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Sodium in PDB 5yky: Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6

Enzymatic activity of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6

All present enzymatic activity of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6:
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6, PDB code: 5yky was solved by H.Tabe, H.Takahashi, T.Shimoi, S.Abe, T.Ueno, Y.Yamada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.48 / 1.88
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.458, 78.458, 36.647, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 23.7

Other elements in 5yky:

The structure of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6 also contains other interesting chemical elements:

Platinum (Pt) 2 atoms
Chlorine (Cl) 12 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6 (pdb code 5yky). 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 Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6, PDB code: 5yky:

Sodium binding site 1 out of 1 in 5yky

Go back to Sodium Binding Sites List in 5yky
Sodium binding site 1 out of 1 in the Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:40.6
occ:1.00
 O A:SER60 2.3 32.9 1.0
O A:HOH332 2.4 35.0 1.0
O A:CYS64 2.4 28.0 1.0
O A:ARG73 2.5 38.6 1.0
OG A:SER72 2.6 46.0 1.0
O A:HOH323 2.6 27.1 1.0
CB A:SER72 3.3 45.5 1.0
C A:SER60 3.4 31.0 1.0
C A:CYS64 3.5 26.4 1.0
C A:ARG73 3.6 41.2 1.0
CA A:ASN65 3.9 28.3 1.0
N A:ARG73 4.0 37.0 1.0
N A:ASN65 4.1 27.7 1.0
C A:SER72 4.1 45.7 1.0
O A:ARG61 4.1 38.6 1.0
CA A:SER60 4.1 26.1 1.0
CA A:SER72 4.3 45.4 1.0
N A:CYS64 4.3 26.8 1.0
C A:ARG61 4.4 40.0 1.0
CA A:ARG73 4.4 43.6 1.0
N A:ASN74 4.4 38.0 1.0
N A:ARG61 4.4 31.3 1.0
CB A:SER60 4.4 24.6 1.0
CA A:ASN74 4.5 33.3 1.0
CA A:CYS64 4.6 26.6 1.0
O A:SER72 4.6 39.1 1.0
O A:HOH330 4.6 26.8 1.0
N A:ASP66 4.6 25.5 1.0
OD1 A:ASN65 4.6 32.8 1.0
CA A:ARG61 4.7 37.7 1.0
CB A:ASN74 4.8 36.1 1.0
CB A:ASN65 4.8 28.0 1.0
CB A:THR69 4.8 30.6 1.0
C A:ASN65 4.8 24.3 1.0
N A:TRP62 4.9 34.0 1.0
N A:TRP63 4.9 28.7 1.0

Reference:

H.Tabe, H.Takahashi, T.Shimoi, Y.Yamada. Photocatalytic Hydrogen Evolution Systems Constructed in Cross-Linked Porous Protein Crystals Appl Catal B V. 237 1124 2018.
ISSN: ISSN 0926-3373
DOI: 10.1016/J.APCATB.2018.01.046
Page generated: Tue Dec 15 11:51:01 2020

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