Chlorine in PDB 6aek: Crystal Structure of ENPP1 in Complex with Papg

Protein crystallography data

The structure of Crystal Structure of ENPP1 in Complex with Papg, PDB code: 6aek 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 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.486, 94.071, 74.680, 90.00, 96.86, 90.00
R / Rfree (%) 18.3 / 20.8

Other elements in 6aek:

The structure of Crystal Structure of ENPP1 in Complex with Papg also contains other interesting chemical elements:

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

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of ENPP1 in Complex with Papg (pdb code 6aek). 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 Papg, PDB code: 6aek:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6aek

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Chlorine binding site 1 out of 6 in the Crystal Structure of ENPP1 in Complex with Papg


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 Papg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1012

b:38.6
occ:1.00
O1 A:EDO1021 2.4 47.4 1.0
O A:HOH1222 3.2 48.8 1.0
NH2 A:ARG440 3.3 33.2 0.5
NH1 A:ARG440 3.3 28.1 0.5
C A:MET261 3.6 31.1 1.0
N A:MET261 3.6 31.1 1.0
CZ A:ARG440 3.7 31.7 0.5
CA A:MET261 3.7 29.9 1.0
C A:LYS260 3.8 32.0 1.0
C1 A:EDO1021 3.8 43.5 1.0
O A:MET261 3.8 33.2 1.0
N A:TYR262 3.9 31.0 1.0
O A:LYS260 4.0 32.9 1.0
CB A:LYS260 4.0 38.9 1.0
CG2 A:VAL432 4.1 36.2 1.0
C2 A:EDO1021 4.4 39.7 1.0
CA A:LYS260 4.5 34.2 1.0
CB A:TYR262 4.6 33.2 1.0
O A:HOH1177 4.6 31.5 1.0
NH2 A:ARG438 4.7 30.7 1.0
CA A:TYR262 4.7 32.8 1.0

Chlorine binding site 2 out of 6 in 6aek

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Chlorine binding site 2 out of 6 in the Crystal Structure of ENPP1 in Complex with Papg


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 Papg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1013

b:51.4
occ:1.00
N A:GLN885 3.2 41.2 1.0
CZ A:ARG884 3.5 40.2 1.0
NE A:ARG884 3.5 39.6 1.0
NH1 A:ARG884 3.6 41.2 1.0
CG A:GLN885 3.7 58.6 1.0
CB A:GLN885 3.7 50.1 1.0
CD A:ARG884 3.7 40.5 1.0
CA A:ARG884 3.9 36.8 1.0
C A:ARG884 4.0 38.9 1.0
NH2 A:ARG884 4.0 41.9 1.0
CA A:GLN885 4.1 44.0 1.0
CB A:ARG884 4.4 37.0 1.0
OE1 A:GLU886 4.4 47.1 1.0
CG A:ARG884 4.7 36.9 1.0
O A:ASP883 4.7 39.9 1.0
CD A:GLN885 5.0 64.6 1.0

Chlorine binding site 3 out of 6 in 6aek

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Chlorine binding site 3 out of 6 in the Crystal Structure of ENPP1 in Complex with Papg


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 Papg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1014

b:36.4
occ:1.00
OG A:SER486 3.1 26.6 1.0
CE A:LYS284 3.2 50.7 1.0
O A:HOH1327 3.3 45.0 1.0
CB A:SER486 3.8 25.6 1.0
NE A:ARG488 3.9 33.1 1.0
CZ A:ARG488 3.9 32.8 1.0
CA A:GLY255 3.9 28.9 1.0
CD A:LYS284 4.0 45.2 1.0
NH2 A:ARG488 4.0 31.0 1.0
CD A:ARG488 4.0 28.4 1.0
CA A:SER486 4.3 29.6 1.0
NH1 A:ARG488 4.5 34.0 1.0
NZ A:LYS284 4.5 54.9 1.0
CG A:ARG488 4.6 28.6 1.0
N A:ASP487 4.6 31.7 1.0
O A:GLU252 4.7 31.4 1.0
O A:GLY255 4.7 28.3 1.0
N A:GLY255 4.7 28.4 1.0
C A:GLY255 4.8 27.9 1.0
C A:SER486 4.9 30.9 1.0
CG A:LYS284 5.0 37.1 1.0

