Magnesium in PDB 3qbt: Crystal Structure of OCRL1 540-678 in Complex with RAB8A:Gppnhp

All present enzymatic activity of Crystal Structure of OCRL1 540-678 in Complex with RAB8A:Gppnhp:
3.1.3.36;

The structure of Crystal Structure of OCRL1 540-678 in Complex with RAB8A:Gppnhp, PDB code: 3qbt was solved by X.Hou, N.Hagemann, S.Schoebel, W.Blankenfeldt, R.S.Goody, K.S.Erdmann, A.Itzen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.38 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	157.147, 55.340, 173.836, 90.00, 91.93, 90.00
R / Rfree (%)	20.8 / 24.1

The binding sites of Magnesium atom in the Crystal Structure of OCRL1 540-678 in Complex with RAB8A:Gppnhp (pdb code 3qbt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of OCRL1 540-678 in Complex with RAB8A:Gppnhp, PDB code: 3qbt:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of OCRL1 540-678 in Complex with RAB8A:Gppnhp


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 OCRL1 540-678 in Complex with RAB8A:Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:24.1 occ:1.00 O2G A:GNP200 2.0 22.3 1.0 O2B A:GNP200 2.1 23.0 1.0 OG1 A:THR22 2.1 23.5 1.0 O A:HOH219 2.2 26.5 1.0 O A:HOH566 2.2 22.7 1.0 OG1 A:THR40 2.2 25.2 1.0 PG A:GNP200 3.2 24.0 1.0 CB A:THR22 3.2 23.0 1.0 CB A:THR40 3.3 28.4 1.0 PB A:GNP200 3.3 23.8 1.0 N3B A:GNP200 3.5 24.2 1.0 N A:THR40 3.7 30.8 1.0 N A:THR22 3.9 23.2 1.0 OD2 A:ASP63 4.0 27.9 1.0 O3G A:GNP200 4.1 25.0 1.0 CA A:THR40 4.1 28.9 1.0 CA A:THR22 4.1 22.3 1.0 O2A A:GNP200 4.1 24.5 1.0 O A:HOH565 4.2 31.7 1.0 OD1 A:ASP63 4.2 25.0 1.0 O1B A:GNP200 4.3 18.5 1.0 CG2 A:THR22 4.3 24.7 1.0 O1G A:GNP200 4.3 26.4 1.0 O3A A:GNP200 4.3 23.2 1.0 CG2 A:THR40 4.4 27.6 1.0 O A:THR64 4.4 23.8 1.0 CG A:ASP63 4.5 23.1 1.0 PA A:GNP200 4.5 26.8 1.0 O A:ILE38 4.6 35.4 1.0 O1A A:GNP200 4.6 23.1 1.0 C A:SER39 4.7 33.7 1.0 CA A:SER39 4.8 35.5 1.0 CB A:LYS21 4.9 23.7 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of OCRL1 540-678 in Complex with RAB8A:Gppnhp


