Magnesium in PDB 5jcz: RAB11 Bound to Myova-Gtd

The structure of RAB11 Bound to Myova-Gtd, PDB code: 5jcz was solved by O.Pylypenko, W.Attanda, C.Gauquelin, G.Malherbes, A.Houdusse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.88 / 2.06
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	215.790, 128.420, 89.020, 90.00, 98.27, 90.00
R / Rfree (%)	18 / 20.8

The structure of RAB11 Bound to Myova-Gtd also contains other interesting chemical elements:

Fluorine

(F)

9 atoms

The binding sites of Magnesium atom in the RAB11 Bound to Myova-Gtd (pdb code 5jcz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the RAB11 Bound to Myova-Gtd, PDB code: 5jcz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the RAB11 Bound to Myova-Gtd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of RAB11 Bound to Myova-Gtd within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:43.0 occ:1.00 O1B A:GDP202 2.0 35.9 1.0 OG1 A:THR43 2.1 40.4 1.0 O A:HOH326 2.1 40.1 1.0 OG A:SER25 2.1 39.0 1.0 O A:HOH316 2.1 38.8 1.0 F3 A:BEF203 2.1 40.8 1.0 BE A:BEF203 3.2 43.3 1.0 CB A:SER25 3.2 39.5 1.0 PB A:GDP202 3.2 38.0 1.0 CB A:THR43 3.3 36.9 1.0 O3B A:GDP202 3.3 38.0 1.0 N A:THR43 3.8 42.8 1.0 N A:SER25 3.9 39.7 1.0 F1 A:BEF203 3.9 38.7 1.0 O2A A:GDP202 4.0 41.8 1.0 OD2 A:ASP66 4.0 46.1 1.0 CA A:THR43 4.0 40.8 1.0 CA A:SER25 4.1 39.3 1.0 F2 A:BEF203 4.2 40.2 1.0 O A:HOH383 4.2 41.0 1.0 O2B A:GDP202 4.2 37.0 1.0 OD1 A:ASP66 4.2 41.6 1.0 O3A A:GDP202 4.3 41.4 1.0 CG2 A:THR43 4.4 36.2 1.0 PA A:GDP202 4.5 43.0 1.0 CG A:ASP66 4.5 41.2 1.0 O1A A:GDP202 4.6 39.7 1.0 O A:LYS41 4.6 44.6 1.0 O A:THR67 4.7 35.9 1.0 C A:SER42 4.8 43.8 1.0 O A:HOH452 4.8 61.0 1.0 CB A:LYS24 4.8 36.5 1.0 CE A:LYS24 4.9 39.3 1.0 C A:LYS24 5.0 40.7 1.0

Magnesium binding site 2 out of 4 in the RAB11 Bound to Myova-Gtd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of RAB11 Bound to Myova-Gtd within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1905 b:85.2 occ:1.00 O E:HOH2091 2.3 63.0 1.0 O C:ARG1809 2.3 75.7 1.0 O E:HOH2096 2.4 70.3 1.0 O C:ARG1807 2.5 72.9 1.0 OD1 E:ASN1590 2.7 67.3 1.0 C C:ARG1809 3.6 62.8 1.0 C C:ARG1807 3.6 70.6 1.0 CG E:ASN1590 3.7 67.1 1.0 CA E:ASN1590 3.7 59.1 1.0 O E:ASN1590 3.9 64.6 1.0 CB E:ASN1590 4.0 61.5 1.0 O C:HOH2006 4.2 66.1 1.0 O E:THR1589 4.2 67.3 1.0 O C:HOH2007 4.2 72.5 1.0 C E:ASN1590 4.3 58.0 1.0 CA C:ARG1807 4.3 72.0 1.0 N C:ARG1809 4.3 72.7 1.0 C C:ASP1808 4.4 80.8 1.0 N C:LYS1810 4.4 63.2 1.0 CA C:LYS1810 4.5 66.8 1.0 OD1 E:ASN1522 4.5 63.6 1.0 O E:HOH2161 4.5 77.4 1.0 CA C:ARG1809 4.5 64.8 1.0 O C:ASP1808 4.6 86.2 1.0 N C:ASP1808 4.6 70.1 1.0 N E:ASN1590 4.8 61.0 1.0 O C:LEU1806 4.8 69.2 1.0 CA C:ASP1808 4.8 80.5 1.0 ND2 E:ASN1590 4.9 67.0 1.0 C E:THR1589 4.9 68.5 1.0

