Magnesium in PDB 7y9g: Crystal Structure of Diterpene Synthase Vena From Streptomyces Venezuelae Atcc 15439 in Complex with Pyrophosphate

The structure of Crystal Structure of Diterpene Synthase Vena From Streptomyces Venezuelae Atcc 15439 in Complex with Pyrophosphate, PDB code: 7y9g 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)	36.02 / 2.18
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	92.789, 92.789, 81.048, 90, 90, 120
R / Rfree (%)	17.5 / 23.8

The binding sites of Magnesium atom in the Crystal Structure of Diterpene Synthase Vena From Streptomyces Venezuelae Atcc 15439 in Complex with Pyrophosphate (pdb code 7y9g). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Diterpene Synthase Vena From Streptomyces Venezuelae Atcc 15439 in Complex with Pyrophosphate, PDB code: 7y9g:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of Diterpene Synthase Vena From Streptomyces Venezuelae Atcc 15439 in Complex with Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Diterpene Synthase Vena From Streptomyces Venezuelae Atcc 15439 in Complex with Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:31.5 occ:1.00 O A:HOH614 2.1 29.2 1.0 O3 A:POP401 2.1 31.6 1.0 OD2 A:ASP115 2.1 39.2 1.0 O6 A:POP401 2.1 32.7 1.0 O A:HOH528 2.1 31.4 1.0 O A:HOH589 2.1 28.2 1.0 CG A:ASP115 3.1 43.6 1.0 P1 A:POP401 3.2 31.7 1.0 MG A:MG403 3.2 34.1 1.0 P2 A:POP401 3.4 32.0 1.0 OD1 A:ASP115 3.4 40.3 1.0 O A:POP401 3.5 31.3 1.0 O2 A:POP401 3.6 35.8 1.0 NZ A:LYS263 3.7 46.4 1.0 NH1 A:ARG344 4.2 31.9 1.0 O A:HOH508 4.2 21.8 1.0 O4 A:POP401 4.3 31.0 1.0 OE2 A:GLU264 4.3 34.0 1.0 CB A:ASP115 4.5 39.1 1.0 O5 A:POP401 4.5 34.4 1.0 O1 A:POP401 4.5 31.7 1.0 OG A:SER119 4.6 78.4 1.0 O A:ASP115 4.6 46.9 1.0 CB A:SER119 4.7 67.1 1.0 OD2 A:ASP269 4.7 53.1 1.0 CE A:LYS263 4.8 48.2 1.0 O A:HOH565 4.8 34.0 1.0 O A:HOH587 4.8 38.6 1.0 MG A:MG404 4.9 31.6 1.0 O A:HOH510 4.9 27.3 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of Diterpene Synthase Vena From Streptomyces Venezuelae Atcc 15439 in Complex with Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Diterpene Synthase Vena From Streptomyces Venezuelae Atcc 15439 in Complex with Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:34.1 occ:1.00 O A:HOH510 2.0 27.3 1.0 O A:HOH508 2.1 21.8 1.0 OD1 A:ASP115 2.1 40.3 1.0 O3 A:POP401 2.1 31.6 1.0 O A:HOH528 2.1 31.4 1.0 O A:HOH565 2.2 34.0 1.0 CG A:ASP115 3.0 43.6 1.0 MG A:MG402 3.2 31.5 1.0 OD2 A:ASP115 3.3 39.2 1.0 P1 A:POP401 3.3 31.7 1.0 OE2 A:GLU192 