Magnesium in PDB 2d7c: Crystal Structure of Human RAB11 in Complex with FIP3 Rab- Binding Domain

The structure of Crystal Structure of Human RAB11 in Complex with FIP3 Rab- Binding Domain, PDB code: 2d7c was solved by T.Shiba, H.Koga, H.W.Shin, M.Kawasaki, R.Kato, K.Nakayama, S.Wakatsuki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.75
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	108.717, 120.565, 36.249, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 22.4

The binding sites of Magnesium atom in the Crystal Structure of Human RAB11 in Complex with FIP3 Rab- Binding Domain (pdb code 2d7c). 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 Human RAB11 in Complex with FIP3 Rab- Binding Domain, PDB code: 2d7c:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human RAB11 in Complex with FIP3 Rab- Binding Domain


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 Human RAB11 in Complex with FIP3 Rab- Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:12.0 occ:1.00 O2G A:GTP1001 2.0 9.5 1.0 O2B A:GTP1001 2.1 8.7 1.0 OG A:SER25 2.1 10.1 1.0 OG1 A:THR43 2.1 9.7 1.0 O A:HOH1031 2.2 10.8 1.0 O A:HOH1036 2.3 14.8 1.0 CB A:SER25 3.2 10.8 1.0 CB A:THR43 3.2 10.8 1.0 PG A:GTP1001 3.3 11.1 1.0 PB A:GTP1001 3.3 9.9 1.0 O3B A:GTP1001 3.5 8.6 1.0 N A:THR43 3.7 11.8 1.0 OD1 A:ASP66 3.9 11.1 1.0 N A:SER25 3.9 9.5 1.0 O A:HOH1033 4.0 15.2 1.0 O3G A:GTP1001 4.0 13.1 1.0 CA A:THR43 4.0 11.6 1.0 O2A A:GTP1001 4.0 10.1 1.0 CA A:SER25 4.1 9.5 1.0 OD2 A:ASP66 4.2 12.4 1.0 O1B A:GTP1001 4.3 10.1 1.0 O3A A:GTP1001 4.4 11.0 1.0 O1G A:GTP1001 4.4 10.9 1.0 CG2 A:THR43 4.4 10.7 1.0 CG A:ASP66 4.5 10.7 1.0 O A:LYS41 4.6 16.3 1.0 PA A:GTP1001 4.6 10.7 1.0 C A:SER42 4.7 15.2 1.0 O1A A:GTP1001 4.7 9.3 1.0 O A:HOH1038 4.8 28.8 1.0 O A:THR67 4.8 12.2 1.0 CA A:SER42 4.9 16.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human RAB11 in Complex with FIP3 Rab- Binding Domain


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 Human RAB11 in Complex with FIP3 Rab- Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1102 b:11.6 occ:1.00 O2G B:GTP1101 2.0 9.2 1.0 O2B B:GTP1101 2.0 10.2 1.0 OG1 B:THR43 2.1 11.3 1.0 OG B:SER25 2.1 9.3 1.0 O B:HOH1138 2.2 8.4 1.0 O B:HOH1139 2.2 11.5 1.0 CB B:SER25 3.2 10.3 1.0 CB B:THR43 3.2 13.0 1.0 PG B:GTP1101 3.2 11.0 1.0 PB B:GTP1101 3.3 9.4 1.0 O3B B:GTP1101 3.5 9.7 1.0 N B:THR43 3.7 13.7 1.0 OD1 B:ASP66 3.9 12.0 1.0 O3G B:GTP1101 3.9 11.1 1.0 N B:SER25 3.9 11.2 1.0 O B:HOH1135 4.0 15.8 1.0 CA B:THR43 4.0 12.4 1.0 CA B:SER25 4.1 10.3 1.0 O2A B:GTP1101 4.2 7.6 1.0 OD2 B:ASP66 4.2 11.6 1.0 O1B B:GTP1101 4.3 9.9 1.0 CG2 B:THR43 4.3 12.8 1.0 O3A B:GTP1101 4.3 6.8 1.0 O1G B:GTP1101 4.3 11.2 1.0 CG B:ASP66 4.5 11.8 1.0 PA B:GTP1101 4.6 9.0 1.0 O B:LYS41 4.6 16.1 1.0 C B:SER42 4.7 15.3 1.0 O1A B:GTP1101 4.8 8.2 1.0 O B:THR67 4.8 12.7 1.0 O B:HOH1137 4.8 28.7 1.0 CA B:SER42 5.0 15.3 1.0 CB B:LYS24 5.0 10.6 1.0

T.Shiba, H.Koga, H.W.Shin, M.Kawasaki, R.Kato, K.Nakayama, S.Wakatsuki. Structural Basis For RAB11-Dependent Membrane Recruitment of A Family of RAB11-Interacting Protein 3 (FIP3)/Arfophilin-1. Proc.Natl.Acad.Sci.Usa V. 103 15416 2006.
ISSN: ISSN 0027-8424
PubMed: 17030804
DOI: 10.1073/PNAS.0605357103