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Sodium in PDB 4yop: 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: 4yop 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 (%) 15.7 / 19.1

Other elements in 4yop:

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 4yop). 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: 4yop:

Sodium binding site 1 out of 1 in 4yop

Go back to Sodium Binding Sites List in 4yop
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:45.7
occ:1.00
O A:SER60 2.3 39.7 1.0
O A:CYS64 2.4 37.3 1.0
OG A:SER72 2.4 44.8 1.0
O A:HOH1122 2.5 37.5 1.0
O A:ARG73 2.6 44.1 1.0
O A:HOH1120 2.6 45.8 1.0
CB A:SER72 3.2 46.3 1.0
C A:SER60 3.4 36.6 1.0
C A:CYS64 3.5 38.3 1.0
C A:ARG73 3.6 44.9 1.0
N A:ARG73 3.9 44.9 1.0
CA A:ASN65 4.0 39.1 1.0
C A:SER72 4.1 49.2 1.0
CA A:SER60 4.1 35.2 1.0
N A:ASN65 4.2 35.8 1.0
CA A:SER72 4.3 46.3 1.0
CB A:SER60 4.3 35.5 1.0
CA A:ARG73 4.4 46.0 1.0
N A:CYS64 4.4 36.1 1.0
O A:ARG61 4.5 41.6 1.0
C A:ARG61 4.5 43.6 1.0
N A:ASN74 4.5 40.8 1.0
N A:ARG61 4.5 36.4 1.0
O A:SER72 4.6 46.6 1.0
CA A:CYS64 4.6 37.5 1.0
CA A:ASN74 4.6 41.7 1.0
CB A:THR69 4.7 40.7 1.0
OD1 A:ASN65 4.8 43.9 1.0
CA A:ARG61 4.8 42.9 1.0
N A:TRP62 4.8 41.1 1.0
N A:ASP66 4.8 35.5 1.0
CB A:ASN74 4.8 41.6 1.0
O A:THR69 4.9 46.3 1.0
CB A:ASN65 4.9 38.3 1.0
O A:HOH1137 4.9 39.7 1.0
C A:ASN65 4.9 32.5 1.0
N A:TRP63 5.0 37.8 1.0

Reference:

T.Nakane, C.Song, M.Suzuki, E.Nango, J.Kobayashi, T.Masuda, S.Inoue, E.Mizohata, T.Nakatsu, T.Tanaka, R.Tanaka, T.Shimamura, K.Tono, Y.Joti, T.Kameshima, T.Hatsui, M.Yabashi, O.Nureki, S.Iwata, M.Sugahara. Native Sulfur/Chlorine Sad Phasing For Serial Femtosecond Crystallography Acta Crystallogr.,Sect.D V. 71 2519 2015.
ISSN: ESSN 1399-0047
PubMed: 26627659
DOI: 10.1107/S139900471501857X
Page generated: Tue Dec 15 10:04:20 2020

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