Sodium in PDB 4z46: X-Ray Structure of the Bis-Platinum Lysozyme Adduct Formed in the Reaction Between the Protein and the Two Drugs Cisplatin and Oxaliplatin

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

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:
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, PDB code: 4z46 was solved by A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.67 / 1.85
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.318, 77.318, 37.325, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 21.8

Other elements in 4z46:

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 also contains other interesting chemical elements:

Platinum (Pt) 2 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium 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 (pdb code 4z46). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium 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, PDB code: 4z46:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4z46

Go back to Sodium Binding Sites List in 4z46
Sodium 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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na212

b:52.6
occ:1.00
 O A:HOH400 2.3 41.4 1.0
O A:HOH359 2.4 53.4 1.0
O A:HOH336 2.6 28.2 1.0
O3 A:NO3210 2.7 39.9 1.0
OE1 A:GLU35 2.7 21.1 1.0
O1 A:NO3210 2.7 37.5 1.0
N A:NO3210 2.9 38.4 1.0
OD2 A:ASP52 3.3 26.7 1.0
CD A:GLU35 3.6 18.8 1.0
OE2 A:GLU35 3.8 19.8 1.0
O A:HOH327 4.0 45.8 1.0
O2 A:NO3210 4.0 31.1 1.0
CB A:GLN57 4.2 17.9 1.0
O A:HOH306 4.3 35.5 1.0
O A:HOH331 4.3 41.7 1.0
CG A:ASP52 4.4 22.0 1.0
CG A:GLN57 4.6 18.1 1.0
OE1 A:GLN57 5.0 18.6 1.0

Sodium binding site 2 out of 2 in 4z46

Go back to Sodium Binding Sites List in 4z46
Sodium 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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na213

b:32.2
occ:1.00
 O3 A:NO3207 2.3 50.6 1.0
O A:HOH395 2.6 47.4 1.0
OH A:TYR23 3.0 17.4 1.0
N A:NO3207 3.5 45.4 1.0
CE2 A:TYR23 3.6 17.9 1.0
CZ A:TYR23 3.7 17.1 1.0
CA A:GLY104 3.7 19.6 1.0
O2 A:NO3207 4.1 44.9 1.0
N A:GLY104 4.3 17.7 1.0
O1 A:NO3207 4.4 47.8 1.0
O A:ARG21 4.5 24.5 1.0
CD2 A:TYR23 4.9 19.3 1.0
CE1 A:TYR23 5.0 15.9 1.0
O A:VAL99 5.0 24.1 1.0
C A:GLY104 5.0 18.9 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: Tue Dec 15 10:05:19 2020

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