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Sodium in PDB 4ym8: Crystal Structure of Hen Egg-White Lysozyme

Enzymatic activity of Crystal Structure of Hen Egg-White Lysozyme

All present enzymatic activity of Crystal Structure of Hen Egg-White Lysozyme:
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of Hen Egg-White Lysozyme, PDB code: 4ym8 was solved by M.Sugahara, T.Nakane, M.Suzuki, E.Nango, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.00 / 2.10
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.200, 79.200, 37.900, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 17.9

Other elements in 4ym8:

The structure of Crystal Structure of Hen Egg-White Lysozyme also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Hen Egg-White Lysozyme (pdb code 4ym8). 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 Hen Egg-White Lysozyme, PDB code: 4ym8:

Sodium binding site 1 out of 1 in 4ym8

Go back to Sodium Binding Sites List in 4ym8
Sodium binding site 1 out of 1 in the Crystal Structure of Hen Egg-White Lysozyme


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 Hen Egg-White Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1001

b:44.5
occ:1.00
O A:SER60 2.3 37.9 1.0
O A:CYS64 2.4 35.7 1.0
O A:HOH1123 2.5 38.2 1.0
O A:ARG73 2.6 42.9 1.0
OG A:SER72 2.6 45.4 1.0
O A:HOH1108 2.7 46.0 1.0
CB A:SER72 3.4 44.9 1.0
C A:CYS64 3.4 37.9 1.0
C A:SER60 3.5 37.5 1.0
C A:ARG73 3.6 43.2 1.0
CA A:ASN65 4.0 39.6 1.0
N A:ARG73 4.0 43.8 1.0
C A:SER72 4.1 50.4 1.0
N A:ASN65 4.1 35.7 1.0
CA A:SER60 4.1 34.9 1.0
N A:CYS64 4.3 36.8 1.0
CA A:SER72 4.4 46.1 1.0
CB A:SER60 4.4 35.5 1.0
N A:ASN74 4.4 41.4 1.0
CA A:ARG73 4.5 44.7 1.0
C A:ARG61 4.5 42.5 1.0
O A:ARG61 4.5 40.3 1.0
CA A:CYS64 4.5 35.5 1.0
CA A:ASN74 4.5 38.6 1.0
O A:SER72 4.5 45.1 1.0
N A:ARG61 4.5 37.3 1.0
CB A:ASN74 4.7 40.5 1.0
OD1 A:ASN65 4.7 43.7 1.0
CA A:ARG61 4.8 42.5 1.0
N A:TRP62 4.8 39.4 1.0
N A:ASP66 4.8 34.5 1.0
CB A:THR69 4.8 37.7 1.0
CB A:ASN65 4.8 37.8 1.0
C A:ASN65 4.9 30.6 1.0
N A:TRP63 4.9 36.2 1.0
O A:THR69 5.0 45.1 1.0
C A:TRP62 5.0 36.9 1.0

Reference:

M.Sugahara, T.Nakane, M.Suzuki, E.Nango. Crystal Structure of Hen Egg-White Lysozyme To Be Published.
Page generated: Tue Dec 15 10:03:57 2020

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