Magnesium in PDB 3fht: Crystal Structure of Human DBP5 in Complex with Amppnp and Rna

The structure of Crystal Structure of Human DBP5 in Complex with Amppnp and Rna, PDB code: 3fht was solved by H.Von Moeller, E.Conti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.52 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.600, 79.660, 124.540, 90.00, 90.02, 90.00
R / Rfree (%)	16.8 / 22.5

The binding sites of Magnesium atom in the Crystal Structure of Human DBP5 in Complex with Amppnp and Rna (pdb code 3fht). 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 Human DBP5 in Complex with Amppnp and Rna, PDB code: 3fht:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human DBP5 in Complex with Amppnp and Rna


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 Human DBP5 in Complex with Amppnp and Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1 b:15.8 occ:1.00 O1G A:ANP480 1.8 14.1 1.0 O1B A:ANP480 1.9 12.2 1.0 O A:HOH17 1.9 4.6 1.0 O A:HOH59 2.0 10.1 1.0 O A:HOH564 2.2 12.5 1.0 O A:HOH43 2.2 11.4 1.0 PB A:ANP480 3.2 12.2 1.0 PG A:ANP480 3.2 16.0 1.0 N3B A:ANP480 3.5 8.0 1.0 OG1 A:THR145 3.6 15.1 1.0 OD2 A:ASP242 3.9 13.8 1.0 OE2 A:GLU243 3.9 19.3 1.0 OD1 A:ASP242 4.0 11.9 1.0 O3G A:ANP480 4.1 15.9 1.0 CA A:GLY396 4.1 11.2 1.0 O3A A:ANP480 4.2 11.2 1.0 O2A A:ANP480 4.2 13.4 1.0 O2B A:ANP480 4.2 12.3 1.0 O2G A:ANP480 4.3 11.9 1.0 CG A:ASP242 4.3 15.6 1.0 CE A:LYS144 4.4 3.2 1.0 O A:GLY396 4.4 12.3 1.0 PA A:ANP480 4.6 13.5 1.0 O1A A:ANP480 4.6 17.5 1.0 O A:HOH20 4.6 12.9 1.0 O A:HOH49 4.7 12.6 1.0 N A:THR145 4.7 10.7 1.0 C A:GLY396 4.8 12.4 1.0 CB A:LYS144 4.9 9.8 1.0 NZ A:LYS144 4.9 7.5 1.0 CB A:THR145 5.0 13.9 1.0 CD A:GLU243 5.0 16.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human DBP5 in Complex with Amppnp and Rna


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 Human DBP5 in Complex with Amppnp and Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1 b:16.4 occ:1.00 O B:HOH565 1.9 5.2 1.0 O1G B:ANP2 1.9 17.7 1.0 O B:HOH33 2.1 6.9 1.0 O1B B:ANP2 2.1 11.8 1.0 O B:HOH32 2.2 10.6 1.0 O B:HOH545 2.2 13.5 1.0 PB B:ANP2 3.3 14.6 1.0 PG B:ANP2 3.3 17.5 1.0 N3B B:ANP2 3.5 12.5 1.0 OG1 B:THR145 3.6 13.3 1.0 OD2 B:ASP242 3.8 18.9 1.0 OE2 B:GLU243 3.8 16.1 1.0 OD1 B:ASP242 4.0 15.4 1.0 CA B:GLY396 4.1 13.2 1.0 O3G B:ANP2 4.1 19.5 1.0 O1A B:ANP2 4.3 19.6 1.0 O3A B:ANP2 4.3 15.9 1.0 CG B:ASP242 4.3 14.8 1.0 O B:GLY396 4.3 12.8 1.0 O2G B:ANP2 4.4 13.2 1.0 O2B B:ANP2 4.5 12.6 1.0 PA B:ANP2 4.5 13.7 1.0 O B:HOH483 4.6 23.2 1.0 O B:HOH480 4.6 13.8 1.0 O2A B:ANP2 4.6 15.3 1.0 CE B:LYS144 4.6 3.5 1.0 C B:GLY396 4.7 13.2 1.0 O B:HOH499 4.8 9.3 1.0 N B:THR145 4.8 9.8 1.0 NH2 B:ARG432 4.8 13.6 1.0 CB B:LYS144 4.9 9.4 1.0 CB B:THR145 4.9 11.7 1.0 CD B:GLU243 5.0 17.8 1.0

H.Von Moeller, C.Basquin, E.Conti. The Mrna Export Protein DBP5 Binds Rna and the Cytoplasmic Nucleoporin NUP214 in A Mutually Exclusive Manner Nat.Struct.Mol.Biol. V. 16 247 2009.
ISSN: ISSN 1545-9993
PubMed: 19219046
DOI: 10.1038/NSMB.1561