Potassium 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
Magnesium (Mg) 3 atoms

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total 3 binding sites of Potassium where determined in the Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion, PDB code: 5yew:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 5yew

Go back to Potassium Binding Sites List in 5yew
Potassium 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 Potassium with other atoms in the K 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:K803

b:70.3
occ:1.00
F3 A:BEF802 2.2 64.5 1.0
O A:GLY104 2.6 60.5 1.0
O A:GLY106 2.7 48.5 1.0
OG A:SER85 2.8 68.9 1.0
O3B A:GDP801 2.9 65.9 1.0
O3A A:GDP801 3.0 75.3 1.0
O5' A:GDP801 3.2 54.9 1.0
BE A:BEF802 3.5 59.7 1.0
PB A:GDP801 3.6 78.6 1.0
PA A:GDP801 3.7 65.0 1.0
C A:GLY104 3.8 59.8 1.0
CB A:SER85 3.9 65.2 1.0
CA A:SER85 3.9 60.4 1.0
C A:GLY106 4.0 49.1 1.0
N A:SER85 4.1 59.9 1.0
CB A:ILE108 4.1 64.0 1.0
F1 A:BEF802 4.1 69.9 1.0
N A:ILE108 4.3 63.4 1.0
C5' A:GDP801 4.4 52.9 1.0
CG1 A:ILE108 4.4 63.1 1.0
N A:GLY106 4.5 47.4 1.0
N A:GLY104 4.5 67.2 1.0
O2A A:GDP801 4.5 77.1 1.0
C A:ILE105 4.5 51.5 1.0
O2B A:GDP801 4.6 45.1 1.0
CG2 A:THR84 4.6 61.6 1.0
CD1 A:ILE108 4.7 60.5 1.0
N A:ILE105 4.7 56.1 1.0
CA A:ILE105 4.7 52.0 1.0
O1B A:GDP801 4.7 89.9 1.0
CA A:GLY104 4.8 65.4 1.0
CA A:HIS107 4.8 50.8 1.0
C4' A:GDP801 4.8 55.9 1.0
O1A A:GDP801 4.8 70.0 1.0
CA A:ILE108 4.8 63.7 1.0
N A:HIS107 4.8 48.8 1.0
CA A:GLY106 4.9 47.4 1.0
C A:HIS107 4.9 58.4 1.0
F2 A:BEF802 4.9 53.5 1.0
O B:GLU209 4.9 47.7 1.0
O A:ILE105 4.9 59.5 1.0
C A:THR84 5.0 55.4 1.0

Potassium binding site 2 out of 3 in 5yew

Go back to Potassium Binding Sites List in 5yew
Potassium 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 Potassium with other atoms in the K 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:K803

b:78.7
occ:1.00
F1 B:BEF802 2.2 99.4 1.0
O B:GLY106 2.7 62.1 1.0
O B:GLY104 2.7 60.9 1.0
O3B B:GDP801 2.8 73.5 1.0
OG B:SER85 2.9 70.2 1.0
O1A B:GDP801 3.3 63.5 1.0
O3A B:GDP801 3.5 61.7 1.0
PB B:GDP801 3.7 66.2 1.0
BE B:BEF802 3.9 76.0 1.0
C B:GLY106 3.9 63.3 1.0
C B:GLY104 4.0 69.5 1.0
CB B:SER85 4.0 70.9 1.0
CA B:SER85 4.0 68.4 1.0
CB B:ILE108 4.0 79.4 1.0
PA B:GDP801 4.0 57.6 1.0
C5' B:GDP801 4.0 69.8 1.0
N B:SER85 4.1 63.8 1.0
N B:ILE108 4.1 68.5 1.0
CG1 B:ILE108 4.4 84.7 1.0
O2B B:GDP801 4.4 57.1 1.0
CG2 B:THR84 4.5 62.3 1.0
N B:GLY106 4.5 62.5 1.0
O5' B:GDP801 4.5 69.8 1.0
C B:ILE105 4.6 65.2 1.0
N B:GLY104 4.6 75.8 1.0
CD1 B:ILE108 4.7 86.7 1.0
CA B:HIS107 4.7 65.0 1.0
CA B:ILE108 4.7 77.5 1.0
C B:HIS107 4.7 67.5 1.0
N B:HIS107 4.7 67.6 1.0
CA B:ILE105 4.8 69.5 1.0
MG B:MG804 4.8 46.2 1.0
N B:ILE105 4.8 68.7 1.0
F2 B:BEF802 4.8 76.3 1.0
CA B:GLY106 4.9 60.7 1.0
CA B:GLY104 4.9 70.2 1.0
C B:THR84 4.9 58.0 1.0
O A:GLU209 4.9 62.6 1.0
O B:ILE105 5.0 64.3 1.0
O1B B:GDP801 5.0 87.4 1.0

Potassium binding site 3 out of 3 in 5yew

Go back to Potassium Binding Sites List in 5yew
Potassium 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 Potassium with other atoms in the K 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:K803

b:65.5
occ:1.00
F1 C:BEF802 2.6 48.9 1.0
O C:GLY106 2.8 45.0 1.0
O C:GLY104 2.9 49.2 1.0
O3B C:GDP801 2.9 60.1 1.0
OG C:SER85 3.0 58.5 1.0
O3A C:GDP801 3.1 57.8 1.0
O1A C:GDP801 3.6 68.0 1.0
PB C:GDP801 3.7 60.2 1.0
PA C:GDP801 3.8 56.1 1.0
O5' C:GDP801 3.8 52.8 1.0
BE C:BEF802 3.9 57.3 1.0
CA C:SER85 4.0 52.2 1.0
N C:SER85 4.0 47.8 1.0
CB C:SER85 4.0 55.0 1.0
C C:GLY106 4.1 46.2 1.0
CB C:ILE108 4.1 53.2 1.0
N C:ILE108 4.1 51.9 1.0
C C:GLY104 4.2 57.5 1.0
C5' C:GDP801 4.4 53.3 1.0
CG2 C:THR84 4.4 44.9 1.0
O1B C:GDP801 4.5 77.8 1.0
CG1 C:ILE108 4.5 54.0 1.0
MG C:MG804 4.5 37.4 1.0
N C:GLY104 4.7 61.9 1.0
CA C:HIS107 4.7 44.4 1.0
CA C:ILE108 4.7 53.4 1.0
N C:GLY106 4.7 46.6 1.0
C C:HIS107 4.8 48.8 1.0
F2 C:BEF802 4.8 70.1 1.0
O2B C:GDP801 4.8 56.4 1.0
CD1 C:ILE108 4.8 55.4 1.0
C C:ILE105 4.8 45.5 1.0
N C:HIS107 4.8 44.3 1.0
C C:THR84 4.9 46.4 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 Dec 14 00:13:58 2020

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