Chlorine in PDB 3cpj: Crystal Structure of YPT31 in Complex with Yeast Rab-Gdi

The structure of Crystal Structure of YPT31 in Complex with Yeast Rab-Gdi, PDB code: 3cpj was solved by S.Kravchenko, A.Ignatev, R.S.Goody, A.Rak, O.Pylypenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.79 / 2.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.940, 61.430, 92.750, 90.00, 103.68, 90.00
R / Rfree (%)	19.9 / 25.5

The structure of Crystal Structure of YPT31 in Complex with Yeast Rab-Gdi also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Chlorine atom in the Crystal Structure of YPT31 in Complex with Yeast Rab-Gdi (pdb code 3cpj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of YPT31 in Complex with Yeast Rab-Gdi, PDB code: 3cpj:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of YPT31 in Complex with Yeast Rab-Gdi


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of YPT31 in Complex with Yeast Rab-Gdi within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl2001 b:31.7 occ:1.00 OG1 G:THR189 2.9 32.0 1.0 O G:HOH4011 3.0 24.1 1.0 N G:GLY186 3.0 30.4 1.0 NE G:ARG147 3.2 28.9 1.0 NH2 G:ARG147 3.3 30.6 1.0 CB G:THR189 3.4 31.4 1.0 CZ G:ARG147 3.7 30.2 1.0 CA G:LEU185 3.7 29.6 1.0 CG G:GLU144 3.8 31.5 1.0 C G:LEU185 3.9 30.0 1.0 CG2 G:THR189 3.9 30.9 1.0 CA G:GLY186 4.0 30.9 1.0 CA G:GLU144 4.0 32.0 1.0 CB G:GLU144 4.2 31.8 1.0 CD2 G:LEU185 4.2 27.3 1.0 O G:GLY184 4.3 29.5 1.0 CD G:ARG147 4.4 30.3 1.0 CB G:LEU185 4.4 29.1 1.0 CB G:ARG147 4.5 30.5 1.0 O G:GLU144 4.5 31.2 1.0 O G:GLY186 4.6 31.4 1.0 OE2 G:GLU144 4.6 34.1 1.0 CD G:GLU144 4.7 32.4 1.0 C G:GLY186 4.8 31.5 1.0 C G:GLU144 4.8 31.6 1.0 N G:LEU185 4.8 29.9 1.0 CA G:THR189 4.9 31.6 1.0 C G:GLY184 4.9 29.9 1.0 O G:HOH4330 4.9 43.2 1.0 CG G:LEU185 5.0 28.4 1.0 CG G:ARG147 5.0 30.3 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of YPT31 in Complex with Yeast Rab-Gdi


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of YPT31 in Complex with Yeast Rab-Gdi within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl2002 b:29.5 occ:1.00 O G:HOH4005 2.9 24.2 1.0 O G:HOH4022 3.0 33.4 1.0 N G:MET90 3.2 26.4 1.0 N G:PHE421 3.4 25.3 1.0 CB G:PHE421 3.6 25.1 1.0 CA G:LEU89 3.7 25.5 1.0 N G:GLU422 3.8 25.2 1.0 CA G:PHE421 3.8 25.2 1.0 C G:PHE421 3.9 25.3 1.0 CB G:MET90 3.9 27.5 1.0 C G:LEU89 3.9 26.0 1.0 CG G:MET90 4.1 28.5 1.0 O G:PHE88 4.1 24.5 1.0 CA G:MET90 4.1 27.1 1.0 CB G:HIS420 4.1 26.1 1.0 OE1 G:GLU422 4.2 24.7 1.0 CB G:LEU89 4.3 25.2 1.0 CG G:GLU422 4.3 25.5 1.0 O G:MET90 4.4 27.6 1.0 C G:HIS420 4.5 25.7 1.0 CA G:GLU422 4.5 25.6 1.0 ND1 G:HIS420 4.5 27.0 1.0 CB G:LEU95 4.6 28.0 1.0 O G:PHE421 4.6 25.0 1.0 CG G:HIS420 4.6 26.8 1.0 CD G:GLU422 4.8 26.6 1.0 N G:LEU89 4.8 25.2 1.0 CA G:GLY93 4.8 28.4 1.0 CG G:PHE421 4.8 25.4 1.0 C G:MET90 4.8 27.5 1.0 CA G:HIS420 4.8 26.1 1.0 CG G:LEU89 4.8 25.4 1.0 C G:PHE88 4.9 24.9 1.0 CB G:GLU422 5.0 25.4 1.0 CD2 G:PHE421 5.0 27.0 1.0 N G:LEU95 5.0 28.3 1.0

A.Ignatev, S.Kravchenko, A.Rak, R.S.Goody, O.Pylypenko. A Structural Model of the Gdp Dissociation Inhibitor Rab Membrane Extraction Mechanism. J.Biol.Chem. V. 283 18377 2008.
ISSN: ISSN 0021-9258
PubMed: 18426803
DOI: 10.1074/JBC.M709718200