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

Protein crystallography data

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

Other elements in 5yew:

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

Magnesium Binding Sites:

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 5yew

Go back to Magnesium Binding Sites List in 5yew
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 5yew

Go back to Magnesium Binding Sites List in 5yew
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 5yew

Go back to Magnesium Binding Sites List in 5yew
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

Reference:

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
Page generated: Mon Sep 30 11:06:55 2024

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