Sodium in PDB 5urb: Crystal Structure of Methionyl-Trna Synthetase (Metrs) From Acinetobacter Baumannii with Bound L-Methionine

Enzymatic activity of Crystal Structure of Methionyl-Trna Synthetase (Metrs) From Acinetobacter Baumannii with Bound L-Methionine

All present enzymatic activity of Crystal Structure of Methionyl-Trna Synthetase (Metrs) From Acinetobacter Baumannii with Bound L-Methionine:
6.1.1.10;

Protein crystallography data

The structure of Crystal Structure of Methionyl-Trna Synthetase (Metrs) From Acinetobacter Baumannii with Bound L-Methionine, PDB code: 5urb was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	37.73 / 1.90
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	69.910, 108.410, 78.570, 90.00, 90.69, 90.00
*R / R_free (%)*	15.6 / 19.4

Other elements in 5urb:

The structure of Crystal Structure of Methionyl-Trna Synthetase (Metrs) From Acinetobacter Baumannii with Bound L-Methionine also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Methionyl-Trna Synthetase (Metrs) From Acinetobacter Baumannii with Bound L-Methionine (pdb code 5urb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Methionyl-Trna Synthetase (Metrs) From Acinetobacter Baumannii with Bound L-Methionine, PDB code: 5urb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5urb

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Sodium Binding Sites List in 5urb

Sodium binding site 1 out of 2 in the Crystal Structure of Methionyl-Trna Synthetase (Metrs) From Acinetobacter Baumannii with Bound L-Methionine

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Methionyl-Trna Synthetase (Metrs) From Acinetobacter Baumannii with Bound L-Methionine within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na601 b:37.3 occ:1.00	O	A:HOH919	2.3	30.6	1.0
	OD1	A:ASN321	2.4	18.9	0.4
	O	A:LYS364	2.4	34.7	1.0
	O	A:HOH866	2.5	26.6	1.0
	O	A:SER362	2.5	32.0	1.0
	CG	A:ASN321	3.4	27.3	0.4
	C	A:LYS364	3.5	34.3	1.0
	C	A:SER362	3.6	36.6	1.0
	NE2	A:GLN27	3.9	25.2	1.0
	N	A:LYS364	4.0	28.0	1.0
	N	A:SER362	4.1	28.9	1.0
	C	A:ASP363	4.2	26.1	1.0
	CB	A:ASN321	4.2	29.1	0.4
	ND2	A:ASN321	4.2	22.9	0.4
	O	A:HOH783	4.2	35.0	1.0
	O	A:VAL320	4.3	25.1	1.0
	CA	A:LYS364	4.4	35.6	1.0
	N	A:VAL365	4.4	31.2	1.0
	CA	A:ASN321	4.4	27.1	0.4
	CD2	A:LEU361	4.5	32.6	1.0
	N	A:ASP363	4.5	30.9	1.0
	CA	A:SER362	4.5	30.2	1.0
	CA	A:ASN321	4.5	26.4	0.6
	CA	A:ASP363	4.5	28.3	1.0
	CB	A:ASN321	4.6	29.5	0.6
	CA	A:VAL365	4.6	30.6	1.0
	O	A:ASP363	4.6	32.8	1.0
	O	A:HOH831	4.6	33.9	1.0
	N	A:GLU366	4.7	34.3	1.0
	OG	A:SER362	4.7	33.9	1.0
	CG	A:GLU366	4.7	43.2	1.0
	OE2	A:GLU366	4.8	50.2	1.0
	CD	A:GLN27	4.9	25.4	1.0

Sodium binding site 2 out of 2 in 5urb

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Sodium Binding Sites List in 5urb

Sodium binding site 2 out of 2 in the Crystal Structure of Methionyl-Trna Synthetase (Metrs) From Acinetobacter Baumannii with Bound L-Methionine

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Methionyl-Trna Synthetase (Metrs) From Acinetobacter Baumannii with Bound L-Methionine within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Na601 b:35.8 occ:1.00	O	B:HOH903	2.2	29.0	1.0
	OD1	B:ASN321	2.4	25.4	0.6
	O	B:SER362	2.4	26.4	1.0
	O	B:HOH1012	2.5	28.3	1.0
	O	B:LYS364	2.5	36.2	1.0
	CG	B:ASN321	3.4	22.9	0.6
	C	B:SER362	3.5	25.8	1.0
	C	B:LYS364	3.6	36.9	1.0
	N	B:SER362	4.0	26.7	1.0
	NE2	B:GLN27	4.0	25.3	1.0
	N	B:LYS364	4.0	36.4	1.0
	C	B:ASP363	4.1	35.2	1.0
	CB	B:ASN321	4.2	27.0	0.6
	O	B:HOH814	4.2	33.4	1.0
	O	B:VAL320	4.3	25.4	1.0
	N	B:ASP363	4.3	25.4	1.0
	CA	B:SER362	4.3	22.2	1.0
	ND2	B:ASN321	4.4	24.2	0.6
	CB	B:ASN321	4.4	26.9	0.4
	CA	B:ASP363	4.4	28.7	1.0
	OG	B:SER362	4.4	31.5	1.0
	CA	B:LYS364	4.5	38.7	1.0
	CA	B:ASN321	4.5	25.9	0.6
	O	B:HOH852	4.5	30.7	1.0
	CA	B:ASN321	4.5	25.9	0.4
	N	B:VAL365	4.5	30.4	1.0
	CD2	B:LEU361	4.6	23.1	1.0
	O	B:ASP363	4.6	34.7	1.0
	CA	B:VAL365	4.6	25.0	1.0
	N	B:GLU366	4.7	31.5	1.0
	CG	B:GLU366	4.7	35.9	1.0
	O	B:HOH992	4.9	41.8	1.0
	OE2	B:GLU366	4.9	52.2	1.0
	O	B:GLU366	5.0	32.6	1.0
	CD	B:GLN27	5.0	23.7	1.0

Reference:

D.M.Dranow, D.D.Lorimer, T.E.Edwards. Crystal Structure of Methionyl-Trna Synthetase (Metrs) From Acinetobacter Baumannii with Bound L-Methionine To Be Published.

Page generated: Tue Oct 8 00:39:16 2024

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