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Chlorine in PDB 5ii3: The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 3, 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 3, 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 3, 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 3, A Platin(II) Compound Containing A O, S Bidentate Ligand, PDB code: 5ii3 was solved by G.Ferraro, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.30 / 1.78
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.206, 78.206, 37.005, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 19

Other elements in 5ii3:

The structure of The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 3, 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 3, A Platin(II) Compound Containing A O, S Bidentate Ligand (pdb code 5ii3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 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 3, A Platin(II) Compound Containing A O, S Bidentate Ligand, PDB code: 5ii3:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5ii3

Go back to Chlorine Binding Sites List in 5ii3
Chlorine binding site 1 out of 5 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 3, 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 3, A Platin(II) Compound Containing A O, S Bidentate Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:53.9
occ:1.00
 OH A:TYR20 2.9 20.9 1.0
O A:HOH374 3.4 31.6 1.0
CE1 A:TYR20 3.4 18.3 1.0
CZ A:TYR20 3.6 18.5 1.0
O A:HOH425 3.8 45.7 1.0
CD A:LYS96 4.0 17.4 1.0
CB A:LYS96 4.6 15.4 1.0
CD1 A:TYR20 4.7 19.2 1.0
CG A:LYS96 4.8 15.9 1.0
CE A:LYS96 4.9 20.2 1.0
O A:HOH313 4.9 31.3 1.0
CE2 A:TYR20 4.9 17.7 1.0
NZ A:LYS96 5.0 24.3 1.0

Chlorine binding site 2 out of 5 in 5ii3

Go back to Chlorine Binding Sites List in 5ii3
Chlorine binding site 2 out of 5 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 3, 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 3, A Platin(II) Compound Containing A O, S Bidentate Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:31.4
occ:1.00
 O A:HOH311 3.0 38.5 1.0
O A:HOH328 3.2 23.4 1.0
N A:ILE88 3.3 18.1 1.0
CG1 A:ILE88 3.7 16.4 1.0
CA A:ASP87 3.8 18.2 1.0
O A:SER86 4.0 20.7 1.0
C A:ASP87 4.1 16.3 1.0
CZ A:PHE3 4.1 17.9 1.0
CB A:ALA11 4.1 18.2 1.0
OD1 A:ASP87 4.2 24.9 1.0
NE2 A:HIS15 4.2 25.2 1.0
CB A:ILE88 4.2 16.6 1.0
CG2 A:ILE88 4.3 18.2 1.0
CA A:ILE88 4.3 17.1 1.0
NH1 A:ARG14 4.4 43.5 1.0
CD1 A:ILE88 4.6 17.1 1.0
CG A:ASP87 4.6 27.4 1.0
CE2 A:PHE3 4.7 16.9 1.0
CB A:ASP87 4.7 21.3 1.0
N A:ASP87 4.8 17.5 1.0
CD2 A:HIS15 4.8 22.1 1.0
C A:SER86 4.8 18.5 1.0

Chlorine binding site 3 out of 5 in 5ii3

Go back to Chlorine Binding Sites List in 5ii3
Chlorine binding site 3 out of 5 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 3, 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 3, A Platin(II) Compound Containing A O, S Bidentate Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:20.5
occ:1.00
 OH A:TYR23 3.0 15.1 1.0
O A:HOH340 3.3 18.3 1.0
CZ A:TYR23 3.7 14.6 1.0
CE2 A:TYR23 3.7 15.3 1.0
CA A:GLY104 4.2 15.4 1.0
O A:ARG21 4.5 18.1 1.0
N A:GLY104 4.7 16.6 1.0
CE1 A:TYR23 4.9 14.4 1.0
CD2 A:TYR23 4.9 14.3 1.0

Chlorine binding site 4 out of 5 in 5ii3

Go back to Chlorine Binding Sites List in 5ii3
Chlorine binding site 4 out of 5 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 3, 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 3, A Platin(II) Compound Containing A O, S Bidentate Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:19.7
occ:1.00
 O A:HOH424 3.1 21.5 1.0
O A:HOH361 3.1 13.7 1.0
O A:HOH377 3.2 22.8 1.0
N A:THR69 3.3 17.5 1.0
O A:HOH337 3.3 29.2 1.0
C A:GLY67 3.4 17.7 1.0
N A:ARG68 3.5 16.9 1.0
O A:THR69 3.5 14.7 1.0
OG A:SER72 3.5 19.7 1.0
CA A:GLY67 3.5 15.9 1.0
N A:GLY67 3.6 14.7 1.0
OD1 A:ASN65 3.7 17.5 1.0
C A:THR69 3.8 17.2 1.0
O A:HOH380 3.9 15.6 1.0
CA A:THR69 4.0 16.9 1.0
O A:GLY67 4.1 16.1 1.0
C A:ARG68 4.3 17.0 1.0
CA A:ARG68 4.3 17.7 1.0
CB A:THR69 4.3 18.9 1.0
OD1 A:ASP66 4.3 13.4 1.0
N A:PRO70 4.7 17.4 1.0
NA A:NA203 4.7 15.6 1.0
C A:ASP66 4.7 14.4 1.0
CB A:SER72 4.8 19.2 1.0
O A:HOH323 4.9 15.5 0.5
O A:HOH423 4.9 34.8 1.0
N A:ASP66 4.9 13.0 1.0
OG1 A:THR69 4.9 16.0 1.0
CG A:ASN65 4.9 16.4 1.0

Chlorine binding site 5 out of 5 in 5ii3

Go back to Chlorine Binding Sites List in 5ii3
Chlorine binding site 5 out of 5 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 3, 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 5 of The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 3, A Platin(II) Compound Containing A O, S Bidentate Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:25.7
occ:1.00
 OG A:SER24 3.1 21.1 1.0
N A:GLY26 3.1 15.7 1.0
CB A:SER24 3.5 20.0 1.0
CA A:GLY26 3.5 16.2 1.0
CA A:GLN121 3.5 24.3 1.0
N A:GLN121 3.8 20.6 1.0
CD1 A:ILE124 3.8 28.9 1.0
OE1 A:GLN121 3.8 66.3 1.0
CB A:GLN121 3.9 30.3 1.0
C A:VAL120 4.2 21.0 1.0
CG1 A:ILE124 4.2 25.5 1.0
N A:LEU25 4.3 17.0 1.0
CG2 A:VAL120 4.3 22.3 1.0
C A:LEU25 4.3 17.6 1.0
O A:VAL120 4.3 20.6 1.0
C A:SER24 4.3 18.1 1.0
CA A:SER24 4.5 18.0 1.0
C A:GLY26 4.5 15.9 1.0
CG A:GLN121 4.6 40.8 1.0
N A:ASN27 4.7 14.9 1.0
CA A:LEU25 4.7 16.6 1.0
CD A:GLN121 4.7 57.2 1.0
O A:SER24 4.8 18.6 1.0
C A:GLN121 4.8 20.1 1.0
O A:HOH382 5.0 15.1 0.5
CB A:VAL120 5.0 21.4 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 09:20:20 2024

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