Chlorine in PDB 6ael: Crystal Structure of ENPP1 in Complex with 3'3'-Cgamp

The structure of Crystal Structure of ENPP1 in Complex with 3'3'-Cgamp, PDB code: 6ael was solved by K.Kato, H.Nishimasu, S.Hirano, H.Hirano, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.00 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.169, 94.063, 74.274, 90.00, 95.93, 90.00
R / Rfree (%)	16.6 / 20.2

The structure of Crystal Structure of ENPP1 in Complex with 3'3'-Cgamp also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Calcium	(Ca)	1 atom

The binding sites of Chlorine atom in the Crystal Structure of ENPP1 in Complex with 3'3'-Cgamp (pdb code 6ael). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of ENPP1 in Complex with 3'3'-Cgamp, PDB code: 6ael:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Crystal Structure of ENPP1 in Complex with 3'3'-Cgamp


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 ENPP1 in Complex with 3'3'-Cgamp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1011 b:40.4 occ:1.00 O1 A:EDO1019 2.4 45.5 1.0 NH2 A:ARG440 3.1 24.5 0.5 NH1 A:ARG440 3.2 18.4 0.5 O A:HOH1270 3.3 43.1 1.0 CZ A:ARG440 3.5 26.8 0.5 C A:MET261 3.6 24.3 1.0 N A:MET261 3.6 21.4 1.0 C1 A:EDO1019 3.8 35.0 1.0 C A:LYS260 3.8 22.4 1.0 CA A:MET261 3.8 23.6 1.0 O A:MET261 3.9 22.4 1.0 O A:LYS260 3.9 26.1 1.0 N A:TYR262 4.0 21.3 1.0 CB A:LYS260 4.0 29.4 1.0 CG2 A:VAL432 4.1 29.4 1.0 C2 A:EDO1019 4.3 31.6 1.0 CA A:LYS260 4.5 23.9 1.0 O A:HOH1168 4.6 18.9 1.0 CB A:TYR262 4.6 21.0 1.0 NH2 A:ARG438 4.7 20.9 1.0 CA A:TYR262 4.8 22.1 1.0 NE A:ARG440 4.8 26.7 0.5

Chlorine binding site 2 out of 6 in the Crystal Structure of ENPP1 in Complex with 3'3'-Cgamp


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 ENPP1 in Complex with 3'3'-Cgamp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1012 b:41.1 occ:1.00 N A:GLN885 3.2 34.6 1.0 NE A:ARG884 3.5 31.3 1.0 CZ A:ARG884 3.6 34.2 1.0 CD A:ARG884 3.6 27.2 1.0 NH1 A:ARG884 3.7 34.1 1.0 CG A:GLN885 3.7 51.1 1.0 CA A:ARG884 3.7 28.4 1.0 CB A:GLN885 3.8 38.0 1.0 C A:ARG884 3.9 33.4 1.0 CA A:GLN885 4.1 36.2 1.0 O A:HOH1447 4.1 53.0 1.0 NH2 A:ARG884 4.2 34.7 1.0 CB A:ARG884 4.3 30.6 1.0 O A:HOH1128 4.4 41.4 1.0 OE1 A:GLU886 4.4 39.6 1.0 CG A:ARG884 4.6 25.3 1.0 O A:ASP883 4.6 28.8 1.0 CD A:GLN885 4.6 63.4 1.0 N A:ARG884 4.9 26.9 1.0

Chlorine binding site 3 out of 6 in the Crystal Structure of ENPP1 in Complex with 3'3'-Cgamp


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 ENPP1 in Complex with 3'3'-Cgamp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1013 b:41.0 occ:1.00 O A:HOH1358 3.0 34.2 1.0 OG A:SER486 3.1 22.4 1.0 O A:HOH1185 3.6 47.3 1.0 NE A:ARG488 3.9 22.7 1.0 CB A:SER486 3.9 19.3 1.0 CD A:ARG488 3.9 19.5 1.0 NH2 A:ARG488 3.9 19.2 1.0 CZ A:ARG488 3.9 22.1 1.0 CA A:GLY255 4.0 20.9 1.0 CA A:SER486 4.3 20.2 1.0 N A:ASP487 4.5 21.8 1.0 NH1 A:ARG488 4.6 22.4 1.0 O A:GLU252 4.7 19.3 1.0 CG A:ARG488 4.7 19.1 1.0 N A:GLY255 4.8 20.7 1.0 O A:GLY255 4.8 21.3 1.0 CG A:LYS284 4.9 25.1 1.0 C A:SER486 4.9 19.2 1.0 CE A:LYS284 4.9 40.3 1.0 C A:GLY255 5.0 21.3 1.0

