Magnesium in PDB 7vqa: Structure of MA1831 From Methanosarcina Acetivorans in Complex with Dimethylallyl Diphosphate.

The structure of Structure of MA1831 From Methanosarcina Acetivorans in Complex with Dimethylallyl Diphosphate., PDB code: 7vqa was solved by L.L.Zhang, C.C.Chen, W.D.Liu, J.W.Huang, X.W.Zhang, B.B.Liu, R.T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.45 / 1.79
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	111.848, 81.567, 60.044, 90, 103.74, 90
R / Rfree (%)	15.2 / 20.2

The binding sites of Magnesium atom in the Structure of MA1831 From Methanosarcina Acetivorans in Complex with Dimethylallyl Diphosphate. (pdb code 7vqa). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of MA1831 From Methanosarcina Acetivorans in Complex with Dimethylallyl Diphosphate., PDB code: 7vqa:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of MA1831 From Methanosarcina Acetivorans in Complex with Dimethylallyl Diphosphate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of MA1831 From Methanosarcina Acetivorans in Complex with Dimethylallyl Diphosphate. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:12.8 occ:1.00 O A:HOH525 2.0 16.7 1.0 O1A A:DMA302 2.1 29.0 1.0 O A:HOH424 2.1 16.8 1.0 O2A A:DMA301 2.2 16.5 1.0 O3B A:DMA301 2.2 13.6 1.0 OD1 A:ASP23 2.2 15.1 1.0 CG A:ASP23 3.2 14.9 1.0 PB A:DMA301 3.3 15.4 1.0 PA A:DMA301 3.4 16.3 1.0 OD2 A:ASP23 3.5 14.4 1.0 PA A:DMA302 3.5 24.2 1.0 O2B A:DMA301 3.6 15.6 1.0 O3A A:DMA301 3.7 15.5 1.0 NH2 A:ARG74 4.0 20.0 1.0 O3B A:DMA302 4.1 27.3 1.0 O1 A:DMA301 4.1 17.7 1.0 O A:HOH564 4.1 30.0 1.0 NH2 A:ARG27 4.2 16.4 1.0 O3A A:DMA302 4.3 23.0 1.0 O A:HOH416 4.4 38.7 1.0 O2A A:DMA302 4.4 32.9 1.0 C1 A:DMA301 4.4 18.3 1.0 O1 A:DMA302 4.5 34.5 1.0 CB A:ASP23 4.6 13.9 1.0 O1B A:DMA301 4.6 14.5 1.0 O A:HOH486 4.6 45.9 1.0 O1A A:DMA301 4.6 16.4 1.0 PB A:DMA302 4.6 23.3 1.0 N A:GLY24 4.7 14.9 1.0 C1 A:DMA302 4.7 27.3 1.0 O A:HOH568 4.7 44.2 1.0 O1B A:DMA302 4.7 32.4 1.0 C5 A:DMA301 4.8 26.9 1.0 NH2 A:ARG26 4.9 20.8 1.0 C2 A:DMA302 5.0 24.6 1.0

Magnesium binding site 2 out of 2 in the Structure of MA1831 From Methanosarcina Acetivorans in Complex with Dimethylallyl Diphosphate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of MA1831 From Methanosarcina Acetivorans in Complex with Dimethylallyl Diphosphate. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:14.5 occ:1.00 O1A B:DMA302 1.9 27.2 1.0 O1A B:DMA301 2.2 18.1 1.0 OD1 B:ASP23 2.2 15.3 1.0 O B:HOH500 2.2 21.0 1.0 O1B B:DMA301 2.3 15.9 1.0 O B:HOH407 2.3 20.2 1.0 CG B:ASP23 3.2 17.0 1.0 PB B:DMA301 3.3 17.8 1.0 PA B:DMA301 3.4 18.0 1.0 PA B:DMA302 3.4 23.0 1.0 OD2 B:ASP23 3.5 15.7 1.0 O3A B:DMA301 3.6 19.2 1.0 O3B B:DMA301 3.7 20.4 1.0 O1 B:DMA301 3.9 20.0 1.0 O3B B:DMA302 4.0 28.0 1.0 NH2 B:ARG74 4.1 20.3 1.0 O1 B:DMA302 4.2 35.5 1.0 C1 B:DMA301 4.3 22.6 1.0 O B:HOH506 4.3 27.6 1.0 NH2 B:ARG27 4.3 20.5 1.0 O B:HOH411 4.3 36.1 1.0 O3A B:DMA302 4.3 23.7 1.0 O2A B:DMA302 4.5 26.6 1.0 CB B:ASP23 4.5 16.3 1.0 N B:GLY24 4.6 16.9 1.0 O2A B:DMA301 4.6 17.5 1.0 O2B B:DMA301 4.6 18.6 1.0 O B:HOH528 4.7 45.5 1.0 PB B:DMA302 4.7 24.6 1.0 C5 B:DMA301 4.7 23.6 1.0 C1 B:DMA302 4.8 29.1 1.0 O B:HOH495 4.8 52.1 1.0 CA B:ASP23 5.0 15.2 1.0 O2B B:DMA302 5.0 32.4 1.0 C2 B:DMA302 5.0 28.3 1.0 NH2 B:ARG173 5.0 16.8 1.0

L.Zhang, X.Zhang, J.Min, B.Liu, J.W.Huang, Y.Yang, W.Liu, L.Dai, Y.Yang, C.C.Chen, R.T.Guo. Structural Insights to A Bi-Functional Isoprenyl Diphosphate Synthase That Can Catalyze Head-to-Tail and Head-to-Middle Condensation. Int.J.Biol.Macromol. V. 214 492 2022.
ISSN: ISSN 0141-8130
PubMed: 35764165
DOI: 10.1016/J.IJBIOMAC.2022.06.146