Magnesium in PDB 5yew: Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion

The structure of Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion, PDB code: 5yew was solved by L.Yan, Y.Qi, X.Huang, C.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.20
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	207.942, 207.942, 107.893, 90.00, 90.00, 120.00
R / Rfree (%)	22.3 / 25.7

The structure of Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion also contains other interesting chemical elements:

Fluorine	(F)	9 atoms
Potassium	(K)	3 atoms

The binding sites of Magnesium atom in the Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion (pdb code 5yew). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion, PDB code: 5yew:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg804 b:52.4 occ:1.00 O1B A:GDP801 1.7 89.9 1.0 OG A:SER89 1.7 65.3 1.0 OG1 A:THR109 1.9 61.8 1.0 F1 A:BEF802 2.6 69.9 1.0 CB A:THR109 2.9 61.2 1.0 CB A:SER89 3.1 67.3 1.0 PB A:GDP801 3.1 78.6 1.0 OD1 A:ASP178 3.2 66.7 1.0 O3A A:GDP801 3.3 75.3 1.0 OD2 A:ASP178 3.3 71.8 1.0 CG2 A:THR109 3.6 64.9 1.0 N A:SER89 3.6 71.4 1.0 CG A:ASP178 3.7 73.5 1.0 CA A:SER89 3.8 66.5 1.0 O3B A:GDP801 3.9 65.9 1.0 O A:SER179 4.0 70.8 1.0 O A:PRO102 4.0 67.0 1.0 O2B A:GDP801 4.1 45.1 1.0 BE A:BEF802 4.1 59.7 1.0 CA A:THR109 4.1 57.4 1.0 N A:THR109 4.2 57.1 1.0 PA A:GDP801 4.5 65.0 1.0 O1A A:GDP801 4.6 70.0 1.0 CB A:LYS88 4.6 63.4 1.0 CE A:LYS88 4.7 69.8 1.0 C A:LYS88 4.8 68.3 1.0

Magnesium binding site 2 out of 3 in the Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg804 b:46.2 occ:1.00 OG1 B:THR109 2.0 88.1 1.0 OG B:SER89 2.2 62.3 1.0 O3B B:GDP801 2.3 73.5 1.0 O1B B:GDP801 2.4 87.4 1.0 PB B:GDP801 2.8 66.2 1.0 CB B:THR109 3.1 78.8 1.0 CG2 B:THR109 3.3 80.8 1.0 CB B:SER89 3.4 66.6 1.0 F2 B:BEF802 3.9 76.3 1.0 BE B:BEF802 3.9 76.0 1.0 N B:SER89 3.9 63.3 1.0 OD1 B:ASP178 3.9 76.4 1.0 O1A B:GDP801 3.9 63.5 1.0 O2B B:GDP801 4.0 57.1 1.0 O B:PRO102 4.0 77.2 1.0 O3A B:GDP801 4.0 61.7 1.0 N B:THR109 4.0 76.0 1.0 OD2 B:ASP178 4.1 87.0 1.0 CA B:THR109 4.2 75.6 1.0 CA B:SER89 4.2 64.9 1.0 F1 B:BEF802 4.3 99.4 1.0 PA B:GDP801 4.3 57.6 1.0 O B:SER179 4.3 58.0 1.0 O2A B:GDP801 4.4 62.4 1.0 CG B:ASP178 4.5 80.1 1.0 F3 B:BEF802 4.7 1.0 1.0 CE B:LYS88 4.7 79.2 1.0 K B:K803 4.8 78.7 1.0 CB B:LYS88 4.8 66.4 1.0 CG2 B:ILE108 4.8 82.4 1.0 NZ B:LYS88 4.9 79.5 1.0

Magnesium binding site 3 out of 3 in the Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg804 b:37.4 occ:1.00 O1B C:GDP801 2.0 77.8 1.0 OG1 C:THR109 2.0 47.4 1.0 OG C:SER89 2.3 57.7 1.0 O3B C:GDP801 2.9 60.1 1.0 PB C:GDP801 2.9 60.2 1.0 CB C:THR109 3.0 49.8 1.0 F1 C:BEF802 3.2 48.9 1.0 O1A C:GDP801 3.5 68.0 1.0 CB C:SER89 3.6 57.4 1.0 F2 C:BEF802 3.8 70.1 1.0 OD1 C:ASP178 3.9 46.8 1.0 O3A C:GDP801 3.9 57.8 1.0 BE C:BEF802 3.9 57.3 1.0 CG2 C:THR109 4.0 51.8 1.0 N C:THR109 4.0 51.5 1.0 N C:SER89 4.1 54.8 1.0 CA C:THR109 4.1 48.2 1.0 O C:SER179 4.1 44.5 1.0 OD2 C:ASP178 4.2 59.5 1.0 O2B C:GDP801 4.2 56.4 1.0 O C:PRO102 4.2 68.4 1.0 PA C:GDP801 4.3 56.1 1.0 CA C:SER89 4.4 54.1 1.0 CG C:ASP178 4.5 53.2 1.0 CE C:LYS88 4.5 66.1 1.0 K C:K803 4.5 65.5 1.0 NZ C:LYS88 4.7 77.6 1.0 CB C:LYS88 4.8 56.4 1.0 CG2 C:ILE108 4.9 60.2 1.0 O2A C:GDP801 5.0 48.8 1.0

L.Yan, Y.Qi, X.Huang, C.Yu, L.Lan, X.Guo, Z.Rao, J.Hu, Z.Lou. Structural Basis For Gtp Hydrolysis and Conformational Change of MFN1 in Mediating Membrane Fusion Nat. Struct. Mol. Biol. V. 25 233 2018.
ISSN: ESSN 1545-9985
PubMed: 29483649
DOI: 10.1038/S41594-018-0034-8