Magnesium in PDB 2j59: Crystal Structure of the ARF1:ARHGAP21-Arfbd Complex

The structure of Crystal Structure of the ARF1:ARHGAP21-Arfbd Complex, PDB code: 2j59 was solved by J.Menetrey, M.Perderiset, J.Cicolari, T.Dubois, N.El Khatib, F.El Khadali, M.Franco, P.Chavrier, A.Houdusse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.1
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.636, 132.136, 146.283, 90.00, 90.01, 90.00
R / Rfree (%)	20.5 / 24.3

The binding sites of Magnesium atom in the Crystal Structure of the ARF1:ARHGAP21-Arfbd Complex (pdb code 2j59). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of the ARF1:ARHGAP21-Arfbd Complex, PDB code: 2j59:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of the ARF1:ARHGAP21-Arfbd Complex


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 ARF1:ARHGAP21-Arfbd Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1182 b:16.0 occ:1.00 O2B A:GTP1181 2.1 13.6 1.0 O3G A:GTP1181 2.1 16.2 1.0 OG1 A:THR31 2.1 12.8 1.0 OG1 A:THR48 2.1 13.2 1.0 O A:HOH3074 2.1 14.5 1.0 O A:HOH3188 2.2 13.9 1.0 CB A:THR48 3.2 14.7 1.0 CB A:THR31 3.2 13.9 1.0 PG A:GTP1181 3.2 14.9 1.0 PB A:GTP1181 3.3 12.8 1.0 O3B A:GTP1181 3.5 14.5 1.0 O2G A:GTP1181 3.7 15.8 1.0 N A:THR48 3.8 14.2 1.0 N A:THR31 4.0 13.3 1.0 OD2 A:ASP67 4.0 14.0 1.0 OD1 A:ASP67 4.1 15.0 1.0 CA A:THR48 4.1 14.7 1.0 O M:HOH3061 4.1 10.9 1.0 O2A A:GTP1181 4.1 13.9 1.0 CA A:THR31 4.2 13.8 1.0 CG2 A:THR31 4.2 12.8 1.0 O A:ILE46 4.2 14.9 1.0 CG2 A:THR48 4.3 14.9 1.0 O3A A:GTP1181 4.3 13.4 1.0 O1B A:GTP1181 4.3 13.8 1.0 O1G A:GTP1181 4.4 13.8 1.0 CG A:ASP67 4.5 15.2 1.0 PA A:GTP1181 4.6 13.5 1.0 O1A A:GTP1181 4.6 12.5 1.0 C A:PRO47 4.8 14.7 1.0 ND2 A:ASN52 4.8 16.1 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of the ARF1:ARHGAP21-Arfbd Complex


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 ARF1:ARHGAP21-Arfbd Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1182 b:14.9 occ:1.00 OG1 B:THR31 2.0 12.6 1.0 O3G B:GTP1181 2.0 14.4 1.0 OG1 B:THR48 2.1 12.7 1.0 O2B B:GTP1181 2.1 13.5 1.0 O B:HOH3064 2.1 13.4 1.0 O B:HOH3033 2.2 14.8 1.0 CB B:THR31 3.1 12.7 1.0 CB B:THR48 3.1 14.0 1.0 PG B:GTP1181 3.2 14.1 1.0 PB B:GTP1181 3.3 12.8 1.0 O3B B:GTP1181 3.6 12.7 1.0 O2G B:GTP1181 3.8 15.7 1.0 N B:THR48 3.8 13.3 1.0 N B:THR31 3.8 12.5 1.0 OD1 B:ASP67 4.0 14.2 1.0 OD2 B:ASP67 4.0 14.7 1.0 CA B:THR31 4.0 12.8 1.0 CA B:THR48 4.1 14.2 1.0 O2A B:GTP1181 4.1 14.3 1.0 O N:HOH3046 4.2 15.3 1.0 CG2 B:THR48 4.2 13.8 1.0 CG2 B:THR31 4.2 11.9 1.0 O3A B:GTP1181 4.3 14.3 1.0 O B:ILE46 4.4 13.9 1.0 O1B B:GTP1181 4.4 12.5 1.0 CG B:ASP67 4.4 14.7 1.0 O1G B:GTP1181 4.5 14.3 1.0 PA B:GTP1181 4.5 13.4 1.0 O1A B:GTP1181 4.5 13.5 1.0 ND2 B:ASN52 4.7 13.1 1.0 C B:PRO47 4.9 14.1 1.0 C B:LYS30 5.0 12.8 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of the ARF1:ARHGAP21-Arfbd Complex


