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Sodium in PDB 5apf: Hen Egg White Lysozyme Reference Dataset Even Frames

Enzymatic activity of Hen Egg White Lysozyme Reference Dataset Even Frames

All present enzymatic activity of Hen Egg White Lysozyme Reference Dataset Even Frames:
3.2.1.17;

Protein crystallography data

The structure of Hen Egg White Lysozyme Reference Dataset Even Frames, PDB code: 5apf was solved by I.Lundholm, H.Rodilla, W.Y.Wahlgren, A.Duelli, G.Bourenkov, J.Vukusic, R.Friedman, J.Stake, T.Schneider, G.Katona, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.09 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.240, 79.240, 37.500, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 19.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Hen Egg White Lysozyme Reference Dataset Even Frames (pdb code 5apf). 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 Hen Egg White Lysozyme Reference Dataset Even Frames, PDB code: 5apf:

Sodium binding site 1 out of 1 in 5apf

Go back to Sodium Binding Sites List in 5apf
Sodium binding site 1 out of 1 in the Hen Egg White Lysozyme Reference Dataset Even Frames


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hen Egg White Lysozyme Reference Dataset Even Frames within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1130

b:29.4
occ:1.00
O A:SER60 2.3 25.1 1.0
O A:HOH2017 2.4 35.1 1.0
O A:CYS64 2.4 22.8 1.0
O A:ARG73 2.5 35.3 1.0
O A:HOH2016 2.5 27.8 1.0
OG A:SER72 2.6 36.0 1.0
CB A:SER72 3.3 35.9 1.0
C A:CYS64 3.4 22.4 1.0
C A:SER60 3.5 22.6 1.0
C A:ARG73 3.5 34.9 1.0
CA A:ASN65 3.8 25.2 1.0
N A:ARG73 4.0 32.4 1.0
N A:ASN65 4.0 22.5 1.0
C A:SER72 4.1 38.2 1.0
CA A:SER60 4.1 21.2 1.0
CA A:SER72 4.3 36.4 1.0
N A:ASN74 4.3 30.2 1.0
CB A:SER60 4.3 23.8 1.0
CA A:ARG73 4.4 33.4 1.0
N A:CYS64 4.4 22.0 1.0
O A:ARG61 4.5 31.3 1.0
CA A:ASN74 4.5 27.7 1.0
C A:ARG61 4.5 28.4 1.0
N A:ARG61 4.6 23.7 1.0
CA A:CYS64 4.6 22.1 1.0
OD1 A:ASN65 4.6 36.3 1.0
O A:HOH2018 4.6 28.5 1.0
O A:SER72 4.6 36.6 1.0
CB A:ASN65 4.7 26.6 1.0
N A:ASP66 4.7 21.7 1.0
CB A:THR69 4.7 24.6 1.0
CB A:ASN74 4.8 29.7 1.0
CA A:ARG61 4.8 28.8 1.0
C A:ASN65 4.8 21.7 1.0
N A:TRP62 4.9 26.1 1.0
O A:THR69 5.0 29.3 1.0

Reference:

I.Lundholm, H.Rodilla, W.Y.Wahlgren, A.Duelli, G.Bourenkov, J.Vukusic, R.Friedman, J.Stake, T.Schneider, G.Katona. Terahertz Radiation Induces Non-Thermal Structural Changes Associated with Frohlich Condensation in A Protein Crystal Struct.Dyn. V. 2 54702 2015.
ISSN: ESSN 2329-7778
PubMed: 26798828
DOI: 10.1063/1.4931825
Page generated: Tue Dec 15 10:23:38 2020

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