Chlorine in PDB 8ezp: Lysozyme Anomalous Dataset at 260 K and 7.1 Kev

Enzymatic activity of Lysozyme Anomalous Dataset at 260 K and 7.1 Kev

All present enzymatic activity of Lysozyme Anomalous Dataset at 260 K and 7.1 Kev:
3.2.1.17;

Protein crystallography data

The structure of Lysozyme Anomalous Dataset at 260 K and 7.1 Kev, PDB code: 8ezp 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) 38.78 / 1.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.502, 77.502, 37.177, 90, 90, 90
R / Rfree (%) 13 / 17.3

Other elements in 8ezp:

The structure of Lysozyme Anomalous Dataset at 260 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 260 K and 7.1 Kev (pdb code 8ezp). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Lysozyme Anomalous Dataset at 260 K and 7.1 Kev, PDB code: 8ezp:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 8ezp

Go back to Chlorine Binding Sites List in 8ezp
Chlorine binding site 1 out of 7 in the Lysozyme Anomalous Dataset at 260 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 260 K and 7.1 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:19.3
occ:1.00
 OH A:TYR23 2.9 12.3 1.0
O A:HOH355 3.4 22.0 1.0
CZ A:TYR23 3.7 13.1 1.0
CE2 A:TYR23 3.7 12.6 1.0
CA A:GLY104 4.1 12.8 1.0
O A:ARG21 4.5 18.0 1.0
N A:GLY104 4.7 14.2 1.0
CE1 A:TYR23 4.9 11.0 1.0
CD2 A:TYR23 4.9 12.5 1.0
O A:HOH339 5.0 19.8 1.0

Chlorine binding site 2 out of 7 in 8ezp

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Chlorine binding site 2 out of 7 in the Lysozyme Anomalous Dataset at 260 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 260 K and 7.1 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:20.4
occ:0.77
 OG A:SER24 3.0 14.6 1.0
N A:GLY26 3.1 12.5 1.0
CA A:GLY26 3.5 13.2 1.0
CB A:SER24 3.5 14.9 1.0
CA A:GLN121 3.7 22.1 1.0
CD1 A:ILE124 4.0 27.5 1.0
CB A:GLN121 4.0 27.3 1.0
N A:LEU25 4.0 12.7 1.0
N A:GLN121 4.1 18.0 1.0
C A:SER24 4.2 12.3 1.0
C A:LEU25 4.2 12.2 1.0
CG A:GLN121 4.3 42.5 1.0
CG1 A:ILE124 4.3 25.0 1.0
O A:VAL120 4.3 17.6 1.0
CG2 A:VAL120 4.3 17.0 1.0
C A:VAL120 4.4 16.6 1.0
CA A:SER24 4.5 13.2 1.0
C A:GLY26 4.6 10.9 1.0
CA A:LEU25 4.6 12.7 1.0
O A:SER24 4.7 12.9 1.0
N A:ASN27 4.7 11.1 1.0
C A:GLN121 4.9 21.7 1.0
CB A:LEU25 5.0 14.0 1.0

Chlorine binding site 3 out of 7 in 8ezp

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Chlorine binding site 3 out of 7 in the Lysozyme Anomalous Dataset at 260 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 260 K and 7.1 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:22.8
occ:0.73
 O A:HOH311 2.9 38.3 1.0
O A:HOH366 3.0 16.0 1.0
N A:THR69 3.1 17.8 1.0
O A:THR69 3.2 20.8 1.0
O A:HOH399 3.3 36.6 1.0
N A:ARG68 3.6 15.6 1.0
OG A:SER72 3.6 33.5 1.0
OD1 A:ASN65 3.6 24.2 1.0
C A:GLY67 3.6 16.9 1.0
C A:THR69 3.7 21.2 1.0
N A:GLY67 3.7 14.5 1.0
CA A:GLY67 3.7 16.4 1.0
CA A:THR69 3.8 17.5 1.0
O A:HOH369 3.9 22.7 1.0
C A:ARG68 4.1 19.7 1.0
CB A:THR69 4.2 17.4 1.0
OD1 A:ASP66 4.2 12.2 1.0
CA A:ARG68 4.3 18.1 1.0
O A:GLY67 4.3 19.3 1.0
N A:PRO70 4.6 25.3 1.0
NA A:NA208 4.6 23.9 0.9
OG1 A:THR69 4.7 14.9 1.0
N A:ASP66 4.8 13.8 1.0
C A:ASP66 4.8 13.9 1.0
CB A:SER72 4.8 31.7 1.0
CG A:ASN65 4.8 23.5 1.0
O A:HOH348 4.9 24.1 0.5

