Chlorine in PDB 8f00: Lysozyme Anomalous Dataset at 293 K and 12 Kev

Enzymatic activity of Lysozyme Anomalous Dataset at 293 K and 12 Kev

All present enzymatic activity of Lysozyme Anomalous Dataset at 293 K and 12 Kev:
3.2.1.17;

Protein crystallography data

The structure of Lysozyme Anomalous Dataset at 293 K and 12 Kev, PDB code: 8f00 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) 33.53 / 1.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.794, 77.794, 37.127, 90, 90, 90
R / Rfree (%) 12.1 / 14.6

Other elements in 8f00:

The structure of Lysozyme Anomalous Dataset at 293 K and 12 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 12 Kev (pdb code 8f00). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Lysozyme Anomalous Dataset at 293 K and 12 Kev, PDB code: 8f00:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 8f00

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Chlorine binding site 1 out of 10 in the Lysozyme Anomalous Dataset at 293 K and 12 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 12 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:21.6
occ:1.00
 OH A:TYR23 3.0 16.1 1.0
O A:HOH375 3.6 56.2 1.0
CZ A:TYR23 3.7 15.2 1.0
CE2 A:TYR23 3.7 15.3 1.0
CA A:GLY104 4.2 16.2 1.0
O A:ARG21 4.6 21.8 1.0
N A:GLY104 4.7 17.3 1.0
CE1 A:TYR23 4.9 15.0 1.0
CD2 A:TYR23 4.9 15.2 1.0

Chlorine binding site 2 out of 10 in 8f00

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Chlorine binding site 2 out of 10 in the Lysozyme Anomalous Dataset at 293 K and 12 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 12 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:26.7
occ:0.75
 OE1 A:GLN121 2.7 53.0 0.5
OG A:SER24 3.0 22.8 1.0
N A:GLY26 3.1 15.1 1.0
CB A:SER24 3.5 19.9 1.0
CA A:GLY26 3.5 14.9 1.0
CD A:GLN121 3.7 40.9 0.5
CA A:GLN121 3.7 24.9 0.5
CA A:GLN121 3.7 24.9 0.5
CD1 A:ILE124 4.0 36.0 1.0
N A:LEU25 4.0 15.7 1.0
N A:GLN121 4.1 22.5 1.0
CB A:GLN121 4.1 29.9 0.5
CB A:GLN121 4.2 36.3 0.5
C A:SER24 4.2 15.6 1.0
C A:LEU25 4.2 15.5 1.0
O A:VAL120 4.3 21.3 1.0
CG2 A:VAL120 4.3 23.4 1.0
CG1 A:ILE124 4.4 24.7 1.0
C A:VAL120 4.4 19.2 1.0
CG A:GLN121 4.4 60.9 0.5
CG A:GLN121 4.4 49.5 0.5
CA A:SER24 4.5 16.3 1.0
C A:GLY26 4.6 14.4 1.0
CA A:LEU25 4.6 15.6 1.0
O A:SER24 4.6 16.1 1.0
NE2 A:GLN121 4.7 46.3 0.5
N A:ASN27 4.7 13.6 1.0
CB A:LEU25 4.9 16.9 1.0
C A:GLN121 4.9 21.5 1.0

Chlorine binding site 3 out of 10 in 8f00

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Chlorine binding site 3 out of 10 in the Lysozyme Anomalous Dataset at 293 K and 12 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 12 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:24.1
occ:0.60
 O A:THR69 3.1 23.4 1.0
O A:HOH343 3.1 23.6 1.0
N A:THR69 3.2 17.0 1.0
OD1 A:ASN65 3.5 30.6 1.0
N A:ARG68 3.6 17.9 1.0
C A:THR69 3.6 19.3 1.0
C A:GLY67 3.6 19.6 1.0
OG A:SER72 3.7 35.1 1.0
N A:GLY67 3.7 17.8 1.0
CA A:GLY67 3.7 19.4 1.0
CA A:THR69 3.8 17.6 1.0
O A:HOH351 3.9 33.7 1.0
CB A:THR69 4.1 18.1 1.0
C A:ARG68 4.2 20.2 1.0
OD1 A:ASP66 4.2 16.1 1.0
O A:GLY67 4.3 24.5 1.0
CA A:ARG68 4.3 17.4 1.0
N A:PRO70 4.6 25.0 1.0
NA A:NA208 4.7 21.0 0.6
CG A:ASN65 4.7 29.0 1.0
N A:ASP66 4.7 15.9 1.0
C A:ASP66 4.7 17.2 1.0
OG1 A:THR69 4.8 16.6 1.0
CB A:SER72 4.9 39.1 1.0
O A:HOH348 4.9 33.1 0.5