3.6 37.5 1.0 O1 A:POP401 3.7 31.7 1.0 OE1 A:GLU192 4.0 34.5 1.0 O2 A:POP401 4.3 35.8 1.0 CD A:GLU192 4.3 36.6 1.0 O A:SER214 4.3 27.8 1.0 CB A:ASP115 4.4 39.1 1.0 NH1 A:ARG211 4.4 29.9 1.0 O A:HOH614 4.4 29.2 1.0 O A:POP401 4.5 31.3 1.0 O A:HOH587 4.5 38.6 1.0 O A:HOH589 4.8 28.2 1.0 O6 A:POP401 4.8 32.7 1.0 O A:HOH693 4.9 49.9 1.0 OG A:SER214 5.0 27.8 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of Diterpene Synthase Vena From Streptomyces Venezuelae Atcc 15439 in Complex with Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Diterpene Synthase Vena From Streptomyces Venezuelae Atcc 15439 in Complex with Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:31.6 occ:1.00 OE2 A:GLU264 2.1 34.0 1.0 OD1 A:ASN256 2.1 27.2 1.0 O2 A:POP401 2.1 35.8 1.0 O A:HOH521 2.1 28.6 1.0 O4 A:POP401 2.1 31.0 1.0 OG A:SER260 2.1 31.1 1.0 CB A:SER260 3.0 27.8 1.0 CD A:GLU264 3.1 33.1 1.0 CG A:ASN256 3.2 28.1 1.0 P2 A:POP401 3.3 32.0 1.0 P1 A:POP401 3.4 31.7 1.0 O A:POP401 3.5 31.3 1.0 OE1 A:GLU264 3.5 32.1 1.0 ND2 A:ASN256 3.7 29.2 1.0 O A:ASN256 3.9 28.4 1.0 O6 A:POP401 3.9 32.7 1.0 NH2 A:ARG211 4.1 30.6 1.0 O A:HOH587 4.2 38.6 1.0 O A:HOH614 4.2 29.2 1.0 O1 A:POP401 4.2 31.7 1.0 C A:ASN256 4.3 26.8 1.0 CG A:GLU264 4.3 31.4 1.0 O3 A:POP401 4.4 31.6 1.0 OD1 A:ASP257 4.4 25.8 1.0 CA A:SER260 4.4 29.4 1.0 CB A:ASN256 4.4 29.3 1.0 O5 A:POP401 4.5 34.4 1.0 N A:ASP257 4.7 27.8 1.0 CA A:ASP257 4.8 26.2 1.0 MG A:MG402 4.9 31.5 1.0 CZ A:ARG211 4.9 29.7 1.0 CA A:ASN256 4.9 27.6 1.0 OH A:TYR345 4.9 26.6 1.0 C A:SER260 4.9 30.1 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of Diterpene Synthase Vena From Streptomyces Venezuelae Atcc 15439 in Complex with Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Diterpene Synthase Vena From Streptomyces Venezuelae Atcc 15439 in Complex with Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:34.4 occ:1.00 O6 B:POP401 2.1 29.8 1.0 OE2 B:GLU264 2.1 36.5 1.0 OD1 B:ASN256 2.1 36.3 1.0 O2 B:POP401 2.1 34.6 1.0 O B:HOH557 2.1 31.2 1.0 OG B:SER260 2.1 33.6 1.0 CD B:GLU264 3.0 42.5 1.0 CB B:SER260 3.1 31.8 1.0 CG B:ASN256 3.1 35.9 1.0 P1 B:POP401 3.3 38.9 1.0 P2 B:POP401 3.3 34.5 1.0 OE1 B:GLU264 3.4 40.5 1.0 O B:POP401 3.5 33.3 1.0 ND2 B:ASN256 3.6 29.8 1.0 O B:HOH578 3.9 33.2 1.0 NH2 B:ARG211 3.9 41.5 1.0 O B:ASN256 3.9 38.2 1.0 O3 B:POP401 3.9 34.4 1.0 O B:HOH536 4.0 36.5 1.0 O4 B:POP401 4.2 35.1 1.0 C B:ASN256 4.3 36.0 1.0 CG B:GLU264 4.3 42.0 1.0 O5 B:POP401 4.4 32.5 1.0 CB B:ASN256 4.4 33.0 1.0 CA B:SER260 