Magnesium in PDB 7opq: RAB27A Fusion with SLP2A-RBDA1 Effector Covalent Adduct with CA1 in C188

All present enzymatic activity of RAB27A Fusion with SLP2A-RBDA1 Effector Covalent Adduct with CA1 in C188:
3.6.5.2;

The structure of RAB27A Fusion with SLP2A-RBDA1 Effector Covalent Adduct with CA1 in C188, PDB code: 7opq was solved by M.Jamshidiha, M.Tersa, T.Lanyon-Hogg, I.Perez-Dorado, C.L.Sutherell, E.Devita, R.M.L.Morgan, E.W.Tate, E.Cota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.52 / 2.23
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.71, 76.816, 117.818, 90, 90, 90
R / Rfree (%)	17.7 / 22.4

The binding sites of Magnesium atom in the RAB27A Fusion with SLP2A-RBDA1 Effector Covalent Adduct with CA1 in C188 (pdb code 7opq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the RAB27A Fusion with SLP2A-RBDA1 Effector Covalent Adduct with CA1 in C188, PDB code: 7opq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the RAB27A Fusion with SLP2A-RBDA1 Effector Covalent Adduct with CA1 in C188


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of RAB27A Fusion with SLP2A-RBDA1 Effector Covalent Adduct with CA1 in C188 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:27.1 occ:1.00 O2B A:GNP202 2.0 28.5 1.0 O3G A:GNP202 2.0 29.7 1.0 O A:HOH301 2.1 28.2 1.0 O A:HOH324 2.1 28.1 1.0 OG1 A:THR22 2.1 33.3 1.0 OG1 A:THR40 2.1 34.4 1.0 CB A:THR40 3.1 33.6 1.0 CB A:THR22 3.2 32.0 1.0 PB A:GNP202 3.2 26.7 1.0 PG A:GNP202 3.2 27.6 1.0 N3B A:GNP202 3.5 26.1 1.0 N A:THR40 3.7 31.8 1.0 OD2 A:ASP73 3.9 40.2 1.0 N A:THR22 4.0 28.3 1.0 O1G A:GNP202 4.0 22.9 1.0 CA A:THR40 4.0 31.1 1.0 OD1 A:ASP73 4.0 36.8 1.0 O A:HOH306 4.1 39.4 1.0 O2A A:GNP202 4.1 32.4 1.0 CA A:THR22 4.2 35.2 1.0 CG2 A:THR22 4.2 27.5 1.0 O1B A:GNP202 4.3 30.0 1.0 O3A A:GNP202 4.3 30.6 1.0 CG2 A:THR40 4.3 32.6 1.0 CG A:ASP73 4.4 38.0 1.0 O2G A:GNP202 4.5 28.5 1.0 PA A:GNP202 4.6 30.9 1.0 O A:ILE38 4.6 30.8 1.0 O1A A:GNP202 4.7 27.2 1.0 C A:THR39 4.7 30.9 1.0 O A:THR74 4.7 37.8 1.0 CA A:THR39 4.9 36.0 1.0 O A:HOH305 5.0 37.4 1.0

Magnesium binding site 2 out of 2 in the RAB27A Fusion with SLP2A-RBDA1 Effector Covalent Adduct with CA1 in C188


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of RAB27A Fusion with SLP2A-RBDA1 Effector Covalent Adduct with CA1 in C188 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:32.3 occ:1.00 O3G B:GNP202 2.0 34.1 1.0 O B:HOH328 2.0 31.3 1.0 O B:HOH315 2.1 31.2 1.0 O2B B:GNP202 2.1 27.9 1.0 OG1 B:THR40 2.1 38.6 1.0 OG1 B:THR22 2.1 32.9 1.0 CB B:THR40 3.1 34.2 1.0 PG B:GNP202 3.2 32.9 1.0 CB B:THR22 3.2 32.7 1.0 PB B:GNP202 3.3 32.3 1.0 N3B B:GNP202 3.5 37.1 1.0 N B:THR40 3.7 35.3 1.0 O1G B:GNP202 3.8 32.2 1.0 N B:THR22 4.0 31.9 1.0 CA B:THR40 4.0 35.1 1.0 OD2 B:ASP73 4.1 43.5 1.0 OD1 B:ASP73 4.1 41.4 1.0 O2A B:GNP202 4.2 33.1 1.0 CG2 B:THR40 4.2 31.9 1.0 CA B:THR22 4.2 35.8 1.0 O B:HOH309 4.3 37.9 1.0 CG2 B:THR22 4.3 29.8 1.0 O1B B:GNP202 4.3 34.3 1.0 O3A B:GNP202 4.4 30.8 1.0 O2G B:GNP202 4.4 34.9 1.0 CG B:ASP73 4.4 45.4 1.0 O B:THR74 4.5 39.9 1.0 PA B:GNP202 4.6 33.1 1.0 C B:THR39 4.7 36.6 1.0 O B:ILE38 4.7 39.8 1.0 O1A B:GNP202 4.8 31.4 1.0 CE B:LYS21 5.0 34.9 1.0 CA B:THR39 5.0 36.8 1.0

M.Jamshidiha, T.Lanyon-Hogg, C.L.Sutherell, G.B.Craven, M.Tersa, E.De Vita, D.Brustur, I.Perez-Dorado, S.Hassan, R.Petracca, R.M.Morgan, M.Sanz-Hernandez, J.C.Norman, A.Armstrong, D.J.Mann, E.Cota, E.W.Tate. Identification of the First Structurally Validated Covalent Ligands of the Small Gtpase RAB27A. Rsc Med Chem V. 13 150 2022.
ISSN: ESSN 2632-8682
PubMed: 35308027
DOI: 10.1039/D1MD00225B