Sodium in PDB 6yjx: Structure of Hen Egg-White Lysozyme Crystallized with Pas Polypeptide

Enzymatic activity of Structure of Hen Egg-White Lysozyme Crystallized with Pas Polypeptide

All present enzymatic activity of Structure of Hen Egg-White Lysozyme Crystallized with Pas Polypeptide:
3.2.1.17;

Protein crystallography data

The structure of Structure of Hen Egg-White Lysozyme Crystallized with Pas Polypeptide, PDB code: 6yjx was solved by A.Schiefner, A.Skerra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.11 / 1.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.468, 79.468, 37.848, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 17.5

Other elements in 6yjx:

The structure of Structure of Hen Egg-White Lysozyme Crystallized with Pas Polypeptide also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Hen Egg-White Lysozyme Crystallized with Pas Polypeptide (pdb code 6yjx). 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 Structure of Hen Egg-White Lysozyme Crystallized with Pas Polypeptide, PDB code: 6yjx:

Sodium binding site 1 out of 1 in 6yjx

Go back to Sodium Binding Sites List in 6yjx
Sodium binding site 1 out of 1 in the Structure of Hen Egg-White Lysozyme Crystallized with Pas Polypeptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Hen Egg-White Lysozyme Crystallized with Pas Polypeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:18.5
occ:1.00
 O A:SER60 2.3 18.9 1.0
O A:ARG73 2.3 23.0 1.0
O A:HOH413 2.4 25.0 1.0
OG A:SER72 2.5 22.2 1.0
O A:HOH385 2.5 14.8 1.0
O A:CYS64 2.6 12.4 1.0
CB A:SER72 3.3 22.3 1.0
C A:SER60 3.4 14.2 1.0
C A:ARG73 3.5 23.7 1.0
C A:CYS64 3.6 12.0 1.0
N A:ARG73 4.0 21.8 1.0
CA A:ASN65 4.0 12.7 1.0
CA A:SER60 4.1 12.1 1.0
C A:SER72 4.2 27.3 1.0
N A:ASN65 4.2 12.3 1.0
CA A:SER72 4.3 26.9 1.0
N A:ASN74 4.4 17.2 1.0
CA A:ARG73 4.4 22.7 1.0
CB A:SER60 4.4 11.6 1.0
O A:ARG61 4.4 21.4 0.5
N A:ARG61 4.4 16.3 0.5
N A:ARG61 4.5 16.4 0.5
C A:ARG61 4.5 17.8 0.5
O A:ARG61 4.5 21.7 0.5
C A:ARG61 4.5 16.9 0.5
N A:CYS64 4.6 12.8 1.0
CA A:ASN74 4.7 15.5 1.0
CA A:ARG61 4.7 19.6 0.5
CL A:CL202 4.7 23.9 1.0
CB A:THR69 4.7 13.2 1.0
CA A:ARG61 4.7 19.4 0.5
OD1 A:ASN65 4.7 17.3 1.0
O A:SER72 4.7 29.1 1.0
N A:ASP66 4.8 11.0 1.0
CA A:CYS64 4.8 12.6 1.0
CB A:ASN74 4.8 15.8 1.0
CB A:ASN65 4.9 13.0 1.0
N A:TRP62 4.9 13.9 1.0
C A:ASN65 4.9 10.7 1.0
O A:THR69 5.0 16.8 1.0

Reference:

A.Schiefner, R.Walser, M.Gebauer, A.Skerra. Proline/Alanine-Rich Sequence (Pas) Polypeptides As An Alternative to Peg Precipitants For Protein Crystallization. Acta Crystallogr.,Sect.F V. 76 320 2020.
ISSN: ESSN 2053-230X
PubMed: 32627748
DOI: 10.1107/S2053230X20008328
Page generated: Tue Dec 15 16:29:48 2020

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