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Sodium in PDB 5wrb: 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: 5wrb was solved by M.Sugahara, M.Suzuki, T.Masuda, S.Inoue, E.Nango, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.14 / 2.01
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.600, 79.600, 38.200, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 20.2

Other elements in 5wrb:

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 5wrb). 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: 5wrb:

Sodium binding site 1 out of 1 in 5wrb

Go back to Sodium Binding Sites List in 5wrb
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:37.1
occ:1.00
O A:SER60 2.3 39.0 1.0
O A:CYS64 2.3 32.2 1.0
O A:HOH1125 2.5 37.0 1.0
OG A:SER72 2.6 41.2 1.0
O A:HOH1129 2.6 42.9 1.0
O A:ARG73 2.7 38.6 1.0
CB A:SER72 3.3 40.6 1.0
C A:CYS64 3.4 33.4 1.0
C A:SER60 3.4 34.9 1.0
C A:ARG73 3.7 43.8 1.0
CA A:ASN65 4.0 38.4 1.0
CA A:SER60 4.0 34.2 1.0
N A:ARG73 4.1 40.6 1.0
N A:ASN65 4.1 35.5 1.0
C A:SER72 4.2 43.4 1.0
CB A:SER60 4.3 32.7 1.0
N A:CYS64 4.3 34.2 1.0
CA A:SER72 4.4 43.0 1.0
CA A:CYS64 4.5 32.1 1.0
CA A:ARG73 4.5 43.3 1.0
N A:ARG61 4.5 34.6 1.0
C A:ARG61 4.5 40.7 1.0
O A:ARG61 4.5 39.7 1.0
N A:ASN74 4.6 38.6 1.0
CA A:ASN74 4.6 39.0 1.0
CB A:THR69 4.7 36.6 1.0
N A:ASP66 4.8 32.3 1.0
O A:SER72 4.8 41.8 1.0
CA A:ARG61 4.8 40.3 1.0
OD1 A:ASN65 4.8 42.1 1.0
CB A:ASN74 4.8 37.9 1.0
N A:TRP62 4.9 35.8 1.0
CB A:ASN65 4.9 35.2 1.0
O A:HOH1142 4.9 36.5 1.0
C A:ASN65 4.9 33.0 1.0
N A:TRP63 5.0 34.9 1.0
OG A:SER60 5.0 33.9 1.0
O A:THR69 5.0 43.0 1.0

Reference:

M.Sugahara, T.Nakane, T.Masuda, M.Suzuki, S.Inoue, C.Song, R.Tanaka, T.Nakatsu, E.Mizohata, F.Yumoto, K.Tono, Y.Joti, T.Kameshima, T.Hatsui, M.Yabashi, O.Nureki, K.Numata, E.Nango, S.Iwata. Hydroxyethyl Cellulose Matrix Applied to Serial Crystallography Sci Rep V. 7 703 2017.
ISSN: ESSN 2045-2322
PubMed: 28386083
DOI: 10.1038/S41598-017-00761-0
Page generated: Tue Dec 15 11:48:07 2020

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