Chlorine in PDB 8ezu: Lysozyme Anomalous Dataset at 273 K and 7.1 Kev

Enzymatic activity of Lysozyme Anomalous Dataset at 273 K and 7.1 Kev

All present enzymatic activity of Lysozyme Anomalous Dataset at 273 K and 7.1 Kev:
3.2.1.17;

Protein crystallography data

The structure of Lysozyme Anomalous Dataset at 273 K and 7.1 Kev, PDB code: 8ezu 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) 38.66 / 1.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.322, 77.322, 37.082, 90, 90, 90
R / Rfree (%) 13.3 / 17.1

Other elements in 8ezu:

The structure of Lysozyme Anomalous Dataset at 273 K and 7.1 Kev also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Chlorine atom in the Lysozyme Anomalous Dataset at 273 K and 7.1 Kev (pdb code 8ezu). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 11 binding sites of Chlorine where determined in the Lysozyme Anomalous Dataset at 273 K and 7.1 Kev, PDB code: 8ezu:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 11 in 8ezu

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Chlorine binding site 1 out of 11 in the Lysozyme Anomalous Dataset at 273 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 273 K and 7.1 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:21.6
occ:0.93
 OH A:TYR23 3.0 16.8 1.0
O A:HOH341 3.4 25.3 1.0
CZ A:TYR23 3.7 17.7 1.0
CE2 A:TYR23 3.7 17.0 1.0
CA A:GLY104 4.1 17.7 1.0
O A:ARG21 4.5 21.3 1.0
N A:GLY104 4.7 19.2 1.0
O A:HOH324 4.9 26.0 1.0
CE1 A:TYR23 5.0 15.3 1.0
CD2 A:TYR23 5.0 16.8 1.0

Chlorine binding site 2 out of 11 in 8ezu

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Chlorine binding site 2 out of 11 in the Lysozyme Anomalous Dataset at 273 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 273 K and 7.1 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:19.4
occ:0.55
 OG A:SER24 2.9 20.3 1.0
N A:GLY26 3.0 15.1 1.0
CB A:SER24 3.5 18.4 1.0
CA A:GLY26 3.5 17.7 1.0
CA A:GLN121 3.7 26.6 1.0
CD1 A:ILE124 3.9 30.8 1.0
N A:LEU25 4.0 17.7 1.0
CB A:GLN121 4.0 31.7 1.0
N A:GLN121 4.1 22.3 1.0
CG A:GLN121 4.1 52.7 1.0
C A:SER24 4.1 17.8 1.0
C A:LEU25 4.2 16.5 1.0
CG1 A:ILE124 4.3 28.6 1.0
CG2 A:VAL120 4.3 24.4 1.0
O A:VAL120 4.4 22.0 1.0
C A:VAL120 4.4 21.3 1.0
CA A:SER24 4.4 17.2 1.0
C A:GLY26 4.6 16.1 1.0
CA A:LEU25 4.6 18.0 1.0
O A:SER24 4.6 16.5 1.0
N A:ASN27 4.7 14.8 1.0
C A:GLN121 4.9 26.9 1.0
CB A:LEU25 5.0 19.5 1.0

Chlorine binding site 3 out of 11 in 8ezu

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Chlorine binding site 3 out of 11 in the Lysozyme Anomalous Dataset at 273 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 273 K and 7.1 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:21.9
occ:0.51
 O A:HOH349 2.9 22.1 1.0
N A:THR69 3.1 22.6 1.0
O A:THR69 3.2 25.6 1.0
O A:HOH375 3.4 45.5 1.0
OD1 A:ASN65 3.5 29.9 1.0
N A:ARG68 3.6 20.1 1.0
OG A:SER72 3.6 37.6 1.0
C A:THR69 3.7 25.4 1.0
C A:GLY67 3.7 23.1 1.0
N A:GLY67 3.7 19.7 1.0
CA A:GLY67 3.7 22.1 1.0
CA A:THR69 3.8 21.3 1.0
O A:HOH362 3.8 27.0 1.0
C A:ARG68 4.1 26.0 1.0
CB A:THR69 4.1 22.5 1.0
OD1 A:ASP66 4.2 16.1 1.0
CA A:ARG68 4.3 24.1 1.0
O A:GLY67 4.3 24.9 1.0
N A:PRO70 4.6 30.9 1.0
NA A:NA208 4.6 29.9 0.9
OG1 A:THR69 4.7 18.4 1.0
N A:ASP66 4.7 19.9 1.0
CG A:ASN65 4.8 30.9 1.0
C A:ASP66 4.8 19.9 1.0
CB A:SER72 4.8 36.4 1.0
O A:HOH342 4.9 33.4 0.5

Chlorine binding site 4 out of 11 in 8ezu

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Chlorine binding site 4 out of 11 in the Lysozyme Anomalous Dataset at 273 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 273 K and 7.1 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:39.7
occ:0.62
 NH2 A:ARG14 2.9 32.9 0.5
N A:ILE88 3.4 20.0 1.0
CG1 A:ILE88 3.6 27.1 1.0
CZ A:ARG14 3.9 28.0 0.5
CA A:ASP87 4.0 25.0 1.0
NH1 A:ARG14 4.0 22.9 0.5
OD1 A:ASP87 4.0 30.6 1.0
O A:SER86 4.0 29.1 1.0
C A:ASP87 4.2 22.3 1.0
CB A:ILE88 4.2 20.2 1.0
NE2 A:HIS15 4.3 27.8 1.0
CG2 A:ILE88 4.3 24.3 1.0
CB A:ALA11 4.3 23.5 1.0
CA A:ILE88 4.3 18.9 1.0
CZ A:PHE3 4.4 25.5 1.0
NH2 A:ARG14 4.4 22.2 0.5
CD1 A:ILE88 4.5 27.8 1.0
CG A:ASP87 4.8 37.6 1.0
CB A:ASP87 4.8 27.5 1.0
CD2 A:HIS15 4.8 25.8 1.0
CE2 A:PHE3 4.8 23.3 1.0
C A:SER86 4.9 25.8 1.0
N A:ASP87 5.0 23.1 1.0
N A:THR89 5.0 21.6 1.0

