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Sodium in PDB 7ynv: Crystal Structure of Photolysed Hen Egg White Lysozyme Introduced with O-(2-Nitrobenzyl)-L-Tyrosine

Enzymatic activity of Crystal Structure of Photolysed Hen Egg White Lysozyme Introduced with O-(2-Nitrobenzyl)-L-Tyrosine

All present enzymatic activity of Crystal Structure of Photolysed Hen Egg White Lysozyme Introduced with O-(2-Nitrobenzyl)-L-Tyrosine:
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of Photolysed Hen Egg White Lysozyme Introduced with O-(2-Nitrobenzyl)-L-Tyrosine, PDB code: 7ynv was solved by T.Hosaka, M.Shirouzu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.14 / 1.39
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.28, 78.28, 37.37, 90, 90, 90
R / Rfree (%) 17.4 / 19.2

Other elements in 7ynv:

The structure of Crystal Structure of Photolysed Hen Egg White Lysozyme Introduced with O-(2-Nitrobenzyl)-L-Tyrosine also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Photolysed Hen Egg White Lysozyme Introduced with O-(2-Nitrobenzyl)-L-Tyrosine (pdb code 7ynv). 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 Photolysed Hen Egg White Lysozyme Introduced with O-(2-Nitrobenzyl)-L-Tyrosine, PDB code: 7ynv:

Sodium binding site 1 out of 1 in 7ynv

Go back to Sodium Binding Sites List in 7ynv
Sodium binding site 1 out of 1 in the Crystal Structure of Photolysed Hen Egg White Lysozyme Introduced with O-(2-Nitrobenzyl)-L-Tyrosine


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 Photolysed Hen Egg White Lysozyme Introduced with O-(2-Nitrobenzyl)-L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:13.9
occ:0.83
 O A:SER60 2.4 14.6 1.0
O A:CYS64 2.4 14.2 1.0
O A:ARG73 2.4 18.1 1.0
O A:HOH369 2.5 19.4 1.0
O A:HOH361 2.5 15.5 1.0
OG A:SER72 2.6 18.5 1.0
CB A:SER72 3.3 18.3 1.0
C A:CYS64 3.4 12.7 1.0
C A:ARG73 3.5 19.4 1.0
C A:SER60 3.5 13.9 1.0
CA A:ASN65 4.0 13.9 1.0
N A:ARG73 4.0 18.1 1.0
CA A:SER60 4.1 13.6 1.0
N A:ASN65 4.1 13.5 1.0
C A:SER72 4.2 22.0 1.0
CB A:SER60 4.3 13.3 1.0
N A:ASN74 4.3 16.9 1.0
CA A:ARG73 4.3 20.8 1.0
N A:CYS64 4.4 13.4 1.0
CA A:SER72 4.4 19.8 1.0
CA A:ASN74 4.5 17.5 1.0
C A:ARG61 4.6 17.1 1.0
CA A:CYS64 4.6 14.3 1.0
O A:ARG61 4.6 18.0 1.0
N A:ARG61 4.6 14.2 1.0
CB A:ASN74 4.7 18.2 1.0
O A:HOH414 4.7 36.0 1.0
O A:SER72 4.7 22.9 1.0
N A:ASP66 4.7 14.7 1.0
OD1 A:ASN65 4.7 19.3 1.0
CB A:THR69 4.8 19.8 1.0
CL A:CL205 4.8 18.1 0.7
N A:TRP62 4.8 15.8 1.0
CA A:ARG61 4.8 15.3 1.0
CB A:ASN65 4.9 18.5 1.0
C A:ASN65 4.9 13.6 1.0

Reference:

T.Hosaka, K.Katsura, Y.Ishizuka-Katsura, K.Hanada, K.Ito, Y.Tomabechi, M.Inoue, R.Akasaka, C.Takemoto, M.Shirouzu. Crystal Structure of An Archaeal Tyrosyl-Trna Synthetase Bound to Photocaged L-Tyrosine and Its Potential Application to Time-Resolved X-Ray Crystallography. Int J Mol Sci V. 23 2022.
ISSN: ESSN 1422-0067
PubMed: 36142308
DOI: 10.3390/IJMS231810399
Page generated: Mon Aug 18 12:42:04 2025

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