Magnesium in PDB 2bme: High Resolution Structure of Gppnhp-Bound Human RAB4A

All present enzymatic activity of High Resolution Structure of Gppnhp-Bound Human RAB4A:
3.6.5.2;

The structure of High Resolution Structure of Gppnhp-Bound Human RAB4A, PDB code: 2bme was solved by A.J.Scheidig, S.K.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.54 / 1.57
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	99.790, 99.790, 95.540, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 22.9

The binding sites of Magnesium atom in the High Resolution Structure of Gppnhp-Bound Human RAB4A (pdb code 2bme). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the High Resolution Structure of Gppnhp-Bound Human RAB4A, PDB code: 2bme:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the High Resolution Structure of Gppnhp-Bound Human RAB4A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of High Resolution Structure of Gppnhp-Bound Human RAB4A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1184 b:19.2 occ:1.00 O2B A:GNP1180 2.0 18.6 1.0 O A:HOH2032 2.0 22.1 1.0 O2G A:GNP1180 2.0 20.0 1.0 OG A:SER24 2.1 22.3 1.0 O A:HOH2063 2.1 18.5 1.0 OG1 A:THR42 2.2 21.4 1.0 CB A:SER24 3.2 20.7 1.0 PB A:GNP1180 3.2 18.6 1.0 PG A:GNP1180 3.2 19.2 1.0 CB A:THR42 3.2 23.4 1.0 N3B A:GNP1180 3.4 19.3 1.0 N A:THR42 3.8 25.2 1.0 N A:SER24 3.8 19.4 1.0 O3G A:GNP1180 4.0 20.8 1.0 O A:HOH2039 4.1 34.9 1.0 CA A:SER24 4.1 19.6 1.0 CA A:THR42 4.1 24.0 1.0 OD2 A:ASP65 4.2 22.1 1.0 OD1 A:ASP65 4.2 20.8 1.0 O3A A:GNP1180 4.2 19.5 1.0 O1B A:GNP1180 4.3 18.6 1.0 O2A A:GNP1180 4.3 20.4 1.0 CG2 A:THR42 4.3 20.1 1.0 O1G A:GNP1180 4.5 20.5 1.0 O A:ASN40 4.5 29.5 1.0 PA A:GNP1180 4.5 19.9 1.0 CG A:ASP65 4.6 18.2 1.0 O A:THR66 4.6 20.0 1.0 O A:HOH2028 4.6 34.1 1.0 O1A A:GNP1180 4.7 20.6 1.0 C A:HIS41 4.8 27.3 1.0 CB A:LYS23 4.8 16.6 1.0 O A:HOH2155 4.9 23.3 1.0 C A:LYS23 4.9 18.5 1.0

Magnesium binding site 2 out of 4 in the High Resolution Structure of Gppnhp-Bound Human RAB4A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of High Resolution Structure of Gppnhp-Bound Human RAB4A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1179 b:15.8 occ:1.00 O2G B:GNP1178 2.0 15.8 1.0 O B:HOH2093 2.1 17.3 1.0 O2B B:GNP1178 2.1 14.6 1.0 O B:HOH2040 2.1 19.1 1.0 OG1 B:THR42 2.1 18.8 1.0 OG B:SER24 2.2 16.2 1.0 CB B:THR42 3.1 18.9 1.0 PG B:GNP1178 3.1 14.9 1.0 CB B:SER24 3.2 14.8 1.0 PB B:GNP1178 3.3 15.0 1.0 N3B B:GNP1178 3.4 15.3 1.0 N B:THR42 3.7 20.8 1.0 O3G B:GNP1178 3.9 15.5 1.0 N B:SER24 4.0 13.3 1.0 CA B:THR42 4.0 19.5 1.0 CA B:SER24 4.1 14.4 1.0 OD2 B:ASP65 4.1 19.8 1.0 OD1 B:ASP65 4.2 16.4 1.0 O B:HOH2054 4.2 32.1 1.0 CG2 B:THR42 4.2 21.2 1.0 O3A B:GNP1178 4.3 14.7 1.0 O1B B:GNP1178 4.3 15.1 1.0 O2A B:GNP1178 4.3 16.6 1.0 O1G B:GNP1178 4.4 17.0 1.0 O B:ASN40 4.6 23.0 1.0 CG B:ASP65 4.6 19.2 1.0 PA B:GNP1178 4.6 15.3 1.0 O B:THR66 4.6 16.5 1.0 O1A B:GNP1178 4.6 15.8 1.0 C B:HIS41 4.7 21.6 1.0 O B:HOH2212 4.9 18.8 1.0 CB B:LYS23 4.9 14.9 1.0 O B:HOH2038 4.9 30.6 1.0 CA B:HIS41 5.0 22.8 1.0

