Sodium in PDB 5t9b: Crystal Structure of B. Subtilis 168 Glpq in Complex with Glycerol-3- Phosphate (5 Minute Soak)

Enzymatic activity of Crystal Structure of B. Subtilis 168 Glpq in Complex with Glycerol-3- Phosphate (5 Minute Soak)

All present enzymatic activity of Crystal Structure of B. Subtilis 168 Glpq in Complex with Glycerol-3- Phosphate (5 Minute Soak):
3.1.4.46;

Protein crystallography data

The structure of Crystal Structure of B. Subtilis 168 Glpq in Complex with Glycerol-3- Phosphate (5 Minute Soak), PDB code: 5t9b was solved by F.K.K.Li, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	43.83 / 1.62
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	50.463, 60.225, 88.418, 90.00, 90.00, 90.00
*R / R_free (%)*	17.6 / 21.6

Other elements in 5t9b:

The structure of Crystal Structure of B. Subtilis 168 Glpq in Complex with Glycerol-3- Phosphate (5 Minute Soak) also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of B. Subtilis 168 Glpq in Complex with Glycerol-3- Phosphate (5 Minute Soak) (pdb code 5t9b). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of B. Subtilis 168 Glpq in Complex with Glycerol-3- Phosphate (5 Minute Soak), PDB code: 5t9b:

Sodium binding site 1 out of 1 in 5t9b

Go back to

Sodium Binding Sites List in 5t9b

Sodium binding site 1 out of 1 in the Crystal Structure of B. Subtilis 168 Glpq in Complex with Glycerol-3- Phosphate (5 Minute Soak)

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 B. Subtilis 168 Glpq in Complex with Glycerol-3- Phosphate (5 Minute Soak) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
G:Na303 b:47.3 occ:0.83	O	G:HOH426	2.2	35.8	1.0
	O	G:HOH518	2.2	34.8	0.9
	O	G:THR93	2.4	32.0	1.0
	O	G:HOH539	2.5	62.9	1.0
	O	G:ASP90	2.5	30.4	1.0
	O	G:HOH546	2.6	53.2	0.9
	C	G:THR93	3.6	33.1	1.0
	C	G:ASP90	3.7	29.6	1.0
	CA	G:ASN94	4.3	31.9	1.0
	O	G:GLY95	4.4	33.2	1.0
	N	G:ASN94	4.4	33.5	1.0
	CA	G:ASP90	4.4	28.4	1.0
	O	G:ARG91	4.4	29.4	1.0
	O	G:HOH583	4.4	52.9	1.0
	N	G:THR93	4.5	30.3	1.0
	C	G:ARG91	4.6	29.5	1.0
	O	G:HOH573	4.6	61.0	1.0
	CA	G:THR93	4.7	32.4	1.0
	N	G:ARG91	4.7	28.8	1.0
	C	G:ASN94	4.8	37.0	1.0
	CA	G:ARG91	4.9	28.6	1.0
	N	G:GLY95	5.0	34.6	1.0
	O	G:LEU89	5.0	31.9	1.0

Reference:

C.L.Myers, F.K.Li, B.M.Koo, O.M.El-Halfawy, S.French, C.A.Gross, N.C.Strynadka, E.D.Brown. Identification of Two Phosphate Starvation-Induced Wall Teichoic Acid Hydrolases Provides First Insights Into the Degradative Pathway of A Key Bacterial Cell Wall Component. J. Biol. Chem. V. 291 26066 2016.
ISSN: ESSN 1083-351X
PubMed: 27780866
DOI: 10.1074/JBC.M116.760447

Page generated: Tue Oct 8 00:04:55 2024

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