Magnesium in PDB 6b9f: Human ATL1 Mutant - F151S Bound to GDPALF4-

The structure of Human ATL1 Mutant - F151S Bound to GDPALF4-, PDB code: 6b9f was solved by J.P.O'donnell, H.Sondermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.68 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.613, 115.721, 184.300, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 22.2

The structure of Human ATL1 Mutant - F151S Bound to GDPALF4- also contains other interesting chemical elements:

Fluorine	(F)	8 atoms
Aluminium	(Al)	2 atoms

The binding sites of Magnesium atom in the Human ATL1 Mutant - F151S Bound to GDPALF4- (pdb code 6b9f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human ATL1 Mutant - F151S Bound to GDPALF4-, PDB code: 6b9f:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human ATL1 Mutant - F151S Bound to GDPALF4-


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human ATL1 Mutant - F151S Bound to GDPALF4- within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:19.2 occ:1.00 O1B A:GDP506 2.0 13.1 1.0 O A:HOH663 2.0 20.2 1.0 F3 A:ALF507 2.0 17.8 1.0 OG A:SER81 2.1 21.2 1.0 OG1 A:THR120 2.1 15.9 1.0 O A:HOH677 2.4 22.8 1.0 PB A:GDP506 3.1 17.5 1.0 CB A:THR120 3.2 18.1 1.0 CB A:SER81 3.2 21.8 1.0 O3B A:GDP506 3.4 17.8 1.0 AL A:ALF507 3.5 18.8 1.0 F1 A:ALF507 3.6 22.4 1.0 N A:SER81 3.8 19.7 1.0 OD2 A:ASP146 4.0 24.9 1.0 CA A:SER81 4.1 19.4 1.0 N A:THR120 4.1 22.6 1.0 CG2 A:THR120 4.2 22.1 1.0 OD1 A:ASP146 4.2 23.2 1.0 O A:HOH670 4.2 22.7 1.0 O2B A:GDP506 4.2 17.4 1.0 CA A:THR120 4.2 18.6 1.0 F2 A:ALF507 4.2 16.2 1.0 O2A A:GDP506 4.2 20.3 1.0 O3A A:GDP506 4.3 15.2 1.0 O A:SER111 4.3 21.8 1.0 O A:THR147 4.3 19.5 1.0 CG A:ASP146 4.5 24.9 1.0 O1A A:GDP506 4.5 14.9 1.0 PA A:GDP506 4.5 20.9 1.0 O A:HOH658 4.6 17.9 1.0 CB A:LYS80 4.8 17.1 1.0 C A:LYS80 4.9 16.0 1.0 NZ A:LYS80 4.9 15.3 1.0 CE A:LYS80 5.0 14.3 1.0

Magnesium binding site 2 out of 2 in the Human ATL1 Mutant - F151S Bound to GDPALF4-


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human ATL1 Mutant - F151S Bound to GDPALF4- within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg505 b:23.4 occ:1.00 F2 B:ALF507 1.9 25.1 1.0 O2B B:GDP506 2.0 19.8 1.0 O B:HOH681 2.1 20.7 1.0 OG1 B:THR120 2.1 22.8 1.0 O B:HOH665 2.1 22.4 1.0 OG B:SER81 2.1 25.2 1.0 CB B:THR120 3.1 20.4 1.0 PB B:GDP506 3.1 20.5 1.0 CB B:SER81 3.3 19.9 1.0 O3B B:GDP506 3.4 24.9 1.0 AL B:ALF507 3.5 22.9 1.0 F4 B:ALF507 3.6 26.1 1.0 N B:SER81 3.7 23.0 1.0 OD2 B:ASP146 4.0 27.9 1.0 CA B:SER81 4.1 20.5 1.0 CG2 B:THR120 4.1 24.0 1.0 O1B B:GDP506 4.1 17.9 1.0 N B:THR120 4.1 29.0 1.0 F3 B:ALF507 4.2 23.9 1.0 O B:HOH637 4.2 25.9 1.0 OD1 B:ASP146 4.2 29.4 1.0 CA B:THR120 4.3 23.0 1.0 O3A B:GDP506 4.3 20.5 1.0 O B:THR147 4.3 23.9 1.0 O1A B:GDP506 4.4 20.6 1.0 O B:SER111 4.4 25.0 1.0 O2A B:GDP506 4.5 23.9 1.0 CG B:ASP146 4.5 29.8 1.0 CB B:LYS80 4.6 17.2 1.0 PA B:GDP506 4.6 22.4 1.0 O B:HOH646 4.6 20.8 1.0 C B:LYS80 4.8 31.6 1.0 CE B:LYS80 4.8 12.5 1.0 NZ B:LYS80 4.9 17.5 1.0

J.P.O'donnell, L.J.Byrnes, R.B.Cooley, H.Sondermann. A Hereditary Spastic Paraplegia-Associated Atlastin Variant Exhibits Defective Allosteric Coupling in the Catalytic Core. J. Biol. Chem. V. 293 687 2018.
ISSN: ESSN 1083-351X
PubMed: 29180453
DOI: 10.1074/JBC.RA117.000380