Sodium in PDB 8c6o: Crystal Structure of H64F Obelin Mutant From Obelia Longissima at 2.2 Angstrom Resolution

The structure of Crystal Structure of H64F Obelin Mutant From Obelia Longissima at 2.2 Angstrom Resolution, PDB code: 8c6o was solved by P.V.Natashin, L.P.Burakova, M.I.Kovaleva, M.B.Schevtsov, D.A.Dmitrieva, E.V.Eremeeva, S.V.Markova, A.V.Mishin, V.I.Borshchevskiy, E.S.Vysotski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.76 / 2.20
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	77.51, 77.51, 180.22, 90, 90, 120
R / Rfree (%)	16.7 / 19.9

The binding sites of Sodium atom in the Crystal Structure of H64F Obelin Mutant From Obelia Longissima at 2.2 Angstrom Resolution (pdb code 8c6o). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of H64F Obelin Mutant From Obelia Longissima at 2.2 Angstrom Resolution, PDB code: 8c6o:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of H64F Obelin Mutant From Obelia Longissima at 2.2 Angstrom Resolution


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 H64F Obelin Mutant From Obelia Longissima at 2.2 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1102 b:45.3 occ:1.00 O A:LYS36 2.0 35.8 1.0 OD1 A:ASP30 2.3 41.1 1.0 OD1 A:ASN32 2.3 55.7 1.0 O A:HOH1226 2.3 48.7 1.0 OD1 A:ASN34 2.4 44.2 1.0 O A:HOH1251 2.6 45.3 1.0 H A:LYS36 3.0 45.4 1.0 HA A:ASP30 3.1 47.8 1.0 CG A:ASN34 3.2 46.1 1.0 H A:ASN34 3.2 52.9 1.0 C A:LYS36 3.2 35.7 1.0 CG A:ASP30 3.3 41.9 1.0 CG A:ASN32 3.4 55.3 1.0 HD21 A:ASN32 3.4 63.1 1.0 HD21 A:ASN34 3.5 59.2 1.0 HG22 A:ILE37 3.7 46.1 1.0 ND2 A:ASN34 3.7 49.3 1.0 N A:LYS36 3.7 37.8 1.0 H A:ASN32 3.8 59.1 1.0 ND2 A:ASN32 3.8 52.6 1.0 CA A:ASP30 3.8 39.8 1.0 HA A:ILE37 3.8 53.1 1.0 HB2 A:LYS36 3.9 48.0 1.0 CB A:ASP30 3.9 43.1 1.0 CA A:LYS36 4.0 36.0 1.0 HB2 A:ASP30 4.0 51.8 1.0 N A:ASN34 4.0 44.1 1.0 H A:GLY33 4.2 59.2 1.0 OD2 A:ASP30 4.2 40.5 1.0 H A:GLY35 4.2 52.2 1.0 C A:ASP30 4.2 43.6 1.0 H A:ILE31 4.2 51.4 1.0 N A:ILE37 4.3 33.6 1.0 CB A:ASN34 4.3 44.0 1.0 OE2 A:GLU41 4.4 67.1 1.0 HD22 A:ASN34 4.4 59.2 1.0 N A:ASN32 4.4 49.2 1.0 N A:GLY35 4.4 43.5 1.0 N A:ILE31 4.4 42.8 1.0 CB A:LYS36 4.5 40.0 1.0 OE1 A:GLU41 4.5 52.5 1.0 CA A:ILE37 4.5 44.2 1.0 CG2 A:ILE37 4.5 38.4 1.0 CA A:ASN34 4.5 45.1 1.0 N A:GLY33 