Magnesium in PDB 1k5d: Crystal Structure of Ran-Gppnhp-RANBP1-Rangap Complex

The structure of Crystal Structure of Ran-Gppnhp-RANBP1-Rangap Complex, PDB code: 1k5d was solved by M.J.Seewald, C.Koerner, A.Wittinghofer, I.R.Vetter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	101.551, 103.109, 120.177, 71.59, 80.55, 67.78
R / Rfree (%)	23.7 / 26.7

The binding sites of Magnesium atom in the Crystal Structure of Ran-Gppnhp-RANBP1-Rangap Complex (pdb code 1k5d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Ran-Gppnhp-RANBP1-Rangap Complex, PDB code: 1k5d:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Ran-Gppnhp-RANBP1-Rangap 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 Ran-Gppnhp-RANBP1-Rangap Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1251 b:29.5 occ:1.00 O A:HOH1254 1.6 23.1 1.0 O A:HOH1253 1.9 46.6 1.0 O2B A:GNP1250 1.9 37.5 1.0 O1G A:GNP1250 2.0 37.5 1.0 OG1 A:THR42 2.1 17.3 1.0 OG1 A:THR24 2.4 27.1 1.0 PB A:GNP1250 3.1 37.5 1.0 PG A:GNP1250 3.1 37.5 1.0 CB A:THR24 3.3 27.1 1.0 CB A:THR42 3.3 17.3 1.0 N3B A:GNP1250 3.4 37.5 1.0 O2G A:GNP1250 3.9 37.5 1.0 N A:THR42 3.9 35.1 1.0 O1B A:GNP1250 4.1 37.5 1.0 N A:THR24 4.1 36.9 1.0 OD1 A:ASP65 4.1 37.8 1.0 O3A A:GNP1250 4.2 37.5 1.0 OD2 A:ASP65 4.2 37.8 1.0 CA A:THR42 4.2 35.1 1.0 CA A:THR24 4.3 36.9 1.0 O A:HOH1255 4.3 29.5 1.0 O3G A:GNP1250 4.3 37.5 1.0 O A:HOH1252 4.3 51.6 1.0 CG2 A:THR24 4.3 27.1 1.0 CG2 A:THR42 4.3 17.3 1.0 O2A A:GNP1250 4.4 37.5 1.0 CG A:ASP65 4.5 37.8 1.0 O1A A:GNP1250 4.5 37.5 1.0 PA A:GNP1250 4.6 37.5 1.0 C A:ALA41 4.7 30.0 1.0 O A:VAL40 4.8 30.2 1.0 O A:THR66 4.8 42.7 1.0 NZ A:LYS23 5.0 27.4 1.0 CB A:LYS23 5.0 27.4 1.0 CA A:ALA41 5.0 30.0 1.0 CE A:LYS23 5.0 27.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Ran-Gppnhp-RANBP1-Rangap 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 Ran-Gppnhp-RANBP1-Rangap Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2251 b:44.2 occ:1.00 O D:HOH2254 1.7 29.9 1.0 O2B D:GNP2250 1.9 37.2 1.0 O D:HOH2253 2.0 41.9 1.0 O1G D:GNP2250 2.1 37.2 1.0 OG1 D:THR42 2.1 22.3 1.0 OG1 D:THR24 2.4 33.7 1.0 PB D:GNP2250 3.0 37.2 1.0 PG D:GNP2250 3.1 37.2 1.0 CB D:THR24 3.3 33.7 1.0 CB D:THR42 3.3 22.3 1.0 N3B D:GNP2250 3.4 37.2 1.0 O2G D:GNP2250 3.8 37.2 1.0 N D:THR42 3.9 33.5 1.0 O1B D:GNP2250 4.0 37.2 1.0 O D:HOH2252 4.0 37.2 1.0 N D:THR24 4.1 30.5 1.0 OD1 D:ASP65 4.1 52.1 1.0 O3A D:GNP2250 4.1 37.2 1.0 OD2 D:ASP65 4.1 52.1 1.0 CA D:THR42 4.2 33.5 1.0 CA D:THR24 4.2 30.5 1.0 O3G D:GNP2250 4.3 37.2 1.0 CG2 D:THR24 4.3 33.7 1.0 CG2 D:THR42 4.3 22.3 1.0 O2A D:GNP2250 4.4 37.2 1.0 CG D:ASP65 4.5 52.1 1.0 O1A D:GNP2250 4.5 37.2 1.0 PA D:GNP2250 4.6 37.2 1.0 O D:HOH2270 4.6 49.7 1.0 C D:ALA41 4.8 30.3 1.0 O D:THR66 4.8 27.2 1.0 O D:VAL40 4.8 30.2 1.0 CB D:LYS23 4.9 26.5 1.0 CE D:LYS23 5.0 26.5 1.0 NZ D:LYS23 5.0 26.5 1.0 CA D:ALA41 5.0 30.