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 / R_free (%)*	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

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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

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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

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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

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