Chlorine binding site 4 out of 6 in the Crystal Structure of ENPP1 in Complex with 3'3'-Cgamp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of ENPP1 in Complex with 3'3'-Cgamp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1014 b:27.2 occ:1.00 N A:HIS468 3.3 28.4 1.0 O A:HOH1384 3.6 51.7 1.0 CA A:GLN467 3.9 33.6 1.0 CD2 A:HIS468 4.0 42.0 1.0 CG A:GLN467 4.0 25.5 1.0 CD1 A:PHE469 4.0 26.9 1.0 O A:HOH1248 4.0 44.6 1.0 C A:GLN467 4.1 27.2 1.0 CB A:HIS468 4.1 31.8 1.0 CG A:GLU464 4.1 38.2 1.0 CA A:HIS468 4.2 24.0 1.0 CE1 A:PHE469 4.2 23.3 1.0 CB A:GLU464 4.3 35.9 1.0 CG A:HIS468 4.4 38.5 1.0 CG2 A:VAL417 4.4 29.4 1.0 CB A:GLN467 4.5 31.7 1.0 N A:PHE469 4.6 22.2 1.0 CZ3 A:TRP500 4.7 33.8 1.0 OH A:TYR422 4.7 37.3 1.0 C A:HIS468 4.8 25.4 1.0 CH2 A:TRP500 4.8 36.1 1.0 O A:ASN466 4.9 47.4 1.0 CD A:GLU464 5.0 43.2 1.0 N A:GLN467 5.0 37.3 1.0

Chlorine binding site 5 out of 6 in the Crystal Structure of ENPP1 in Complex with 3'3'-Cgamp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of ENPP1 in Complex with 3'3'-Cgamp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1015 b:30.2 occ:1.00 NAS A:4BW1007 3.3 72.7 1.0 OAG A:4BW1007 3.3 63.3 1.0 O A:HIS517 3.4 23.6 1.0 N A:HIS517 3.4 21.5 1.0 CE1 A:HIS362 3.5 29.6 1.0 CA A:PHE516 3.7 28.7 1.0 CB A:PHE516 3.9 28.4 1.0 NAA A:4BW1007 4.0 71.9 1.0 CBA A:4BW1007 4.0 73.0 1.0 CBI A:4BW1007 4.0 66.5 1.0 C A:PHE516 4.1 25.8 1.0 NE2 A:HIS517 4.2 28.4 1.0 CD2 A:HIS517 4.2 26.1 1.0 C A:HIS517 4.2 21.4 1.0 ND1 A:HIS362 4.2 31.4 1.0 CBG A:4BW1007 4.2 70.9 1.0 CE1 A:HIS517 4.3 23.8 1.0 CG A:HIS517 4.3 25.4 1.0 CBO A:4BW1007 4.4 68.5 1.0 CA A:HIS517 4.4 24.2 1.0 ND1 A:HIS517 4.4 23.4 1.0 NE2 A:HIS362 4.4 32.1 1.0 CE A:LYS237 4.4 34.8 1.0 NBQ A:4BW1007 4.6 69.7 1.0 O A:GLY515 4.8 28.7 1.0 CD A:LYS237 4.8 23.1 1.0 CB A:HIS517 5.0 25.8 1.0 CG A:PHE516 5.0 24.9 1.0

Chlorine binding site 6 out of 6 in the Crystal Structure of ENPP1 in Complex with 3'3'-Cgamp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of ENPP1 in Complex with 3'3'-Cgamp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1016 b:37.3 occ:1.00 CB A:ALA536 3.6 31.8 1.0 ND2 A:ASN399 3.6 33.0 1.0 N A:ALA536 3.7 34.9 1.0 CA A:ALA536 3.8 34.5 1.0 CG A:PRO192 3.9 42.0 1.0 CB A:PRO535 3.9 38.2 1.0 CG A:PRO183 4.2 48.7 1.0 C A:PRO535 4.2 34.1 1.0 OD1 A:ASN399 4.3 36.2 1.0 CG A:ASN399 4.4 31.8 1.0 CD A:PRO192 4.7 45.3 1.0 CA A:PRO535 4.7 32.8 1.0 CG A:PRO535 4.7 38.9 1.0 O A:PRO535 4.9 33.4 1.0 CD A:PRO183 5.0 45.6 1.0

K.Kato, H.Nishimasu, D.Oikawa, S.Hirano, H.Hirano, G.Kasuya, R.Ishitani, F.Tokunaga, O.Nureki. Structural Insights Into Cgamp Degradation By Ecto-Nucleotide Pyrophosphatase Phosphodiesterase 1. Nat Commun V. 9 4424 2018.
ISSN: ESSN 2041-1723
PubMed: 30356045
DOI: 10.1038/S41467-018-06922-7