Chlorine binding site 5 out of 11 in 8ezu

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Chlorine binding site 5 out of 11 in the Lysozyme Anomalous Dataset at 273 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 273 K and 7.1 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:40.1
occ:0.58
 CE2 A:PHE38 3.7 19.5 1.0
NZ A:LYS33 3.9 33.5 1.0
CZ3 A:TRP123 4.1 27.7 1.0
CD A:ARG5 4.2 25.1 1.0
CD A:LYS33 4.3 24.2 1.0
O A:HOH354 4.3 36.7 1.0
CE A:LYS33 4.3 33.5 1.0
CZ A:PHE38 4.4 15.8 1.0
CB A:ARG5 4.4 25.5 1.0
CD2 A:PHE38 4.7 19.7 1.0
NE A:ARG5 4.7 26.5 1.0
CG A:ARG5 4.7 25.5 1.0
CE3 A:TRP123 4.9 23.7 1.0
CH2 A:TRP123 4.9 25.6 1.0

Chlorine binding site 6 out of 11 in 8ezu

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Chlorine binding site 6 out of 11 in the Lysozyme Anomalous Dataset at 273 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 273 K and 7.1 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:53.9
occ:0.73
 N A:ASN74 2.9 29.1 1.0
O A:HOH310 3.0 53.7 1.0
NE A:ARG73 3.4 54.2 1.0
CB A:ARG73 3.6 33.6 1.0
C A:ASN74 3.6 23.5 1.0
O A:ASN74 3.6 22.6 1.0
CA A:ARG73 3.7 30.5 1.0
CA A:ASN74 3.7 22.8 1.0
C A:ARG73 3.8 36.8 1.0
NH2 A:ARG73 4.0 50.9 1.0
CB A:ASN74 4.0 23.1 1.0
N A:LEU75 4.1 22.6 1.0
CZ A:ARG73 4.2 55.0 1.0
CD2 A:LEU75 4.2 33.8 1.0
CD A:ARG73 4.3 46.5 1.0
CG A:ARG73 4.6 37.3 1.0
CA A:LEU75 4.6 26.5 1.0
CG A:LEU75 4.7 29.5 1.0
O A:ARG73 5.0 29.2 1.0

Chlorine binding site 7 out of 11 in 8ezu

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Chlorine binding site 7 out of 11 in the Lysozyme Anomalous Dataset at 273 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 273 K and 7.1 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:22.6
occ:0.44
 NH1 A:ARG68 3.1 24.4 1.0
CD A:ARG68 3.7 24.9 1.0
CZ A:ARG68 4.1 25.7 1.0
NE A:ARG68 4.4 23.2 1.0
CG A:ARG68 5.0 22.4 1.0

Chlorine binding site 8 out of 11 in 8ezu

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Chlorine binding site 8 out of 11 in the Lysozyme Anomalous Dataset at 273 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 273 K and 7.1 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl210

b:16.2
occ:0.37
 O A:HOH369 2.3 40.9 1.0
O A:HOH348 3.0 51.6 1.0
N A:SER24 3.1 19.7 1.0
OG A:SER24 3.3 20.3 1.0
O A:GLY22 3.3 20.4 1.0
ND2 A:ASN27 3.4 20.6 1.0
CB A:SER24 3.5 18.4 1.0
CA A:SER24 3.9 17.2 1.0
CA A:TYR23 4.0 17.5 1.0
C A:TYR23 4.1 18.3 1.0
C A:GLY22 4.3 17.4 1.0
CG A:ASN27 4.6 19.6 1.0
N A:TYR23 4.7 17.4 1.0
OD1 A:ASN19 4.8 46.3 1.0

Chlorine binding site 9 out of 11 in 8ezu

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Chlorine binding site 9 out of 11 in the Lysozyme Anomalous Dataset at 273 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 9 of Lysozyme Anomalous Dataset at 273 K and 7.1 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl211

b:24.4
occ:0.45
 ND2 A:ASN65 3.0 37.8 1.0
CA A:GLY67 3.7 22.1 1.0
CG A:ASN65 4.0 30.9 1.0
N A:GLY67 4.1 19.7 1.0
O A:HOH329 4.2 38.4 1.0
OD1 A:ASN65 4.4 29.9 1.0
C A:ASP66 4.6 19.9 1.0

Chlorine binding site 10 out of 11 in 8ezu

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Chlorine binding site 10 out of 11 in the Lysozyme Anomalous Dataset at 273 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 10 of Lysozyme Anomalous Dataset at 273 K and 7.1 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl212

b:37.2
occ:0.54
 O A:HOH374 3.0 58.0 0.5
N A:ARG45 3.2 19.7 1.0
CB A:ARG45 3.8 24.2 0.5
CA A:ASN44 3.8 15.2 1.0
CB A:ARG45 3.8 27.3 0.5
C A:ASN44 4.0 17.7 1.0
CA A:ARG45 4.0 21.2 0.5
CA A:ARG45 4.0 22.2 0.5
OD1 A:ASN44 4.2 22.0 1.0
O A:ARG45 4.4 27.9 1.0
CB A:ASN44 4.4 17.9 1.0
O A:HOH364 4.5 35.7 0.5
O A:THR43 4.7 18.4 1.0
C A:ARG45 4.8 23.3 1.0
CG A:ASN44 4.8 19.9 1.0
N A:ASN44 5.0 14.0 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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