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Chlorine in PDB 5lvi: Hen Egg White Lysozyme Soaked with [Hisq][Trans-RUCL4(Dmso)(Isq)]

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

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

Protein crystallography data

The structure of Hen Egg White Lysozyme Soaked with [Hisq][Trans-RUCL4(Dmso)(Isq)], PDB code: 5lvi 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) 14.80 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.482, 77.482, 37.159, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 21.7

Other elements in 5lvi:

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

Chlorine binding site 1 out of 6 in 5lvi

Go back to Chlorine Binding Sites List in 5lvi
Chlorine binding site 1 out of 6 in the Hen Egg White Lysozyme Soaked with [Hisq][Trans-RUCL4(Dmso)(Isq)]


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 [Hisq][Trans-RUCL4(Dmso)(Isq)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:31.3
occ:0.50
 OG1 A:THR43 2.7 11.8 1.0
O A:HOH402 2.7 31.5 1.0
CB A:THR43 3.4 11.8 1.0
C A:THR43 3.8 11.7 1.0
O A:THR43 3.8 11.9 1.0
N A:ASN44 4.1 12.8 1.0
CA A:THR43 4.2 11.4 1.0
CG2 A:THR51 4.3 7.8 1.0
CA A:ASN44 4.4 13.3 1.0
CG2 A:THR43 4.5 12.8 1.0
N A:ARG45 4.5 13.1 1.0
NH2 A:ARG68 4.6 13.4 1.0
C A:ASN44 4.6 13.4 1.0
O A:HOH393 4.8 29.9 1.0

Chlorine binding site 2 out of 6 in 5lvi

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Chlorine binding site 2 out of 6 in the Hen Egg White Lysozyme Soaked with [Hisq][Trans-RUCL4(Dmso)(Isq)]


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 [Hisq][Trans-RUCL4(Dmso)(Isq)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:32.3
occ:1.00
 O A:HOH414 3.1 21.3 1.0
OD1 A:ASN65 3.2 26.0 1.0
CB A:PRO79 3.8 13.7 1.0
CA A:PRO79 3.8 12.7 1.0
CB A:ASN65 3.8 13.9 1.0
CG A:ASN65 3.9 15.3 1.0
N A:PRO79 4.1 14.0 1.0
O A:ASN65 4.3 11.6 1.0
CD A:PRO79 4.4 15.7 1.0
CG A:PRO79 4.5 16.3 1.0
C A:ILE78 4.7 15.5 1.0
O A:ILE78 4.8 13.3 1.0
ND2 A:ASN74 4.9 15.1 1.0
O A:HOH412 4.9 15.8 1.0
CA A:ASN65 4.9 11.6 1.0
C A:ASN65 4.9 11.0 1.0

Chlorine binding site 3 out of 6 in 5lvi

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Chlorine binding site 3 out of 6 in the Hen Egg White Lysozyme Soaked with [Hisq][Trans-RUCL4(Dmso)(Isq)]


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 [Hisq][Trans-RUCL4(Dmso)(Isq)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:24.6
occ:1.00
 OG A:SER24 3.0 14.0 1.0
N A:GLY26 3.1 11.8 1.0
CA A:GLY26 3.5 12.1 1.0
CB A:SER24 3.5 13.6 1.0
CA A:GLN121 3.6 19.1 1.0
CD1 A:ILE124 3.9 25.6 1.0
CB A:GLN121 3.9 23.7 1.0
N A:GLN121 4.0 16.2 1.0
N A:LEU25 4.1 12.6 1.0
CG1 A:ILE124 4.2 22.9 1.0
C A:SER24 4.2 13.5 1.0
C A:LEU25 4.2 12.7 1.0
O A:VAL120 4.3 16.1 1.0
CG A:GLN121 4.3 29.0 1.0
CG2 A:VAL120 4.3 14.9 1.0
C A:VAL120 4.3 15.8 1.0
CA A:SER24 4.5 13.4 1.0
C A:GLY26 4.6 10.9 1.0
CA A:LEU25 4.6 12.6 1.0
N A:ASN27 4.6 11.0 1.0
O A:SER24 4.7 13.4 1.0
C A:GLN121 4.9 18.0 1.0
CB A:LEU25 4.9 12.8 1.0

Chlorine binding site 4 out of 6 in 5lvi

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Chlorine binding site 4 out of 6 in the Hen Egg White Lysozyme Soaked with [Hisq][Trans-RUCL4(Dmso)(Isq)]


