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Sodium in PDB 5l3h: Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties

Enzymatic activity of Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties

All present enzymatic activity of Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties:
3.2.1.17;

Protein crystallography data

The structure of Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties, PDB code: 5l3h was solved by J.R.Helliwell, S.W.M.Tanley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.93 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.832, 78.832, 37.021, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 24.8

Other elements in 5l3h:

The structure of Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties also contains other interesting chemical elements:

Platinum (Pt) 5 atoms
Chlorine (Cl) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties (pdb code 5l3h). 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 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties, PDB code: 5l3h:

Sodium binding site 1 out of 1 in 5l3h

Go back to Sodium Binding Sites List in 5l3h
Sodium binding site 1 out of 1 in the Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties


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 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:13.2
occ:1.00
 O A:SER60 2.3 12.8 1.0
O A:HOH344 2.4 13.2 1.0
O A:HOH339 2.4 9.4 1.0
O A:CYS64 2.5 9.9 1.0
OG A:SER72 2.5 14.0 1.0
O A:ARG73 2.5 14.1 1.0
HB2 A:SER72 2.8 17.0 1.0
HA A:ASN65 2.9 13.7 1.0
CB A:SER72 3.2 14.1 1.0
C A:CYS64 3.5 10.6 1.0
C A:ARG73 3.5 13.9 1.0
C A:SER60 3.5 12.3 1.0
HB2 A:SER60 3.7 11.9 1.0
CA A:ASN65 3.8 11.4 1.0
HB3 A:SER72 3.8 17.0 1.0
HB A:THR69 3.8 13.7 1.0
N A:ARG73 3.8 13.7 1.0
H A:ARG73 3.9 16.4 1.0
HB2 A:ASN74 3.9 14.4 1.0
HA A:SER60 4.0 13.8 1.0
N A:ASN65 4.0 10.5 1.0
H A:ASP66 4.0 12.3 1.0
C A:SER72 4.0 15.6 1.0
H A:CYS64 4.1 11.9 1.0
HA A:ASN74 4.2 14.8 1.0
CA A:SER60 4.2 11.5 1.0
CA A:SER72 4.2 14.1 1.0
HB2 A:ASN65 4.3 13.9 1.0
CA A:ARG73 4.3 12.9 1.0
CB A:SER60 4.4 10.0 1.0
HA A:ARG61 4.4 15.9 0.5
N A:ASN74 4.4 13.3 1.0
HA A:ARG61 4.5 15.9 0.5
N A:CYS64 4.5 9.9 1.0
C A:ARG61 4.6 14.4 0.5
CB A:ASN65 4.6 11.6 1.0
N A:ARG61 4.6 13.3 0.5
N A:ARG61 4.6 13.3 0.5
C A:ARG61 4.6 14.4 0.5
O A:ARG61 4.6 14.9 0.5
O A:SER72 4.6 15.6 1.0
CL A:CL201 4.6 13.4 1.0
HA A:ARG73 4.6 15.4 1.0
CA A:CYS64 4.6 10.4 1.0
OD1 A:ASN65 4.6 13.5 1.0
CA A:ASN74 4.6 12.3 1.0
O A:ARG61 4.7 14.9 0.5
N A:ASP66 4.7 10.3 1.0
CB A:THR69 4.7 11.4 1.0
CB A:ASN74 4.7 12.0 1.0
CA A:ARG61 4.8 13.2 0.5
C A:ASN65 4.8 9.9 1.0
CA A:ARG61 4.8 13.2 0.5
HA A:SER72 4.8 16.9 1.0
H A:ASN65 4.8 12.6 1.0
HG21 A:THR69 4.8 15.1 1.0
N A:TRP62 4.9 13.1 1.0
O A:THR69 5.0 12.6 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 Oct 7 22:16:23 2024

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