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Chlorine in PDB 5lvh: Hen Egg White Lysozyme Soaked with Trans-Ru(Dmso)4CL2

Enzymatic activity of Hen Egg White Lysozyme Soaked with Trans-Ru(Dmso)4CL2

All present enzymatic activity of Hen Egg White Lysozyme Soaked with Trans-Ru(Dmso)4CL2:
3.2.1.17;

Protein crystallography data

The structure of Hen Egg White Lysozyme Soaked with Trans-Ru(Dmso)4CL2, PDB code: 5lvh 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) 15.23 / 1.55
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.683, 77.683, 37.195, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 21.1

Other elements in 5lvh:

The structure of Hen Egg White Lysozyme Soaked with Trans-Ru(Dmso)4CL2 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 Trans-Ru(Dmso)4CL2 (pdb code 5lvh). 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 Trans-Ru(Dmso)4CL2, PDB code: 5lvh:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 5lvh

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Chlorine binding site 1 out of 8 in the Hen Egg White Lysozyme Soaked with Trans-Ru(Dmso)4CL2


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 Trans-Ru(Dmso)4CL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:35.1
occ:1.00
 RU A:RU201 3.1 32.0 0.7
N A:ILE88 3.4 17.0 1.0
CG1 A:ILE88 3.5 15.8 1.0
NE2 A:HIS15 3.6 25.6 1.0
OD1 A:ASP87 4.0 31.7 1.0
CA A:ASP87 4.0 21.6 1.0
NH1 A:ARG14 4.0 25.5 0.7
O A:HOH331 4.0 41.1 0.8
O A:HOH310 4.0 41.1 1.0
CB A:ILE88 4.2 14.7 1.0
C A:ASP87 4.2 19.6 1.0
CG2 A:ILE88 4.3 16.0 1.0
CD2 A:HIS15 4.3 24.5 1.0
CB A:ALA11 4.3 15.3 1.0
CA A:ILE88 4.3 15.1 1.0
NH2 A:ARG14 4.3 22.8 0.7
O A:SER86 4.4 25.9 1.0
CD1 A:ILE88 4.4 18.4 1.0
CZ A:PHE3 4.6 19.0 1.0
CE1 A:HIS15 4.6 27.3 1.0
CZ A:ARG14 4.7 22.7 0.7
CG A:ASP87 4.7 31.6 1.0
CB A:ASP87 4.8 25.7 1.0
N A:THR89 4.9 15.9 1.0

Chlorine binding site 2 out of 8 in 5lvh

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Chlorine binding site 2 out of 8 in the Hen Egg White Lysozyme Soaked with Trans-Ru(Dmso)4CL2


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 Trans-Ru(Dmso)4CL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:22.6
occ:1.00
 OG A:SER24 3.0 16.1 1.0
N A:GLY26 3.2 12.0 1.0
CB A:SER24 3.5 14.5 1.0
CA A:GLY26 3.5 11.6 1.0
CA A:GLN121 3.6 18.6 1.0
CD1 A:ILE124 3.8 24.2 1.0
N A:GLN121 3.9 17.7 1.0
CB A:GLN121 3.9 24.8 1.0
CG A:GLN121 4.2 29.4 1.0
N A:LEU25 4.2 13.8 1.0
O A:VAL120 4.3 15.6 1.0
CG2 A:VAL120 4.3 17.4 1.0
C A:VAL120 4.3 17.0 1.0
C A:LEU25 4.3 12.9 1.0
CG1 A:ILE124 4.4 21.4 1.0
C A:SER24 4.4 14.2 1.0
C A:GLY26 4.6 12.2 1.0
CA A:SER24 4.6 15.0 1.0
N A:ASN27 4.6 11.0 1.0
CA A:LEU25 4.7 14.2 1.0
O A:SER24 4.8 14.2 1.0
C A:GLN121 4.9 16.3 1.0

Chlorine binding site 3 out of 8 in 5lvh

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Chlorine binding site 3 out of 8 in the Hen Egg White Lysozyme Soaked with Trans-Ru(Dmso)4CL2


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 Trans-Ru(Dmso)4CL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:21.8
occ:1.00
 N A:THR69 3.1 14.1 1.0
O A:HOH363 3.1 13.3 1.0
O A:THR69 3.2 16.6 1.0
O A:HOH408 3.2 26.6 1.0
O A:HOH320 3.2 38.1 1.0
N A:ARG68 3.5 12.6 1.0
C A:GLY67 3.6 14.7 1.0
CA A:GLY67 3.6 13.6 1.0
C A:THR69 3.6 15.5 1.0
OD1 A:ASN65 3.6 16.3 1.0
N A:GLY67 3.6 13.1 1.0
OG A:SER72 3.7 21.1 1.0
CA A:THR69 3.8 15.0 1.0
O A:HOH382 4.0 17.9 1.0
CB A:THR69 4.1 13.9 1.0
C A:ARG68 4.1 15.7 1.0
OD1 A:ASP66 4.2 10.4 1.0
O A:GLY67 4.2 17.2 1.0
CA A:ARG68 4.2 14.5 1.0
N A:PRO70 4.5 21.2 1.0
NA A:NA210 4.5 20.9 1.0
OG1 A:THR69 4.7 12.5 1.0
C A:ASP66 4.7 11.6 1.0
N A:ASP66 4.8 10.5 1.0
CG A:ASN65 4.8 15.3 1.0
CL A:CL206 4.9 35.5 0.5
CB A:SER72 5.0 23.6 1.0
CA A:PRO70 5.0 24.9 1.0

