Chlorine in PDB 3vm6: Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakarensis KOD1 in Complex with Alpha-D-Ribose-1,5- Bisphosphate

The structure of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakarensis KOD1 in Complex with Alpha-D-Ribose-1,5- Bisphosphate, PDB code: 3vm6 was solved by A.Nakamura, M.Fujihashi, R.Aono, T.Sato, Y.Nishiba, S.Yoshida, A.Yano, H.Atomi, T.Imanaka, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.97 / 2.85
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	146.537, 146.537, 99.649, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 26.2

The structure of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakarensis KOD1 in Complex with Alpha-D-Ribose-1,5- Bisphosphate also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Chlorine atom in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakarensis KOD1 in Complex with Alpha-D-Ribose-1,5- Bisphosphate (pdb code 3vm6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakarensis KOD1 in Complex with Alpha-D-Ribose-1,5- Bisphosphate, PDB code: 3vm6:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakarensis KOD1 in Complex with Alpha-D-Ribose-1,5- Bisphosphate


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 Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakarensis KOD1 in Complex with Alpha-D-Ribose-1,5- Bisphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl411 b:38.6 occ:1.00 O A:HOH616 2.8 13.3 1.0 O A:HOH615 3.0 22.0 1.0 NZ A:LYS213 3.3 19.9 1.0 CD A:LYS162 3.5 25.1 1.0 CG A:LYS162 3.5 22.8 1.0 OE1 A:GLN164 3.7 25.6 1.0 CB A:LYS162 3.9 23.2 1.0 CD A:LYS213 4.0 17.7 1.0 CD A:PRO161 4.1 23.5 1.0 CE A:LYS213 4.1 18.7 1.0 CE A:LYS162 4.3 26.5 1.0 CD A:GLN164 4.3 25.4 1.0 CG A:PRO161 4.4 24.1 1.0 CE A:MET17 4.4 29.8 1.0 N A:LYS162 4.5 22.8 1.0 SD A:MET17 4.7 31.6 1.0 NE2 A:GLN164 4.8 24.1 1.0 OE1 A:GLU258 4.8 35.3 1.0 CA A:LYS162 4.9 23.2 1.0 N A:PRO161 4.9 23.8 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakarensis KOD1 in Complex with Alpha-D-Ribose-1,5- Bisphosphate


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 Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakarensis KOD1 in Complex with Alpha-D-Ribose-1,5- Bisphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl411 b:41.4 occ:1.00 NZ B:LYS24 2.8 22.5 1.0 O B:HOH671 3.3 15.2 1.0 CE B:LYS24 3.4 22.2 1.0 N B:ARG20 3.4 26.0 1.0 O B:GLU18 3.5 32.0 1.0 CD B:LYS24 3.6 22.2 1.0 CA B:ILE19 3.8 28.6 1.0 O B:ARG20 3.9 25.4 1.0 CG B:ARG20 3.9 21.7 1.0 C B:ILE19 4.1 27.2 1.0 C B:GLU18 4.3 31.9 1.0 CA B:ARG20 4.4 25.1 1.0 N B:ILE19 4.5 30.1 1.0 C B:ARG20 4.5 25.1 1.0 CB B:ARG20 4.8 23.6 1.0 NH1 B:ARG20 4.8 25.0 1.0 CG B:LYS24 4.8 21.9 1.0 CB B:ILE19 4.9 29.5 1.0 CG2 B:ILE19 5.0 28.6 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakarensis KOD1 in Complex with Alpha-D-Ribose-1,5- Bisphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakarensis KOD1 in Complex with Alpha-D-Ribose-1,5- Bisphosphate within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl412 b:38.4 occ:1.00 O C:HOH703 3.1 9.1 1.0 O C:HOH634 3.3 20.7 1.0 NZ C:LYS213 3.3 16.4 1.0 CD C:LYS162 3.5 22.1 1.0 CE C:LYS213 3.5 18.1 1.0 CG C:LYS162 3.7 19.7 1.0 CD C:LYS213 4.0 17.4 1.0 CB C:LYS162 4.1 17.9 1.0 CD C:PRO161 4.2 18.0 1.0 OE1 C:GLN164 4.3 24.3 1.0 CB C:ALA278 4.3 17.1 1.0 CE C:LYS162 4.4 23.5 1.0 CE C:MET17 4.4 27.1 1.0 SD C:MET17 4.6 29.7 1.0 CG C:PRO161 4.6 19.0 1.0 OE1 C:GLU258 4.6 34.1 1.0 CA C:ALA278 4.7 18.4 1.0 CD C:ARG254 4.7 22.7 1.0 N C:LYS162 4.8 18.8 1.0 O C:ALA278 4.8 19.5 1.0 CD C:GLN164 4.9 23.2 1.0

A.Nakamura, M.Fujihashi, R.Aono, T.Sato, Y.Nishiba, S.Yoshida, A.Yano, H.Atomi, T.Imanaka, K.Miki. Dynamic, Ligand-Dependent Conformational Change Triggers Reaction of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakarensis KOD1 J.Biol.Chem. V. 287 20784 2012.
ISSN: ISSN 0021-9258
PubMed: 22511789
DOI: 10.1074/JBC.M112.349423