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 ARF1:ARHGAP21-Arfbd Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1182 b:17.5 occ:1.00 OG1 C:THR31 1.9 14.6 1.0 O2B C:GTP1181 2.0 13.6 1.0 O C:HOH3060 2.1 19.3 1.0 O3G C:GTP1181 2.1 17.0 1.0 O C:HOH3036 2.1 15.6 1.0 OG1 C:THR48 2.2 15.8 1.0 CB C:THR31 3.1 13.6 1.0 PB C:GTP1181 3.2 14.7 1.0 CB C:THR48 3.2 16.7 1.0 PG C:GTP1181 3.3 17.8 1.0 O3B C:GTP1181 3.6 16.5 1.0 O2G C:GTP1181 3.8 16.9 1.0 N C:THR31 3.8 13.4 1.0 N C:THR48 3.9 16.6 1.0 O2A C:GTP1181 4.0 17.4 1.0 OD2 C:ASP67 4.0 13.4 1.0 CA C:THR31 4.0 13.4 1.0 OD1 C:ASP67 4.1 11.4 1.0 CG2 C:THR31 4.2 11.8 1.0 CA C:THR48 4.2 16.7 1.0 O O:HOH3031 4.2 9.8 1.0 O3A C:GTP1181 4.3 15.5 1.0 CG2 C:THR48 4.3 16.0 1.0 O C:ILE46 4.3 16.4 1.0 O1B C:GTP1181 4.3 15.5 1.0 PA C:GTP1181 4.5 16.8 1.0 CG C:ASP67 4.5 13.4 1.0 O1G C:GTP1181 4.5 18.7 1.0 O1A C:GTP1181 4.6 16.2 1.0 ND2 C:ASN52 4.8 13.6 1.0 C C:PRO47 4.9 16.8 1.0 C C:LYS30 5.0 13.7 1.0 CB C:LYS30 5.0 13.8 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of the ARF1:ARHGAP21-Arfbd Complex


