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Chlorine in PDB 6sim: Sad Structure of Hen Egg White Lysozyme Recovered By Inverse Beam Geometry Data Collection and Univariate Analysis

Enzymatic activity of Sad Structure of Hen Egg White Lysozyme Recovered By Inverse Beam Geometry Data Collection and Univariate Analysis

All present enzymatic activity of Sad Structure of Hen Egg White Lysozyme Recovered By Inverse Beam Geometry Data Collection and Univariate Analysis:
3.2.1.17;

Protein crystallography data

The structure of Sad Structure of Hen Egg White Lysozyme Recovered By Inverse Beam Geometry Data Collection and Univariate Analysis, PDB code: 6sim was solved by M.J.Garcia-Bonete, G.Katona, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.54 / 1.61
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.070, 79.070, 36.980, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 17.4

Other elements in 6sim:

The structure of Sad Structure of Hen Egg White Lysozyme Recovered By Inverse Beam Geometry Data Collection and Univariate Analysis also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Sad Structure of Hen Egg White Lysozyme Recovered By Inverse Beam Geometry Data Collection and Univariate Analysis (pdb code 6sim). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Sad Structure of Hen Egg White Lysozyme Recovered By Inverse Beam Geometry Data Collection and Univariate Analysis, PDB code: 6sim:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 6sim

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Chlorine binding site 1 out of 8 in the Sad Structure of Hen Egg White Lysozyme Recovered By Inverse Beam Geometry Data Collection and Univariate Analysis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Sad Structure of Hen Egg White Lysozyme Recovered By Inverse Beam Geometry Data Collection and Univariate Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:26.8
occ:1.00
 O A:HOH397 3.3 38.4 1.0
NZ A:LYS51 3.6 21.3 1.0
CE2 A:PHE56 3.7 13.8 1.0
O A:HOH393 3.9 45.5 1.0
CZ3 A:TRP141 3.9 15.1 1.0
CE A:LYS51 4.1 20.1 1.0
CD A:ARG23 4.2 18.6 1.0
CD A:LYS51 4.2 11.8 1.0
CB A:ARG23 4.3 19.1 1.0
O A:HOH390 4.3 41.8 1.0
CZ A:PHE56 4.4 12.5 1.0
CD2 A:PHE56 4.6 13.8 1.0
CG A:ARG23 4.7 20.1 1.0
CE3 A:TRP141 4.7 14.5 1.0
NE A:ARG23 4.8 23.6 1.0
CH2 A:TRP141 4.8 15.8 1.0
C1 A:EDO203 4.9 33.1 1.0

Chlorine binding site 2 out of 8 in 6sim

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Chlorine binding site 2 out of 8 in the Sad Structure of Hen Egg White Lysozyme Recovered By Inverse Beam Geometry Data Collection and Univariate Analysis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Sad Structure of Hen Egg White Lysozyme Recovered By Inverse Beam Geometry Data Collection and Univariate Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:26.7
occ:1.00
 O A:HOH409 3.0 23.6 1.0
ND2 A:ASN83 3.3 20.3 1.0
CB A:PRO97 3.7 13.8 1.0
CA A:PRO97 3.8 11.6 1.0
CB A:ASN83 3.9 13.5 1.0
N A:PRO97 4.0 12.5 1.0
CG A:ASN83 4.1 18.8 1.0
CD A:PRO97 4.2 16.4 1.0
CG A:PRO97 4.3 19.3 1.0
O A:ASN83 4.3 13.3 1.0
C A:ILE96 4.6 15.6 1.0
O A:ILE96 4.7 13.5 1.0
ND2 A:ASN92 4.9 14.7 1.0
C A:ASN83 5.0 13.7 1.0
CA A:ASN83 5.0 11.7 1.0

