1.0
O E:HOH1181 3.3 32.6 1.0
CG E:GLN744 3.7 39.3 1.0
C E:PHE743 3.8 30.5 1.0
O3' F:A38 3.9 42.2 1.0
P F:A39 4.0 49.7 1.0
MG F:MG101 4.0 93.9 1.0
C5' F:A39 4.1 53.4 1.0
OE2 E:GLU807 4.2 100.0 1.0
CG1 E:VAL742 4.2 23.9 1.0
NE2 E:GLN744 4.4 35.5 1.0
N E:PHE743 4.4 28.0 1.0
O5' F:A39 4.5 53.9 1.0
CD E:GLN744 4.6 39.1 1.0
N E:GLN744 4.6 31.3 1.0
CA E:GLN744 4.7 33.9 1.0
CA E:PHE743 4.7 30.8 1.0
CB E:GLN744 4.8 37.5 1.0
O2' F:A38 4.9 40.6 1.0
CD E:GLU807 4.9 95.6 1.0

Magnesium binding site 10 out of 12 in 7ka0

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Magnesium binding site 10 out of 12 in the Crystal Structure of the Complex of M. Tuberculosis Phers 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 Crystal Structure of the Complex of M. Tuberculosis Phers with Cognate Precursor Trna and Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg903

b:54.3
occ:1.00
 OG1 E:THR793 2.5 28.0 1.0
O6 F:G35 2.8 45.3 1.0
OG E:SER791 2.9 23.4 1.0
OD2 E:ASP778 3.1 47.0 1.0
OG E:SER747 3.2 27.4 0.5
N1 F:A36 3.4 34.6 1.0
CB E:SER791 3.4 21.2 1.0
NH1 E:ARG830 3.5 38.6 1.0
O E:SER791 3.6 32.7 1.0
C E:SER791 3.6 31.9 1.0
CB E:THR793 3.8 29.4 1.0
C6 F:A36 3.9 35.4 1.0
C6 F:G35 3.9 48.2 1.0
N E:THR793 3.9 24.9 1.0
N6 F:A36 4.0 39.7 1.0
C E:LEU792 4.0 29.3 1.0
N E:LEU792 4.0 29.2 1.0
C2 F:A36 4.0 37.5 1.0
OG E:SER747 4.1 27.9 0.5
CA E:SER791 4.1 27.1 1.0
CG E:ASP778 4.2 39.7 1.0
CB E:PHE780 4.2 31.8 1.0
N1 F:G35 4.2 49.4 1.0
CA E:LEU792 4.3 28.1 1.0
CA E:THR793 4.3 28.4 1.0
O E:LEU792 4.3 29.4 1.0
CB E:SER747 4.4 26.4 0.5
CB E:SER747 4.4 26.5 0.5
CB E:ASP778 4.5 31.1 1.0
O E:ASP778 4.6 40.1 1.0
C5 F:A36 4.8 41.2 1.0
CZ E:ARG830 4.8 40.4 1.0
N E:PHE780 4.9 33.6 1.0
CG2 E:THR793 4.9 28.5 1.0
N3 F:A36 4.9 42.6 1.0
C E:ASP778 4.9 34.5 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 22:10:13 2024

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