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 the ARF1:ARHGAP21-Arfbd Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1182 b:15.7 occ:1.00 O3G D:GTP1181 2.1 15.2 1.0 OG1 D:THR31 2.1 15.2 1.0 O2B D:GTP1181 2.1 12.2 1.0 O D:HOH3063 2.1 9.8 1.0 OG1 D:THR48 2.2 16.6 1.0 O D:HOH3035 2.2 13.9 1.0 CB D:THR48 3.1 16.6 1.0 CB D:THR31 3.2 14.3 1.0 PG D:GTP1181 3.2 15.4 1.0 PB D:GTP1181 3.3 12.5 1.0 O3B D:GTP1181 3.5 13.3 1.0 O2G D:GTP1181 3.8 14.4 1.0 N D:THR31 3.9 13.8 1.0 N D:THR48 3.9 16.8 1.0 OD1 D:ASP67 3.9 15.1 1.0 OD2 D:ASP67 4.0 14.5 1.0 CA D:THR31 4.1 14.1 1.0 CA D:THR48 4.1 16.7 1.0 CG2 D:THR48 4.2 16.1 1.0 CG2 D:THR31 4.3 13.9 1.0 O2A D:GTP1181 4.3 15.1 1.0 O P:HOH3032 4.3 10.9 1.0 O1B D:GTP1181 4.4 12.3 1.0 O3A D:GTP1181 4.4 12.6 1.0 CG D:ASP67 4.4 15.2 1.0 O D:ILE46 4.4 15.6 1.0 O1G D:GTP1181 4.5 15.5 1.0 PA D:GTP1181 4.7 14.8 1.0 O1A D:GTP1181 4.7 14.3 1.0 ND2 D:ASN52 4.8 13.1 1.0 C D:PRO47 4.9 16.8 1.0 CB D:LYS30 4.9 13.7 1.0 C D:LYS30 5.0 13.4 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of the ARF1:ARHGAP21-Arfbd Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the ARF1:ARHGAP21-Arfbd Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1182 b:14.6 occ:1.00 O3G E:GTP1181 2.0 15.2 1.0 O2B E:GTP1181 2.0 12.0 1.0 O E:HOH3076 2.1 14.6 1.0 OG1 E:THR31 2.1 11.0 1.0 OG1 E:THR48 2.2 12.5 1.0 O E:HOH3038 2.2 11.7 1.0 PG E:GTP1181 3.2 15.4 1.0 CB E:THR31 3.2 12.9 1.0 PB E:GTP1181 3.2 12.9 1.0 CB E:THR48 3.3 13.8 1.0 O3B E:GTP1181 3.5 13.7 1.0 O2G E:GTP1181 3.8 16.2 1.0 N E:THR31 3.8 12.5 1.0 N E:THR48 3.9 14.0 1.0 OD1 E:ASP67 4.0 12.9 1.0 OD2 E:ASP67 4.1 12.6 1.0 CA E:THR31 4.1 12.8 1.0 O2A E:GTP1181 4.1 14.7 1.0 O E:HOH3040 4.2 10.2 1.0 CA E:THR48 4.2 13.9 1.0 CG2 E:THR31 4.3 12.3 1.0 O1B E:GTP1181 4.3 11.9 1.0 O3A E:GTP1181 4.3 14.5 1.0 CG2 E:THR48 4.4 13.4 1.0 O E:ILE46 4.4 12.8 1.0 O1G E:GTP1181 4.4 15.9 1.0 CG E:ASP67 4.5 13.1 1.0 PA E:GTP1181 4.5 14.0 1.0 O1A E:GTP1181 4.6 14.1 1.0 ND2 E:ASN52 4.9 12.2 1.0 C E:PRO47 4.9 14.0 1.0 C E:LYS30 4.9 12.9 1.0 CB E:LYS30 5.0 12.1 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of the ARF1:ARHGAP21-Arfbd Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the ARF1:ARHGAP21-Arfbd Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1182 b:20.0 occ:1.00 OG1 F:THR31 2.0 17.8 1.0 O3G F:GTP1181 2.1 18.7 1.0 OG1 F:THR48 2.1 21.5 1.0 O F:HOH3157 2.1 15.4 1.0 O F:HOH3059 2.1 15.9 1.0 O2B F:GTP1181 2.1 14.5 1.0 CB F:THR31 3.1 16.7 1.0 CB F:THR48 3.2 20.4 1.0 PG F:GTP1181 3.3 17.5 1.0 PB F:GTP1181 3.3 16.4 1.0 O3B F:GTP1181 3.6 17.6 1.0 O2G F:GTP1181 3.8 17.5 1.0 N F:THR48 3.9 20.0 1.0 N F:THR31 3.9 16.0 1.0 OD2 F:ASP67 4.0 19.6 1.0 OD1 F:ASP67 4.0 17.9 1.0 CA F:THR31 4.1 16.4 1.0 CA F:THR48 4.1 20.7 1.0 O R:HOH3031 4.2 14.3 1.0 CG2 F:THR31 4.2 16.6 1.0 CG2 F:THR48 4.2 20.0 1.0 O2A F:GTP1181 4.3 16.5 1.0 O1B F:GTP1181 4.4 18.4 1.0 O F:ILE46 4.4 17.6 1.0 O3A F:GTP1181 4.4 16.1 1.0 CG F:ASP67 4.5 18.7 1.0 O1G F:GTP1181 4.5 18.4 1.0 O1A F:GTP1181 4.6 15.7 1.0 PA F:GTP1181 4.6 17.3 1.0 ND2 F:ASN52 4.8 20.1 1.0 C F:PRO47 4.9 19.9 1.0

J.Menetrey, M.Perderiset, J.Cicolari, T.Dubois, N.El Khatib, F.El Khadali, M.Franco, P.Chavrier, A.Houdusse. Structural Basis For ARF1-Mediated Recruitment of ARHGAP21 to Golgi Membranes. Embo J. V. 26 1953 2007.
ISSN: ISSN 0261-4189
PubMed: 17347647
DOI: 10.1038/SJ.EMBOJ.7601634