Chlorine in PDB 8ezx: Lysozyme Anomalous Dataset at 293 K and 7.1 Kev

Enzymatic activity of Lysozyme Anomalous Dataset at 293 K and 7.1 Kev

All present enzymatic activity of Lysozyme Anomalous Dataset at 293 K and 7.1 Kev:
3.2.1.17;

Protein crystallography data

The structure of Lysozyme Anomalous Dataset at 293 K and 7.1 Kev, PDB code: 8ezx was solved by T.Doukov, F.Yabukarski, D.Herschlag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.88 / 1.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.706, 77.706, 37.121, 90, 90, 90
R / Rfree (%) 13 / 16.6

Other elements in 8ezx:

The structure of Lysozyme Anomalous Dataset at 293 K and 7.1 Kev also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Lysozyme Anomalous Dataset at 293 K and 7.1 Kev (pdb code 8ezx). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Lysozyme Anomalous Dataset at 293 K and 7.1 Kev, PDB code: 8ezx:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 8ezx

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Chlorine binding site 1 out of 8 in the Lysozyme Anomalous Dataset at 293 K and 7.1 Kev


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Lysozyme Anomalous Dataset at 293 K and 7.1 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:25.4
occ:1.00
 OH A:TYR23 2.9 17.3 1.0
O A:HOH347 3.5 29.5 1.0
CZ A:TYR23 3.7 18.2 1.0
CE2 A:TYR23 3.7 17.5 1.0
CA A:GLY104 4.1 16.2 1.0
O A:ARG21 4.5 26.7 1.0
N A:GLY104 4.7 18.1 1.0
O A:HOH313 4.8 28.4 1.0
CE1 A:TYR23 4.9 16.5 1.0
CD2 A:TYR23 4.9 18.2 1.0

Chlorine binding site 2 out of 8 in 8ezx

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Chlorine binding site 2 out of 8 in the Lysozyme Anomalous Dataset at 293 K and 7.1 Kev


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Lysozyme Anomalous Dataset at 293 K and 7.1 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:23.1
occ:0.62
 OG A:SER24 3.0 19.3 1.0
N A:GLY26 3.1 16.8 1.0
CB A:SER24 3.5 21.1 1.0
CA A:GLY26 3.5 17.9 1.0
CA A:GLN121 3.7 28.3 1.0
CD1 A:ILE124 3.8 32.2 1.0
N A:LEU25 3.9 16.1 1.0
CB A:GLN121 4.0 35.1 1.0
N A:GLN121 4.1 25.1 1.0
C A:SER24 4.2 17.9 1.0
C A:LEU25 4.2 16.2 1.0
CG A:GLN121 4.2 60.9 1.0
CG1 A:ILE124 4.3 30.8 1.0
O A:VAL120 4.3 24.2 1.0
CG2 A:VAL120 4.4 23.6 1.0
C A:VAL120 4.4 25.0 1.0
CA A:SER24 4.4 17.9 1.0
CA A:LEU25 4.6 16.9 1.0
C A:GLY26 4.6 16.2 1.0
O A:SER24 4.7 19.3 1.0
N A:ASN27 4.7 16.2 1.0
C A:GLN121 4.9 28.3 1.0
CB A:LEU25 5.0 18.8 1.0

Chlorine binding site 3 out of 8 in 8ezx

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Chlorine binding site 3 out of 8 in the Lysozyme Anomalous Dataset at 293 K and 7.1 Kev


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Lysozyme Anomalous Dataset at 293 K and 7.1 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:26.4
occ:0.54
 O A:HOH352 2.9 25.1 1.0
O A:THR69 3.1 26.9 1.0
N A:THR69 3.1 23.6 1.0
O A:HOH373 3.3 52.7 1.0
OD1 A:ASN65 3.4 31.0 1.0
N A:ARG68 3.5 20.0 1.0
OG A:SER72 3.6 43.1 1.0
C A:THR69 3.6 27.2 1.0
C A:GLY67 3.7 21.4 1.0
N A:GLY67 3.7 18.8 1.0
CA A:THR69 3.8 22.8 1.0
CA A:GLY67 3.8 20.8 1.0
O A:HOH314 3.8 39.2 1.0
CB A:THR69 4.1 21.2 1.0
C A:ARG68 4.1 24.3 1.0
OD1 A:ASP66 4.2 16.5 1.0
CA A:ARG68 4.3 23.2 1.0
O A:GLY67 4.4 23.7 1.0
N A:PRO70 4.6 31.4 1.0
NA A:NA207 4.6 25.3 0.7
CG A:ASN65 4.7 29.3 1.0
CB A:SER72 4.7 43.8 1.0
N A:ASP66 4.7 19.6 1.0
OG1 A:THR69 4.7 19.4 1.0
C A:ASP66 4.8 18.7 1.0
O A:HOH333 5.0 37.0 0.5

Chlorine binding site 4 out of 8 in 8ezx

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Chlorine binding site 4 out of 8 in the Lysozyme Anomalous Dataset at 293 K and 7.1 Kev


