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Sodium in PDB 6p4d: Hen Egg Lysozyme (Hel) Containing Three Point Mutations (HEL3X): R21Q, R73E, and D101R

Enzymatic activity of Hen Egg Lysozyme (Hel) Containing Three Point Mutations (HEL3X): R21Q, R73E, and D101R

All present enzymatic activity of Hen Egg Lysozyme (Hel) Containing Three Point Mutations (HEL3X): R21Q, R73E, and D101R:
3.2.1.17;

Protein crystallography data

The structure of Hen Egg Lysozyme (Hel) Containing Three Point Mutations (HEL3X): R21Q, R73E, and D101R, PDB code: 6p4d was solved by D.B.Langley, D.Christ, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.77 / 1.05
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.550, 77.550, 37.770, 90.00, 90.00, 90.00
R / Rfree (%) 12.2 / 14.5

Other elements in 6p4d:

The structure of Hen Egg Lysozyme (Hel) Containing Three Point Mutations (HEL3X): R21Q, R73E, and D101R also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Hen Egg Lysozyme (Hel) Containing Three Point Mutations (HEL3X): R21Q, R73E, and D101R (pdb code 6p4d). 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 Lysozyme (Hel) Containing Three Point Mutations (HEL3X): R21Q, R73E, and D101R, PDB code: 6p4d:

Sodium binding site 1 out of 1 in 6p4d

Go back to Sodium Binding Sites List in 6p4d
Sodium binding site 1 out of 1 in the Hen Egg Lysozyme (Hel) Containing Three Point Mutations (HEL3X): R21Q, R73E, and D101R


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hen Egg Lysozyme (Hel) Containing Three Point Mutations (HEL3X): R21Q, R73E, and D101R within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:17.8
occ:0.50
 O A:HOH305 1.5 27.6 1.0
OG A:SER72 1.8 24.1 0.5
O A:SER60 2.2 14.8 1.0
O A:HOH389 2.5 12.3 1.0
CB A:SER72 2.5 20.4 0.5
O A:GLU73 2.5 18.6 0.5
CB A:SER72 2.6 18.7 0.5
O A:CYS64 2.6 11.4 1.0
O A:HOH309 2.8 28.5 1.0
OG A:SER72 3.1 26.5 0.5
CA A:SER72 3.2 16.9 0.5
C A:SER60 3.3 11.2 1.0
CA A:SER72 3.6 24.7 0.5
C A:GLU73 3.6 18.2 0.5
C A:CYS64 3.6 9.8 1.0
N A:GLU73 3.7 13.0 0.5
O A:ARG61 3.7 22.8 1.0
C A:SER72 3.8 16.1 0.5
C A:SER72 3.8 23.2 0.5
N A:ASN74 3.9 10.4 0.5
N A:GLU73 4.0 19.3 0.5
CA A:ASN65 4.0 10.4 1.0
C A:ARG61 4.1 13.6 1.0
CA A:SER60 4.1 10.2 1.0
N A:ASN65 4.2 9.9 1.0
CA A:ARG61 4.3 13.5 1.0
N A:ARG61 4.3 11.2 1.0
CA A:ASN74 4.4 11.0 0.5
N A:ASN74 4.4 17.3 0.5
O A:SER72 4.5 25.8 0.5
CA A:GLU73 4.5 20.0 0.5
O A:HOH387 4.5 19.6 1.0
CB A:SER60 4.5 10.0 1.0
N A:CYS64 4.5 10.5 1.0
N A:SER72 4.6 17.5 0.5
CA A:ASN74 4.6 14.1 0.5
CB A:ASN74 4.6 11.9 0.5
CB A:THR69 4.7 11.9 1.0
CA A:CYS64 4.8 10.2 1.0
C A:GLU73 4.8 12.4 0.5
N A:TRP62 4.8 11.8 0.5
N A:TRP62 4.8 11.1 0.5
N A:ASP66 4.8 9.4 1.0
CB A:ASN74 4.8 14.1 0.5
OD1 A:ASN65 4.8 16.6 1.0
CA A:GLU73 4.9 13.2 0.5
N A:SER72 4.9 22.8 0.5
CB A:ASN65 4.9 12.3 1.0
O A:SER72 4.9 17.8 0.5
C A:ASN65 5.0 9.2 1.0
O A:THR69 5.0 16.6 1.0
N A:TRP63 5.0 9.6 1.0

Reference:

D.B.Langley, D.Christ. Resolution of Self-Reactivity Upon Vaccination with A Conformationally Flexible Antigen. To Be Published.
Page generated: Tue Oct 8 12:40:29 2024

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