Chlorine binding site 4 out of 10 in 8f00

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Chlorine binding site 4 out of 10 in the Lysozyme Anomalous Dataset at 293 K and 12 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 12 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:39.6
occ:0.50
 N A:ILE88 3.3 19.7 1.0
NE2 A:HIS15 3.4 27.4 1.0
OD1 A:ASP87 3.5 30.1 1.0
CG1 A:ILE88 3.6 21.5 1.0
NH2 A:ARG14 3.7 26.9 0.5
NH2 A:ARG14 3.8 36.5 0.5
CA A:ASP87 3.9 21.8 1.0
C A:ASP87 4.0 22.0 1.0
NH1 A:ARG14 4.1 41.5 0.5
CA A:ILE88 4.2 17.7 1.0
CD2 A:HIS15 4.2 27.4 1.0
CZ A:ARG14 4.3 31.1 0.5
CG A:ASP87 4.3 36.9 1.0
CB A:ILE88 4.3 18.5 1.0
N A:THR89 4.4 19.9 1.0
CE1 A:HIS15 4.4 30.7 1.0
OG1 A:THR89 4.5 24.2 1.0
CD1 A:ILE88 4.6 24.3 1.0
CB A:ASP87 4.6 27.9 1.0
C A:ILE88 4.6 18.6 1.0
CB A:ALA11 4.6 22.3 1.0
O A:SER86 4.6 27.6 1.0
O A:HOH319 4.7 48.4 1.0
CG2 A:ILE88 4.8 21.4 1.0
CZ A:ARG14 4.9 26.9 0.5

Chlorine binding site 5 out of 10 in 8f00

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Chlorine binding site 5 out of 10 in the Lysozyme Anomalous Dataset at 293 K and 12 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 12 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:45.9
occ:0.58
 CE2 A:PHE38 3.8 20.9 1.0
O A:HOH374 4.1 51.1 1.0
NZ A:LYS33 4.1 39.0 1.0
CZ3 A:TRP123 4.2 26.6 1.0
CD A:ARG5 4.2 22.3 1.0
CD A:LYS33 4.3 23.4 1.0
CE A:LYS33 4.3 30.3 1.0
CZ A:PHE38 4.5 18.1 1.0
CB A:ARG5 4.5 22.6 1.0
CD2 A:PHE38 4.7 19.3 1.0
NE A:ARG5 4.8 26.2 1.0
CG A:ARG5 4.8 24.4 1.0
CE3 A:TRP123 5.0 23.5 1.0
CH2 A:TRP123 5.0 26.6 1.0

Chlorine binding site 6 out of 10 in 8f00

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Chlorine binding site 6 out of 10 in the Lysozyme Anomalous Dataset at 293 K and 12 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 12 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:56.4
occ:0.73
 N A:ASN74 2.5 25.8 1.0
O A:HOH304 3.1 54.2 1.0
C A:ASN74 3.2 22.8 1.0
CA A:ASN74 3.3 22.0 1.0
CB A:ARG73 3.3 31.1 1.0
CA A:ARG73 3.3 29.4 1.0
O A:ASN74 3.4 23.6 1.0
C A:ARG73 3.4 27.8 1.0
NE A:ARG73 3.5 53.3 1.0
CB A:ASN74 3.7 22.3 1.0
N A:LEU75 3.7 21.2 1.0
CD2 A:LEU75 4.1 30.3 1.0
CD A:ARG73 4.2 50.3 1.0
CA A:LEU75 4.3 22.5 1.0
CG A:ARG73 4.4 32.7 1.0
NH2 A:ARG73 4.4 59.3 1.0
CZ A:ARG73 4.5 80.1 1.0
CG A:LEU75 4.5 26.9 1.0
O A:ARG73 4.6 30.1 1.0
N A:ARG73 4.8 34.8 1.0
CG A:ASN74 5.0 22.1 1.0
CB A:LEU75 5.0 23.1 1.0

