Magnesium in PDB 9ikq: Crystal Structure of Optn Lzd in Complex with Gtp-Bound RAB8A(Q67L)

All present enzymatic activity of Crystal Structure of Optn Lzd in Complex with Gtp-Bound RAB8A(Q67L):
3.6.5.2;

The structure of Crystal Structure of Optn Lzd in Complex with Gtp-Bound RAB8A(Q67L), PDB code: 9ikq was solved by J.Zhang, L.F.Pan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.19 / 1.93
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.218, 69.432, 110.337, 90, 90, 90
R / Rfree (%)	17.4 / 21.8

The binding sites of Magnesium atom in the Crystal Structure of Optn Lzd in Complex with Gtp-Bound RAB8A(Q67L) (pdb code 9ikq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Optn Lzd in Complex with Gtp-Bound RAB8A(Q67L), PDB code: 9ikq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Optn Lzd in Complex with Gtp-Bound RAB8A(Q67L)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Optn Lzd in Complex with Gtp-Bound RAB8A(Q67L) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:19.8 occ:1.00 O1G A:GTP201 2.0 17.4 1.0 O2B A:GTP201 2.0 15.9 1.0 OG1 A:THR22 2.1 21.7 1.0 O A:HOH321 2.1 17.2 1.0 OG1 A:THR40 2.1 17.0 1.0 O A:HOH303 2.1 15.2 1.0 CB A:THR22 3.2 18.8 1.0 CB A:THR40 3.2 22.2 1.0 PG A:GTP201 3.2 19.9 1.0 PB A:GTP201 3.2 18.4 1.0 O3B A:GTP201 3.5 17.8 1.0 N A:THR40 3.7 20.9 1.0 O3G A:GTP201 3.9 15.8 1.0 N A:THR22 3.9 16.6 1.0 OD2 A:ASP63 4.0 21.3 1.0 CA A:THR40 4.0 22.8 1.0 O1A A:GTP201 4.1 13.4 1.0 OD1 A:ASP63 4.1 18.8 1.0 CA A:THR22 4.1 15.7 1.0 CG2 A:THR22 4.2 18.1 1.0 O A:HOH356 4.2 23.4 1.0 O1B A:GTP201 4.3 13.1 1.0 O3A A:GTP201 4.3 20.1 1.0 CG2 A:THR40 4.3 17.6 1.0 O2G A:GTP201 4.4 19.5 1.0 CG A:ASP63 4.5 21.2 1.0 O2A A:GTP201 4.5 17.5 1.0 PA A:GTP201 4.5 21.3 1.0 O A:ILE38 4.6 25.2 1.0 C A:SER39 4.7 27.1 1.0 O A:THR64 4.7 17.9 1.0 CA A:SER39 4.9 26.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Optn Lzd in Complex with Gtp-Bound RAB8A(Q67L)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Optn Lzd in Complex with Gtp-Bound RAB8A(Q67L) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg206 b:17.9 occ:1.00 O1G B:GTP201 2.1 16.0 1.0 OG1 B:THR22 2.1 17.8 1.0 O B:HOH347 2.1 16.2 1.0 O2B B:GTP201 2.1 14.2 1.0 O B:HOH321 2.1 18.0 1.0 OG1 B:THR40 2.2 18.9 1.0 CB B:THR22 3.1 18.6 1.0 CB B:THR40 3.2 23.5 1.0 PB B:GTP201 3.3 18.7 1.0 PG B:GTP201 3.3 19.7 1.0 O3B B:GTP201 3.5 21.3 1.0 N B:THR40 3.7 19.9 1.0 N B:THR22 3.9 17.6 1.0 O3G B:GTP201 4.0 18.2 1.0 OD2 B:ASP63 4.0 18.1 1.0 CA B:THR40 4.1 21.2 1.0 CA B:THR22 4.1 15.4 1.0 OD1 B:ASP63 4.1 22.7 1.0 O1A B:GTP201 4.1 16.7 1.0 O B:HOH313 4.2 30.5 1.0 CG2 B:THR22 4.2 16.2 1.0 O1B B:GTP201 4.3 18.2 1.0 O3A B:GTP201 4.3 22.3 1.0 CG2 B:THR40 4.4 17.9 1.0 CG B:ASP63 4.4 21.4 1.0 O2G B:GTP201 4.5 20.7 1.0 O2A B:GTP201 4.5 19.8 1.0 PA B:GTP201 4.6 19.5 1.0 O B:ILE38 4.7 28.8 1.0 O B:THR64 4.7 19.0 1.0 C B:SER39 4.8 29.9 1.0 CE B:LYS21 5.0 12.9 1.0

J.Zhang, L.Liu, M.Li, H.Liu, X.Gong, Y.Tang, Y.Zhang, X.Zhou, Z.Lin, H.Guo, L.Pan. Molecular Basis of the Recognition of the Active RAB8A By Optineurin. J.Mol.Biol. V. 436 68811 2024.
ISSN: ESSN 1089-8638
PubMed: 39374890
DOI: 10.1016/J.JMB.2024.168811