Sodium in PDB 8cwd: 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose

All present enzymatic activity of 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose:
3.2.1.17;

The structure of 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose, PDB code: 8cwd was solved by A.M.Wolff, M.C.Thompson, J.S.Fraser, E.Nango, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.74 / 1.48
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	77.061, 77.061, 37.223, 90, 90, 90
R / Rfree (%)	13 / 16.3

The structure of 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Sodium atom in the 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose (pdb code 8cwd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose, PDB code: 8cwd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:16.6 occ:1.00 O A:SER60 2.3 14.2 1.0 O A:CYS64 2.3 12.9 1.0 O A:ARG73 2.4 18.3 1.0 O A:HOH380 2.4 20.5 1.0 OG A:SER72 2.4 18.9 1.0 O A:HOH350 2.5 18.1 1.0 HB2 A:SER72 2.9 22.4 1.0 HA A:ASN65 2.9 17.6 1.0 CB A:SER72 3.2 18.7 1.0 C A:SER60 3.4 10.5 1.0 C A:CYS64 3.4 12.9 1.0 C A:ARG73 3.4 19.4 1.0 HB2 A:SER60 3.4 14.1 1.0 HA A:SER60 3.7 12.5 1.0 HB A:THR69 3.7 17.8 1.0 CA A:ASN65 3.8 14.7 1.0 H A:CYS64 3.8 15.8 1.0 HB2 A:ASN74 3.8 19.8 1.0 HB3 A:SER72 3.8 22.4 1.0 N A:ARG73 3.9 19.0 1.0 CA A:SER60 3.9 10.4 1.0 HA A:ASN74 3.9 20.3 1.0 H A:ARG73 3.9 22.8 1.0 H A:ASP66 4.0 17.1 1.0 N A:ASN65 4.0 14.0 1.0 C A:SER72 4.0 19.3 1.0 CB A:SER60 4.1 11.8 1.0 CA A:SER72 4.2 20.1 1.0 N A:ASN74 4.3 18.6 1.0 CA A:ARG73 4.3 21.0 1.0 N A:CYS64 4.3 13.2 1.0 CA A:ASN74 4.4 16.9 1.0 HA A:ARG61 4.4 17.5 1.0 N A:ARG61 4.5 12.6 1.0 C A:ARG61 4.5 12.8 1.0 O A:ARG61 4.5 14.9 1.0 HB2 A:ASN65 4.5 20.6 1.0 CA A:CYS64 4.5 12.2 1.0 CB A:ASN74 4.6 16.5 1.0 O A:SER72 4.6 22.2 1.0 CB A:THR69 4.6 14.9 1.0 HG21 A:THR69 4.6 18.7 1.0 N A:ASP66 4.6 14.3 1.0 CL A:CL204 4.7 32.2 1.0 OD1 A:ASN65 4.7 25.0 1.0 CA A:ARG61 4.7 14.6 1.0 CB A:ASN65 4.7 17.2 1.0 HA A:ARG73 4.7 25.1 1.0 O A:THR69 4.8 18.8 1.0 C A:ASN65 4.8 14.8 1.0 HG A:SER60 4.8 14.5 1.0 N A:TRP62 4.8 13.0 1.0 H A:TRP63 4.8 15.0 1.0 HB3 A:SER60 4.8 14.1 1.0 O A:HOH384 4.8 36.3 1.0 H A:ASN65 4.8 16.8 1.0 HA A:SER72 4.9 24.1 1.0 H A:SER72 5.0 25.2 1.0 OG A:SER60 5.0 12.1 1.0

Sodium binding site 2 out of 2 in the 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:93.2 occ:1.00 O A:HOH342 2.1 24.8 1.0 O A:HOH320 2.1 19.4 1.0 H21 A:VY5202 2.2 26.0 1.0 O3 A:VY5202 2.2 13.3 1.0 OE1 A:GLU35 2.3 13.5 1.0 O8 A:VY5202 2.5 21.7 1.0 H20 A:VY5202 2.9 15.1 1.0 H10 A:VY5202 3.0 14.1 1.0 C10 A:VY5202 3.0 11.7 1.0 C6 A:VY5202 3.1 13.6 1.0 HB3 A:GLN57 3.2 14.2 1.0 C11 A:VY5202 3.2 17.4 1.0 CD A:GLU35 3.3 11.9 1.0 H6 A:VY5202 3.4 16.3 1.0 H11 A:VY5202 3.4 20.8 1.0 O7 A:VY5202 3.4 12.6 1.0 O A:HOH349 3.5 32.1 1.0 HG3 A:GLN57 3.5 13.0 1.0 HB2 A:GLN57 3.6 14.2 1.0 OE2 A:GLU35 3.7 14.1 1.0 CB A:GLN57 3.7 11.9 1.0 HA A:GLU35 4.0 12.1 1.0 CG A:GLN57 4.0 10.9 1.0 O A:HOH310 4.1 28.9 1.0 H12 A:VY5202 4.2 20.8 1.0 OE1 A:GLN57 4.2 13.4 1.0 HB A:VAL109 4.3 15.8 1.0 HB3 A:GLU35 4.3 13.1 1.0 C7 A:VY5202 4.4 11.4 1.0 C1 A:VY5202 4.4 13.9 1.0 OD2 A:ASP52 4.5 17.2 1.0 HB3 A:ASP52 4.5 13.4 1.0 H A:ALA110 4.6 12.4 1.0 CG A:GLU35 4.6 11.7 1.0 CD A:GLN57 4.6 10.9 1.0 H7 A:VY5202 4.6 13.7 1.0 HB2 A:ALA110 4.7 14.2 1.0 CG A:ASP52 4.7 14.0 1.0 H1 A:VY5202 4.7 16.6 1.0 HB2 A:ASP52 4.7 13.4 1.0 O A:GLU35 4.7 13.7 1.0 O A:GLN57 4.8 12.1 1.0 CA A:GLU35 4.8 10.1 1.0 CB A:GLU35 4.8 10.9 1.0 HG2 A:GLN57 4.9 13.0 1.0 CB A:ASP52 4.9 11.2 1.0

A.M.Wolff, E.Nango, I.D.Young, A.S.Brewster, M.Kubo, T.Nomura, M.Sugahara, S.Owada, B.A.Barad, K.Ito, A.Bhowmick, S.Carbajo, T.Hino, J.M.Holton, D.Im, L.J.O'riordan, T.Tanaka, R.Tanaka, R.G.Sierra, F.Yumoto, K.Tono, S.Iwata, N.K.Sauter, J.S.Fraser, M.C.Thompson. Mapping Protein Dynamics at High-Resolution with Temperature-Jump X-Ray Crystallography Biorxiv 2022.
DOI: 10.1101/2022.06.10.495662