Chlorine binding site 3 out of 8 in 6sim

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Chlorine binding site 3 out of 8 in the Sad Structure of Hen Egg White Lysozyme Recovered By Inverse Beam Geometry Data Collection and Univariate Analysis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Sad Structure of Hen Egg White Lysozyme Recovered By Inverse Beam Geometry Data Collection and Univariate Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl209

b:32.1
occ:1.00
 N A:ASN92 3.0 18.5 1.0
NE A:ARG91 3.3 26.2 1.0
O A:HOH440 3.7 45.6 1.0
C A:ASN92 3.7 16.1 1.0
O A:ASN92 3.7 18.2 1.0
CB A:ARG91 3.7 17.6 1.0
CA A:ASN92 3.8 14.0 1.0
CD A:ARG91 3.9 22.4 1.0
CA A:ARG91 3.9 16.2 1.0
C A:ARG91 4.0 19.9 1.0
CD2 A:LEU93 4.0 25.3 1.0
CB A:ASN92 4.2 13.9 1.0
N A:LEU93 4.2 15.2 1.0
CZ A:ARG91 4.3 26.1 1.0
NH2 A:ARG91 4.4 27.7 1.0
CG A:ARG91 4.4 19.6 1.0
CA A:LEU93 4.6 16.6 1.0
CG A:LEU93 4.7 21.8 1.0

Chlorine binding site 4 out of 8 in 6sim

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Chlorine binding site 4 out of 8 in the Sad Structure of Hen Egg White Lysozyme Recovered By Inverse Beam Geometry Data Collection and Univariate Analysis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Sad Structure of Hen Egg White Lysozyme Recovered By Inverse Beam Geometry Data Collection and Univariate Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl210

b:29.2
occ:1.00
 O A:HOH443 2.9 40.2 1.0
N A:ILE106 3.2 15.9 1.0
O A:HOH420 3.4 26.7 1.0
O A:HOH334 3.5 27.4 1.0
CG1 A:ILE106 3.6 14.2 1.0
CA A:ASP105 3.8 14.8 1.0
CE1 A:HIS33 3.9 24.6 1.0
C A:ASP105 4.0 14.2 1.0
O A:SER104 4.0 21.5 1.0
OD1 A:ASP105 4.1 20.0 1.0
O A:HOH370 4.1 39.9 1.0
CG2 A:ILE106 4.2 17.8 1.0
CB A:ILE106 4.2 12.4 1.0
CA A:ILE106 4.2 12.5 1.0
CG A:ASP105 4.3 28.5 1.0
CZ A:PHE21 4.3 17.3 1.0
CB A:ALA29 4.3 17.2 1.0
CD1 A:ILE106 4.5 15.2 1.0
CB A:ASP105 4.6 21.0 1.0
NE2 A:HIS33 4.6 28.4 1.0
ND1 A:HIS33 4.6 22.4 1.0
N A:ASP105 4.8 14.6 1.0
OD2 A:ASP105 4.8 33.9 1.0
C A:SER104 4.8 20.1 1.0
CE2 A:PHE21 4.9 15.3 1.0
N A:THR107 4.9 13.3 1.0

Chlorine binding site 5 out of 8 in 6sim

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Chlorine binding site 5 out of 8 in the Sad Structure of Hen Egg White Lysozyme Recovered By Inverse Beam Geometry Data Collection and Univariate Analysis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Sad Structure of Hen Egg White Lysozyme Recovered By Inverse Beam Geometry Data Collection and Univariate Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl211

b:18.4
occ:1.00
 O A:HOH377 3.1 12.0 1.0
N A:THR87 3.2 14.7 1.0
O A:HOH424 3.2 31.3 1.0
O A:THR87 3.2 16.2 1.0
O A:HOH434 3.4 23.2 1.0
N A:ARG86 3.5 14.5 0.5
O A:HOH328 3.5 28.1 1.0
N A:ARG86 3.5 14.4 0.5
C A:GLY85 3.5 15.9 1.0
CA A:GLY85 3.6 14.5 1.0
OG A:SER90 3.6 18.9 1.0
C A:THR87 3.6 15.9 1.0
N A:GLY85 3.7 14.7 1.0
OD1 A:ASN83 3.7 17.1 1.0
CA A:THR87 3.8 15.6 1.0
O A:HOH381 4.0 17.7 1.0
C A:ARG86 4.1 16.9 0.5
O A:GLY85 4.1 19.1 1.0
CB A:THR87 4.2 14.0 1.0
C A:ARG86 4.2 16.4 0.5
OD1 A:ASP84 4.2 11.4 1.0
CA A:ARG86 4.2 15.9 0.5
CA A:ARG86 4.3 15.7 0.5
N A:PRO88 4.6 17.2 1.0
NA A:NA206 4.7 18.1 1.0
C A:ASP84 4.8 11.9 1.0
OG1 A:THR87 4.8 13.2 1.0
O A:HOH366 4.8 20.0 0.5
CB A:SER90 4.9 18.5 1.0
CG A:ASN83 4.9 18.8 1.0
N A:ASP84 4.9 11.6 1.0

