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Chlorine in PDB 8d8d: Crystal Structure of Hen Egg White Lysozyme at 300 Kelvin (Duplicate)

Enzymatic activity of Crystal Structure of Hen Egg White Lysozyme at 300 Kelvin (Duplicate)

All present enzymatic activity of Crystal Structure of Hen Egg White Lysozyme at 300 Kelvin (Duplicate):
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of Hen Egg White Lysozyme at 300 Kelvin (Duplicate), PDB code: 8d8d 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) 22.58 / 1.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.484, 79.484, 37.86, 90, 90, 90
R / Rfree (%) 17.6 / 20.3

Other elements in 8d8d:

The structure of Crystal Structure of Hen Egg White Lysozyme at 300 Kelvin (Duplicate) 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 300 Kelvin (Duplicate) (pdb code 8d8d). 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 300 Kelvin (Duplicate), PDB code: 8d8d:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 8d8d

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Chlorine binding site 1 out of 7 in the Crystal Structure of Hen Egg White Lysozyme at 300 Kelvin (Duplicate)


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 300 Kelvin (Duplicate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:22.9
occ:1.00
 OH A:TYR23 2.9 14.7 1.0
CZ A:TYR23 3.7 12.9 1.0
CE2 A:TYR23 3.7 12.4 1.0
CA A:GLY104 4.1 15.8 1.0
O A:ARG21 4.6 20.0 1.0
N A:GLY104 4.7 15.5 1.0
O A:HOH311 4.8 30.9 1.0
CE1 A:TYR23 4.9 12.9 1.0
CD2 A:TYR23 4.9 12.8 1.0

Chlorine binding site 2 out of 7 in 8d8d

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Chlorine binding site 2 out of 7 in the Crystal Structure of Hen Egg White Lysozyme at 300 Kelvin (Duplicate)


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 300 Kelvin (Duplicate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:32.1
occ:1.00
 O A:HOH328 3.0 20.0 1.0
O A:THR69 3.2 20.0 1.0
N A:THR69 3.2 17.4 1.0
ND2 A:ASN65 3.4 22.9 1.0
N A:ARG68 3.6 16.5 1.0
C A:THR69 3.7 18.1 1.0
C A:GLY67 3.7 18.4 1.0
N A:GLY67 3.7 16.5 1.0
OG A:SER72 3.7 24.6 1.0
CA A:GLY67 3.7 16.4 1.0
CA A:THR69 3.9 17.0 1.0
O A:HOH342 4.0 27.6 1.0
CB A:THR69 4.2 16.9 1.0
C A:ARG68 4.2 18.9 1.0
OD1 A:ASP66 4.2 13.8 1.0
O A:GLY67 4.3 23.2 1.0
CA A:ARG68 4.4 18.3 1.0
N A:PRO70 4.5 21.6 1.0
NA A:NA201 4.7 19.3 1.0
CG A:ASN65 4.7 22.4 1.0
N A:ASP66 4.8 12.6 1.0
C A:ASP66 4.8 15.0 1.0
OG1 A:THR69 4.8 16.1 1.0
CA A:PRO70 4.9 24.1 1.0
CB A:SER72 4.9 24.7 1.0

Chlorine binding site 3 out of 7 in 8d8d

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Chlorine binding site 3 out of 7 in the Crystal Structure of Hen Egg White Lysozyme at 300 Kelvin (Duplicate)


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 300 Kelvin (Duplicate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:31.8
occ:1.00
 OG A:SER24 3.0 22.1 1.0
N A:GLY26 3.1 14.1 1.0
CB A:SER24 3.4 18.1 1.0
CA A:GLY26 3.6 13.7 1.0
CA A:GLN121 3.7 22.8 1.0
CD1 A:ILE124 3.8 27.4 1.0
N A:GLN121 4.0 20.5 1.0
N A:LEU25 4.1 15.4 1.0
CB A:GLN121 4.1 31.1 1.0
C A:SER24 4.2 15.0 1.0
C A:LEU25 4.2 15.1 1.0
CG A:GLN121 4.2 41.2 1.0
CG1 A:ILE124 4.3 22.9 1.0
O A:VAL120 4.3 19.9 1.0
CG2 A:VAL120 4.3 21.6 1.0
C A:VAL120 4.3 21.5 1.0
CA A:SER24 4.4 15.9 1.0
C A:GLY26 4.6 12.7 1.0
CA A:LEU25 4.6 15.1 1.0
O A:SER24 4.7 15.5 1.0
N A:ASN27 4.7 11.8 1.0
C A:GLN121 4.9 19.9 1.0
CB A:LEU25 4.9 17.1 1.0