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Lysozyme Anomalous Dataset at 293 K and 7.1 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:42.9
occ:0.63
 NH2 A:ARG14 2.8 42.8 0.5
N A:ILE88 3.4 20.8 1.0
CG1 A:ILE88 3.6 25.6 1.0
OD1 A:ASP87 3.7 33.0 1.0
NE2 A:HIS15 3.7 28.8 1.0
CZ A:ARG14 3.7 33.6 0.5
NH1 A:ARG14 4.0 35.5 0.5
CA A:ASP87 4.0 26.1 1.0
C A:ASP87 4.2 22.8 1.0
NH2 A:ARG14 4.2 25.4 0.5
CB A:ILE88 4.3 20.5 1.0
CA A:ILE88 4.3 18.4 1.0
O A:SER86 4.4 33.9 1.0
CD2 A:HIS15 4.4 26.6 1.0
CB A:ALA11 4.4 24.4 1.0
CD1 A:ILE88 4.5 27.3 1.0
CG2 A:ILE88 4.5 26.6 1.0
CG A:ASP87 4.6 42.1 1.0
N A:THR89 4.7 19.5 1.0
NE A:ARG14 4.8 33.8 0.5
CB A:ASP87 4.8 29.4 1.0
CE1 A:HIS15 4.8 31.4 1.0
C A:ILE88 4.8 19.0 1.0
CZ A:PHE3 4.9 22.1 1.0
OG1 A:THR89 5.0 27.7 1.0

Chlorine binding site 5 out of 8 in 8ezx

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Chlorine binding site 5 out of 8 in the Lysozyme Anomalous Dataset at 293 K and 7.1 Kev


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Lysozyme Anomalous Dataset at 293 K and 7.1 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:52.6
occ:0.67
 CE2 A:PHE38 3.8 20.0 1.0
O A:HOH363 4.0 42.2 1.0
NZ A:LYS33 4.1 35.3 1.0
CZ3 A:TRP123 4.2 29.4 1.0
CD A:ARG5 4.2 26.2 1.0
CB A:ARG5 4.4 26.8 1.0
CZ A:PHE38 4.5 17.9 1.0
CD A:LYS33 4.5 25.2 1.0
CE A:LYS33 4.5 31.3 1.0
CD2 A:PHE38 4.7 20.7 1.0
NE A:ARG5 4.7 28.5 1.0
CG A:ARG5 4.8 28.2 1.0
CE3 A:TRP123 4.9 24.0 1.0

Chlorine binding site 6 out of 8 in 8ezx

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Chlorine binding site 6 out of 8 in the Lysozyme Anomalous Dataset at 293 K and 7.1 Kev


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Lysozyme Anomalous Dataset at 293 K and 7.1 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:28.5
occ:0.51
 NH1 A:ARG68 3.0 27.5 1.0
CD A:ARG68 3.7 25.7 1.0
CZ A:ARG68 4.0 27.8 1.0
NE A:ARG68 4.3 23.3 1.0
CG A:ARG68 4.9 21.9 1.0

Chlorine binding site 7 out of 8 in 8ezx

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Chlorine binding site 7 out of 8 in the Lysozyme Anomalous Dataset at 293 K and 7.1 Kev


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Lysozyme Anomalous Dataset at 293 K and 7.1 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl209

b:21.0
occ:0.47
 O A:HOH368 2.4 41.4 1.0
N A:SER24 3.2 19.7 1.0
O A:GLY22 3.3 21.6 1.0
OG A:SER24 3.3 19.3 1.0
ND2 A:ASN27 3.4 21.9 1.0
CB A:SER24 3.5 21.1 1.0
CA A:SER24 3.9 17.9 1.0
CA A:TYR23 4.0 17.0 1.0
C A:TYR23 4.1 18.6 1.0
C A:GLY22 4.3 18.1 1.0
N A:TYR23 4.6 17.1 1.0
CG A:ASN27 4.7 21.3 1.0
OD1 A:ASN19 4.8 49.8 1.0

Chlorine binding site 8 out of 8 in 8ezx

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Chlorine binding site 8 out of 8 in the Lysozyme Anomalous Dataset at 293 K and 7.1 Kev


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Lysozyme Anomalous Dataset at 293 K and 7.1 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl210

b:24.5
occ:0.49
 O A:HOH369 2.6 33.7 1.0
N A:GLU7 3.1 23.8 1.0
N A:CYS6 3.4 21.7 1.0
CA A:GLY4 3.6 23.7 1.0
C A:GLY4 3.6 21.4 1.0
CB A:GLU7 3.7 22.7 1.0
CB A:CYS6 3.7 26.7 1.0
N A:ARG5 3.8 22.7 1.0
CA A:CYS6 3.8 24.5 1.0
C A:CYS6 3.9 24.6 1.0
CA A:GLU7 4.0 22.8 1.0
O A:GLY4 4.2 19.8 1.0
C A:ARG5 4.3 21.8 1.0
N A:GLY4 4.5 23.0 1.0
CA A:ARG5 4.6 23.9 1.0
SG A:CYS6 4.9 28.3 1.0

Reference:

T.Doukov, D.Herschlag, F.Yabukarski. Obtaining Anomalous and Ensemble Information From Protein Crystals From 220 K Up to Physiological Temperatures Acta Crystallogr.,Sect.D V. D79 212 2023.
ISSN: ESSN 1399-0047
DOI: 10.1107/S205979832300089X
Page generated: Tue Jul 30 09:07:38 2024

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