Magnesium binding site 3 out of 4 in the RAB11 Bound to Myova-Gtd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of RAB11 Bound to Myova-Gtd within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:47.5 occ:1.00 OG D:SER25 2.1 44.7 1.0 O D:HOH309 2.1 40.6 1.0 O D:HOH326 2.1 42.6 1.0 F3 D:BEF203 2.1 46.0 1.0 O2B D:GDP202 2.1 41.7 1.0 OG1 D:THR43 2.1 51.0 1.0 CB D:SER25 3.2 46.6 1.0 BE D:BEF203 3.2 46.8 1.0 CB D:THR43 3.3 51.6 1.0 PB D:GDP202 3.3 47.0 1.0 O1B D:GDP202 3.4 45.9 1.0 N D:THR43 3.7 47.3 1.0 O1A D:GDP202 3.9 49.1 1.0 F1 D:BEF203 3.9 49.2 1.0 OD2 D:ASP66 3.9 46.4 1.0 O D:HOH320 4.0 43.9 1.0 N D:SER25 4.0 44.6 1.0 CA D:THR43 4.0 47.3 1.0 CA D:SER25 4.1 48.8 1.0 F2 D:BEF203 4.2 49.3 1.0 O3B D:GDP202 4.2 48.9 1.0 OD1 D:ASP66 4.3 47.1 1.0 O3A D:GDP202 4.4 49.2 1.0 CG2 D:THR43 4.4 45.9 1.0 PA D:GDP202 4.5 49.2 1.0 O D:LYS41 4.5 52.5 1.0 CG D:ASP66 4.5 47.6 1.0 O2A D:GDP202 4.6 49.5 1.0 O D:THR67 4.7 45.7 1.0 C D:SER42 4.7 48.0 1.0 C D:THR67 5.0 48.2 1.0 CB D:LYS24 5.0 43.6 1.0 CA D:SER42 5.0 54.2 0.5 CA D:SER42 5.0 54.3 0.5

Magnesium binding site 4 out of 4 in the RAB11 Bound to Myova-Gtd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of RAB11 Bound to Myova-Gtd within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg201 b:42.1 occ:0.30 O I:HOH301 2.1 56.8 1.0 O I:HOH303 2.1 88.1 1.0 OG I:SER25 2.1 40.0 0.3 OG1 I:THR43 2.1 43.1 0.3 F3 I:BEF203 2.1 40.8 0.3 O1B I:GDP202 2.1 48.1 0.3 BE I:BEF203 3.1 41.9 0.3 CB I:SER25 3.1 48.2 0.3 CB I:THR43 3.2 44.3 0.3 PB I:GDP202 3.3 45.6 0.3 O3B I:GDP202 3.3 45.8 0.3 N I:THR43 3.6 47.9 0.3 O2A I:GDP202 3.8 53.8 0.3 CA I:THR43 3.9 47.3 0.3 OD2 I:ASP66 4.0 33.9 0.3 F1 I:BEF203 4.0 40.1 0.3 N I:SER25 4.0 46.1 0.3 F2 I:BEF203 4.0 40.2 0.3 CA I:SER25 4.1 46.6 0.3 O2B I:GDP202 4.3 44.0 0.3 O3A I:GDP202 4.4 54.1 0.3 O I:LYS41 4.4 50.0 0.3 PA I:GDP202 4.4 54.8 0.3 CG2 I:THR43 4.4 45.4 0.3 OD1 I:ASP66 4.5 46.2 0.3 O1A I:GDP202 4.5 52.1 0.3 C I:SER42 4.6 47.9 0.3 CG I:ASP66 4.6 42.3 0.3 CA I:SER42 4.9 52.5 0.3 O I:HOH307 4.9 91.8 1.0 O I:THR67 5.0 55.1 0.3

O.Pylypenko, T.Welz, J.Tittel, M.Kollmar, F.Chardon, G.Malherbe, S.Weiss, C.I.Michel, A.Samol-Wolf, A.T.Grasskamp, A.Hume, B.Goud, B.Baron, P.England, M.A.Titus, P.Schwille, T.Weidemann, A.Houdusse, E.Kerkhoff. Coordinated Recruitment of Spir Actin Nucleators and Myosin V Motors to RAB11 Vesicle Membranes. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27623148
DOI: 10.7554/ELIFE.17523