Chlorine binding site 4 out of 7 in 8ezp

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Chlorine binding site 4 out of 7 in the Lysozyme Anomalous Dataset at 260 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 260 K and 7.1 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:36.3
occ:0.75
 N A:ILE88 3.4 15.1 1.0
CG1 A:ILE88 3.5 20.0 1.0
O A:HOH301 3.9 28.9 1.0
CA A:ASP87 4.0 20.0 1.0
O A:SER86 4.1 25.0 1.0
OD1 A:ASP87 4.1 24.1 1.0
NE2 A:HIS15 4.1 23.3 1.0
C A:ASP87 4.2 17.7 1.0
CB A:ILE88 4.2 14.9 1.0
CB A:ALA11 4.3 19.1 1.0
CA A:ILE88 4.3 14.0 1.0
CG2 A:ILE88 4.3 18.0 1.0
NH2 A:ARG14 4.4 34.3 1.0
CZ A:PHE3 4.4 19.4 1.0
CD1 A:ILE88 4.5 20.2 1.0
CG A:ASP87 4.7 29.1 1.0
CD2 A:HIS15 4.7 20.2 1.0
CB A:ASP87 4.8 21.5 1.0
CE2 A:PHE3 4.9 18.7 1.0
N A:THR89 4.9 16.4 1.0
C A:SER86 4.9 21.6 1.0
N A:ASP87 4.9 19.2 1.0
C A:ILE88 5.0 14.3 1.0

Chlorine binding site 5 out of 7 in 8ezp

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Chlorine binding site 5 out of 7 in the Lysozyme Anomalous Dataset at 260 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 260 K and 7.1 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:35.2
occ:0.63
 CE2 A:PHE38 3.7 14.2 1.0
NZ A:LYS33 4.0 27.3 1.0
CZ3 A:TRP123 4.1 21.5 1.0
CE A:LYS33 4.2 25.9 1.0
CD A:ARG5 4.2 18.9 1.0
O A:HOH370 4.3 35.0 1.0
CZ A:PHE38 4.4 11.7 1.0
CD A:LYS33 4.4 18.9 1.0
CB A:ARG5 4.4 18.4 1.0
CD2 A:PHE38 4.6 13.8 1.0
CG A:ARG5 4.8 19.4 1.0
NE A:ARG5 4.8 21.8 1.0
CH2 A:TRP123 4.9 21.6 1.0
CE3 A:TRP123 4.9 19.8 1.0

Chlorine binding site 6 out of 7 in 8ezp

Go back to Chlorine Binding Sites List in 8ezp
Chlorine binding site 6 out of 7 in the Lysozyme Anomalous Dataset at 260 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 260 K and 7.1 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:42.9
occ:0.64
 N A:ASN74 2.8 22.2 1.0
O A:HOH337 3.0 45.3 1.0
CB A:ARG73 3.5 27.9 1.0
C A:ASN74 3.5 18.2 1.0
NE A:ARG73 3.5 47.0 1.0
CA A:ARG73 3.6 26.0 1.0
O A:ASN74 3.6 18.1 1.0
CA A:ASN74 3.6 18.6 1.0
C A:ARG73 3.7 26.9 1.0
N A:LEU75 3.9 17.8 1.0
CB A:ASN74 3.9 19.1 1.0
NH2 A:ARG73 4.1 48.5 1.0
CD2 A:LEU75 4.2 27.0 1.0
CZ A:ARG73 4.3 49.7 1.0
CD A:ARG73 4.3 43.1 1.0
CA A:LEU75 4.4 20.6 1.0
CG A:ARG73 4.5 33.4 1.0
CG A:LEU75 4.6 22.9 1.0
O A:ARG73 4.9 25.2 1.0
N A:ARG73 5.0 24.9 1.0

Chlorine binding site 7 out of 7 in 8ezp

Go back to Chlorine Binding Sites List in 8ezp
Chlorine binding site 7 out of 7 in the Lysozyme Anomalous Dataset at 260 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 260 K and 7.1 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:29.5
occ:0.75
 NH1 A:ARG68 3.0 18.4 1.0
CD A:ARG68 3.7 17.3 1.0
CZ A:ARG68 4.1 17.0 1.0
NE A:ARG68 4.4 15.7 1.0
NH2 A:ARG45 4.8 40.3 0.5
NH1 A:ARG45 4.9 24.5 0.5
CG A:ARG68 5.0 16.3 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 09:06:22 2024

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