Magnesium in PDB 2zet: Crystal Structure of the Small Gtpase RAB27B Complexed with the Slp Homology Domain of SLAC2-A/Melanophilin

The structure of Crystal Structure of the Small Gtpase RAB27B Complexed with the Slp Homology Domain of SLAC2-A/Melanophilin, PDB code: 2zet was solved by M.Kukimoto-Niino, A.Sakamoto, E.Kanno, K.Hanawa-Suetsugu, T.Terada, M.Shirouzu, M.Fukuda, S.Yokoyama, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.28 / 3.00
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	82.208, 82.208, 325.484, 90.00, 90.00, 90.00
R / Rfree (%)	24.7 / 29.6

The structure of Crystal Structure of the Small Gtpase RAB27B Complexed with the Slp Homology Domain of SLAC2-A/Melanophilin also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Small Gtpase RAB27B Complexed with the Slp Homology Domain of SLAC2-A/Melanophilin (pdb code 2zet). 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 the Small Gtpase RAB27B Complexed with the Slp Homology Domain of SLAC2-A/Melanophilin, PDB code: 2zet:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Small Gtpase RAB27B Complexed with the Slp Homology Domain of SLAC2-A/Melanophilin


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 the Small Gtpase RAB27B Complexed with the Slp Homology Domain of SLAC2-A/Melanophilin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:55.0 occ:1.00 O1G A:GTP203 2.4 64.3 1.0 O2B A:GTP203 2.5 51.9 1.0 OG1 A:THR41 2.5 82.4 1.0 OG1 A:THR23 2.6 61.8 1.0 O3B A:GTP203 2.7 58.6 1.0 PB A:GTP203 3.1 54.0 1.0 O2A A:GTP203 3.1 51.0 1.0 PG A:GTP203 3.1 59.9 1.0 CB A:THR23 3.2 48.9 1.0 O1A A:GTP203 3.4 69.7 1.0 PA A:GTP203 3.6 54.5 1.0 N A:THR41 3.7 81.9 1.0 CB A:THR41 3.7 85.7 1.0 O3A A:GTP203 3.8 61.8 1.0 N A:THR23 4.0 51.9 1.0 CA A:THR23 4.2 54.3 1.0 CG2 A:THR23 4.2 46.7 1.0 O3G A:GTP203 4.3 61.0 1.0 CA A:THR41 4.3 81.5 1.0 O2G A:GTP203 4.3 35.5 1.0 O A:ILE39 4.3 90.7 1.0 OD2 A:ASP74 4.3 91.6 1.0 O1B A:GTP203 4.4 62.3 1.0 C A:THR40 4.6 88.1 1.0 CA A:THR40 4.6 88.2 1.0 CG2 A:THR41 4.9 86.5 1.0 C A:ILE39 4.9 94.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Small Gtpase RAB27B Complexed with the Slp Homology Domain of SLAC2-A/Melanophilin


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 the Small Gtpase RAB27B Complexed with the Slp Homology Domain of SLAC2-A/Melanophilin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:42.5 occ:1.00 OG1 B:THR23 2.2 59.3 1.0 O1G B:GTP203 2.4 80.0 1.0 O2B B:GTP203 2.4 65.3 1.0 OG1 B:THR41 2.5 63.3 1.0 O3B B:GTP203 2.8 73.4 1.0 CB B:THR23 2.8 44.1 1.0 PG B:GTP203 3.1 67.4 1.0 PB B:GTP203 3.1 63.8 1.0 O2A B:GTP203 3.3 62.0 1.0 O1A B:GTP203 3.5 78.8 1.0 PA B:GTP203 3.7 74.7 1.0 CB B:THR41 3.7 78.8 1.0 N B:THR41 3.8 80.2 1.0 N B:THR23 3.8 61.7 1.0 CG2 B:THR23 3.9 29.1 1.0 CA B:THR23 3.9 52.8 1.0 O3A B:GTP203 4.0 73.8 1.0 O2G B:GTP203 4.2 64.8 1.0 OD2 B:ASP74 4.2 0.1 1.0 O3G B:GTP203 4.3 75.0 1.0 CA B:THR41 4.3 76.8 1.0 O1B B:GTP203 4.4 69.4 1.0 C B:THR40 4.7 85.0 1.0 OD1 B:ASP74 4.7 0.8 1.0 CA B:THR40 4.8 86.5 1.0 CG2 B:THR41 4.8 81.5 1.0 CG B:ASP74 4.9 0.0 1.0 O B:ILE39 4.9 96.6 1.0

M.Kukimoto-Niino, A.Sakamoto, E.Kanno, K.Hanawa-Suetsugu, T.Terada, M.Shirouzu, M.Fukuda, S.Yokoyama. Structural Basis For the Exclusive Specificity of SLAC2-A/Melanophilin For the RAB27 Gtpases. Structure V. 16 1478 2008.
ISSN: ISSN 0969-2126
PubMed: 18940604
DOI: 10.1016/J.STR.2008.07.014