4.5 49.3 1.0 O A:HOH1203 4.5 53.4 1.0 HB3 A:ASN34 4.6 52.8 1.0 C A:ASN34 4.6 41.7 1.0 HG23 A:ILE37 4.6 46.1 1.0 HD22 A:ASN32 4.6 63.1 1.0 CB A:ASN32 4.7 49.1 1.0 HA A:LYS36 4.8 43.2 1.0 HB3 A:ASP30 4.9 51.8 1.0 CD A:GLU41 4.9 70.7 1.0 O A:ASP30 4.9 42.6 1.0 CA A:ASN32 4.9 52.0 1.0 C A:GLY35 4.9 33.9 1.0 C A:ASN32 4.9 51.1 1.0 HB3 A:LYS36 4.9 48.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of H64F Obelin Mutant From Obelia Longissima at 2.2 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of H64F Obelin Mutant From Obelia Longissima at 2.2 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1102 b:45.0 occ:1.00 OD1 B:ASN34 2.1 54.0 1.0 O B:LYS36 2.2 40.1 1.0 OD1 B:ASN32 2.3 56.3 1.0 OD1 B:ASP30 2.3 46.0 1.0 O B:HOH1278 2.8 45.4 1.0 CG B:ASN34 3.1 53.5 1.0 H B:LYS36 3.2 47.8 1.0 H B:ASN34 3.2 64.5 1.0 CG B:ASN32 3.3 54.0 1.0 HD21 B:ASN32 3.3 67.4 1.0 HD21 B:ASN34 3.3 67.2 1.0 C B:LYS36 3.4 36.3 1.0 CG B:ASP30 3.5 50.2 1.0 HA B:ASP30 3.5 52.1 1.0 ND2 B:ASN34 3.6 56.0 1.0 ND2 B:ASN32 3.7 56.2 1.0 H B:ASN32 3.7 65.0 1.0 H B:GLY33 3.8 61.2 1.0 HB2 B:LYS36 3.9 51.5 1.0 N B:LYS36 3.9 39.8 1.0 HA B:ILE37 4.0 46.4 1.0 N B:ASN34 4.0 53.7 1.0 HG22 B:ILE37 4.1 44.2 1.0 CA B:LYS36 4.1 43.8 1.0 CA B:ASP30 4.2 43.4 1.0 OD2 B:ASP30 4.3 45.5 1.0 CB B:ASN34 4.3 50.4 1.0 CB B:ASP30 4.3 46.6 1.0 H B:ILE31 4.3 60.4 1.0 H B:GLY35 4.3 55.2 1.0 N B:GLY33 4.4 51.0 1.0 HD22 B:ASN34 4.4 67.2 1.0 N B:ILE37 4.4 36.9 1.0 N B:ASN32 4.4 54.2 1.0 C B:ASP30 4.4 44.2 1.0 HB2 B:ASP30 4.5 56.0 1.0 N B:ILE31 4.5 50.3 1.0 CB B:LYS36 4.5 42.9 1.0 HB3 B:ASN34 4.5 60.5 1.0 HD22 B:ASN32 4.6 67.4 1.0 CA B:ASN34 4.6 49.3 1.0 N B:GLY35 4.6 46.0 1.0 O B:HOH1290 4.6 51.4 1.0 CB B:ASN32 4.7 52.4 1.0 CA B:ILE37 4.7 38.6 1.0 OE1 B:GLU41 4.7 58.3 1.0 OE2 B:GLU41 4.7 74.6 1.0 C B:ASN34 4.8 48.1 1.0 C B:ASN32 4.9 53.7 1.0 CA B:ASN32 4.9 55.9 1.0 HG23 B:ILE37 4.9 44.2 1.0 CG2 B:ILE37 4.9 36.9 1.0

P.V.Natashin, L.P.Burakova, M.I.Kovaleva, M.B.Shevtsov, D.A.Dmitrieva, E.V.Eremeeva, S.V.Markova, A.V.Mishin, V.I.Borshchevskiy, E.S.Vysotski. Role of Tyr-His-Trp Triad and Water Molecule Near the N1-Atom of 2-Hydroperoxycoelenterazine in Bioluminescence of Hydromedusan Photoproteins: Structural and Mutagenesis Study To Be Published 2023.