Chlorine binding site 4 out of 7 in 8d8d

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Chlorine binding site 4 out of 7 in the Crystal Structure of Hen Egg White Lysozyme at 300 Kelvin (Duplicate)


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 300 Kelvin (Duplicate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:61.5
occ:1.00
 O A:HOH334 3.6 37.5 1.0
CE2 A:PHE38 3.7 18.3 1.0
CZ3 A:TRP123 4.1 24.2 1.0
CD A:ARG5 4.1 23.2 1.0
CB A:ARG5 4.2 19.6 1.0
O1 A:GOL209 4.2 70.4 1.0
CE A:LYS33 4.3 30.3 1.0
CZ A:PHE38 4.4 16.4 1.0
NZ A:LYS33 4.4 35.3 1.0
CD A:LYS33 4.4 22.8 1.0
CG A:ARG5 4.6 21.5 1.0
CD2 A:PHE38 4.7 16.4 1.0
NE A:ARG5 4.7 27.3 1.0
CE3 A:TRP123 4.8 20.8 1.0
CH2 A:TRP123 5.0 23.3 1.0

Chlorine binding site 5 out of 7 in 8d8d

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Chlorine binding site 5 out of 7 in the Crystal Structure of Hen Egg White Lysozyme at 300 Kelvin (Duplicate)


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 300 Kelvin (Duplicate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:65.4
occ:1.00
 ND2 A:ASN74 3.4 23.1 1.0
N A:PRO79 3.5 16.9 1.0
C A:ILE78 3.5 17.0 1.0
O A:ILE78 3.8 17.3 1.0
CD A:PRO79 3.8 18.5 1.0
CB A:ASN65 4.0 16.5 1.0
CA A:PRO79 4.0 15.4 1.0
CA A:ILE78 4.1 19.8 1.0
N A:ILE78 4.2 20.7 1.0
OD1 A:ASN65 4.4 34.3 1.0
CB A:PRO79 4.4 16.9 1.0
CG A:PRO79 4.5 22.1 1.0
CG A:ASN74 4.6 21.1 1.0
C A:ASN77 4.7 22.9 1.0
CG A:ASN65 4.7 22.4 1.0
O A:ASN77 4.9 23.0 1.0
OD1 A:ASN74 5.0 20.7 1.0

Chlorine binding site 6 out of 7 in 8d8d

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Chlorine binding site 6 out of 7 in the Crystal Structure of Hen Egg White Lysozyme at 300 Kelvin (Duplicate)


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 300 Kelvin (Duplicate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:50.9
occ:1.00
 N A:ILE88 3.3 17.9 1.0
CG1 A:ILE88 3.6 19.5 1.0
CA A:ASP87 3.8 19.8 1.0
O A:SER86 3.9 25.4 1.0
OD1 A:ASP87 3.9 27.7 1.0
C A:ASP87 4.0 19.1 1.0
CB A:ILE88 4.2 16.5 1.0
CA A:ILE88 4.3 16.9 1.0
NE2 A:HIS15 4.4 29.3 1.0
CZ A:PHE3 4.4 22.0 1.0
CG2 A:ILE88 4.4 19.3 1.0
CB A:ALA11 4.5 19.1 1.0
CG A:ASP87 4.5 29.2 1.0
CD1 A:ILE88 4.6 21.1 1.0
CB A:ASP87 4.7 23.8 1.0
C A:SER86 4.7 20.6 1.0
N A:ASP87 4.7 20.1 1.0
CE2 A:PHE3 4.9 20.3 1.0
CD2 A:HIS15 4.9 24.5 1.0
N A:THR89 4.9 17.5 1.0

Chlorine binding site 7 out of 7 in 8d8d

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Chlorine binding site 7 out of 7 in the Crystal Structure of Hen Egg White Lysozyme at 300 Kelvin (Duplicate)


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 300 Kelvin (Duplicate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:62.9
occ:1.00
 N A:ASN74 3.0 22.1 1.0
NE A:ARG73 3.3 54.7 1.0
C A:ASN74 3.6 18.8 1.0
NH2 A:ARG73 3.6 57.7 1.0
CA A:ASN74 3.7 20.4 1.0
O A:ASN74 3.7 19.4 1.0
CA A:ARG73 3.8 24.5 1.0
CB A:ARG73 3.8 27.1 1.0
C A:ARG73 3.9 24.0 1.0
CZ A:ARG73 3.9 57.2 1.0
CB A:ASN74 3.9 21.0 1.0
N A:LEU75 4.2 20.4 1.0
CD A:ARG73 4.3 45.7 1.0
CD2 A:LEU75 4.6 31.1 1.0
CG A:ARG73 4.6 36.6 1.0
CA A:LEU75 4.7 20.9 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: Sun Jul 13 10:42:28 2025

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