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Chlorine in PDB 5lvk: Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)]

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

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

Protein crystallography data

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

Resolution Low / High (Å) 14.37 / 2.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.039, 64.100, 111.311, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 28.1

Other elements in 5lvk:

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

Ruthenium (Ru) 2 atoms
Sodium (Na) 3 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 5 in 5lvk

Go back to Chlorine Binding Sites List in 5lvk
Chlorine binding site 1 out of 5 in the Human 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 Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:26.8
occ:1.00
 O A:HOH322 3.6 12.8 1.0
N A:ASN60 3.6 11.4 1.0
NE1 A:TRP64 3.7 12.7 1.0
CD1 A:TRP64 3.7 8.1 1.0
NE1 A:TRP109 3.9 13.8 1.0
CB A:ASN60 3.9 11.5 1.0
O A:GLN58 4.1 11.8 1.0
CA A:ILE59 4.1 7.9 1.0
CD1 A:TRP109 4.3 11.2 1.0
CE2 A:TRP109 4.4 10.1 1.0
C A:ILE59 4.4 7.7 1.0
O A:HOH395 4.4 19.9 1.0
CA A:ASN60 4.4 14.8 1.0
CZ2 A:TRP109 4.8 10.5 1.0
CE2 A:TRP64 4.8 9.1 1.0
CG A:TRP64 4.9 9.0 1.0
CG A:TRP109 4.9 8.3 1.0
CB A:ILE59 4.9 12.3 1.0
CG2 A:ILE59 5.0 6.5 1.0
OD1 A:ASP53 5.0 7.7 1.0

Chlorine binding site 2 out of 5 in 5lvk

Go back to Chlorine Binding Sites List in 5lvk
Chlorine binding site 2 out of 5 in the Human 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 Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:41.8
occ:1.00
 NH2 B:ARG115 3.9 21.9 1.0
O B:HOH398 3.9 14.8 1.0
NH2 A:ARG98 4.0 8.2 1.0
CB A:ALA76 4.9 7.4 1.0

Chlorine binding site 3 out of 5 in 5lvk

Go back to Chlorine Binding Sites List in 5lvk
Chlorine binding site 3 out of 5 in the Human 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 Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:35.6
occ:1.00
 NH1 A:ARG119 3.6 13.8 1.0
NH2 A:ARG119 4.3 19.6 1.0
CZ A:ARG119 4.4 13.1 1.0
O A:HOH308 4.6 9.3 1.0

Chlorine binding site 4 out of 5 in 5lvk

Go back to Chlorine Binding Sites List in 5lvk
Chlorine binding site 4 out of 5 in the Human 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 Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:27.7
occ:1.00
 O A:HOH389 2.8 29.9 1.0
N A:GLY127 3.3 19.3 1.0
OE1 A:GLN126 3.8 45.9 1.0
CA A:GLY127 3.9 18.8 1.0
N A:GLY129 4.1 15.4 1.0
C A:GLN126 4.3 26.3 1.0
CA A:GLN126 4.3 27.0 1.0
N A:CYS128 4.4 20.1 1.0
C A:GLY127 4.4 25.0 1.0
CA A:GLY129 4.6 9.9 1.0
CB A:GLN126 4.7 26.7 1.0
CD A:GLN126 4.9 55.1 1.0

Chlorine binding site 5 out of 5 in 5lvk

Go back to Chlorine Binding Sites List in 5lvk
Chlorine binding site 5 out of 5 in the Human 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 Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:27.9
occ:1.00
 NE1 B:TRP109 3.7 7.3 1.0
NE1 B:TRP64 3.7 8.3 1.0
CD1 B:TRP64 3.8 10.2 1.0
N B:ASN60 4.0 10.8 1.0
CD1 B:TRP109 4.1 11.6 1.0
CE2 B:TRP109 4.1 12.4 1.0
O B:GLN58 4.2 6.5 1.0
CA B:ILE59 4.3 6.9 1.0
CB B:ASN60 4.4 8.4 1.0
O B:HOH310 4.4 13.1 1.0
CZ2 B:TRP109 4.6 4.0 1.0
O B:HOH388 4.7 27.9 1.0
C B:ILE59 4.7 11.1 1.0
CG B:TRP109 4.7 6.2 1.0
CE2 B:TRP64 4.7 6.5 1.0
CD2 B:TRP109 4.8 5.3 1.0
CA B:ASN60 4.9 10.5 1.0
O B:ALA108 4.9 8.0 1.0
CG2 B:VAL99 4.9 7.2 1.0
CG2 B:ILE59 4.9 9.1 1.0
CG B:TRP64 4.9 8.3 1.0
CB B:ALA108 5.0 10.3 1.0
CB B:ILE59 5.0 7.0 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: Sat Dec 12 12:04:25 2020

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