Chlorine in PDB 8d5s: Crystal Structure of Hen Egg White Lysozyme at 100 Kelvin

Enzymatic activity of Crystal Structure of Hen Egg White Lysozyme at 100 Kelvin

All present enzymatic activity of Crystal Structure of Hen Egg White Lysozyme at 100 Kelvin:
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of Hen Egg White Lysozyme at 100 Kelvin, PDB code: 8d5s was solved by F.S.Ribeiro, L.M.T.R.Lima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.62 / 1.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.835, 78.835, 37.241, 90, 90, 90
R / Rfree (%) 18 / 21.3

Other elements in 8d5s:

The structure of Crystal Structure of Hen Egg White Lysozyme at 100 Kelvin also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Hen Egg White Lysozyme at 100 Kelvin (pdb code 8d5s). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of Hen Egg White Lysozyme at 100 Kelvin, PDB code: 8d5s:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 8d5s

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Chlorine binding site 1 out of 7 in the Crystal Structure of Hen Egg White Lysozyme at 100 Kelvin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Hen Egg White Lysozyme at 100 Kelvin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:12.5
occ:1.00
 OH A:TYR23 3.0 8.8 1.0
O A:HOH332 3.3 12.2 1.0
CZ A:TYR23 3.7 6.6 1.0
CE2 A:TYR23 3.7 6.6 1.0
CA A:GLY104 4.2 9.2 1.0
O A:ARG21 4.6 10.0 1.0
N A:GLY104 4.8 10.6 1.0
CE1 A:TYR23 4.9 7.0 1.0
CD2 A:TYR23 4.9 6.8 1.0

Chlorine binding site 2 out of 7 in 8d5s

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Chlorine binding site 2 out of 7 in the Crystal Structure of Hen Egg White Lysozyme at 100 Kelvin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Hen Egg White Lysozyme at 100 Kelvin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:14.7
occ:1.00
 N A:THR69 3.1 10.3 1.0
O A:HOH363 3.1 9.8 1.0
O A:THR69 3.3 12.1 1.0
O A:HOH319 3.5 26.9 1.0
N A:ARG68 3.5 9.9 1.0
C A:GLY67 3.5 10.5 1.0
CA A:GLY67 3.6 9.7 1.0
N A:GLY67 3.6 9.2 1.0
C A:THR69 3.6 11.2 1.0
OG A:SER72 3.7 15.0 1.0
ND2 A:ASN65 3.7 8.6 1.0
CA A:THR69 3.8 11.5 1.0
O A:HOH381 4.0 13.8 1.0
O A:GLY67 4.1 13.2 1.0
C A:ARG68 4.1 11.9 1.0
CB A:THR69 4.2 10.3 1.0
OD1 A:ASP66 4.2 6.2 1.0
CA A:ARG68 4.3 10.9 1.0
N A:PRO70 4.5 13.5 1.0
NA A:NA201 4.7 13.5 1.0
C A:ASP66 4.7 8.0 1.0
OG1 A:THR69 4.7 9.6 1.0
N A:ASP66 4.9 6.6 1.0
CB A:SER72 4.9 15.9 1.0
O A:HOH358 4.9 12.6 0.5
CG A:ASN65 5.0 9.5 1.0

Chlorine binding site 3 out of 7 in 8d5s

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Chlorine binding site 3 out of 7 in the Crystal Structure of Hen Egg White Lysozyme at 100 Kelvin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Hen Egg White Lysozyme at 100 Kelvin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:15.6
occ:1.00
 O A:HOH389 2.9 31.4 1.0
OG A:SER24 3.0 12.3 1.0
N A:GLY26 3.2 9.2 1.0
CA A:GLY26 3.5 8.1 1.0
CB A:SER24 3.5 9.4 1.0
CA A:GLN121 3.6 13.0 1.0
CD1 A:ILE124 3.7 19.9 1.0
CB A:GLN121 3.9 16.4 1.0
N A:GLN121 4.0 11.1 1.0
CG A:GLN121 4.2 18.9 1.0
O A:VAL120 4.2 10.2 1.0
CG1 A:ILE124 4.2 15.6 1.0
C A:VAL120 4.3 10.3 1.0
CG2 A:VAL120 4.3 10.7 1.0
N A:LEU25 4.3 11.5 1.0
C A:LEU25 4.4 10.3 1.0
C A:SER24 4.5 10.1 1.0
C A:GLY26 4.5 7.3 1.0
CA A:SER24 4.6 9.4 1.0
N A:ASN27 4.6 6.9 1.0
C A:GLN121 4.8 11.5 1.0
CA A:LEU25 4.9 11.2 1.0
O A:SER24 4.9 10.1 1.0

