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

Go back to

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

Go back to

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW

	© Copyright 2008-2020 by atomistry.com
Home \| Site Map \| Copyright \| Contact us \| Privacy