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Chlorine in PDB 5ilf: The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 4, A Platin(II) Compound Containing A O, S Bidentate Ligand

Enzymatic activity of The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 4, A Platin(II) Compound Containing A O, S Bidentate Ligand

All present enzymatic activity of The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 4, A Platin(II) Compound Containing A O, S Bidentate Ligand:
3.2.1.17;

Protein crystallography data

The structure of The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 4, A Platin(II) Compound Containing A O, S Bidentate Ligand, PDB code: 5ilf was solved by A.Merlino, G.Ferraro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.14 / 1.85
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.983, 77.983, 37.281, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 23.3

Other elements in 5ilf:

The structure of The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 4, A Platin(II) Compound Containing A O, S Bidentate Ligand also contains other interesting chemical elements:

Platinum (Pt) 1 atom
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 4, A Platin(II) Compound Containing A O, S Bidentate Ligand (pdb code 5ilf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 4, A Platin(II) Compound Containing A O, S Bidentate Ligand, PDB code: 5ilf:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5ilf

Go back to Chlorine Binding Sites List in 5ilf
Chlorine binding site 1 out of 4 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 4, A Platin(II) Compound Containing A O, S Bidentate Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 4, A Platin(II) Compound Containing A O, S Bidentate Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:28.1
occ:1.00
 O A:HOH411 3.1 33.3 1.0
O A:HOH357 3.2 16.1 1.0
N A:THR69 3.2 19.7 1.0
O A:THR69 3.3 19.9 1.0
N A:ARG68 3.5 19.4 1.0
C A:GLY67 3.5 23.8 1.0
CA A:GLY67 3.6 19.4 1.0
C A:THR69 3.7 21.6 1.0
OG A:SER72 3.7 30.9 1.0
N A:GLY67 3.7 18.6 1.0
OD1 A:ASN65 3.7 20.0 1.0
CA A:THR69 3.8 20.5 1.0
O A:HOH368 4.1 22.7 1.0
C A:ARG68 4.1 21.5 1.0
CB A:THR69 4.2 21.4 1.0
O A:GLY67 4.2 22.9 1.0
CA A:ARG68 4.2 22.5 1.0
OD1 A:ASP66 4.2 16.9 1.0
N A:PRO70 4.6 22.7 1.0
NA A:NA208 4.7 25.7 1.0
OG1 A:THR69 4.8 17.7 1.0
C A:ASP66 4.8 17.9 1.0
O A:HOH347 4.9 21.9 0.5
CG A:ASN65 4.9 22.4 1.0
N A:ASP66 5.0 16.3 1.0
CB A:SER72 5.0 30.3 1.0

Chlorine binding site 2 out of 4 in 5ilf

Go back to Chlorine Binding Sites List in 5ilf
Chlorine binding site 2 out of 4 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 4, A Platin(II) Compound Containing A O, S Bidentate Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 4, A Platin(II) Compound Containing A O, S Bidentate Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:28.6
occ:1.00
 OG A:SER24 3.1 21.5 1.0
N A:GLY26 3.2 18.2 1.0
CB A:SER24 3.4 20.8 1.0
CA A:GLY26 3.5 18.8 1.0
CA A:GLN121 3.6 24.4 1.0
N A:GLN121 3.9 23.1 1.0
CD1 A:ILE124 3.9 29.7 1.0
CB A:GLN121 4.1 33.2 1.0
O A:VAL120 4.2 21.5 1.0
C A:VAL120 4.2 21.3 1.0
N A:LEU25 4.3 19.8 1.0
CG1 A:ILE124 4.3 26.1 1.0
CG2 A:VAL120 4.3 23.9 1.0
C A:LEU25 4.4 18.5 1.0
C A:SER24 4.4 19.9 1.0
NE2 A:GLN121 4.5 52.1 1.0
CA A:SER24 4.5 19.8 1.0
C A:GLY26 4.6 18.5 1.0
N A:ASN27 4.7 16.4 1.0
CA A:LEU25 4.8 20.3 1.0
C A:GLN121 4.8 23.1 1.0
O A:HOH401 4.8 55.4 1.0
O A:SER24 5.0 18.6 1.0

Chlorine binding site 3 out of 4 in 5ilf

Go back to Chlorine Binding Sites List in 5ilf
Chlorine binding site 3 out of 4 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 4, A Platin(II) Compound Containing A O, S Bidentate Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 4, A Platin(II) Compound Containing A O, S Bidentate Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:26.9
occ:1.00
 OH A:TYR23 3.0 16.5 1.0
O A:HOH332 3.4 21.7 1.0
CZ A:TYR23 3.7 16.9 1.0
CE2 A:TYR23 3.7 17.7 1.0
CA A:GLY104 4.2 20.2 1.0
O A:ARG21 4.6 22.0 1.0
CE1 A:TYR23 4.8 16.4 1.0
O A:HOH310 4.9 23.3 1.0
N A:GLY104 5.0 20.3 1.0
CD2 A:TYR23 5.0 18.4 1.0

Chlorine binding site 4 out of 4 in 5ilf

Go back to Chlorine Binding Sites List in 5ilf
Chlorine binding site 4 out of 4 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 4, A Platin(II) Compound Containing A O, S Bidentate Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 4, A Platin(II) Compound Containing A O, S Bidentate Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:36.3
occ:1.00
 N A:ILE88 3.2 21.9 1.0
O A:HOH317 3.5 33.7 1.0
CA A:ASP87 3.7 24.5 1.0
CG1 A:ILE88 3.7 18.8 1.0
NE2 A:HIS15 3.9 26.8 1.0
C A:ASP87 4.0 22.9 1.0
O A:SER86 4.1 27.9 1.0
CG A:ASP87 4.2 33.1 1.0
OD1 A:ASP87 4.2 32.2 1.0
CB A:ILE88 4.2 20.2 1.0
CB A:ALA11 4.2 23.1 1.0
CA A:ILE88 4.2 22.4 1.0
CG2 A:ILE88 4.2 19.4 1.0
CZ A:PHE3 4.3 22.7 1.0
NH1 A:ARG14 4.4 47.1 1.0
OD2 A:ASP87 4.5 39.0 1.0
CB A:ASP87 4.5 29.9 1.0
CD2 A:HIS15 4.5 25.3 1.0
CD1 A:ILE88 4.6 20.6 1.0
N A:ASP87 4.7 24.0 1.0
C A:SER86 4.9 23.9 1.0
CE1 A:HIS15 4.9 28.6 1.0
N A:THR89 5.0 21.4 1.0
CE2 A:PHE3 5.0 22.0 1.0

Reference:

J.Hildebrandt, N.Hafner, H.Gorls, D.Kritsch, G.Ferraro, M.Durst, I.B.Runnebaum, A.Merlino, W.Weigand. Platinum(II) O,S Complexes As Potential Metallodrugs Against Cisplatin Resistance. Dalton Trans V. 45 18876 2016.
ISSN: ESSN 1477-9234
PubMed: 27897281
DOI: 10.1039/C6DT01388K
Page generated: Fri Jul 26 09:23:44 2024

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