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Chlorine in PDB 5lvj: Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)]

Enzymatic activity of Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)]

All present enzymatic activity of Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)]:
3.2.1.17;

Protein crystallography data

The structure of Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)], PDB code: 5lvj was solved by K.Kurpiewska, P.Halajko, K.Lewinski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.83 / 1.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.609, 77.609, 37.205, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 21.4

Other elements in 5lvj:

The structure of Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)] also contains other interesting chemical elements:

Ruthenium (Ru) 1 atom
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)] (pdb code 5lvj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)], PDB code: 5lvj:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 5lvj

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Chlorine binding site 1 out of 8 in the Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:32.0
occ:0.50
 O A:HOH394 2.7 25.2 1.0
OG1 A:THR43 2.7 11.8 1.0
CB A:THR43 3.3 12.1 1.0
C A:THR43 3.8 11.4 1.0
O A:THR43 3.9 12.6 1.0
N A:ASN44 4.1 12.8 1.0
CA A:THR43 4.2 12.0 1.0
CG2 A:THR51 4.3 10.1 1.0
CA A:ASN44 4.4 13.6 1.0
CG2 A:THR43 4.5 13.1 1.0
N A:ARG45 4.5 14.5 1.0
C A:ASN44 4.6 13.6 1.0
NH2 A:ARG68 4.6 15.2 1.0
O A:HOH405 4.8 26.0 1.0

Chlorine binding site 2 out of 8 in 5lvj

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Chlorine binding site 2 out of 8 in the Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:36.3
occ:1.00
 O A:HOH421 3.1 21.4 1.0
OD1 A:ASN65 3.2 21.0 1.0
CA A:PRO79 3.7 13.3 1.0
CB A:PRO79 3.8 13.7 1.0
CB A:ASN65 3.9 12.3 1.0
CG A:ASN65 4.0 13.2 1.0
N A:PRO79 4.0 14.6 1.0
CG A:PRO79 4.2 16.9 1.0
O A:ASN65 4.3 11.0 1.0
CD A:PRO79 4.3 15.3 1.0
C A:ILE78 4.6 15.6 1.0
O A:ILE78 4.7 13.5 1.0
ND2 A:ASN74 4.8 16.3 1.0
C A:ASN65 4.9 11.0 1.0
O A:HOH418 4.9 13.7 1.0
CA A:ASN65 5.0 10.9 1.0

Chlorine binding site 3 out of 8 in 5lvj

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Chlorine binding site 3 out of 8 in the Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:24.0
occ:1.00
 N A:GLY26 3.1 12.5 1.0
OG A:SER24 3.1 12.7 1.0
CA A:GLY26 3.4 12.5 1.0
CB A:SER24 3.5 12.9 1.0
CA A:GLN121 3.7 18.3 1.0
CD1 A:ILE124 4.0 25.2 1.0
N A:GLN121 4.0 16.6 1.0
CB A:GLN121 4.0 23.2 1.0
N A:LEU25 4.1 11.9 1.0
CG A:GLN121 4.3 27.6 1.0
O A:VAL120 4.3 16.2 1.0
C A:LEU25 4.3 12.7 1.0
C A:SER24 4.3 12.7 1.0
CG1 A:ILE124 4.3 21.1 1.0
C A:VAL120 4.3 16.3 1.0
CG2 A:VAL120 4.4 15.9 1.0
C A:GLY26 4.5 11.6 1.0
CA A:SER24 4.6 12.3 1.0
CA A:LEU25 4.6 11.9 1.0
N A:ASN27 4.6 10.5 1.0
O A:HOH302 4.7 29.0 1.0
O A:SER24 4.8 13.2 1.0
C A:GLN121 4.9 16.7 1.0
CB A:LEU25 4.9 13.2 1.0

Chlorine binding site 4 out of 8 in 5lvj

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Chlorine binding site 4 out of 8 in the Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:17.2
occ:1.00
 ND2 A:ASN113 3.3 14.4 1.0
CB A:ASN113 3.6 13.0 1.0
CA A:ALA110 3.8 13.8 1.0
CG1 A:VAL109 4.0 13.5 0.5
CG A:ASN113 4.0 12.7 1.0
O A:VAL109 4.2 14.8 1.0
N A:ALA110 4.2 12.8 1.0
CB A:ALA110 4.3 14.9 1.0
CD A:ARG114 4.3 14.8 1.0
C A:VAL109 4.4 13.4 1.0
CG A:ARG114 4.4 13.6 1.0
CG1 A:VAL109 4.5 15.4 0.5
O A:HOH447 4.6 27.9 1.0
CG2 A:VAL109 4.8 16.7 0.5
C A:ALA110 4.9 13.2 1.0
CA A:ASN113 4.9 12.8 1.0
O A:ALA110 5.0 14.3 1.0

