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

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

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

Protein crystallography data

The structure of Crystal Structure of Hen Egg White Lysozyme Introduced with O-(2- Nitrobenzyl)-L-Tyrosine, PDB code: 7ynu 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) 39.84 / 1.44
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.68, 79.68, 37.05, 90, 90, 90
R / Rfree (%) 19.1 / 22.3

Other elements in 7ynu:

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

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Hen Egg White Lysozyme Introduced with O-(2- Nitrobenzyl)-L-Tyrosine (pdb code 7ynu). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Hen Egg White Lysozyme Introduced with O-(2- Nitrobenzyl)-L-Tyrosine, PDB code: 7ynu:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 7ynu

Go back to Chlorine Binding Sites List in 7ynu
Chlorine binding site 1 out of 5 in the Crystal Structure of Hen Egg White Lysozyme Introduced with O-(2- Nitrobenzyl)-L-Tyrosine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Hen Egg White Lysozyme Introduced with O-(2- Nitrobenzyl)-L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:19.7
occ:0.90
 OH A:TYR23 3.1 19.1 1.0
O A:HOH345 3.2 21.2 1.0
CZ A:TYR23 3.8 16.2 1.0
CE1 A:TYR23 3.8 16.7 1.0
CA A:GLY104 4.1 17.0 1.0
O A:ARG21 4.5 24.2 1.0
N A:GLY104 4.7 18.1 1.0
CE2 A:TYR23 5.0 16.4 1.0

Chlorine binding site 2 out of 5 in 7ynu

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Chlorine binding site 2 out of 5 in the Crystal Structure of Hen Egg White Lysozyme Introduced with O-(2- Nitrobenzyl)-L-Tyrosine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Hen Egg White Lysozyme Introduced with O-(2- Nitrobenzyl)-L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:27.8
occ:0.51
 NZ A:LYS33 3.3 31.8 1.0
O A:HOH361 3.5 41.7 1.0
CE2 A:PHE38 3.7 18.7 1.0
CE A:LYS33 4.0 26.4 1.0
CB A:ARG5 4.1 26.3 1.0
CD A:ARG5 4.1 26.1 1.0
CD A:LYS33 4.2 24.6 1.0
CZ3 A:TRP123 4.4 31.8 1.0
CZ A:PHE38 4.4 19.5 1.0
CG A:ARG5 4.5 25.7 1.0
CD2 A:PHE38 4.6 22.2 1.0
NE A:ARG5 4.8 30.1 1.0

Chlorine binding site 3 out of 5 in 7ynu

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Chlorine binding site 3 out of 5 in the Crystal Structure of Hen Egg White Lysozyme Introduced with O-(2- Nitrobenzyl)-L-Tyrosine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Hen Egg White Lysozyme Introduced with O-(2- Nitrobenzyl)-L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:25.9
occ:0.83
 OG A:SER24 3.0 25.1 1.0
N A:GLY26 3.0 19.9 1.0
CB A:SER24 3.5 23.7 1.0
CA A:GLY26 3.5 17.9 1.0
CA A:GLN121 3.6 25.9 1.0
CD1 A:ILE124 3.8 29.1 1.0
N A:GLN121 3.9 23.3 1.0
N A:LEU25 3.9 21.3 1.0
CB A:GLN121 4.0 29.6 1.0
C A:SER24 4.2 19.6 1.0
C A:LEU25 4.2 22.3 1.0
C A:VAL120 4.3 23.3 1.0
CG2 A:VAL120 4.3 22.5 1.0
CG1 A:ILE124 4.3 26.0 1.0
O A:VAL120 4.3 22.7 1.0
CG A:GLN121 4.4 36.1 1.0
CA A:SER24 4.5 20.1 1.0
CA A:LEU25 4.5 18.6 1.0
C A:GLY26 4.6 14.9 1.0
O A:SER24 4.6 20.1 1.0
N A:ASN27 4.7 16.8 1.0
C A:GLN121 4.9 22.8 1.0
CB A:LEU25 4.9 21.0 1.0

Chlorine binding site 4 out of 5 in 7ynu

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Chlorine binding site 4 out of 5 in the Crystal Structure of Hen Egg White Lysozyme Introduced with O-(2- Nitrobenzyl)-L-Tyrosine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Hen Egg White Lysozyme Introduced with O-(2- Nitrobenzyl)-L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:24.1
occ:0.83
 O A:HOH385 2.9 38.8 1.0
O A:HOH339 3.2 21.1 1.0
N A:THR69 3.2 22.7 1.0
O A:THR69 3.3 23.1 1.0
O A:HOH390 3.3 39.5 1.0
O A:HOH333 3.4 43.5 1.0
N A:ARG68 3.6 24.8 1.0
C A:THR69 3.6 24.3 1.0
OD1 A:ASN65 3.6 26.0 1.0
C A:GLY67 3.6 28.7 1.0
OG A:SER72 3.7 25.1 1.0
N A:GLY67 3.7 22.8 1.0
CA A:GLY67 3.7 24.1 1.0
CA A:THR69 3.8 22.0 1.0
O A:HOH360 4.0 24.5 1.0
CB A:THR69 4.2 22.4 1.0
OD1 A:ASP66 4.2 20.7 1.0
C A:ARG68 4.3 29.2 1.0
O A:GLY67 4.3 30.7 1.0
N A:PRO70 4.4 25.4 1.0
CA A:ARG68 4.4 27.0 1.0
NA A:NA201 4.7 20.5 1.0
CG A:ASN65 4.8 28.1 1.0
C A:ASP66 4.8 21.9 1.0
CA A:PRO70 4.8 25.3 1.0
OG1 A:THR69 4.8 21.0 1.0
N A:ASP66 4.9 20.9 1.0
CB A:SER72 5.0 24.0 1.0

Chlorine binding site 5 out of 5 in 7ynu

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Chlorine binding site 5 out of 5 in the Crystal Structure of Hen Egg White Lysozyme Introduced with O-(2- Nitrobenzyl)-L-Tyrosine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Hen Egg White Lysozyme Introduced with O-(2- Nitrobenzyl)-L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:38.1
occ:0.79
 O A:HOH397 2.5 50.2 1.0
N A:ILE88 3.4 26.8 1.0
O A:HOH343 3.4 43.0 1.0
CG1 A:ILE88 3.5 25.6 1.0
O A:HOH388 3.8 46.5 1.0
CA A:ASP87 3.8 31.1 1.0
OD2 A:ASP87 3.9 43.5 1.0
CE1 A:HIS15 4.0 41.2 1.0
C A:ASP87 4.1 23.8 1.0
CZ A:PHE3 4.1 28.6 1.0
O A:SER86 4.2 31.8 1.0
CB A:ALA11 4.2 25.5 1.0
CB A:ILE88 4.3 24.9 1.0
CG2 A:ILE88 4.4 26.7 1.0
CA A:ILE88 4.4 23.8 1.0
CD1 A:ILE88 4.5 29.9 1.0
CB A:ASP87 4.6 32.4 1.0
CE1 A:PHE3 4.7 26.5 1.0
CG A:ASP87 4.7 39.2 1.0
ND1 A:HIS15 4.7 37.8 1.0
O A:HOH391 4.8 51.5 1.0
N A:ASP87 4.9 28.0 1.0
C A:SER86 5.0 30.1 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: Tue Jul 30 06:01:29 2024

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