Sodium in PDB 8cl5: Lysozyme in Matrix of Lipidic Cubic Phase of Monoolein (Lcp)

The structure of Lysozyme in Matrix of Lipidic Cubic Phase of Monoolein (Lcp), PDB code: 8cl5 was solved by Q.Bertrand, M.W.Kepa, T.Weinert, M.Wranik, J.Standfuss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.47 / 1.31
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	77.92, 77.92, 37.64, 90, 90, 90
R / Rfree (%)	12.5 / 14.8

The structure of Lysozyme in Matrix of Lipidic Cubic Phase of Monoolein (Lcp) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Lysozyme in Matrix of Lipidic Cubic Phase of Monoolein (Lcp) (pdb code 8cl5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Lysozyme in Matrix of Lipidic Cubic Phase of Monoolein (Lcp), PDB code: 8cl5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Lysozyme in Matrix of Lipidic Cubic Phase of Monoolein (Lcp)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Lysozyme in Matrix of Lipidic Cubic Phase of Monoolein (Lcp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:23.4 occ:1.00 N A:LEU56 2.9 14.7 1.0 O A:TYR53 2.9 13.8 1.0 OG A:SER91 2.9 17.9 1.0 N A:ILE55 3.3 14.2 1.0 C A:GLY54 3.4 13.7 1.0 CA A:GLY54 3.5 14.0 1.0 N A:GLN57 3.5 13.7 1.0 CA A:LEU56 3.5 15.2 1.0 CB A:SER91 3.6 16.6 1.0 CB A:LEU56 3.7 16.2 1.0 C A:LEU56 3.7 15.3 1.0 CD1 A:ILE58 3.8 20.8 1.0 CG1 A:ILE58 3.8 18.0 1.0 C A:TYR53 3.9 12.5 1.0 O A:HOH305 3.9 35.4 1.0 C A:ILE55 3.9 14.4 1.0 O A:GLY54 4.0 13.8 1.0 N A:ILE58 4.1 13.5 1.0 CA A:ILE55 4.1 15.1 1.0 CG2 A:ILE55 4.1 22.0 1.0 N A:GLY54 4.2 13.2 1.0 O A:LEU83 4.2 20.0 1.0 CB A:ILE58 4.3 15.6 1.0 CB A:LEU83 4.3 18.5 1.0 CA A:SER91 4.4 16.8 1.0 O A:LEU56 4.6 17.1 1.0 CA A:GLN57 4.6 13.1 1.0 CD2 A:LEU83 4.7 22.5 1.0 CG A:LEU56 4.7 19.4 1.0 CB A:ILE55 4.7 21.1 1.0 C A:GLN57 4.8 14.2 1.0 CA A:ILE58 4.8 13.8 1.0 CG A:LEU83 4.9 19.7 1.0 CD1 A:LEU83 4.9 20.5 1.0

Sodium binding site 2 out of 2 in the Lysozyme in Matrix of Lipidic Cubic Phase of Monoolein (Lcp)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Lysozyme in Matrix of Lipidic Cubic Phase of Monoolein (Lcp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:23.8 occ:1.00 NE A:ARG68 2.5 22.4 0.3 OG1 A:THR51 2.6 15.7 1.0 OD2 A:ASP66 2.7 15.7 1.0 O A:GLY49 2.8 23.8 1.0 NE A:ARG68 2.9 15.6 0.7 OG1 A:THR69 3.1 17.5 1.0 CD A:ARG68 3.3 21.0 0.3 N A:THR51 3.4 14.5 1.0 CZ A:ARG68 3.4 22.9 0.3 CG A:ARG68 3.4 16.7 0.7 NH2 A:ARG68 3.4 22.2 0.3 CB A:THR51 3.4 14.1 1.0 NE A:ARG45 3.5 24.3 0.5 C A:SER50 3.5 15.9 1.0 O A:ARG68 3.6 18.1 0.3 CG A:ASP66 3.6 15.8 1.0 CA A:SER50 3.6 17.1 1.0 CG A:ARG68 3.7 20.5 0.3 CD A:ARG68 3.7 16.6 0.7 OG A:SER60 3.8 15.3 1.0 NH2 A:ARG68 3.8 15.4 0.7 OD1 A:ASP66 3.8 15.8 1.0 CZ A:ARG68 3.8 14.8 0.7 C A:GLY49 3.9 22.0 1.0 NH2 A:ARG45 3.9 26.4 0.5 NE A:ARG45 3.9 27.0 0.5 CZ A:ARG45 4.0 25.6 0.5 CA A:THR51 4.0 13.1 1.0 O A:SER50 4.1 18.1 1.0 C A:ARG68 4.2 18.8 0.3 N A:SER50 4.3 18.9 1.0 CD A:ARG45 4.3 22.6 0.5 OH A:TYR53 4.3 15.2 1.0 NH2 A:ARG45 4.3 28.4 0.5 CB A:THR69 4.4 18.1 1.0 CZ A:ARG45 4.4 27.8 0.5 O A:ARG68 4.5 19.8 0.7 CB A:ARG68 4.5 19.9 0.3 C A:ARG68 4.5 18.5 0.7 CD A:ARG45 4.6 25.3 0.5 NH1 A:ARG68 4.6 24.1 0.3 N A:THR69 4.7 19.2 1.0 CG2 A:THR51 4.7 15.3 1.0 CB A:SER60 4.7 15.6 1.0 CB A:ARG68 4.7 17.7 0.7 CA A:THR69 4.8 19.1 1.0 CG2 A:THR69 4.9 18.4 1.0 CA A:ARG68 4.9 19.0 0.3 CB A:ASP66 4.9 15.4 1.0 CB A:SER50 4.9 18.2 1.0 NH1 A:ARG45 5.0 26.6 0.5

M.Wranik, M.W.Kepa, E.V.Beale, D.James, Q.Bertrand, T.Weinert, A.Furrer, H.Glover, D.Gashi, M.Carrillo, Y.Kondo, R.T.Stipp, G.Khusainov, K.Nass, D.Ozerov, C.Cirelli, P.J.M.Johnson, F.Dworkowski, J.H.Beale, S.Stubbs, T.Zamofing, M.Schneider, K.Krauskopf, L.Gao, O.Thorn-Seshold, C.Bostedt, C.Bacellar, M.O.Steinmetz, C.Milne, J.Standfuss. A Multi-Reservoir Extruder For Time-Resolved Serial Protein Crystallography and Compound Screening at X-Ray Free-Electron Lasers. Nat Commun V. 14 7956 2023.
ISSN: ESSN 2041-1723
PubMed: 38042952
DOI: 10.1038/S41467-023-43523-5