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 [Hisq][Trans-RUCL4(Dmso)(Isq)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:18.4
occ:1.00
 ND2 A:ASN113 3.3 15.2 1.0
CB A:ASN113 3.6 14.9 1.0
CA A:ALA110 3.8 14.8 1.0
CG1 A:VAL109 3.9 13.9 0.5
CG A:ASN113 3.9 14.7 1.0
O A:VAL109 4.1 17.5 1.0
N A:ALA110 4.2 13.0 1.0
CB A:ALA110 4.3 14.9 1.0
C A:VAL109 4.3 14.8 1.0
CD A:ARG114 4.4 15.3 1.0
CG A:ARG114 4.5 15.0 1.0
CG1 A:VAL109 4.6 14.7 0.5
CG2 A:VAL109 4.6 16.2 0.5
O A:HOH438 4.7 33.7 1.0
CA A:ASN113 4.9 13.9 1.0
C A:ALA110 4.9 13.7 1.0

Chlorine binding site 5 out of 6 in 5lvi

Go back to Chlorine Binding Sites List in 5lvi
Chlorine binding site 5 out of 6 in the Hen Egg White Lysozyme Soaked with [Hisq][Trans-RUCL4(Dmso)(Isq)]


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 [Hisq][Trans-RUCL4(Dmso)(Isq)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:27.6
occ:0.80
 O A:HOH303 2.8 12.7 0.3
RU A:RU211 3.0 49.4 0.3
N A:ILE88 3.3 14.6 1.0
O A:ACT210 3.4 36.7 0.5
NH1 A:ARG14 3.4 20.0 0.3
CG1 A:ILE88 3.6 13.9 1.0
NE2 A:HIS15 3.8 26.5 1.0
NH1 A:ARG14 3.9 24.7 0.7
CA A:ASP87 3.9 20.2 1.0
OD1 A:ASP87 3.9 27.4 1.0
O A:HOH331 3.9 38.6 1.0
C A:ASP87 4.0 16.2 1.0
CA A:ILE88 4.2 14.8 1.0
CB A:ILE88 4.2 12.9 1.0
O A:SER86 4.3 23.7 1.0
CZ A:ARG14 4.3 20.2 0.3
NH2 A:ARG14 4.3 19.0 0.3
CG2 A:ILE88 4.4 13.4 1.0
CB A:ALA11 4.4 15.9 1.0
CZ A:PHE3 4.4 16.7 1.0
CG A:ASP87 4.4 28.6 1.0
CD2 A:HIS15 4.5 25.3 1.0
CD1 A:ILE88 4.6 13.8 1.0
C A:ACT210 4.6 38.3 0.5
CB A:ASP87 4.7 23.2 1.0
CE1 A:HIS15 4.8 24.1 1.0
N A:THR89 4.8 15.2 1.0
N A:ASP87 4.9 18.4 1.0
CE2 A:PHE3 4.9 15.7 1.0
C A:ILE88 5.0 14.7 1.0

Chlorine binding site 6 out of 6 in 5lvi

Go back to Chlorine Binding Sites List in 5lvi
Chlorine binding site 6 out of 6 in the Hen Egg White Lysozyme Soaked with [Hisq][Trans-RUCL4(Dmso)(Isq)]


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 [Hisq][Trans-RUCL4(Dmso)(Isq)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:23.2
occ:1.00
 O A:HOH372 2.9 13.4 1.0
N A:THR69 3.0 15.9 1.0
O A:THR69 3.1 16.9 1.0
O A:HOH427 3.3 27.1 1.0
N A:ARG68 3.5 14.1 1.0
OG A:SER72 3.5 30.9 1.0
C A:THR69 3.5 16.6 1.0
C A:GLY67 3.6 15.6 1.0
ND2 A:ASN65 3.7 13.7 1.0
CA A:THR69 3.7 14.1 1.0
CA A:GLY67 3.7 14.0 1.0
N A:GLY67 3.7 12.6 1.0
CB A:THR69 4.0 14.1 1.0
O A:HOH309 4.0 18.2 1.0
C A:ARG68 4.1 15.0 1.0
OD1 A:ASP66 4.1 11.1 1.0
O A:GLY67 4.2 17.4 1.0
CA A:ARG68 4.2 16.1 1.0
NA A:NA207 4.4 25.4 1.0
N A:PRO70 4.5 20.3 1.0
OG1 A:THR69 4.6 12.0 1.0
CB A:SER72 4.7 32.1 1.0
N A:ASP66 4.7 10.8 1.0
C A:ASP66 4.7 12.0 1.0
CG A:ASN65 4.9 15.3 1.0
CA A:PRO70 5.0 23.0 1.0
O A:HOH313 5.0 23.1 0.5

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 12:15:12 2024

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