Magnesium in PDB 8elf: Structure of GET3D, A Homolog of GET3, From Arabidopsis Thaliana

The structure of Structure of GET3D, A Homolog of GET3, From Arabidopsis Thaliana, PDB code: 8elf was solved by M.S.Manu, A.N.Barlow, W.M.Clemons Jr., S.Ramasamy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.83 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.251, 67.05, 99.398, 90, 97.81, 90
R / Rfree (%)	21.4 / 25.6

The binding sites of Magnesium atom in the Structure of GET3D, A Homolog of GET3, From Arabidopsis Thaliana (pdb code 8elf). 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 GET3D, A Homolog of GET3, From Arabidopsis Thaliana, PDB code: 8elf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of GET3D, A Homolog of GET3, From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of GET3D, A Homolog of GET3, From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:47.9 occ:1.00 H A:THR73 2.5 40.6 1.0 HB A:THR72 2.7 40.1 1.0 O2 A:PO4501 2.8 36.9 1.0 HA2 A:GLY70 3.0 46.8 1.0 O3 A:PO4501 3.0 34.6 1.0 H A:THR72 3.1 39.3 1.0 OG1 A:THR73 3.2 33.7 1.0 N A:THR73 3.3 33.8 1.0 HG1 A:THR73 3.4 40.6 1.0 P A:PO4501 3.5 36.3 1.0 N A:THR72 3.6 32.6 1.0 CB A:THR72 3.6 33.4 1.0 O A:HOH609 3.6 45.8 1.0 O B:HOH628 3.7 48.5 1.0 HB A:THR73 3.7 42.3 1.0 CA A:GLY70 3.7 38.9 1.0 H A:GLY70 3.8 45.1 1.0 C A:GLY70 3.9 35.4 1.0 CB A:THR73 3.9 35.1 1.0 CA A:THR72 3.9 35.3 1.0 HZ3 B:LYS66 4.0 53.6 1.0 C A:THR72 4.0 30.4 1.0 N A:LYS71 4.1 31.8 1.0 H A:LYS71 4.1 38.2 1.0 CA A:THR73 4.2 26.8 1.0 HD11 A:LEU103 4.2 43.7 1.0 OG1 A:THR72 4.2 36.1 1.0 N A:GLY70 4.2 37.5 1.0 O A:GLY70 4.4 31.9 1.0 HZ1 B:LYS66 4.5 53.6 1.0 C A:LYS71 4.5 37.7 1.0 O4 A:PO4501 4.5 37.1 1.0 HA3 A:GLY70 4.5 46.8 1.0 O1 A:PO4501 4.6 40.2 1.0 HA A:THR73 4.6 32.2 1.0 HG22 A:THR72 4.7 42.0 1.0 NZ B:LYS66 4.7 44.6 1.0 CG2 A:THR72 4.7 34.9 1.0 HB3 A:SER99 4.7 37.7 1.0 CA A:LYS71 4.9 34.2 1.0 HA A:THR72 4.9 42.5 1.0 HB2 A:LYS71 5.0 41.1 1.0 HG21 A:THR72 5.0 42.0 1.0 HG1 A:THR72 5.0 43.4 1.0

Magnesium binding site 2 out of 2 in the Structure of GET3D, A Homolog of GET3, From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of GET3D, A Homolog of GET3, From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:49.1 occ:1.00 H B:THR73 2.3 44.5 1.0 O2 B:PO4501 2.5 36.2 1.0 HA2 B:GLY70 2.6 42.9 1.0 HB B:THR72 2.8 45.9 1.0 H B:THR72 2.9 39.0 1.0 O3 B:PO4501 3.1 39.2 1.0 N B:THR73 3.1 37.0 1.0 OG1 B:THR73 3.3 38.0 1.0 P B:PO4501 3.4 34.3 1.0 CA B:GLY70 3.4 35.7 1.0 N B:THR72 3.4 32.4 1.0 O B:HOH616 3.4 50.5 1.0 HG1 B:THR73 3.5 45.8 1.0 HB B:THR73 3.5 41.7 1.0 C B:GLY70 3.5 34.5 1.0 H B:GLY70 3.6 42.9 1.0 CB B:THR72 3.6 38.1 1.0 CB B:THR73 3.8 34.6 1.0 N B:LYS71 3.8 38.0 1.0 CA B:THR72 3.8 36.6 1.0 H B:LYS71 3.9 45.7 1.0 C B:THR72 3.9 33.2 1.0 O B:GLY70 3.9 29.5 1.0 N B:GLY70 4.0 35.6 1.0 CA B:THR73 4.0 34.9 1.0 HA3 B:GLY70 4.2 42.9 1.0 C B:LYS71 4.3 26.8 1.0 O1 B:PO4501 4.3 31.1 1.0 OG1 B:THR72 4.3 37.3 1.0 HZ3 A:LYS66 4.4 70.1 1.0 O4 B:PO4501 4.5 36.1 1.0 HA B:THR73 4.5 42.0 1.0 HZ B:PHE350 4.6 105.5 1.0 CA B:LYS71 4.6 30.2 1.0 HG22 B:THR72 4.6 41.8 1.0 HD11 B:LEU103 4.7 43.8 1.0 H B:ALA74 4.7 37.2 1.0 CG2 B:THR72 4.7 34.8 1.0 HA B:THR72 4.8 44.0 1.0 HB2 B:LYS71 4.9 31.5 1.0

A.N.Barlow, M.S.Manu, S.M.Saladi, P.T.Tarr, Y.Yadav, A.M.M.Thinn, Y.Zhu, A.D.Laganowsky, W.M.Clemons Jr., S.Ramasamy. Structures of GET3D Reveal A Distinct Architecture Associated with the Emergence of Photosynthesis. J.Biol.Chem. 04752 2023.
ISSN: ESSN 1083-351X
PubMed: 37100288
DOI: 10.1016/J.JBC.2023.104752