Magnesium in PDB 2w83: Crystal Structure of the ARF6 Gtpase in Complex with A Specific Effector, JIP4

The structure of Crystal Structure of the ARF6 Gtpase in Complex with A Specific Effector, JIP4, PDB code: 2w83 was solved by T.Isabet, G.Montagnac, K.Regazzoni, B.Raynal, F.El Khadali, M.Franco, P.England, P.Chavrier, A.Houdusse, J.Menetrey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	118.68 / 1.93
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	137.270, 137.270, 165.030, 90.00, 90.00, 120.00
R / Rfree (%)	21.4 / 23.8

The binding sites of Magnesium atom in the Crystal Structure of the ARF6 Gtpase in Complex with A Specific Effector, JIP4 (pdb code 2w83). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the ARF6 Gtpase in Complex with A Specific Effector, JIP4, PDB code: 2w83:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the ARF6 Gtpase in Complex with A Specific Effector, JIP4


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 ARF6 Gtpase in Complex with A Specific Effector, JIP4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1174 b:17.5 occ:1.00 O3G A:GTP1173 2.0 18.9 1.0 OG1 A:THR27 2.1 16.6 1.0 O A:HOH2033 2.1 16.3 1.0 O2B A:GTP1173 2.1 15.5 1.0 OG1 A:THR44 2.1 17.1 1.0 O A:HOH2094 2.2 16.9 1.0 CB A:THR44 3.2 18.2 1.0 CB A:THR27 3.2 17.4 1.0 PG A:GTP1173 3.2 17.5 1.0 PB A:GTP1173 3.3 17.9 1.0 O3B A:GTP1173 3.5 18.0 1.0 O2G A:GTP1173 3.7 17.2 1.0 N A:THR44 3.8 19.5 1.0 N A:THR27 4.0 17.2 1.0 OD2 A:ASP63 4.0 19.2 1.0 CA A:THR44 4.0 18.8 1.0 OD1 A:ASP63 4.1 17.1 1.0 O1A A:GTP1173 4.1 19.4 1.0 CA A:THR27 4.2 16.9 1.0 CG2 A:THR27 4.2 16.4 1.0 O A:HOH2015 4.2 20.8 1.0 CG2 A:THR44 4.3 17.5 1.0 O A:ILE42 4.3 22.1 1.0 O3A A:GTP1173 4.3 17.1 1.0 O1B A:GTP1173 4.4 16.8 1.0 O1G A:GTP1173 4.4 17.3 1.0 CG A:ASP63 4.5 18.1 1.0 PA A:GTP1173 4.6 18.3 1.0 O2A A:GTP1173 4.7 17.2 1.0 C A:PRO43 4.8 20.6 1.0 ND2 A:ASN48 4.9 17.2 1.0 CA A:PRO43 5.0 21.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the ARF6 Gtpase in Complex with A Specific Effector, JIP4


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 ARF6 Gtpase in Complex with A Specific Effector, JIP4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1174 b:30.6 occ:1.00 O2G B:GTP1173 2.0 33.9 1.0 O2B B:GTP1173 2.1 35.0 1.0 OG1 B:THR27 2.1 32.3 1.0 O B:HOH2015 2.2 27.4 1.0 O B:HOH2007 2.2 34.2 1.0 OG1 B:THR44 2.2 37.4 1.0 PG B:GTP1173 3.1 33.4 1.0 PB B:GTP1173 3.3 33.0 1.0 CB B:THR27 3.3 32.4 1.0 CB B:THR44 3.3 37.7 1.0 O3B B:GTP1173 3.5 33.6 1.0 O3G B:GTP1173 3.6 33.8 1.0 N B:THR44 3.9 38.0 1.0 N B:THR27 4.0 32.1 1.0 OD2 B:ASP63 4.1 28.0 1.0 O1A B:GTP1173 4.1 33.3 1.0 CA B:THR44 4.2 37.7 1.0 OD1 B:ASP63 4.2 29.6 1.0 CA B:THR27 4.2 32.3 1.0 O3A B:GTP1173 4.3 34.2 1.0 CG2 B:THR27 4.3 31.9 1.0 O1B B:GTP1173 4.3 32.4 1.0 O1G B:GTP1173 4.3 33.5 1.0 O B:ILE42 4.4 40.4 1.0 CG2 B:THR44 4.4 37.3 1.0 PA B:GTP1173 4.5 32.5 1.0 O2A B:GTP1173 4.6 32.0 1.0 CG B:ASP63 4.6 28.5 1.0 C B:PRO43 4.8 38.6 1.0 CB B:LYS26 5.0 32.5 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the ARF6 Gtpase in Complex with A Specific Effector, JIP4


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 the ARF6 Gtpase in Complex with A Specific Effector, JIP4 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1174 b:17.3 occ:1.00 O E:HOH2029 2.0 15.6 1.0 O3G E:GTP1173 2.0 18.1 1.0 O2B E:GTP1173 2.1 15.5 1.0 OG1 E:THR27 2.1 13.8 1.0 O E:HOH2083 2.1 15.1 1.0 OG1 E:THR44 2.3 17.1 1.0 CB E:THR27 3.1 14.4 1.0 PG E:GTP1173 3.1 17.3 1.0 CB E:THR44 3.2 17.6 1.0 PB E:GTP1173 3.3 16.3 1.0 O3B E:GTP1173 3.5 15.8 1.0 O2G E:GTP1173 3.6 17.5 1.0 N E:THR44 3.8 18.1 1.0 N E:THR27 4.0 14.5 1.0 O1A E:GTP1173 4.1 17.6 1.0 OD2 E:ASP63 4.1 15.8 1.0 CA E:THR44 4.1 18.4 1.0 CG2 E:THR27 4.1 12.3 1.0 CA E:THR27 4.1 14.1 1.0 OD1 E:ASP63 4.1 16.4 1.0 O E:HOH2019 4.3 25.1 1.0 O3A E:GTP1173 4.3 15.7 1.0 CG2 E:THR44 4.3 18.0 1.0 O1B E:GTP1173 4.3 16.7 1.0 O E:ILE42 4.4 19.5 1.0 O1G E:GTP1173 4.4 19.9 1.0 PA E:GTP1173 4.5 17.7 1.0 CG E:ASP63 4.6 15.9 1.0 O2A E:GTP1173 4.6 17.3 1.0 C E:PRO43 4.7 18.8 1.0 ND2 E:ASN48 4.8 17.4 1.0 CA E:PRO43 4.9 19.1 1.0

T.Isabet, G.Montagnac, K.Regazzoni, B.Raynal, F.El Khadali, P.England, M.Franco, P.Chavrier, A.Houdusse, J.Menetrey. The Structural Basis of Arf Effector Specificity: the Crystal Structure of ARF6 in A Complex with JIP4. Embo J. V. 28 2835 2009.
ISSN: ISSN 0261-4189
PubMed: 19644450
DOI: 10.1038/EMBOJ.2009.209