Sodium in PDB 8a9s: Crystal Structure of CA2+-Discharged Obelin in Complex with Coelenteramine-V

The structure of Crystal Structure of CA2+-Discharged Obelin in Complex with Coelenteramine-V, PDB code: 8a9s was solved by M.I.Kovaleva, P.V.Natashin, M.B.Schevtsov, E.V.Eremeeva, S.S.Bukhdrucker, D.A.Dmitrieva, A.V.Mishin, E.S.Vysotski, V.I.Borshchevskiy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.46 / 2.10
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	77.281, 77.281, 182.224, 90, 90, 120
R / Rfree (%)	16 / 21

The binding sites of Sodium atom in the Crystal Structure of CA2+-Discharged Obelin in Complex with Coelenteramine-V (pdb code 8a9s). 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 CA2+-Discharged Obelin in Complex with Coelenteramine-V, PDB code: 8a9s:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of CA2+-Discharged Obelin in Complex with Coelenteramine-V


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 CA2+-Discharged Obelin in Complex with Coelenteramine-V within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:44.2 occ:0.99 OD1 A:ASN32 2.2 49.6 1.0 OD1 A:ASN34 2.2 40.1 1.0 O A:LYS36 2.2 31.5 1.0 O A:HOH805 2.5 53.5 1.0 OD1 A:ASP30 2.5 38.2 1.0 O A:HOH842 2.7 53.8 1.0 H A:LYS36 3.1 40.0 1.0 CG A:ASN34 3.1 41.9 1.0 CG A:ASN32 3.2 48.9 1.0 H A:ASN34 3.2 50.9 1.0 HD21 A:ASN32 3.3 57.8 1.0 C A:LYS36 3.4 32.8 1.0 HD21 A:ASN34 3.5 58.0 1.0 HA A:ASP30 3.5 42.0 1.0 CG A:ASP30 3.6 38.9 1.0 ND2 A:ASN32 3.7 48.2 1.0 ND2 A:ASN34 3.7 48.4 1.0 O A:HOH794 3.8 61.9 1.0 H A:ASN32 3.8 54.4 1.0 N A:LYS36 3.9 33.4 1.0 HG22 A:ILE37 3.9 41.6 1.0 HB2 A:LYS36 4.0 45.2 1.0 N A:ASN34 4.1 42.4 1.0 HA A:ILE37 4.1 47.2 1.0 CA A:LYS36 4.1 36.9 1.0 CA A:ASP30 4.3 35.0 1.0 H A:GLY33 4.3 54.9 1.0 CB A:ASN34 4.3 39.6 1.0 H A:GLY35 4.4 45.8 1.0 HB3 A:ASN34 4.4 47.5 1.0 CB A:ASP30 4.4 33.4 1.0 N A:ASN32 4.5 45.3 1.0 HG23 A:ILE37 4.5 41.6 1.0 N A:ILE37 4.5 34.0 1.0 OD2 A:ASP30 4.5 45.5 1.0 HD22 A:ASN34 4.5 58.0 1.0 H A:ILE31 4.5 48.9 1.0 HD22 A:ASN32 4.5 57.8 1.0 N A:GLY33 4.5 45.7 1.0 C A:ASP30 4.5 39.4 1.0 CA A:ASN34 4.5 40.1 1.0 CB A:LYS36 4.6 37.6 1.0 CB A:ASN32 4.6 47.5 1.0 N A:GLY35 4.6 38.1 1.0 OE1 A:GLU41 4.6 61.1 1.0 CG2 A:ILE37 4.6 34.6 1.0 HB2 A:ASP30 4.6 40.0 1.0 N A:ILE31 4.7 40.8 1.0 C A:ASN34 4.7 38.1 1.0 CA A:ILE37 4.7 39.4 1.0 C A:ASN32 4.8 41.6 1.0 CA A:ASN32 4.8 44.2 1.0 O A:HOH721 4.9 61.0 1.0 HB3 A:ASN32 5.0 56.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of CA2+-Discharged Obelin in Complex with Coelenteramine-V


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 CA2+-Discharged Obelin in Complex with Coelenteramine-V within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:61.5 occ:1.00 O B:LYS36 2.2 40.9 1.0 O B:HOH739 2.3 53.0 1.0 OD1 B:ASN32 2.3 57.2 1.0 OD1 B:ASN34 2.6 50.2 1.0 OD1 B:ASP30 2.6 45.0 1.0 O B:HOH782 2.7 48.4 1.0 HD21 B:ASN32 3.0 65.7 1.0 CG B:ASN32 3.2 55.4 1.0 HD21 B:ASN34 3.2 53.1 1.0 CG B:ASN34 3.3 45.8 1.0 HA B:ASP30 3.4 49.8 1.0 ND2 B:ASN32 3.4 54.8 1.0 C B:LYS36 3.5 41.0 1.0 H B:LYS36 3.5 54.9 1.0 ND2 B:ASN34 3.5 44.2 1.0 H B:ASN34 3.6 55.5 1.0 H B:ASN32 3.7 67.4 1.0 CG B:ASP30 3.7 45.3 1.0 HA B:ILE37 3.8 49.3 1.0 HG21 B:ILE37 4.0 45.9 1.0 OE1 B:GLU41 4.1 71.8 1.0 HB2 B:LYS36 4.1 53.6 1.0 CA B:ASP30 4.2 41.5 1.0 N B:LYS36 4.2 45.7 1.0 HD22 B:ASN32 4.2 65.7 1.0 H B:ILE31 4.2 50.0 1.0 HD22 B:ASN34 4.3 53.1 1.0 CA B:LYS36 4.3 43.3 1.0 H B:GLY33 4.4 53.6 1.0 N B:ASN34 4.4 46.2 1.0 N B:ASN32 4.4 56.2 1.0 N B:ILE37 4.4 40.1 1.0 CB B:ASP30 4.5 45.7 1.0 N B:ILE31 4.5 41.7 1.0 C B:ASP30 4.5 42.2 1.0 CB B:ASN32 4.5 53.2 1.0 CB B:ASN34 4.5 45.4 1.0 CA B:ILE37 4.6 41.1 1.0 OE2 B:GLU41 4.6 77.8 1.0 OD2 B:ASP30 4.6 48.6 1.0 HG22 B:ILE37 4.7 45.9 1.0 N B:GLY33 4.7 44.6 1.0 HB2 B:ASP30 4.7 54.9 1.0 CB B:LYS36 4.7 44.7 1.0 HB3 B:ASN34 4.7 54.5 1.0 CG2 B:ILE37 4.7 38.3 1.0 CD B:GLU41 4.8 73.3 1.0 H B:GLY35 4.8 56.4 1.0 HB3 B:ASN32 4.9 63.8 1.0 CA B:ASN32 4.9 53.5 1.0 CA B:ASN34 4.9 45.6 1.0 C B:ASN32 5.0 47.2 1.0

P.V.Natashin, E.V.Eremeeva, M.B.Shevtsov, M.I.Kovaleva, S.S.Bukhdruker, D.A.Dmitrieva, D.V.Gulnov, E.V.Nemtseva, V.I.Gordeliy, A.V.Mishin, V.I.Borshchevskiy, E.S.Vysotski. Crystal Structure of Semi-Synthetic Obelin-V After Calcium Induced Bioluminescence Implies Coelenteramine As the Main Reaction Product. Sci Rep V. 12 19613 2022.
ISSN: ESSN 2045-2322
PubMed: 36379962
DOI: 10.1038/S41598-022-24117-5