4.4 36.0 1.0 OD1 B:ASP257 4.5 36.9 1.0 O1 B:POP401 4.5 36.7 1.0 N B:ASP257 4.7 35.1 1.0 CA B:ASP257 4.8 36.3 1.0 CZ B:ARG211 4.8 37.8 1.0 MG B:MG403 4.9 36.7 1.0 O B:SER260 4.9 42.8 1.0 CA B:ASN256 4.9 35.0 1.0 C B:SER260 4.9 37.2 1.0 OH B:TYR345 5.0 31.9 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of Diterpene Synthase Vena From Streptomyces Venezuelae Atcc 15439 in Complex with Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Diterpene Synthase Vena From Streptomyces Venezuelae Atcc 15439 in Complex with Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:36.7 occ:1.00 OD2 B:ASP115 2.1 34.9 1.0 O B:HOH529 2.1 34.4 1.0 O5 B:POP401 2.1 32.5 1.0 O3 B:POP401 2.1 34.4 1.0 O B:HOH536 2.1 36.5 1.0 O B:HOH538 2.1 39.0 1.0 CG B:ASP115 3.0 36.3 1.0 MG B:MG404 3.2 35.4 1.0 P2 B:POP401 3.2 34.5 1.0 OD1 B:ASP115 3.2 34.1 1.0 P1 B:POP401 3.3 38.9 1.0 O B:POP401 3.4 33.3 1.0 NZ B:LYS263 3.8 41.8 1.0 O B:ASP115 3.8 38.1 1.0 O6 B:POP401 3.8 29.8 1.0 OG B:SER119 3.9 49.2 1.0 O B:HOH561 4.0 33.5 1.0 NH1 B:ARG344 4.0 34.7 1.0 O B:HOH585 4.1 41.3 1.0 OE2 B:GLU264 4.3 36.5 1.0 O2 B:POP401 4.3 34.6 1.0 CB B:ASP115 4.4 35.7 1.0 O1 B:POP401 4.4 36.7 1.0 O B:HOH519 4.4 37.6 1.0 O4 B:POP401 4.5 35.1 1.0 C B:ASP115 4.6 40.2 1.0 OD2 B:ASP269 4.7 57.0 1.0 O B:HOH578 4.7 33.2 1.0 CE B:LYS263 4.8 39.1 1.0 O B:HOH507 4.8 38.0 1.0 MG B:MG402 4.9 34.4 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of Diterpene Synthase Vena From Streptomyces Venezuelae Atcc 15439 in Complex with Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Diterpene Synthase Vena From Streptomyces Venezuelae Atcc 15439 in Complex with Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:35.4 occ:1.00 O B:HOH507 2.1 38.0 1.0 OD1 B:ASP115 2.1 34.1 1.0 O5 B:POP401 2.1 32.5 1.0 O B:HOH519 2.1 37.6 1.0 O B:HOH561 2.1 33.5 1.0 O B:HOH529 2.1 34.4 1.0 CG B:ASP115 3.1 36.3 1.0 MG B:MG403 3.2 36.7 1.0 P2 B:POP401 3.3 34.5 1.0 OD2 B:ASP115 3.5 34.9 1.0 OE1 B:GLU192 3.5 48.0 1.0 O4 B:POP401 3.7 35.1 1.0 O B:HOH585 3.7 41.3 1.0 OE2 B:GLU192 4.1 51.3 1.0 CD B:GLU192 4.3 52.0 1.0 O6 B:POP401 4.3 29.8 1.0 O B:SER214 4.3 35.8 1.0 O B:HOH536 4.3 36.5 1.0 O B:POP401 4.4 33.3 1.0 NH1 B:ARG211 4.4 38.3 1.0 O B:HOH578 4.4 33.2 1.0 CB B:ASP115 4.4 35.7 1.0 O B:ASP115 4.8 38.1 1.0 O3 B:POP401 4.8 34.4 1.0 O B:HOH673 4.8 54.0 1.0 C B:SER214 4.8 35.6 1.0 CB B:SER214 4.8 40.0 1.0 O B:HOH538 4.9 39.0 1.0 CE1 B:PHE185 4.9 42.0 1.0 SG B:CYS189 5.0 46.2 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