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Sodium in PDB 8f28: Lysozyme Structures From Single-Entity Crystallization Method Nanoac

Enzymatic activity of Lysozyme Structures From Single-Entity Crystallization Method Nanoac

All present enzymatic activity of Lysozyme Structures From Single-Entity Crystallization Method Nanoac:
3.2.1.17;

Protein crystallography data

The structure of Lysozyme Structures From Single-Entity Crystallization Method Nanoac, PDB code: 8f28 was solved by R.Yang, B.Sankaran, E.Ogbonna, G.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.69 / 1.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.592, 78.592, 36.815, 90, 90, 90
R / Rfree (%) 14.2 / 17

Other elements in 8f28:

The structure of Lysozyme Structures From Single-Entity Crystallization Method Nanoac also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Lysozyme Structures From Single-Entity Crystallization Method Nanoac (pdb code 8f28). 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 Lysozyme Structures From Single-Entity Crystallization Method Nanoac, PDB code: 8f28:

Sodium binding site 1 out of 1 in 8f28

Go back to Sodium Binding Sites List in 8f28
Sodium binding site 1 out of 1 in the Lysozyme Structures From Single-Entity Crystallization Method Nanoac


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Lysozyme Structures From Single-Entity Crystallization Method Nanoac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:11.7
occ:1.00
 OG A:SER72 2.1 8.4 0.2
O A:SER60 2.3 12.2 1.0
O A:ARG73 2.4 12.0 0.8
O A:HOH384 2.4 10.7 1.0
O A:CYS64 2.4 10.4 1.0
OG A:SER72 2.5 13.2 0.8
CB A:SER72 3.0 10.6 0.2
CB A:SER72 3.3 12.6 0.8
CA A:SER72 3.4 16.1 0.2
C A:SER60 3.4 10.5 1.0
C A:ARG73 3.4 12.7 0.8
C A:CYS64 3.5 9.5 1.0
N A:ARG73 3.9 12.6 0.8
CA A:ASN65 3.9 10.0 1.0
CA A:SER60 4.0 8.8 1.0
N A:ARG73 4.0 17.2 0.2
N A:ASN65 4.2 9.4 1.0
C A:SER72 4.2 12.7 0.8
C A:SER72 4.2 17.0 0.2
CB A:SER60 4.2 8.9 1.0
CA A:ARG73 4.2 12.4 0.8
N A:ASN74 4.3 12.5 1.0
CA A:SER72 4.3 13.6 0.8
O A:ARG61 4.4 14.5 1.0
C A:ARG61 4.5 13.1 1.0
N A:ARG61 4.5 11.2 1.0
N A:CYS64 4.5 9.2 1.0
CA A:ASN74 4.6 12.0 1.0
N A:SER72 4.6 18.7 0.2
N A:ASP66 4.6 8.8 1.0
CB A:THR69 4.7 11.0 1.0
CA A:CYS64 4.7 9.6 1.0
OD1 A:ASN65 4.7 12.8 1.0
CA A:ARG61 4.7 13.7 1.0
O A:HOH418 4.7 6.6 1.0
CB A:ASN74 4.8 12.6 1.0
O A:SER72 4.8 14.5 0.8
CB A:ASN65 4.8 10.9 1.0
N A:TRP62 4.8 12.9 0.1
C A:ASN65 4.8 8.8 1.0
N A:TRP62 4.8 10.9 0.9

Reference:

R.Yang, M.Kvetny, W.Brown, E.N.Ogbonna, G.Wang. A Single-Entity Method For Actively Controlled Nucleation and High-Quality Protein Crystal Synthesis. Anal.Chem. V. 95 9462 2023.
ISSN: ESSN 1520-6882
PubMed: 37243709
DOI: 10.1021/ACS.ANALCHEM.3C00175
Page generated: Wed Oct 9 11:48:24 2024

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