Chlorine binding site 7 out of 10 in 8f00

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Chlorine binding site 7 out of 10 in the Lysozyme Anomalous Dataset at 293 K and 12 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 12 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:23.4
occ:0.40
 O A:HOH388 2.1 40.1 1.0
NH1 A:ARG68 3.0 20.8 1.0
CD A:ARG68 3.7 21.2 1.0
CZ A:ARG68 4.1 18.9 1.0
NE A:ARG68 4.4 21.5 1.0
NH1 A:ARG45 4.5 90.5 0.5
CG A:ARG68 4.9 19.7 1.0

Chlorine binding site 8 out of 10 in 8f00

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Chlorine binding site 8 out of 10 in the Lysozyme Anomalous Dataset at 293 K and 12 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 12 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl210

b:22.2
occ:0.50
 O A:HOH378 2.7 42.5 1.0
N A:SER24 3.1 16.6 1.0
OG A:SER24 3.2 22.8 1.0
O A:GLY22 3.3 20.3 1.0
ND2 A:ASN27 3.3 17.5 1.0
CB A:SER24 3.5 19.9 1.0
CA A:SER24 3.9 16.3 1.0
CA A:TYR23 4.0 16.7 1.0
C A:TYR23 4.0 16.4 1.0
C A:GLY22 4.3 18.5 1.0
O A:HOH359 4.5 45.9 1.0
CG A:ASN27 4.6 14.6 1.0
N A:TYR23 4.7 17.1 1.0
OD1 A:ASN19 4.7 89.1 0.5
C A:SER24 5.0 15.6 1.0

Chlorine binding site 9 out of 10 in 8f00

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Chlorine binding site 9 out of 10 in the Lysozyme Anomalous Dataset at 293 K and 12 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 293 K and 12 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl211

b:27.6
occ:0.45
 ND2 A:ASN65 3.2 48.7 1.0
CA A:GLY67 3.7 19.4 1.0
N A:GLY67 4.0 17.8 1.0
CG A:ASN65 4.1 29.0 1.0
OD1 A:ASN65 4.3 30.6 1.0
C A:ASP66 4.6 17.2 1.0
O A:HOH368 4.8 53.0 1.0
O A:ASP66 5.0 18.0 1.0

Chlorine binding site 10 out of 10 in 8f00

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Chlorine binding site 10 out of 10 in the Lysozyme Anomalous Dataset at 293 K and 12 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 293 K and 12 Kev within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl212

b:27.9
occ:0.50
 O A:HOH380 2.6 32.8 1.0
N A:GLU7 3.3 20.6 1.0
N A:CYS6 3.5 20.6 1.0
CA A:GLY4 3.6 23.5 1.0
C A:GLY4 3.7 21.2 1.0
N A:ARG5 3.8 20.6 1.0
CB A:CYS6 3.8 23.9 1.0
CB A:GLU7 3.9 21.3 1.0
CA A:CYS6 3.9 23.3 1.0
C A:CYS6 4.0 21.9 1.0
CA A:GLU7 4.2 21.5 1.0
O A:GLY4 4.2 20.2 1.0
C A:ARG5 4.4 20.0 1.0
N A:GLY4 4.6 21.5 1.0
CA A:ARG5 4.6 20.0 1.0
SG A:CYS6 4.9 24.3 0.9

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 09:08:22 2024

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