Chlorine binding site 6 out of 8 in 6sim

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Chlorine binding site 6 out of 8 in the Sad Structure of Hen Egg White Lysozyme Recovered By Inverse Beam Geometry Data Collection and Univariate Analysis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Sad Structure of Hen Egg White Lysozyme Recovered By Inverse Beam Geometry Data Collection and Univariate Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl212

b:19.4
occ:1.00
 O A:HOH425 2.9 30.1 1.0
OG A:SER42 3.0 18.6 1.0
N A:GLY44 3.2 13.6 1.0
CA A:GLY44 3.5 13.2 1.0
CB A:SER42 3.5 15.8 1.0
CA A:GLN139 3.6 15.3 1.0
CD1 A:ILE142 3.8 29.8 1.0
N A:GLN139 4.0 16.1 1.0
CB A:GLN139 4.0 21.8 1.0
CG A:GLN139 4.2 35.3 1.0
CG1 A:ILE142 4.2 24.0 1.0
N A:LEU43 4.2 13.4 1.0
O A:VAL138 4.2 13.9 1.0
CG2 A:VAL138 4.2 17.3 1.0
C A:VAL138 4.3 15.6 1.0
C A:LEU43 4.4 13.0 1.0
C A:SER42 4.4 15.5 1.0
C A:GLY44 4.5 10.5 1.0
CA A:SER42 4.6 14.9 1.0
N A:ASN45 4.6 11.4 1.0
CA A:LEU43 4.8 10.7 1.0
C A:GLN139 4.8 15.8 1.0
O A:SER42 4.9 13.1 1.0

Chlorine binding site 7 out of 8 in 6sim

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Chlorine binding site 7 out of 8 in the Sad Structure of Hen Egg White Lysozyme Recovered By Inverse Beam Geometry Data Collection and Univariate Analysis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Sad Structure of Hen Egg White Lysozyme Recovered By Inverse Beam Geometry Data Collection and Univariate Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl213

b:14.5
occ:1.00
 OH A:TYR41 3.0 12.6 1.0
O A:HOH363 3.3 16.1 1.0
CE2 A:TYR41 3.7 12.1 1.0
CZ A:TYR41 3.7 12.5 1.0
CA A:GLY122 4.1 9.4 1.0
O A:HOH423 4.3 45.8 1.0
O A:ARG39 4.6 15.8 1.0
N A:GLY122 4.7 11.9 1.0
CE1 A:TYR41 4.9 11.3 1.0
CD2 A:TYR41 4.9 10.6 1.0

Chlorine binding site 8 out of 8 in 6sim

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Chlorine binding site 8 out of 8 in the Sad Structure of Hen Egg White Lysozyme Recovered By Inverse Beam Geometry Data Collection and Univariate Analysis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Sad Structure of Hen Egg White Lysozyme Recovered By Inverse Beam Geometry Data Collection and Univariate Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl214

b:33.9
occ:1.00
 N A:LEU43 2.9 13.4 1.0
CB A:LEU43 3.6 15.2 1.0
CA A:SER42 3.6 14.9 1.0
CB A:ASP36 3.7 24.7 1.0
C A:SER42 3.8 15.5 1.0
CB A:SER42 3.8 15.8 1.0
CA A:LEU43 3.9 10.7 1.0
N A:ASN37 3.9 17.9 1.0
CA A:ASP36 4.1 19.2 1.0
C A:ASP36 4.2 19.9 1.0
CB A:ASN37 4.6 21.8 1.0
CA A:ASN37 4.7 15.8 1.0
CG A:ASP36 4.8 29.0 1.0
OD2 A:ASP36 4.8 33.7 1.0
N A:SER42 4.9 14.0 1.0
CG A:LEU43 4.9 16.8 1.0
O A:ASP36 5.0 20.6 1.0
O A:SER42 5.0 13.1 1.0
OG A:SER42 5.0 18.6 1.0

Reference:

M.J.Garcia-Bonete, G.Katona. Bayesian Machine Learning Improves Single-Wavelength Anomalous Diffraction Phasing. Acta Crystallogr.,Sect.A V. 75 851 2019.
ISSN: ESSN 2053-2733
PubMed: 31692460
DOI: 10.1107/S2053273319011446
Page generated: Mon Jul 29 14:59:00 2024

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