Chlorine binding site 4 out of 8 in 5lvh

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Chlorine binding site 4 out of 8 in the Hen Egg White Lysozyme Soaked with Trans-Ru(Dmso)4CL2


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 Trans-Ru(Dmso)4CL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:19.5
occ:1.00
 OH A:TYR23 2.9 12.1 1.0
O A:HOH391 3.1 33.7 1.0
O A:HOH362 3.3 16.6 1.0
CZ A:TYR23 3.6 10.1 1.0
CE2 A:TYR23 3.7 10.2 1.0
CA A:GLY104 4.3 12.6 1.0
O A:ARG21 4.5 16.3 1.0
CE1 A:TYR23 4.8 10.5 1.0
N A:GLY104 4.9 13.1 1.0
CD2 A:TYR23 4.9 10.0 1.0

Chlorine binding site 5 out of 8 in 5lvh

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Chlorine binding site 5 out of 8 in the Hen Egg White Lysozyme Soaked with Trans-Ru(Dmso)4CL2


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 Trans-Ru(Dmso)4CL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:35.5
occ:0.50
 CA A:GLY71 2.9 29.6 1.0
O A:HOH408 3.5 26.6 1.0
CA A:PRO70 3.7 24.9 1.0
C A:GLY71 3.9 30.7 1.0
N A:GLY71 4.0 36.5 1.0
N A:SER72 4.1 29.5 1.0
O A:THR69 4.2 16.6 1.0
C A:PRO70 4.3 27.8 1.0
CB A:PRO70 4.4 27.1 1.0
N A:PRO70 4.8 21.2 1.0
O A:SER72 4.8 30.6 1.0
C A:THR69 4.9 15.5 1.0
CL A:CL204 4.9 21.8 1.0
O A:GLY71 4.9 32.3 1.0

Chlorine binding site 6 out of 8 in 5lvh

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Chlorine binding site 6 out of 8 in the Hen Egg White Lysozyme Soaked with Trans-Ru(Dmso)4CL2


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 Trans-Ru(Dmso)4CL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:35.5
occ:0.50
 O A:HOH373 2.9 29.3 1.0
NH1 A:ARG14 3.2 25.5 0.7
NE A:ARG14 3.4 23.6 0.7
CZ A:ARG14 3.7 22.7 0.7
CB A:ALA10 3.8 17.1 1.0
C A:ALA10 4.1 17.4 1.0
N A:ALA11 4.1 14.8 1.0
O A:ALA10 4.2 18.2 1.0
CA A:ALA11 4.3 15.6 1.0
C3 A:GOL214 4.5 33.5 0.5
CA A:ALA10 4.6 17.2 1.0
CD A:ARG14 4.6 24.5 0.7
C1 A:GOL214 4.9 34.6 0.5
NH2 A:ARG14 4.9 22.8 0.7
CB A:ALA11 4.9 15.3 1.0
O3 A:GOL214 5.0 36.1 0.5
O A:GLU7 5.0 14.3 1.0

Chlorine binding site 7 out of 8 in 5lvh

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Chlorine binding site 7 out of 8 in the Hen Egg White Lysozyme Soaked with Trans-Ru(Dmso)4CL2


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 Trans-Ru(Dmso)4CL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:30.5
occ:1.00
 O A:HOH421 2.8 41.3 1.0
ND2 A:ASN65 3.1 19.6 1.0
CA A:GLY67 3.5 13.6 1.0
N A:GLY67 3.9 13.1 1.0
CG A:ASN65 4.1 15.3 1.0
O A:HOH320 4.4 38.1 1.0
OD1 A:ASN65 4.4 16.3 1.0
C A:ASP66 4.5 11.6 1.0
O A:ASP66 4.8 12.6 1.0
C A:GLY67 4.8 14.7 1.0
CL A:CL209 5.0 37.0 1.0

Chlorine binding site 8 out of 8 in 5lvh

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Chlorine binding site 8 out of 8 in the Hen Egg White Lysozyme Soaked with Trans-Ru(Dmso)4CL2


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 Trans-Ru(Dmso)4CL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl209

b:37.0
occ:1.00
 ND2 A:ASN65 3.3 19.6 1.0
O A:HOH386 3.3 22.4 1.0
CB A:PRO79 3.6 14.8 1.0
CA A:PRO79 3.7 14.2 1.0
CG A:PRO79 3.9 17.9 1.0
CB A:ASN65 3.9 14.6 1.0
N A:PRO79 4.0 14.6 1.0
CG A:ASN65 4.1 15.3 1.0
CD A:PRO79 4.3 16.2 1.0
O A:ASN65 4.3 11.3 1.0
C A:ILE78 4.7 15.9 1.0
O A:ILE78 4.9 13.7 1.0
C A:ASN65 4.9 11.2 1.0
CL A:CL208 5.0 30.5 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 12:14:38 2024

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