Chlorine binding site 4 out of 7 in 8d5s

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Chlorine binding site 4 out of 7 in the Crystal Structure of Hen Egg White Lysozyme at 100 Kelvin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Hen Egg White Lysozyme at 100 Kelvin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:23.1
occ:1.00
 CE2 A:PHE38 3.6 7.5 1.0
NZ A:LYS33 3.8 16.3 1.0
CZ3 A:TRP123 4.0 11.0 1.0
O1 A:GOL209 4.2 37.2 1.0
CB A:ARG5 4.2 12.8 1.0
CD A:ARG5 4.2 13.3 1.0
CE A:LYS33 4.3 12.8 1.0
CZ A:PHE38 4.4 7.6 1.0
CD A:LYS33 4.4 10.9 1.0
CD2 A:PHE38 4.6 6.8 1.0
CG A:ARG5 4.6 12.1 1.0
CE3 A:TRP123 4.7 10.4 1.0
NE A:ARG5 4.8 13.5 1.0
CH2 A:TRP123 4.9 10.6 1.0

Chlorine binding site 5 out of 7 in 8d5s

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Chlorine binding site 5 out of 7 in the Crystal Structure of Hen Egg White Lysozyme at 100 Kelvin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Hen Egg White Lysozyme at 100 Kelvin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:22.7
occ:1.00
 O A:HOH385 3.1 18.1 1.0
OD1 A:ASN65 3.1 14.0 1.0
CA A:PRO79 3.7 10.0 1.0
CB A:PRO79 3.7 10.3 1.0
CB A:ASN65 3.8 8.4 1.0
CG A:ASN65 3.9 9.5 1.0
N A:PRO79 4.0 10.0 1.0
O A:ASN65 4.3 7.6 1.0
CD A:PRO79 4.3 10.4 1.0
CG A:PRO79 4.5 12.8 1.0
C A:ILE78 4.6 9.5 1.0
O A:ILE78 4.7 8.7 1.0
C A:ASN65 4.9 6.6 1.0
CA A:ASN65 4.9 7.3 1.0
ND2 A:ASN74 5.0 13.2 1.0

Chlorine binding site 6 out of 7 in 8d5s

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Chlorine binding site 6 out of 7 in the Crystal Structure of Hen Egg White Lysozyme at 100 Kelvin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Hen Egg White Lysozyme at 100 Kelvin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:19.4
occ:1.00
 O A:HOH388 3.3 23.8 1.0
N A:ILE88 3.4 10.7 1.0
O A:HOH306 3.4 21.3 1.0
CG1 A:ILE88 3.7 10.5 1.0
NE2 A:HIS15 3.7 17.5 1.0
CA A:ASP87 3.8 12.5 1.0
C A:ASP87 4.1 11.2 1.0
O A:SER86 4.2 14.1 0.5
CB A:ALA11 4.2 10.3 1.0
O A:SER86 4.2 14.0 0.5
OD1 A:ASP87 4.2 14.1 1.0
CG2 A:ILE88 4.3 10.6 1.0
CB A:ILE88 4.3 10.0 1.0
CG A:ASP87 4.3 18.5 1.0
CZ A:PHE3 4.4 9.3 1.0
CA A:ILE88 4.4 9.6 1.0
CE1 A:HIS15 4.4 14.9 1.0
CD2 A:HIS15 4.4 13.4 1.0
CB A:ASP87 4.6 14.6 1.0
CD1 A:ILE88 4.6 11.3 1.0
OD2 A:ASP87 4.7 22.3 1.0
O A:HOH355 4.7 23.4 1.0
N A:ASP87 4.9 12.2 1.0
CE2 A:PHE3 4.9 9.0 1.0
C A:SER86 4.9 12.9 0.5
C A:SER86 4.9 12.9 0.5

Chlorine binding site 7 out of 7 in 8d5s

Go back to Chlorine Binding Sites List in 8d5s
Chlorine binding site 7 out of 7 in the Crystal Structure of Hen Egg White Lysozyme at 100 Kelvin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Hen Egg White Lysozyme at 100 Kelvin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:37.5
occ:1.00
 N A:ASN74 3.0 12.1 1.0
NE A:ARG73 3.3 27.6 1.0
C A:ASN74 3.5 10.1 1.0
CB A:ARG73 3.6 17.1 1.0
CA A:ASN74 3.7 10.7 1.0
O A:ASN74 3.7 11.0 1.0
CA A:ARG73 3.8 14.0 1.0
C A:ARG73 3.9 12.9 1.0
NH2 A:ARG73 4.0 36.3 1.0
CZ A:ARG73 4.0 28.8 1.0
N A:LEU75 4.0 10.7 1.0
CD2 A:LEU75 4.0 15.8 1.0
CD A:ARG73 4.0 22.2 1.0
CB A:ASN74 4.1 10.8 1.0
CG A:ARG73 4.4 18.1 1.0
CA A:LEU75 4.5 11.7 1.0
CG A:LEU75 4.6 15.3 1.0

Reference:

F.De Sa Ribeiro, L.M.T.Lima. Linking B-Factor and Temperature-Induced Conformational Transition Biophys.Chem. 07027 2023.
ISSN: ISSN 0301-4622
DOI: 10.1016/J.BPC.2023.107027
Page generated: Tue Jul 30 08:26:25 2024

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