Chlorine binding site 5 out of 8 in 5lvj

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Chlorine binding site 5 out of 8 in the Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:27.2
occ:0.80
 RU A:RU215 3.1 45.2 0.3
N A:ILE88 3.2 15.0 1.0
O A:HOH305 3.3 23.3 0.3
CG1 A:ILE88 3.6 14.6 1.0
CA A:ASP87 3.7 19.7 1.0
OXT A:ACT211 3.8 61.3 1.0
OD1 A:ASP87 3.9 23.9 1.0
C A:ASP87 3.9 16.8 1.0
NH1 A:ARG14 4.0 32.2 1.0
O A:SER86 4.0 24.2 1.0
NE2 A:HIS15 4.0 23.5 1.0
O A:HOH308 4.1 40.2 1.0
CA A:ILE88 4.2 14.6 1.0
CB A:ILE88 4.2 13.5 1.0
CG2 A:ILE88 4.2 13.3 1.0
CZ A:PHE3 4.3 15.1 1.0
CG A:ASP87 4.3 26.1 1.0
CB A:ALA11 4.4 15.6 1.0
CB A:ASP87 4.6 21.0 1.0
CD1 A:ILE88 4.6 14.1 1.0
CD2 A:HIS15 4.6 23.5 1.0
N A:ASP87 4.7 20.4 1.0
C A:SER86 4.8 18.3 1.0
C A:ACT211 4.8 62.4 1.0
N A:THR89 4.9 14.0 1.0
CE2 A:PHE3 4.9 13.9 1.0
C A:ILE88 4.9 14.2 1.0

Chlorine binding site 6 out of 8 in 5lvj

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Chlorine binding site 6 out of 8 in the Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:23.6
occ:1.00
 O A:HOH390 3.0 12.1 1.0
N A:THR69 3.1 15.4 1.0
O A:THR69 3.3 16.0 1.0
O A:HOH434 3.4 25.1 1.0
N A:ARG68 3.5 14.5 1.0
C A:GLY67 3.5 15.4 1.0
CA A:GLY67 3.5 13.4 1.0
ND2 A:ASN65 3.6 12.6 1.0
N A:GLY67 3.6 12.4 1.0
O A:HOH387 3.6 38.2 1.0
C A:THR69 3.7 17.4 1.0
OG A:SER72 3.7 28.1 1.0
CA A:THR69 3.8 15.4 1.0
O A:HOH313 3.9 17.7 1.0
CB A:THR69 4.0 15.3 1.0
C A:ARG68 4.1 15.7 1.0
OD1 A:ASP66 4.1 11.3 1.0
O A:GLY67 4.2 18.1 1.0
CA A:ARG68 4.3 16.1 1.0
NA A:NA209 4.5 24.2 1.0
N A:PRO70 4.6 22.5 1.0
OG1 A:THR69 4.7 13.3 1.0
C A:ASP66 4.7 11.5 1.0
N A:ASP66 4.8 10.5 1.0
CG A:ASN65 4.8 13.2 1.0
CB A:SER72 4.9 31.9 1.0

Chlorine binding site 7 out of 8 in 5lvj

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Chlorine binding site 7 out of 8 in the Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:32.6
occ:0.80
 O A:HOH309 2.9 21.2 1.0
O A:HOH359 2.9 37.4 1.0
N A:VAL109 3.0 13.0 1.0
O A:ALA107 3.2 15.8 1.0
CH3 A:ACT213 3.5 34.5 1.0
CB A:VAL109 3.5 14.3 0.5
CG1 A:VAL109 3.6 15.4 0.5
O A:HOH358 3.6 44.2 1.0
CB A:VAL109 3.7 16.0 0.5
CA A:TRP108 3.7 11.3 1.0
CG2 A:VAL109 3.7 13.3 0.5
O A:HOH311 3.8 21.6 1.0
C A:TRP108 3.8 12.8 1.0
CA A:VAL109 3.9 13.9 1.0
C A:ALA107 4.2 12.7 1.0
OE2 A:GLU35 4.2 12.7 1.0
O A:HOH371 4.3 28.3 1.0
N A:TRP108 4.4 11.1 1.0
C A:ACT213 4.7 33.5 1.0
CB A:TRP108 4.8 11.2 1.0
N A:ALA110 4.8 12.8 1.0
CG1 A:VAL109 4.8 13.5 0.5
C A:VAL109 4.9 13.4 1.0
OXT A:ACT213 4.9 34.2 1.0

Chlorine binding site 8 out of 8 in 5lvj

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Chlorine binding site 8 out of 8 in the Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:34.6
occ:1.00
 O A:HOH456 3.2 39.9 1.0
NZ A:LYS33 3.7 19.7 1.0
O A:HOH406 3.7 35.6 1.0
CE2 A:PHE38 3.7 10.9 1.0
CZ3 A:TRP123 4.0 18.2 1.0
CE A:LYS33 4.1 17.5 1.0
O A:HOH410 4.2 38.9 1.0
CD A:LYS33 4.2 15.8 1.0
O A:HOH466 4.4 39.1 1.0
CZ A:PHE38 4.4 10.3 1.0
CD A:ARG5 4.4 17.9 1.0
CB A:ARG5 4.6 17.1 1.0
CD2 A:PHE38 4.6 11.9 1.0
CH2 A:TRP123 4.8 17.0 1.0
CE3 A:TRP123 4.9 16.2 1.0
CG A:ARG5 4.9 16.9 1.0
NE A:ARG5 4.9 18.9 1.0

Reference:

M.Oszajca, K.Kurpiewska, P.Halajko, A.Szura, K.Lewinski, M.Brindell. Ligand-Dependent Interaction of Anticancer Ruthenium Complexes with Hen Egg White Lysozyme and Human Lysozyme To Be Published.
Page generated: Fri Jul 26 12:15:13 2024

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