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Ran-Gppnhp-RANBP1-Rangap 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 Ran-Gppnhp-RANBP1-Rangap Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg3251 b:36.5 occ:1.00 O G:HOH3254 1.8 36.9 1.0 O G:HOH3253 2.0 62.6 1.0 O1G G:GNP3250 2.0 37.6 1.0 O2B G:GNP3250 2.0 37.6 1.0 OG1 G:THR42 2.1 34.1 1.0 OG1 G:THR24 2.4 28.6 1.0 PG G:GNP3250 3.1 37.6 1.0 PB G:GNP3250 3.1 37.6 1.0 CB G:THR42 3.2 34.1 1.0 CB G:THR24 3.3 28.6 1.0 N3B G:GNP3250 3.4 37.6 1.0 O2G G:GNP3250 3.8 37.6 1.0 N G:THR42 3.9 29.7 1.0 OD1 G:ASP65 4.1 44.6 1.0 O1B G:GNP3250 4.1 37.6 1.0 N G:THR24 4.1 29.2 1.0 CA G:THR42 4.2 29.7 1.0 O G:HOH3252 4.2 59.6 1.0 OD2 G:ASP65 4.2 44.6 1.0 O3A G:GNP3250 4.2 37.6 1.0 CA G:THR24 4.3 29.2 1.0 O3G G:GNP3250 4.3 37.6 1.0 CG2 G:THR42 4.3 34.1 1.0 CG2 G:THR24 4.3 28.6 1.0 O G:HOH3259 4.4 39.5 1.0 O2A G:GNP3250 4.5 37.6 1.0 CG G:ASP65 4.5 44.6 1.0 O1A G:GNP3250 4.6 37.6 1.0 PA G:GNP3250 4.6 37.6 1.0 C G:ALA41 4.7 40.4 1.0 O G:VAL40 4.7 33.2 1.0 O G:THR66 4.7 58.8 1.0 CA G:ALA41 4.9 40.4 1.0 CB G:LYS23 5.0 26.1 1.0 CE G:LYS23 5.0 26.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Ran-Gppnhp-RANBP1-Rangap 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 Ran-Gppnhp-RANBP1-Rangap Complex within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg4251 b:45.0 occ:1.00 O J:HOH4254 1.7 32.0 1.0 O2B J:GNP4250 1.9 36.6 1.0 O J:HOH4253 2.0 60.1 1.0 O1G J:GNP4250 2.1 36.6 1.0 OG1 J:THR42 2.2 20.7 1.0 OG1 J:THR24 2.4 31.3 1.0 PB J:GNP4250 3.0 36.6 1.0 PG J:GNP4250 3.1 36.6 1.0 CB J:THR24 3.2 31.3 1.0 CB J:THR42 3.3 20.7 1.0 N3B J:GNP4250 3.4 36.6 1.0 O2G J:GNP4250 3.8 36.6 1.0 N J:THR42 3.9 30.7 1.0 O1B J:GNP4250 4.0 36.6 1.0 N J:THR24 4.0 29.4 1.0 O J:HOH4252 4.1 36.6 1.0 O3A J:GNP4250 4.1 36.6 1.0 OD1 J:ASP65 4.1 54.7 1.0 OD2 J:ASP65 4.2 54.7 1.0 CA J:THR42 4.2 30.7 1.0 CA J:THR24 4.2 29.4 1.0 CG2 J:THR24 4.3 31.3 1.0 O3G J:GNP4250 4.3 36.6 1.0 CG2 J:THR42 4.4 20.7 1.0 O2A J:GNP4250 4.4 36.6 1.0 O1A J:GNP4250 4.5 36.6 1.0 CG J:ASP65 4.5 54.7 1.0 O J:HOH4282 4.6 22.2 1.0 PA J:GNP4250 4.6 36.6 1.0 O J:VAL40 4.7 22.9 1.0 C J:ALA41 4.7 26.6 1.0 O J:THR66 4.8 35.1 1.0 CB J:LYS23 4.9 35.7 1.0 CE J:LYS23 5.0 35.7 1.0 CA J:ALA41 5.0 26.6 1.0 NZ J:LYS23 5.0 35.7 1.0

M.J.Seewald, C.Korner, A.Wittinghofer, I.R.Vetter. Rangap Mediates Gtp Hydrolysis Without An Arginine Finger. Nature V. 415 662 2002.
ISSN: ISSN 0028-0836
PubMed: 11832950
DOI: 10.1038/415662A