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Sodium in PDB 5l3i: Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15

Enzymatic activity of Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15

All present enzymatic activity of Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15:
3.2.1.17;

Protein crystallography data

The structure of Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15, PDB code: 5l3i 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) 18.39 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.016, 78.016, 37.071, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.2

Other elements in 5l3i:

The structure of Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 also contains other interesting chemical elements:

Platinum (Pt) 5 atoms
Chlorine (Cl) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 (pdb code 5l3i). 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 Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15, PDB code: 5l3i:

Sodium binding site 1 out of 1 in 5l3i

Go back to Sodium Binding Sites List in 5l3i
Sodium binding site 1 out of 1 in the Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:12.0
occ:1.00
 O A:HOH327 2.3 9.6 1.0
O A:HOH336 2.4 12.8 1.0
O A:CYS64 2.4 10.2 1.0
O A:SER60 2.4 12.6 1.0
O A:ARG73 2.5 15.1 1.0
OG A:SER72 2.5 18.1 1.0
HB2 A:SER72 2.8 22.7 1.0
HA A:ASN65 2.9 15.0 1.0
CB A:SER72 3.2 18.9 1.0
HB2 A:SER60 3.4 11.5 1.0
C A:CYS64 3.4 9.8 1.0
C A:ARG73 3.5 17.6 1.0
C A:SER60 3.5 14.8 1.0
HB A:THR69 3.7 20.2 1.0
HB3 A:SER72 3.8 22.7 1.0
CA A:ASN65 3.8 12.5 1.0
HA A:SER60 3.9 14.5 1.0
HB2 A:ASN74 3.9 16.4 1.0
N A:ARG73 3.9 19.2 1.0
H A:CYS64 3.9 11.9 1.0
H A:ARG73 4.0 23.1 1.0
H A:ASP66 4.0 12.7 1.0
N A:ASN65 4.0 10.9 1.0
C A:SER72 4.1 21.9 1.0
CA A:SER60 4.1 12.1 1.0
HA A:ASN74 4.1 17.4 1.0
CB A:SER60 4.2 9.6 1.0
CA A:ARG73 4.3 20.6 1.0
CA A:SER72 4.3 20.2 1.0
N A:ASN74 4.4 14.1 1.0
HB2 A:ASN65 4.4 13.9 1.0
N A:CYS64 4.5 9.9 1.0
CA A:CYS64 4.6 10.7 1.0
CA A:ASN74 4.6 14.5 1.0
N A:ASP66 4.6 10.5 1.0
CL A:CL217 4.6 16.9 1.0
HA A:ARG73 4.6 24.7 1.0
N A:ARG61 4.7 14.6 1.0
O A:SER72 4.7 21.0 1.0
CB A:THR69 4.7 16.9 1.0
OD1 A:ASN65 4.7 15.0 1.0
C A:ARG61 4.7 20.5 1.0
O A:ARG61 4.7 19.0 1.0
CB A:ASN65 4.7 11.6 1.0
CB A:ASN74 4.7 13.7 1.0
HA A:ARG61 4.7 22.8 1.0
HG1 A:THR69 4.7 15.7 0.0
C A:ASN65 4.8 9.7 1.0
HG22 A:THR69 4.8 20.3 1.0
HA A:SER72 4.8 24.2 1.0
HB3 A:SER60 4.8 11.5 1.0
H A:ASN65 4.9 13.1 1.0
CA A:ARG61 4.9 19.0 1.0
N A:TRP62 5.0 15.5 1.0
O A:THR69 5.0 14.3 1.0
H A:TRP63 5.0 16.4 1.0

Reference:

J.R.Helliwell, A.M.M.Schreurs, L.M.J.Kroon-Batenburg, S.Tanley. Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Ligand Distances and Angles, and Their Standard Uncertainties, and Also Reporting A Split Occupancy Effect Arxiv 2016.
DOI: 10.3927/45371856
Page generated: Mon Aug 18 00:48:30 2025

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