Sodium in PDB 3nbz: Crystal Structure of the Hiv-1 Rev Nes-CRM1-Rangtp Nuclear Export Complex (Crystal I)

The structure of Crystal Structure of the Hiv-1 Rev Nes-CRM1-Rangtp Nuclear Export Complex (Crystal I), PDB code: 3nbz was solved by T.Guttler, T.Madl, P.Neumann, D.Deichsel, L.Corsini, T.Monecke, R.Ficner, M.Sattler, D.Gorlich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.90 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.660, 224.617, 164.021, 90.00, 100.82, 90.00
R / Rfree (%)	22.6 / 28.5

The structure of Crystal Structure of the Hiv-1 Rev Nes-CRM1-Rangtp Nuclear Export Complex (Crystal I) also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of the Hiv-1 Rev Nes-CRM1-Rangtp Nuclear Export Complex (Crystal I) (pdb code 3nbz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Hiv-1 Rev Nes-CRM1-Rangtp Nuclear Export Complex (Crystal I), PDB code: 3nbz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Hiv-1 Rev Nes-CRM1-Rangtp Nuclear Export Complex (Crystal I)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Hiv-1 Rev Nes-CRM1-Rangtp Nuclear Export Complex (Crystal I) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1 b:42.2 occ:1.00 CG C:ARG110 3.4 19.8 1.0 OE2 A:GLU176 3.7 60.7 1.0 NE C:ARG110 3.8 46.5 1.0 O A:HOH1119 4.0 23.3 1.0 NZ A:LYS172 4.2 50.3 1.0 CD C:ARG110 4.2 39.0 1.0 CG2 C:VAL109 4.2 21.8 1.0 CE A:LYS172 4.3 41.0 1.0 CB C:ARG110 4.5 29.8 1.0 CD2 A:LEU173 4.5 41.2 1.0 CA C:ARG110 4.5 36.7 1.0 N C:ARG110 4.7 37.0 1.0 CD A:GLU176 4.7 64.3 1.0 OE1 A:GLU176 4.8 61.6 1.0 CZ C:ARG110 4.9 53.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Hiv-1 Rev Nes-CRM1-Rangtp Nuclear Export Complex (Crystal I)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Hiv-1 Rev Nes-CRM1-Rangtp Nuclear Export Complex (Crystal I) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1072 b:52.5 occ:1.00 NE2 D:GLN140 3.5 90.7 1.0 O D:THR89 3.5 58.8 1.0 OE1 D:GLU1024 3.6 94.7 1.0 CD D:LYS92 3.7 61.9 1.0 NZ D:LYS92 3.7 64.4 1.0 CB D:GLU1024 3.8 64.3 1.0 CE D:LYS92 3.9 62.0 1.0 O D:LYS88 3.9 77.8 1.0 C D:THR89 3.9 63.8 1.0 CD D:GLU1024 4.0 91.7 1.0 CG D:LYS92 4.0 44.0 1.0 CG D:GLU1024 4.1 77.8 1.0 CD D:GLN140 4.2 86.7 1.0 N D:LYS92 4.2 62.1 1.0 OE1 D:GLN140 4.3 86.1 1.0 CB D:LYS92 4.3 38.4 1.0 C D:LYS88 4.3 59.1 1.0 N D:TRP91 4.3 50.1 1.0 O D:PHE1025 4.4 72.0 1.0 CA D:THR89 4.5 56.9 1.0 N D:PHE1025 4.5 56.3 1.0 N D:THR89 4.5 56.9 1.0 CB D:TRP91 4.6 61.0 1.0 N D:ARG90 4.6 72.5 1.0 C D:PHE1025 4.6 71.1 1.0 CA D:GLU1024 4.7 60.8 1.0 O D:ILE87 4.7 65.5 1.0 OE2 D:GLU1024 4.8 92.7 1.0 C D:ARG90 4.9 53.5 1.0 CA D:TRP91 4.9 61.1 1.0 CA D:LYS92 4.9 52.8 1.0 N D:ALA1026 5.0 84.3 1.0 C D:GLU1024 5.0 59.4 1.0 CA D:ARG90 5.0 60.1 1.0

T.Guttler, T.Madl, P.Neumann, D.Deichsel, L.Corsini, T.Monecke, R.Ficner, M.Sattler, D.Gorlich. Nes Consensus Redefined By Structures of Pki-Type and Rev-Type Nuclear Export Signals Bound to CRM1. Nat.Struct.Mol.Biol. V. 17 1367 2010.
ISSN: ISSN 1545-9993
PubMed: 20972448
DOI: 10.1038/NSMB.1931