Sodium in PDB 7y9h: Crystal Structure of Diterpene Synthase Vena From Streptomyces Venezuelae Atcc 15439

The structure of Crystal Structure of Diterpene Synthase Vena From Streptomyces Venezuelae Atcc 15439, PDB code: 7y9h was solved by L.L.Zhang, Z.Z.Xie, J.-W.Huang, Y.C.Hu, W.D.Liu, Y.Yang, C.-C.Chen, R.-T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.37 / 2.03
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	93.999, 93.999, 80.747, 90, 90, 120
R / Rfree (%)	16 / 20.6

The binding sites of Sodium atom in the Crystal Structure of Diterpene Synthase Vena From Streptomyces Venezuelae Atcc 15439 (pdb code 7y9h). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Diterpene Synthase Vena From Streptomyces Venezuelae Atcc 15439, PDB code: 7y9h:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Diterpene Synthase Vena From Streptomyces Venezuelae Atcc 15439


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 Diterpene Synthase Vena From Streptomyces Venezuelae Atcc 15439 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:30.3 occ:1.00 O B:HOH674 2.6 20.6 1.0 O A:HOH826 2.6 16.8 1.0 O B:PRO50 2.7 21.9 1.0 O A:HIS49 2.7 18.4 1.0 CB A:TYR48 3.5 20.4 1.0 C B:PRO50 3.6 21.2 1.0 CB A:ALA52 3.8 18.9 1.0 C A:HIS49 3.8 20.9 1.0 O B:HOH551 3.8 24.7 1.0 O B:HOH616 3.9 31.9 1.0 CA B:ASP51 4.0 20.9 1.0 O A:PRO50 4.0 22.4 1.0 O A:TYR48 4.1 21.5 1.0 N A:ALA52 4.1 19.2 1.0 N B:ALA52 4.1 18.9 1.0 CA A:PRO50 4.1 23.1 1.0 C A:PRO50 4.1 22.2 1.0 C A:TYR48 4.2 20.8 1.0 N B:ASP51 4.2 18.6 1.0 C B:ASP51 4.2 19.6 1.0 N B:ALA53 4.2 20.2 1.0 O B:HOH545 4.3 27.0 1.0 N A:PRO50 4.4 21.6 1.0 CB B:ALA53 4.5 21.6 1.0 CG A:TYR48 4.5 21.2 1.0 CA A:TYR48 4.5 20.9 1.0 CA A:ALA52 4.5 19.0 1.0 N A:HIS49 4.6 22.0 1.0 CA B:PRO50 4.7 22.2 1.0 N A:ASP51 4.8 21.3 1.0 O B:HIS49 4.8 21.9 1.0 CD2 A:TYR48 4.9 21.2 1.0 CA A:HIS49 4.9 22.6 1.0 O B:ASP51 4.9 19.3 1.0 CA B:ALA53 5.0 20.9 1.0 N A:ALA53 5.0 18.8 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Diterpene Synthase Vena From Streptomyces Venezuelae Atcc 15439


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 Diterpene Synthase Vena From Streptomyces Venezuelae Atcc 15439 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:29.2 occ:1.00 O B:HOH608 2.7 19.8 1.0 O B:HOH644 2.8 24.6 1.0 O B:HOH614 2.9 17.9 1.0 OD1 B:ASP353 3.1 22.1 1.0 N B:ASP353 3.2 17.8 1.0 CG B:ASP353 3.2 21.9 1.0 OD2 B:ASP353 3.6 23.2 1.0 CB B:ARG368 3.6 25.7 1.0 CA B:TRP352 3.7 18.7 1.0 O B:VAL351 3.7 20.4 1.0 CD1 B:TRP352 3.7 20.0 1.0 C B:TRP352 3.9 19.5 1.0 CB B:ASP353 3.9 21.0 1.0 O B:HOH679 3.9 16.6 1.0 OG B:SER355 4.0 20.0 1.0 O B:HOH673 4.0 20.2 1.0 CA B:ASP353 4.1 19.3 1.0 O B:HOH531 4.3 24.2 1.0 CA B:ARG368 4.3 23.4 1.0 C B:VAL351 4.4 17.8 1.0 O B:HOH606 4.5 19.2 1.0 N B:TRP352 4.5 17.5 1.0 CG B:TRP352 4.6 19.4 1.0 NE1 B:TRP352 4.6 21.4 1.0 CB B:TRP352 4.7 19.1 1.0 CD B:ARG368 4.7 29.0 1.0 CG B:ARG368 4.7 25.3 1.0 N B:GLY354 4.9 19.9 1.0 C B:ASP353 4.9 20.2 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Diterpene Synthase Vena From Streptomyces Venezuelae Atcc 15439


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Diterpene Synthase Vena From Streptomyces Venezuelae Atcc 15439 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:45.7 occ:1.00 NH2 B:ARG344 3.3 55.7 1.0 NE2 B:GLN83 3.4 24.6 1.0 NZ B:LYS263 3.8 62.4 1.0 CE2 B:PHE117 4.0 43.3 1.0 CZ B:PHE117 4.1 41.8 1.0 CZ B:ARG344 4.1 55.5 1.0 CB B:SER116 4.2 39.5 1.0 CE1 B:PHE79 4.3 24.9 1.0 OG B:SER116 4.3 42.3 1.0 CD B:GLN83 4.3 22.1 1.0 OE1 B:GLN83 4.4 24.4 1.0 NH1 B:ARG344 4.4 54.5 1.0 CE B:LYS263 4.4 60.5 1.0 CG B:ARG344 5.0 32.1 1.0 CD2 B:PHE117 5.0 45.1 1.0 NE B:ARG344 5.0 49.4 1.0

Z.Li, L.L.Zhang, K.W.Xu, Y.Y.Jiang, J.Du, X.W.Zhang, L.H.Meng, Q.Wu, L.Du, X.J.Li, Y.C.Hu, Z.Z.Xie, X.K.Jiang, Y.-J.Tang, R.B.Wu, R.-T.Guo, S.Y.Li. Molecular Insights Into the Catalytic Promiscuity of A Bacterial Diterpene Synthase Nat Commun 2023.
ISSN: ESSN 2041-1723