Magnesium binding site 3 out of 4 in the High Resolution Structure of Gppnhp-Bound Human RAB4A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of High Resolution Structure of Gppnhp-Bound Human RAB4A within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1181 b:17.5 occ:1.00 O2G C:GNP1178 2.0 17.6 1.0 O C:HOH2037 2.1 20.6 1.0 O C:HOH2068 2.1 17.1 1.0 OG1 C:THR42 2.1 18.2 1.0 O2B C:GNP1178 2.1 15.6 1.0 OG C:SER24 2.2 15.8 1.0 CB C:THR42 3.2 19.2 1.0 PG C:GNP1178 3.2 17.8 1.0 CB C:SER24 3.2 17.3 1.0 PB C:GNP1178 3.2 16.3 1.0 N3B C:GNP1178 3.4 17.5 1.0 N C:THR42 3.7 21.0 1.0 O3G C:GNP1178 3.9 20.1 1.0 N C:SER24 3.9 15.3 1.0 CA C:THR42 4.0 20.7 1.0 OD2 C:ASP65 4.1 20.1 1.0 CA C:SER24 4.1 16.0 1.0 CG2 C:THR42 4.2 18.8 1.0 OD1 C:ASP65 4.2 17.6 1.0 O C:HOH2047 4.2 26.7 1.0 O3A C:GNP1178 4.3 16.9 1.0 O2A C:GNP1178 4.3 20.4 1.0 O1B C:GNP1178 4.3 17.0 1.0 O1G C:GNP1178 4.4 21.0 1.0 O C:ASN40 4.5 24.8 1.0 PA C:GNP1178 4.6 17.9 1.0 CG C:ASP65 4.6 20.6 1.0 O C:THR66 4.6 18.3 1.0 O1A C:GNP1178 4.7 16.5 1.0 C C:HIS41 4.7 23.8 1.0 O C:HOH2164 4.9 23.7 1.0 CB C:LYS23 4.9 13.9 1.0

Magnesium binding site 4 out of 4 in the High Resolution Structure of Gppnhp-Bound Human RAB4A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of High Resolution Structure of Gppnhp-Bound Human RAB4A within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1180 b:22.5 occ:1.00 OG D:SER24 2.0 23.6 1.0 O2B D:GNP1179 2.0 20.3 1.0 O2G D:GNP1179 2.1 23.6 1.0 O D:HOH2036 2.1 26.2 1.0 O D:HOH2066 2.1 24.9 1.0 OG1 D:THR42 2.2 24.6 1.0 CB D:SER24 3.1 21.3 1.0 CB D:THR42 3.2 28.4 1.0 PG D:GNP1179 3.2 21.4 1.0 PB D:GNP1179 3.2 20.7 1.0 N3B D:GNP1179 3.4 21.5 1.0 N D:THR42 3.8 31.4 1.0 N D:SER24 3.9 20.3 1.0 O D:HOH2041 3.9 39.8 1.0 O3G D:GNP1179 3.9 20.0 1.0 CA D:SER24 4.0 20.9 1.0 CA D:THR42 4.0 31.4 1.0 OD2 D:ASP65 4.1 23.6 1.0 O2A D:GNP1179 4.2 25.0 1.0 OD1 D:ASP65 4.2 27.2 1.0 O3A D:GNP1179 4.2 19.7 1.0 O1B D:GNP1179 4.3 21.9 1.0 CG2 D:THR42 4.3 28.2 1.0 O1G D:GNP1179 4.4 23.9 1.0 PA D:GNP1179 4.6 21.0 1.0 O D:ASN40 4.6 34.6 1.0 CG D:ASP65 4.6 24.8 1.0 O1A D:GNP1179 4.6 23.2 1.0 O D:HOH2034 4.7 32.5 1.0 O D:THR66 4.7 27.2 1.0 C D:HIS41 4.8 34.6 1.0 O D:HOH2137 4.8 26.9 1.0 CB D:LYS23 4.9 19.6 1.0 C D:LYS23 4.9 18.9 1.0

S.K.Huber, A.J.Scheidig. High Resolution Crystal Structures of Human RAB4A in Its Active and Inactive Conformations. Febs Lett. V. 579 2821 2005.
ISSN: ISSN 0014-5793
PubMed: 15907487
DOI: 10.1016/J.FEBSLET.2005.04.020