Chlorine 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:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Photolysed Hen Egg White Lysozyme Introduced with O-(2-Nitrobenzyl)-L-Tyrosine, PDB code: 7ynv:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 7ynv

Go back to Chlorine Binding Sites List in 7ynv
Chlorine binding site 1 out of 5 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 Chlorine with other atoms in the Cl 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:Cl202

b:15.9
occ:0.84
 OH A:TYR23 3.0 13.3 1.0
O A:HOH339 3.2 18.6 1.0
O A:HOH353 3.2 37.9 1.0
CE1 A:TYR23 3.7 13.0 1.0
CZ A:TYR23 3.7 11.8 1.0
CA A:GLY104 4.1 13.3 1.0
O A:ARG21 4.5 18.4 1.0
N A:GLY104 4.7 14.1 1.0
CE2 A:TYR23 4.9 13.0 1.0
CD1 A:TYR23 4.9 13.4 1.0

Chlorine binding site 2 out of 5 in 7ynv

Go back to Chlorine Binding Sites List in 7ynv
Chlorine binding site 2 out of 5 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 Chlorine with other atoms in the Cl binding site number 2 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:Cl203

b:34.9
occ:0.69
 NZ A:LYS33 3.4 42.9 1.0
O A:HOH360 3.6 40.8 1.0
CE2 A:PHE38 3.7 17.1 1.0
O A:HOH380 4.0 39.5 1.0
CD A:ARG5 4.1 21.5 1.0
CE A:LYS33 4.1 32.0 1.0
CB A:ARG5 4.1 20.4 1.0
CZ3 A:TRP123 4.3 25.3 1.0
CZ A:PHE38 4.3 15.4 1.0
CD A:LYS33 4.4 25.1 1.0
CG A:ARG5 4.5 19.4 1.0
CD2 A:PHE38 4.6 17.1 1.0
NE A:ARG5 4.6 26.7 1.0

Chlorine binding site 3 out of 5 in 7ynv

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Chlorine binding site 3 out of 5 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl204

b:20.9
occ:0.69
 OG A:SER24 2.9 21.5 1.0
N A:GLY26 3.1 15.0 1.0
O A:HOH375 3.2 41.3 1.0
CB A:SER24 3.5 18.1 1.0
CA A:GLY26 3.6 14.5 1.0
CA A:GLN121 3.7 25.3 1.0
N A:GLN121 3.9 22.3 1.0
CD1 A:ILE124 4.0 30.8 1.0
N A:LEU25 4.0 14.3 1.0
CB A:GLN121 4.1 26.4 1.0
C A:SER24 4.2 15.7 1.0
C A:LEU25 4.2 14.6 1.0
C A:VAL120 4.3 21.1 1.0
O A:VAL120 4.3 19.7 1.0
CG A:GLN121 4.4 34.1 1.0
CG1 A:ILE124 4.4 26.0 1.0
CG2 A:VAL120 4.4 22.6 1.0
CA A:SER24 4.5 14.9 1.0
CA A:LEU25 4.6 15.4 1.0
O A:SER24 4.6 14.7 1.0
C A:GLY26 4.6 15.5 1.0
N A:ASN27 4.8 13.5 1.0
C A:GLN121 4.9 22.0 1.0
CB A:LEU25 4.9 16.1 1.0

Chlorine binding site 4 out of 5 in 7ynv

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Chlorine binding site 4 out of 5 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl205

b:18.1
occ:0.66
 O A:HOH361 3.1 15.5 1.0
O A:HOH428 3.2 34.0 1.0
O A:HOH416 3.2 32.2 1.0
N A:THR69 3.3 18.3 1.0
O A:THR69 3.3 19.9 1.0
O A:HOH321 3.4 37.9 1.0
N A:ARG68 3.5 19.2 0.5
N A:ARG68 3.6 19.2 0.5
OD1 A:ASN65 3.6 19.3 1.0
C A:GLY67 3.6 22.8 1.0
C A:THR69 3.6 18.5 1.0
CA A:GLY67 3.7 19.5 1.0
N A:GLY67 3.7 17.8 1.0
OG A:SER72 3.8 18.5 1.0
CA A:THR69 3.9 18.0 1.0
O A:HOH369 4.0 19.4 1.0
CB A:THR69 4.3 19.8 1.0
C A:ARG68 4.3 20.8 0.5
O A:GLY67 4.3 23.6 1.0
C A:ARG68 4.3 20.8 0.5
OD1 A:ASP66 4.3 15.2 1.0
CA A:ARG68 4.3 17.9 0.5
N A:PRO70 4.4 20.8 1.0
CA A:ARG68 4.4 18.0 0.5
NA A:NA201 4.8 13.9 0.8
C A:ASP66 4.8 17.0 1.0
CG A:ASN65 4.8 19.1 1.0
OG1 A:THR69 4.9 16.7 1.0
CA A:PRO70 4.9 21.6 1.0
N A:ASP66 4.9 14.7 1.0
O A:HOH308 5.0 38.3 1.0

Chlorine binding site 5 out of 5 in 7ynv

Go back to Chlorine Binding Sites List in 7ynv
Chlorine binding site 5 out of 5 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 Chlorine with other atoms in the Cl binding site number 5 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:Cl206

b:24.2
occ:0.76
 O A:HOH392 2.9 41.7 1.0
O A:HOH341 3.0 40.9 1.0
N A:ILE88 3.3 15.9 1.0
O A:HOH310 3.4 28.9 1.0
CG1 A:ILE88 3.7 17.4 1.0
CA A:ASP87 3.8 19.8 1.0
CB A:ALA11 4.0 17.4 1.0
CZ A:PHE3 4.0 17.2 1.0
C A:ASP87 4.1 17.6 1.0
NH2 A:ARG14 4.1 25.1 1.0
CG A:ASP87 4.1 39.1 1.0
OD2 A:ASP87 4.2 45.7 1.0
O A:SER86 4.2 24.0 0.6
O A:SER86 4.2 23.9 0.4
CG2 A:ILE88 4.3 20.1 1.0
CB A:ILE88 4.3 17.1 1.0
OD1 A:ASP87 4.3 53.3 1.0
CA A:ILE88 4.3 15.9 1.0
NE2 A:HIS15 4.5 22.9 1.0
CE1 A:PHE3 4.5 16.0 1.0
CB A:ASP87 4.5 26.2 1.0
CD1 A:ILE88 4.6 20.5 1.0
N A:ASP87 4.9 16.7 1.0
CD2 A:HIS15 4.9 24.5 1.0
C A:SER86 5.0 18.8 0.6

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 Apr 4 22:18:50 2023

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