Sodium in PDB 7cjz: Room Temperature Structure of Lysozyme Delivered in Lard By Serial Millisecond Crystallography

All present enzymatic activity of Room Temperature Structure of Lysozyme Delivered in Lard By Serial Millisecond Crystallography:
3.2.1.17;

The structure of Room Temperature Structure of Lysozyme Delivered in Lard By Serial Millisecond Crystallography, PDB code: 7cjz 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)	56.18 / 1.75
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.450, 79.450, 38.470, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 18.7

The structure of Room Temperature Structure of Lysozyme Delivered in Lard By Serial Millisecond Crystallography also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Room Temperature Structure of Lysozyme Delivered in Lard By Serial Millisecond Crystallography (pdb code 7cjz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Room Temperature Structure of Lysozyme Delivered in Lard By Serial Millisecond Crystallography, PDB code: 7cjz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Room Temperature Structure of Lysozyme Delivered in Lard By Serial Millisecond Crystallography


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Room Temperature Structure of Lysozyme Delivered in Lard By Serial Millisecond Crystallography within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:54.4 occ:1.00 H A:ILE106 2.4 41.0 1.0 HG12 A:ILE106 2.7 42.5 1.0 HA A:ASP105 2.9 42.0 1.0 N A:ILE106 3.2 34.2 1.0 HE1 A:HIS33 3.5 54.1 1.0 HG22 A:ILE106 3.6 39.5 1.0 CG1 A:ILE106 3.6 35.3 1.0 O A:HOH318 3.6 54.6 1.0 HZ A:PHE21 3.6 44.8 1.0 HB1 A:ALA29 3.8 43.1 1.0 CA A:ASP105 3.8 35.0 1.0 OD1 A:ASP105 3.9 42.1 1.0 O A:SER104 4.0 41.9 1.0 HG13 A:ILE106 4.0 42.5 1.0 C A:ASP105 4.0 35.9 1.0 HH11 A:ARG32 4.2 67.6 1.0 CB A:ILE106 4.2 33.9 1.0 CA A:ILE106 4.3 31.9 1.0 CE1 A:HIS33 4.3 45.1 1.0 CG2 A:ILE106 4.3 32.9 1.0 HB2 A:ALA29 4.4 43.1 1.0 CZ A:PHE21 4.5 37.3 1.0 CB A:ALA29 4.5 35.9 1.0 H A:THR107 4.5 37.0 1.0 HD11 A:ILE106 4.5 43.8 1.0 CD1 A:ILE106 4.5 36.5 1.0 HD12 A:ILE106 4.6 43.8 1.0 CG A:ASP105 4.6 45.6 1.0 HG1 A:THR107 4.6 47.0 1.0 HE2 A:PHE21 4.6 41.2 1.0 CB A:ASP105 4.6 34.5 1.0 N A:ASP105 4.8 34.7 1.0 HB2 A:ASP105 4.8 41.4 1.0 HG23 A:ILE106 4.8 39.5 1.0 C A:SER104 4.8 35.2 1.0 NH1 A:ARG32 4.9 56.3 1.0 HD1 A:HIS33 4.9 52.8 1.0 HH12 A:ARG32 4.9 67.6 1.0 N A:THR107 4.9 30.8 1.0 ND1 A:HIS33 5.0 43.9 1.0 CE2 A:PHE21 5.0 34.3 1.0 HA A:ILE106 5.0 38.3 1.0

Sodium binding site 2 out of 2 in the Room Temperature Structure of Lysozyme Delivered in Lard By Serial Millisecond Crystallography


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Room Temperature Structure of Lysozyme Delivered in Lard By Serial Millisecond Crystallography within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:33.8 occ:1.00 HG A:SER90 2.2 47.5 1.0 O A:ARG91 2.4 38.9 1.0 O A:SER78 2.4 32.2 1.0 O A:CYS82 2.4 27.9 1.0 O A:HOH334 2.5 41.9 1.0 O A:HOH339 2.6 30.3 0.8 OG A:SER90 2.6 39.5 1.0 HA A:ASN83 3.0 33.8 1.0 HB2 A:SER90 3.0 46.0 1.0 CB A:SER90 3.3 38.3 1.0 C A:CYS82 3.5 26.7 1.0 C A:ARG91 3.5 39.2 1.0 C A:SER78 3.6 28.0 1.0 H A:CYS82 3.7 30.8 1.0 HB2 A:SER78 3.8 29.8 1.0 CA A:ASN83 3.9 28.1 1.0 HB A:THR87 3.9 37.1 1.0 HB2 A:ASN92 3.9 40.9 1.0 HA A:SER78 3.9 31.5 1.0 HB3 A:SER90 4.0 46.0 1.0 HA A:ASN92 4.0 40.7 1.0 N A:ARG91 4.0 36.6 1.0 N A:ASN83 4.1 27.5 1.0 H A:ASP84 4.1 32.8 1.0 C A:SER90 4.1 44.1 1.0 H A:ARG91 4.2 43.9 1.0 CA A:SER78 4.2 26.2 1.0 N A:CYS82 4.3 25.7 1.0 CA A:SER90 4.4 41.3 1.0 N A:ASN92 4.4 37.0 1.0 CA A:ARG91 4.4 37.8 1.0 CB A:SER78 4.4 24.8 1.0 HA A:ARG79 4.5 41.6 1.0 HB2 A:ASN83 4.5 36.1 1.0 CA A:ASN92 4.5 33.9 1.0 C A:ARG79 4.5 40.4 1.0 CA A:CYS82 4.6 25.6 1.0 O A:ARG79 4.6 37.5 1.0 N A:ARG79 4.6 28.1 1.0 O A:SER90 4.6 41.5 1.0 OD1 A:ASN83 4.6 39.6 1.0 CB A:ASN92 4.7 34.0 1.0 CB A:ASN83 4.7 30.1 1.0 N A:ASP84 4.7 27.3 1.0 H A:TRP81 4.8 33.8 1.0 CA A:ARG79 4.8 34.7 1.0 HG23 A:THR87 4.8 36.5 1.0 HA A:ARG91 4.8 45.4 1.0 N A:TRP80 4.8 30.8 1.0 CB A:THR87 4.8 30.9 1.0 C A:ASN83 4.9 29.7 1.0 H A:ASN83 4.9 33.0 1.0 O A:HOH357 4.9 34.8 1.0 HA A:SER90 5.0 49.6 1.0 N A:TRP81 5.0 28.1 1.0

K.H.Nam, K.H.Nam. N/A N/A.
ISSN: ESSN 1422-0067
PubMed: 32825186
DOI: 10.3390/IJMS21175977