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 OCRL1 540-678 in Complex with RAB8A:Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:18.6 occ:1.00 O2G C:GNP200 2.0 19.7 1.0 O2B C:GNP200 2.0 17.5 1.0 OG1 C:THR40 2.1 17.4 1.0 OG1 C:THR22 2.1 17.9 1.0 O C:HOH252 2.2 22.6 1.0 O C:HOH211 2.3 18.2 1.0 PG C:GNP200 3.1 20.4 1.0 CB C:THR40 3.2 21.0 1.0 PB C:GNP200 3.2 18.9 1.0 CB C:THR22 3.2 19.0 1.0 N3B C:GNP200 3.5 16.9 1.0 N C:THR40 3.7 24.4 1.0 O3G C:GNP200 3.8 18.6 1.0 N C:THR22 3.9 18.5 1.0 CA C:THR40 4.0 21.6 1.0 OD2 C:ASP63 4.1 23.4 1.0 O2A C:GNP200 4.1 18.0 1.0 CA C:THR22 4.1 18.7 1.0 OD1 C:ASP63 4.2 26.6 1.0 CG2 C:THR40 4.2 18.9 1.0 CG2 C:THR22 4.3 19.8 1.0 O1B C:GNP200 4.3 15.7 1.0 O3A C:GNP200 4.3 16.6 1.0 O1G C:GNP200 4.3 18.4 1.0 O C:HOH177 4.3 30.1 1.0 O C:THR64 4.4 20.1 1.0 PA C:GNP200 4.5 21.1 1.0 CG C:ASP63 4.5 23.2 1.0 O1A C:GNP200 4.5 17.9 1.0 O C:ILE38 4.6 27.7 1.0 C C:SER39 4.7 26.7 1.0 CA C:SER39 4.9 28.5 1.0 CB C:LYS21 5.0 17.7 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of OCRL1 540-678 in Complex with RAB8A:Gppnhp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of OCRL1 540-678 in Complex with RAB8A:Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg201 b:30.2 occ:1.00 O2B E:GNP200 2.0 23.4 1.0 O2G E:GNP200 2.1 29.2 1.0 OG1 E:THR22 2.1 27.8 1.0 O E:HOH309 2.1 27.6 1.0 OG1 E:THR40 2.2 30.4 1.0 O E:HOH187 2.4 25.3 1.0 PG E:GNP200 3.2 28.1 1.0 CB E:THR40 3.2 31.9 1.0 PB E:GNP200 3.2 27.7 1.0 CB E:THR22 3.3 25.7 1.0 N3B E:GNP200 3.5 26.1 1.0 N E:THR40 3.7 33.1 1.0 O3G E:GNP200 3.9 28.9 1.0 N E:THR22 4.0 25.5 1.0 OD2 E:ASP63 4.0 31.1 1.0 CA E:THR40 4.1 31.6 1.0 O2A E:GNP200 4.2 27.4 1.0 OD1 E:ASP63 4.2 28.9 1.0 CA E:THR22 4.2 26.4 1.0 O1B E:GNP200 4.2 26.5 1.0 CG2 E:THR22 4.3 27.0 1.0 O3A E:GNP200 4.4 27.3 1.0 CG2 E:THR40 4.4 30.7 1.0 O E:HOH185 4.4 35.9 1.0 O1G E:GNP200 4.4 25.8 1.0 O E:THR64 4.5 29.3 1.0 CG E:ASP63 4.5 30.1 1.0 PA E:GNP200 4.6 27.5 1.0 O1A E:GNP200 4.7 27.6 1.0 C E:SER39 4.7 33.6 1.0 O E:ILE38 4.7 35.5 1.0 CB E:LYS21 4.8 25.6 1.0 CA E:SER39 5.0 36.1 1.0 C E:LYS21 5.0 25.4 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of OCRL1 540-678 in Complex with RAB8A:Gppnhp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of OCRL1 540-678 in Complex with RAB8A:Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg201 b:23.2 occ:1.00 O2G G:GNP200 2.0 25.9 1.0 OG1 G:THR40 2.0 26.1 1.0 OG1 G:THR22 2.0 21.5 1.0 O2B G:GNP200 2.0 24.0 1.0 O G:HOH302 2.2 23.5 1.0 O G:HOH192 2.2 22.1 1.0 CB G:THR22 3.1 21.5 1.0 CB G:THR40 3.2 26.3 1.0 PG G:GNP200 3.2 25.5 1.0 PB G:GNP200 3.3 23.6 1.0 N3B G:GNP200 3.6 22.0 1.0 N G:THR40 3.6 26.9 1.0 CA G:THR40 4.0 25.9 1.0 OD2 G:ASP63 4.0 27.5 1.0 N G:THR22 4.0 20.5 1.0 O3G G:GNP200 4.0 25.9 1.0 O2A G:GNP200 4.1 21.2 1.0 CG2 G:THR22 4.1 24.6 1.0 CA G:THR22 4.1 21.1 1.0 OD1 G:ASP63 4.3 29.5 1.0 CG2 G:THR40 4.3 22.3 1.0 O1B G:GNP200 4.3 23.2 1.0 O G:ILE38 4.4 31.6 1.0 O1G G:GNP200 4.4 27.8 1.0 O3A G:GNP200 4.4 26.0 1.0 CG G:ASP63 4.5 27.7 1.0 PA G:GNP200 4.5 24.1 1.0 C G:SER39 4.5 27.9 1.0 O G:THR64 4.6 27.2 1.0 O1A G:GNP200 4.7 23.5 1.0 CA G:SER39 4.8 30.5 1.0

X.Hou, N.Hagemann, S.Schoebel, W.Blankenfeldt, R.S.Goody, K.S.Erdmann, A.Itzen. A Structural Basis For Lowe Syndrome Caused By Mutations in the Rab-Binding Domain of OCRL1. Embo J. V. 30 1659 2011.
ISSN: ISSN 0261-4189
PubMed: 21378754
DOI: 10.1038/EMBOJ.2011.60