Sodium in PDB 6qwy: Hewl Lysozyme, Crystallized From Nacl Solution

All present enzymatic activity of Hewl Lysozyme, Crystallized From Nacl Solution:
3.2.1.17;

The structure of Hewl Lysozyme, Crystallized From Nacl Solution, PDB code: 6qwy was solved by A.S.Boikova, P.V.Dorovatovskii, Y.A.Dyakova, K.B.Ilina, I.P.Kuranova, V.A.Lazarenko, M.A.Marchenkova, Y.V.Pisarevsky, V.I.Timofeev, M.V.Kovalchuk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.28 / 1.35
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	77.147, 77.147, 37.139, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 19.9

The structure of Hewl Lysozyme, Crystallized From Nacl Solution also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Hewl Lysozyme, Crystallized From Nacl Solution (pdb code 6qwy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Hewl Lysozyme, Crystallized From Nacl Solution, PDB code: 6qwy:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Hewl Lysozyme, Crystallized From Nacl Solution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hewl Lysozyme, Crystallized From Nacl Solution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:19.2 occ:1.00 O A:SER60 2.2 16.6 1.0 O A:HOH404 2.2 17.7 1.0 O A:ARG73 2.3 21.1 1.0 O A:HOH361 2.4 11.3 1.0 OG A:SER72 2.6 19.7 1.0 O A:CYS64 2.6 10.3 1.0 C A:SER60 3.3 12.7 1.0 CB A:SER72 3.3 19.5 1.0 C A:ARG73 3.4 19.2 1.0 C A:CYS64 3.7 9.2 1.0 N A:ARG73 3.8 22.0 1.0 CA A:SER60 4.0 12.0 1.0 CA A:ASN65 4.0 9.5 1.0 C A:SER72 4.1 25.6 1.0 CA A:ARG73 4.2 20.5 1.0 CB A:SER60 4.2 10.2 1.0 N A:ASN65 4.3 8.9 1.0 N A:ASN74 4.3 15.1 1.0 CA A:SER72 4.3 19.8 1.0 N A:ARG61 4.4 14.4 1.0 C A:ARG61 4.5 16.5 1.0 CB A:THR69 4.6 11.6 1.0 O A:ARG61 4.6 19.8 1.0 OD1 A:ASN65 4.6 13.4 1.0 N A:CYS64 4.6 9.6 1.0 CL A:CL206 4.6 18.7 1.0 CA A:ASN74 4.6 13.7 1.0 N A:ASP66 4.6 8.7 1.0 CA A:ARG61 4.7 17.5 1.0 O A:SER72 4.7 31.0 1.0 N A:TRP62 4.8 13.9 1.0 CA A:CYS64 4.8 9.8 1.0 CB A:ASN74 4.8 14.6 1.0 O A:THR69 4.8 15.6 1.0 CB A:ASN65 4.9 11.3 1.0 C A:ASN65 4.9 8.7 1.0 CG2 A:THR69 5.0 13.0 1.0 OG A:SER60 5.0 9.6 1.0

Sodium binding site 2 out of 3 in the Hewl Lysozyme, Crystallized From Nacl Solution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hewl Lysozyme, Crystallized From Nacl Solution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:29.3 occ:1.00 O A:HOH374 1.8 20.8 1.0 O A:LEU84 2.4 13.8 1.0 O A:HOH306 2.5 23.8 1.0 OG1 A:THR40 2.6 12.1 1.0 N A:SER86 3.3 15.5 1.0 C A:SER85 3.3 15.0 0.5 N A:LYS1 3.3 12.9 1.0 C A:SER85 3.3 14.8 0.5 C A:LEU84 3.5 12.9 1.0 CG A:GLN41 3.6 10.0 1.0 O A:SER85 3.7 14.8 0.5 O A:SER85 3.7 14.5 0.5 CB A:THR40 3.7 9.9 1.0 CA A:SER85 3.8 15.5 0.5 OG A:SER86 3.8 27.6 1.0 CA A:SER85 3.8 15.1 0.5 CA A:SER86 3.9 16.3 1.0 N A:SER85 4.1 13.9 0.5 N A:SER85 4.1 13.9 0.5 O A:HOH382 4.1 26.9 1.0 CD A:GLN41 4.3 10.2 1.0 CB A:SER86 4.4 20.5 1.0 C A:THR40 4.5 8.3 1.0 N A:GLN41 4.6 7.8 1.0 CA A:LYS1 4.6 13.5 1.0 CG2 A:THR40 4.6 9.8 1.0 CB A:LYS1 4.7 15.6 1.0 OE1 A:GLN41 4.7 12.3 1.0 CA A:LEU84 4.8 11.5 1.0 CA A:THR40 4.8 8.9 1.0 CB A:GLN41 4.8 8.5 1.0 O A:THR40 4.9 8.9 1.0 NE2 A:GLN41 4.9 10.9 1.0 CA A:GLN41 4.9 8.1 1.0

Sodium binding site 3 out of 3 in the Hewl Lysozyme, Crystallized From Nacl Solution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Hewl Lysozyme, Crystallized From Nacl Solution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:2.7 occ:1.00 OD2 A:ASP52 2.0 9.5 1.0 O A:HOH352 2.0 12.1 1.0 O A:HOH304 2.1 13.4 1.0 O A:HOH341 2.1 11.5 1.0 O A:HOH315 2.1 13.6 1.0 O A:HOH427 2.2 13.4 1.0 CG A:ASP52 3.0 8.1 1.0 OD1 A:ASP52 3.4 8.5 1.0 O A:HOH302 3.9 10.8 1.0 O A:HOH403 3.9 26.8 1.0 O A:HOH441 4.0 21.6 1.0 O A:HOH353 4.0 11.1 1.0 O A:GLN57 4.1 8.7 1.0 ND2 A:ASN46 4.1 9.6 1.0 O A:HOH414 4.2 28.3 1.0 O A:HOH310 4.2 22.2 1.0 CB A:ASP52 4.3 8.0 1.0 OE1 A:GLU35 4.3 9.6 1.0 O A:HOH351 4.5 19.8 1.0 O A:HOH422 4.6 14.7 1.0 CB A:GLN57 4.6 7.7 1.0 CG A:ASN46 4.9 10.0 1.0 OD1 A:ASN46 4.9 11.6 1.0

A.S.Boikova, P.V.Dorovatovskii, Y.A.Dyakova, K.B.Ilina, I.P.Kuranova, V.A.Lazarenko, M.A.Marchenkova, Y.V.Pisarevsky, V.I.Timofeev, M.V.Kovalchuk. Hewl Lysozyme, Crystallized From Different Chlorides To Be Published.