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Sodium in PDB 6ybi: Rt Structure of Hew Lysozyme Obtained at 1.12 A Resolution From Crystal Grown in A Mylar Microchip.

Enzymatic activity of Rt Structure of Hew Lysozyme Obtained at 1.12 A Resolution From Crystal Grown in A Mylar Microchip.

All present enzymatic activity of Rt Structure of Hew Lysozyme Obtained at 1.12 A Resolution From Crystal Grown in A Mylar Microchip.:
3.2.1.17;

Protein crystallography data

The structure of Rt Structure of Hew Lysozyme Obtained at 1.12 A Resolution From Crystal Grown in A Mylar Microchip., PDB code: 6ybi was solved by J.A.Gavira, S.Martinez-Rodriguez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.58 / 1.12
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.170, 79.170, 37.960, 90.00, 90.00, 90.00
R / Rfree (%) 13.3 / 15.3

Other elements in 6ybi:

The structure of Rt Structure of Hew Lysozyme Obtained at 1.12 A Resolution From Crystal Grown in A Mylar Microchip. also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Rt Structure of Hew Lysozyme Obtained at 1.12 A Resolution From Crystal Grown in A Mylar Microchip. (pdb code 6ybi). 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 Rt Structure of Hew Lysozyme Obtained at 1.12 A Resolution From Crystal Grown in A Mylar Microchip., PDB code: 6ybi:

Sodium binding site 1 out of 1 in 6ybi

Go back to Sodium Binding Sites List in 6ybi
Sodium binding site 1 out of 1 in the Rt Structure of Hew Lysozyme Obtained at 1.12 A Resolution From Crystal Grown in A Mylar Microchip.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Rt Structure of Hew Lysozyme Obtained at 1.12 A Resolution From Crystal Grown in A Mylar Microchip. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:24.3
occ:1.00
 O A:SER60 2.3 19.7 1.0
O A:CYS64 2.4 18.2 1.0
OG A:SER72 2.4 29.0 1.0
O A:HOH377 2.5 33.4 1.0
O A:ARG73 2.5 28.2 0.6
O A:ARG73 2.5 27.0 0.4
O A:HOH357 2.5 22.4 1.0
CB A:SER72 3.2 29.3 1.0
C A:SER60 3.5 17.1 1.0
C A:CYS64 3.5 16.4 1.0
C A:ARG73 3.5 26.3 0.4
C A:ARG73 3.5 26.6 0.6
CA A:ASN65 3.9 17.9 1.0
N A:ARG73 3.9 26.9 0.6
N A:ARG73 3.9 28.1 0.4
C A:SER72 4.1 29.3 1.0
N A:ASN65 4.1 17.3 1.0
CA A:SER60 4.1 16.1 1.0
CA A:SER72 4.2 29.2 1.0
C A:ARG61 4.3 20.7 1.0
O A:ARG61 4.4 22.9 1.0
N A:CYS64 4.4 17.2 1.0
CA A:ARG73 4.4 28.3 0.4
N A:ASN74 4.4 24.8 1.0
CB A:SER60 4.4 16.6 1.0
CA A:ARG73 4.4 27.9 0.6
N A:ARG61 4.5 18.4 1.0
CA A:ASN74 4.5 21.9 1.0
CA A:ARG61 4.6 21.0 1.0
CA A:CYS64 4.6 16.6 1.0
O A:SER72 4.6 32.6 1.0
CB A:ASN74 4.7 23.3 1.0
CB A:THR69 4.7 18.6 1.0
N A:TRP62 4.7 19.7 0.6
N A:TRP62 4.8 20.6 0.4
N A:ASP66 4.8 16.4 1.0
O A:HOH371 4.8 24.2 1.0
CB A:ASN65 4.8 22.0 1.0
OD1 A:ASN65 4.8 28.6 1.0
C A:ASN65 4.9 15.6 1.0
O A:THR69 4.9 23.9 1.0
N A:TRP63 5.0 18.0 1.0
C A:TRP62 5.0 19.7 0.6

Reference:

J.A.Gavira, I.Rodriguez-Ruiz, S.Martinez-Rodriguez, S.Basu, S.Teychene, A.A.Mccarthy, C.Mueller-Dieckman. Attaining Atomic Resolution From in Situ Data Collection at Room Temperature Using Counter-Diffusion-Based Low-Cost Microchips. Acta Crystallogr D Struct V. 76 751 2020BIOL.
ISSN: ISSN 2059-7983
PubMed: 32744257
DOI: 10.1107/S2059798320008475
Page generated: Tue Oct 8 15:01:24 2024

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