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Sodium in PDB 6irj: Crystal Structure of Lysozyme By Fixed-Target Serial Femtosecond Crystallography

Enzymatic activity of Crystal Structure of Lysozyme By Fixed-Target Serial Femtosecond Crystallography

All present enzymatic activity of Crystal Structure of Lysozyme By Fixed-Target Serial Femtosecond Crystallography:
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of Lysozyme By Fixed-Target Serial Femtosecond Crystallography, PDB code: 6irj was solved by K.H.Nam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.31 / 1.65
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.220, 78.220, 37.760, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 22.9

Other elements in 6irj:

The structure of Crystal Structure of Lysozyme By Fixed-Target Serial Femtosecond Crystallography also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Lysozyme By Fixed-Target Serial Femtosecond Crystallography (pdb code 6irj). 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 Lysozyme By Fixed-Target Serial Femtosecond Crystallography, PDB code: 6irj:

Sodium binding site 1 out of 1 in 6irj

Go back to Sodium Binding Sites List in 6irj
Sodium binding site 1 out of 1 in the Crystal Structure of Lysozyme By Fixed-Target Serial Femtosecond Crystallography


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 Lysozyme By Fixed-Target Serial Femtosecond Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:35.3
occ:1.00
 O A:SER78 2.2 36.9 1.0
O A:CYS82 2.4 33.2 1.0
O A:HOH335 2.4 42.0 1.0
O A:ARG91 2.5 43.1 1.0
O A:HOH325 2.6 37.8 1.0
OG A:SER90 2.6 43.2 1.0
HB2 A:SER90 2.8 56.1 1.0
HA A:ASN83 3.0 41.7 1.0
CB A:SER90 3.2 46.7 1.0
HG A:SER90 3.3 51.9 1.0
C A:SER78 3.4 31.2 1.0
C A:CYS82 3.4 33.2 1.0
C A:ARG91 3.5 42.9 1.0
HB2 A:SER78 3.5 37.7 1.0
H A:CYS82 3.7 37.7 1.0
HB3 A:SER90 3.8 56.1 1.0
HB A:THR87 3.9 47.8 1.0
HA A:SER78 3.9 37.2 1.0
CA A:ASN83 3.9 34.8 1.0
HB2 A:ASN92 3.9 46.5 1.0
N A:ARG91 4.0 40.5 1.0
HA A:ASN92 4.0 44.8 1.0
C A:SER90 4.0 46.0 1.0
H A:ASP84 4.0 38.4 1.0
CA A:SER78 4.1 31.0 1.0
H A:ARG91 4.1 48.7 1.0
N A:ASN83 4.1 32.6 1.0
CA A:SER90 4.2 43.8 1.0
CB A:SER78 4.2 31.4 1.0
N A:CYS82 4.3 31.4 1.0
N A:ASN92 4.3 39.3 1.0
HA A:ARG79 4.3 51.5 1.0
CA A:ARG91 4.4 44.5 1.0
O A:SER90 4.5 46.1 1.0
C A:ARG79 4.5 41.8 1.0
N A:ARG79 4.5 33.3 1.0
CA A:ASN92 4.5 37.3 1.0
O A:ARG79 4.5 39.4 1.0
CA A:CYS82 4.5 32.5 1.0
HB2 A:ASN83 4.6 40.8 1.0
HG A:SER78 4.7 35.5 1.0
CA A:ARG79 4.7 42.9 1.0
CB A:ASN92 4.7 38.8 1.0
H A:TRP81 4.7 40.9 1.0
N A:ASP84 4.7 32.0 1.0
O A:HOH341 4.8 38.5 1.0
OD1 A:ASN83 4.8 43.8 1.0
CB A:THR87 4.8 39.8 1.0
HA A:SER90 4.8 52.6 1.0
N A:TRP80 4.8 35.2 1.0
HA A:ARG91 4.8 53.4 1.0
CB A:ASN83 4.8 34.0 1.0
C A:ASN83 4.9 31.4 1.0
N A:TRP81 4.9 34.1 1.0
O A:THR87 4.9 42.4 1.0
C A:TRP80 4.9 36.6 1.0
HB3 A:SER78 4.9 37.7 1.0
H A:ASN83 5.0 39.1 1.0

Reference:

D.Lee, S.Baek, J.Park, K.Lee, J.Kim, S.J.Lee, W.K.Chung, J.L.Lee, Y.Cho, K.H.Nam. Nylon Mesh-Based Sample Holder For Fixed-Target Serial Femtosecond Crystallography. Sci Rep V. 9 6971 2019.
ISSN: ESSN 2045-2322
PubMed: 31061502
DOI: 10.1038/S41598-019-43485-Z
Page generated: Tue Oct 8 09:39:30 2024

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