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Sodium in PDB 5lxw: Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years on the Shelf

Enzymatic activity of Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years on the Shelf

All present enzymatic activity of Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years on the Shelf:
3.2.1.17;

Protein crystallography data

The structure of Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years on the Shelf, PDB code: 5lxw was solved by J.R.Helliwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.39 / 1.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.370, 79.370, 37.840, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 20.3

Other elements in 5lxw:

The structure of Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years on the Shelf also contains other interesting chemical elements:

Platinum (Pt) 3 atoms
Chlorine (Cl) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years on the Shelf (pdb code 5lxw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years on the Shelf, PDB code: 5lxw:

Sodium binding site 1 out of 1 in 5lxw

Go back to Sodium Binding Sites List in 5lxw
Sodium binding site 1 out of 1 in the Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years on the Shelf


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years on the Shelf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:13.3
occ:1.00
 HG A:SER72 2.2 17.5 0.0
O A:SER60 2.3 12.3 1.0
O A:ARG73 2.5 15.1 1.0
O A:CYS64 2.5 12.5 1.0
O A:HOH351 2.5 17.3 1.0
O A:HOH356 2.5 13.3 1.0
OG A:SER72 2.5 14.6 1.0
HB2 A:SER72 2.9 17.2 1.0
HA A:ASN65 3.0 14.6 1.0
CB A:SER72 3.2 14.3 1.0
C A:SER60 3.5 12.1 1.0
C A:CYS64 3.5 12.0 1.0
C A:ARG73 3.5 14.7 1.0
HB2 A:SER60 3.6 14.1 1.0
HB A:THR69 3.9 14.8 1.0
HB3 A:SER72 3.9 17.2 1.0
HA A:SER60 3.9 13.7 1.0
CA A:ASN65 3.9 12.2 1.0
H A:ARG73 4.0 18.1 1.0
N A:ARG73 4.0 15.1 1.0
H A:ASP66 4.0 13.6 0.5
H A:ASP66 4.0 13.6 0.5
H A:CYS64 4.0 15.4 1.0
HB2 A:ASN74 4.0 17.2 1.0
N A:ASN65 4.1 12.1 1.0
C A:SER72 4.2 15.7 1.0
CA A:SER60 4.2 11.4 1.0
HA A:ASN74 4.2 17.6 1.0
CA A:SER72 4.4 14.9 1.0
HA A:ARG61 4.4 16.3 0.5
CB A:SER60 4.4 11.8 1.0
CA A:ARG73 4.4 15.3 1.0
O A:ARG61 4.4 13.9 0.5
HA A:ARG61 4.4 17.3 0.5
N A:ASN74 4.4 15.1 1.0
C A:ARG61 4.5 13.5 0.5
N A:CYS64 4.5 12.9 1.0
N A:ARG61 4.6 12.8 0.5
HB2 A:ASN65 4.6 16.3 1.0
C A:ARG61 4.6 13.4 0.5
N A:ARG61 4.6 12.2 0.5
O A:ARG61 4.6 14.1 0.5
CA A:CYS64 4.6 11.9 1.0
CA A:ASN74 4.7 14.7 1.0
N A:ASP66 4.7 11.3 1.0
OD1 A:ASN65 4.7 14.7 1.0
CA A:ARG61 4.7 14.4 0.5
CA A:ARG61 4.7 13.6 0.5
HA A:ARG73 4.8 18.4 1.0
CL A:CL211 4.8 16.5 1.0
O A:SER72 4.8 16.5 1.0
CB A:THR69 4.8 12.3 1.0
CB A:ASN74 4.8 14.3 1.0
CB A:ASN65 4.8 13.6 1.0
C A:ASN65 4.9 12.3 1.0
HA A:SER72 4.9 17.9 1.0
H A:TRP63 4.9 14.8 1.0
HG21 A:THR69 4.9 16.4 1.0
N A:TRP62 4.9 13.1 1.0
HG A:CYS80 5.0 13.7 1.0
H A:ASN65 5.0 14.5 1.0

Reference:

J.R.Helliwell, T.Simon. Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years 'on the Shelf' Zenodo 2016.
DOI: 10.5281/ZENODO.155068
Page generated: Mon Oct 7 22:26:08 2024

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