Sodium in PDB 5hmj: Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution

Enzymatic activity of Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution

All present enzymatic activity of Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution:
3.2.1.17;

Protein crystallography data

The structure of Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution, PDB code: 5hmj 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) 39.29 / 1.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.580, 78.580, 37.290, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 21.5

Other elements in 5hmj:

The structure of Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution also contains other interesting chemical elements:

Bromine (Br) 15 atoms
Platinum (Pt) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution (pdb code 5hmj). 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 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution, PDB code: 5hmj:

Sodium binding site 1 out of 1 in 5hmj

Go back to Sodium Binding Sites List in 5hmj
Sodium binding site 1 out of 1 in the Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution


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 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na207

b:14.2
occ:1.00
 O A:SER60 2.3 13.7 1.0
O A:CYS64 2.4 13.0 1.0
O A:ARG73 2.4 15.9 1.0
OG A:SER72 2.5 17.0 1.0
O A:HOH339 2.5 14.9 1.0
O A:HOH353 2.5 16.8 1.0
HB2 A:SER72 2.8 20.2 1.0
HA A:ASN65 3.0 16.2 1.0
CB A:SER72 3.2 16.8 1.0
C A:CYS64 3.5 13.6 1.0
C A:ARG73 3.5 16.8 1.0
C A:SER60 3.5 13.2 1.0
HB2 A:SER60 3.5 15.1 1.0
HB3 A:SER72 3.8 20.2 1.0
HB A:THR69 3.8 18.1 1.0
HA A:SER60 3.9 14.1 1.0
H A:CYS64 3.9 17.2 1.0
N A:ARG73 3.9 17.5 1.0
CA A:ASN65 3.9 13.5 1.0
H A:ARG73 3.9 21.0 1.0
HB2 A:ASN74 4.0 19.8 1.0
H A:ASP66 4.0 14.9 1.0
C A:SER72 4.1 18.9 1.0
N A:ASN65 4.1 12.4 1.0
HA A:ASN74 4.1 19.6 1.0
CA A:SER60 4.1 11.7 1.0
CA A:SER72 4.3 17.3 1.0
CB A:SER60 4.3 12.6 1.0
CA A:ARG73 4.3 18.6 1.0
HA A:ARG61 4.4 18.7 1.0
N A:ASN74 4.4 16.9 1.0
O A:ARG61 4.4 18.2 1.0
N A:CYS64 4.4 14.3 1.0
C A:ARG61 4.5 15.9 1.0
N A:ARG61 4.5 14.4 1.0
CA A:ASN74 4.6 16.3 1.0
CA A:CYS64 4.6 13.4 1.0
HB2 A:ASN65 4.6 18.3 1.0
HA A:ARG73 4.6 22.3 1.0
N A:ASP66 4.7 12.4 1.0
O A:SER72 4.7 19.5 1.0
CA A:ARG61 4.7 15.6 1.0
CB A:ASN74 4.7 16.5 1.0
OD1 A:ASN65 4.7 18.7 1.0
CB A:THR69 4.8 15.1 1.0
BR A:BR205 4.8 21.6 0.6
HA A:SER72 4.8 20.8 1.0
O A:HOH369 4.8 34.6 1.0
CB A:ASN65 4.8 15.2 1.0
C A:ASN65 4.8 13.4 1.0
HG21 A:THR69 4.9 18.1 1.0
H A:TRP63 4.9 17.4 1.0
H A:ASN65 4.9 14.9 1.0
HB3 A:SER60 4.9 15.1 1.0
N A:TRP62 5.0 17.2 1.0

Reference:

S.W.Tanley, A.M.Schreurs, L.M.Kroon-Batenburg, J.R.Helliwell. Re-Refinement of 4XAN: Hen Egg-White Lysozyme with Carboplatin in Sodium Bromide Solution. Acta Crystallogr F Struct V. 72 251 2016BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 26919531
DOI: 10.1107/S2053230X16000777
Page generated: Tue Dec 15 11:03:38 2020

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