Sodium in PDB 5vnr: X-Ray Strucutre of Perdeuterated T4 Lysozyme Cysteine-Free Pseudo-Wild Type at Cryogenic Temperature

Enzymatic activity of X-Ray Strucutre of Perdeuterated T4 Lysozyme Cysteine-Free Pseudo-Wild Type at Cryogenic Temperature

All present enzymatic activity of X-Ray Strucutre of Perdeuterated T4 Lysozyme Cysteine-Free Pseudo-Wild Type at Cryogenic Temperature:
3.2.1.17;

Protein crystallography data

The structure of X-Ray Strucutre of Perdeuterated T4 Lysozyme Cysteine-Free Pseudo-Wild Type at Cryogenic Temperature, PDB code: 5vnr was solved by L.Li, S.Shukla, F.Meilleur, R.F.Standaert, J.Pierce, D.A.A.Myles, M.J.Cuneo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	28.55 / 1.63
*Space group*	P 3₂ 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	59.830, 59.830, 95.461, 90.00, 90.00, 120.00
*R / R_free (%)*	15.8 / 18.6

Other elements in 5vnr:

The structure of X-Ray Strucutre of Perdeuterated T4 Lysozyme Cysteine-Free Pseudo-Wild Type at Cryogenic Temperature also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Strucutre of Perdeuterated T4 Lysozyme Cysteine-Free Pseudo-Wild Type at Cryogenic Temperature (pdb code 5vnr). 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 X-Ray Strucutre of Perdeuterated T4 Lysozyme Cysteine-Free Pseudo-Wild Type at Cryogenic Temperature, PDB code: 5vnr:

Sodium binding site 1 out of 1 in 5vnr

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Sodium Binding Sites List in 5vnr

Sodium binding site 1 out of 1 in the X-Ray Strucutre of Perdeuterated T4 Lysozyme Cysteine-Free Pseudo-Wild Type at Cryogenic Temperature

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Strucutre of Perdeuterated T4 Lysozyme Cysteine-Free Pseudo-Wild Type at Cryogenic Temperature within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na202 b:28.8 occ:1.00	O	A:HOH346	2.2	30.3	1.0
	O	A:HOH407	2.9	28.9	1.0
	O	A:GLU11	2.9	17.0	1.0
	OE1	A:GLU11	2.9	19.0	1.0
	OH	A:TYR18	3.0	22.6	1.0
	O	A:HOH372	3.1	29.1	1.0
	O	A:HOH482	3.1	31.5	1.0
	O	A:HOH554	3.2	28.8	1.0
	O	A:HOH434	3.4	38.5	1.0
	O	A:HOH489	3.5	28.1	1.0
	C	A:GLU11	3.8	13.8	1.0
	CZ	A:TYR18	3.8	21.5	1.0
	CE1	A:TYR18	3.8	18.6	1.0
	CA	A:GLU11	3.9	13.0	1.0
	O	A:HOH383	4.0	24.2	1.0
	CA	A:GLY30	4.1	12.7	1.0
	CD	A:GLU11	4.1	19.1	1.0
	CB	A:GLU11	4.2	14.9	1.0
	N	A:GLY30	4.4	11.6	1.0
	CG	A:GLU11	4.8	15.1	1.0
	CG2	A:THR26	5.0	15.6	1.0

Reference:

L.Li, S.Shukla, F.Meilleur, R.F.Standaert, J.Pierce, D.A.A.Myles, M.J.Cuneo. Neutron Crystallographic Studies of T4 Lysozyme at Cryogenic Temperature. Protein Sci. V. 26 2098 2017.
ISSN: ESSN 1469-896X
PubMed: 28707382
DOI: 10.1002/PRO.3231

Page generated: Tue Oct 8 00:52:43 2024

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