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Platinum in PDB 4zee: X-Ray Structure of the Bis-Platinum Lysozyme Adduct Formed in the Reaction Between the Protein and the Two Drugs Cisplatin and Oxaliplatin (Preparation 2)

Enzymatic activity of X-Ray Structure of the Bis-Platinum Lysozyme Adduct Formed in the Reaction Between the Protein and the Two Drugs Cisplatin and Oxaliplatin (Preparation 2)

All present enzymatic activity of X-Ray Structure of the Bis-Platinum Lysozyme Adduct Formed in the Reaction Between the Protein and the Two Drugs Cisplatin and Oxaliplatin (Preparation 2):
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of the Bis-Platinum Lysozyme Adduct Formed in the Reaction Between the Protein and the Two Drugs Cisplatin and Oxaliplatin (Preparation 2), PDB code: 4zee was solved by A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.71 / 1.95
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.377, 77.377, 37.600, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 23

Other elements in 4zee:

The structure of X-Ray Structure of the Bis-Platinum Lysozyme Adduct Formed in the Reaction Between the Protein and the Two Drugs Cisplatin and Oxaliplatin (Preparation 2) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Platinum Binding Sites:

The binding sites of Platinum atom in the X-Ray Structure of the Bis-Platinum Lysozyme Adduct Formed in the Reaction Between the Protein and the Two Drugs Cisplatin and Oxaliplatin (Preparation 2) (pdb code 4zee). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 2 binding sites of Platinum where determined in the X-Ray Structure of the Bis-Platinum Lysozyme Adduct Formed in the Reaction Between the Protein and the Two Drugs Cisplatin and Oxaliplatin (Preparation 2), PDB code: 4zee:
Jump to Platinum binding site number: 1; 2;

Platinum binding site 1 out of 2 in 4zee

Go back to Platinum Binding Sites List in 4zee
Platinum binding site 1 out of 2 in the X-Ray Structure of the Bis-Platinum Lysozyme Adduct Formed in the Reaction Between the Protein and the Two Drugs Cisplatin and Oxaliplatin (Preparation 2)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of X-Ray Structure of the Bis-Platinum Lysozyme Adduct Formed in the Reaction Between the Protein and the Two Drugs Cisplatin and Oxaliplatin (Preparation 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt412

b:55.9
occ:0.40
PT A:1PT412 0.0 55.9 0.4
O A:HOH505 1.7 22.6 0.4
N1 A:1PT412 2.0 33.1 0.4
N2 A:1PT412 2.2 35.0 0.4
OD2 A:ASP119 2.7 43.8 1.0
C1 A:1PT412 2.9 31.6 0.4
C2 A:1PT412 2.9 34.2 0.4
OD1 A:ASP119 2.9 32.7 1.0
CG A:ASP119 3.1 36.9 1.0
NH1 A:ARG125 4.1 80.2 1.0
C6 A:1PT412 4.1 29.6 0.4
C3 A:1PT412 4.3 34.5 0.4
CB A:ASP119 4.6 32.5 1.0
CB A:GLN121 4.6 46.8 1.0
OE1 A:GLN121 4.6 81.9 1.0

Platinum binding site 2 out of 2 in 4zee

Go back to Platinum Binding Sites List in 4zee
Platinum binding site 2 out of 2 in the X-Ray Structure of the Bis-Platinum Lysozyme Adduct Formed in the Reaction Between the Protein and the Two Drugs Cisplatin and Oxaliplatin (Preparation 2)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of X-Ray Structure of the Bis-Platinum Lysozyme Adduct Formed in the Reaction Between the Protein and the Two Drugs Cisplatin and Oxaliplatin (Preparation 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt413

b:63.6
occ:0.35
PT1 A:CPT413 0.0 63.6 0.3
N2 A:CPT413 2.3 52.3 0.3
CL1 A:CPT413 2.3 36.2 0.3
ND1 A:HIS15 2.5 31.7 1.0
CE1 A:HIS15 3.3 29.8 1.0
CG A:HIS15 3.4 28.2 1.0
CB A:HIS15 3.7 26.8 1.0
CA A:HIS15 3.7 24.6 1.0
O A:HIS15 4.3 25.9 1.0
O A:HOH620 4.3 37.5 1.0
NE2 A:HIS15 4.3 28.2 1.0
CD2 A:HIS15 4.4 28.1 1.0
C A:HIS15 4.5 27.0 1.0
OD1 A:ASN93 4.7 49.6 1.0
N A:HIS15 4.8 25.5 1.0
O A:HOH553 4.8 51.8 1.0
O A:ARG14 4.8 24.6 1.0
O A:HOH565 4.8 44.5 1.0
CG2 A:THR89 4.9 26.8 1.0
O A:HOH527 4.9 40.3 1.0

Reference:

D.Marasco, L.Messori, T.Marzo, A.Merlino. Oxaliplatin Vs. Cisplatin: Competition Experiments on Their Binding to Lysozyme. Dalton Trans 2015.
ISSN: ESSN 1477-9234
PubMed: 25974859
DOI: 10.1039/C5DT01279A
Page generated: Wed Dec 16 02:05:07 2020

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