Chlorine binding site 4 out of 6 in 6aek

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Chlorine binding site 4 out of 6 in the Crystal Structure of ENPP1 in Complex with Papg


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 Papg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1015

b:31.0
occ:1.00
N A:HIS468 3.2 36.0 1.0
O A:HOH1114 3.3 53.0 1.0
CD2 A:HIS468 3.8 41.1 1.0
CA A:GLN467 3.9 42.7 1.0
CB A:HIS468 3.9 32.8 1.0
CG A:GLN467 4.0 38.5 1.0
CD1 A:PHE469 4.1 30.4 1.0
C A:GLN467 4.1 39.6 1.0
CG A:GLU464 4.1 44.7 1.0
CA A:HIS468 4.1 31.1 1.0
CE1 A:PHE469 4.2 31.6 1.0
CG A:HIS468 4.2 38.4 1.0
CG2 A:VAL417 4.3 33.2 1.0
CB A:GLU464 4.4 42.4 1.0
CB A:GLN467 4.5 39.9 1.0
OH A:TYR422 4.6 41.3 1.0
N A:PHE469 4.6 30.2 1.0
CZ3 A:TRP500 4.7 36.2 1.0
O A:ASN466 4.7 52.2 1.0
C A:HIS468 4.8 31.1 1.0
CD A:GLU464 4.9 48.5 1.0
CH2 A:TRP500 4.9 38.3 1.0

Chlorine binding site 5 out of 6 in 6aek

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Chlorine binding site 5 out of 6 in the Crystal Structure of ENPP1 in Complex with Papg


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 Papg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1016

b:36.6
occ:1.00
O A:HIS517 3.4 28.2 1.0
N A:HIS517 3.4 25.6 1.0
CE1 A:HIS362 3.5 36.1 1.0
N2 A:G1008 3.5 82.3 1.0
N3 A:G1008 3.7 82.0 1.0
CA A:PHE516 3.7 26.1 1.0
CB A:PHE516 3.8 25.6 1.0
C2 A:G1008 3.8 82.6 1.0
O A:HOH1380 3.8 49.2 1.0
C A:PHE516 4.1 25.0 1.0
NE2 A:HIS517 4.1 31.2 1.0
CD2 A:HIS517 4.2 29.1 1.0
C A:HIS517 4.2 23.6 1.0
CE A:LYS237 4.3 40.5 1.0
CE1 A:HIS517 4.3 30.6 1.0
O2' A:G1008 4.3 76.4 1.0
ND1 A:HIS362 4.3 35.8 1.0
CG A:HIS517 4.4 27.4 1.0
NE2 A:HIS362 4.4 37.9 1.0
CA A:HIS517 4.4 23.8 1.0
ND1 A:HIS517 4.4 27.3 1.0
C4 A:G1008 4.6 81.0 1.0
N1 A:G1008 4.7 82.7 1.0
O A:GLY515 4.9 30.4 1.0
CD A:LYS237 4.9 29.5 1.0
O A:HOH1385 4.9 51.7 1.0
CG A:PHE516 4.9 27.1 1.0
CD2 A:PHE516 5.0 28.4 1.0

Chlorine binding site 6 out of 6 in 6aek

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Chlorine binding site 6 out of 6 in the Crystal Structure of ENPP1 in Complex with Papg


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 Papg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1017

b:41.0
occ:1.00
ND2 A:ASN399 3.4 40.2 1.0
CB A:ALA536 3.7 41.3 1.0
CG A:PRO192 3.8 50.0 1.0
N A:ALA536 3.9 41.2 1.0
CB A:PRO535 3.9 44.7 1.0
CD A:PRO192 4.0 48.7 1.0
CA A:ALA536 4.1 41.8 1.0
OD1 A:ASN399 4.2 38.3 1.0
CG A:ASN399 4.2 37.5 1.0
C A:PRO535 4.5 43.2 1.0
CB A:PRO192 4.5 48.8 1.0
CG A:PRO183 4.6 53.6 1.0
CG A:PRO535 4.6 46.5 1.0
CA A:PRO535 4.8 42.8 1.0

Reference:

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
Page generated: Sat Dec 12 12:43:33 2020

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