Sodium in PDB 8pej: CJGH35 with A Galactosidase Activity-Based Probe

All present enzymatic activity of CJGH35 with A Galactosidase Activity-Based Probe:
3.2.1.23;

The structure of CJGH35 with A Galactosidase Activity-Based Probe, PDB code: 8pej was solved by W.A.Offen, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	82.54 / 1.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	99.316, 116.212, 116.396, 90.24, 89.89, 90.09
R / Rfree (%)	15.7 / 18.1

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 35;

Binding sites:

The binding sites of Sodium atom in the CJGH35 with A Galactosidase Activity-Based Probe (pdb code 8pej). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 35 binding sites of Sodium where determined in the CJGH35 with A Galactosidase Activity-Based Probe, PDB code: 8pej:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 35 in the CJGH35 with A Galactosidase Activity-Based Probe


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of CJGH35 with A Galactosidase Activity-Based Probe within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:29.8 occ:1.00 O A:GLY466 2.3 25.6 1.0 O A:HOH1097 2.3 42.9 1.0 OD1 A:ASP464 2.5 30.1 1.0 OG A:SER518 2.5 31.0 1.0 OE1 A:GLN519 2.5 36.6 1.0 O A:HOH744 2.6 35.6 1.0 HG A:SER518 2.9 30.8 0.0 HB3 A:SER518 3.1 29.8 1.0 CG A:ASP464 3.3 31.4 1.0 CB A:SER518 3.3 29.8 1.0 C A:GLY466 3.3 23.6 1.0 HE22 A:GLN519 3.4 40.7 1.0 NA A:NA605 3.4 34.3 1.0 H A:GLY466 3.4 24.9 1.0 OD2 A:ASP464 3.4 37.8 1.0 HA2 A:GLY466 3.5 25.0 1.0 CD A:GLN519 3.5 44.2 1.0 HB2 A:SER518 3.7 29.8 1.0 CA A:GLY466 3.7 25.7 1.0 NE2 A:GLN519 3.8 39.4 1.0 N A:GLY466 3.9 24.4 1.0 OD1 A:ASP469 4.4 27.4 1.0 O A:HOH1120 4.4 46.7 1.0 N A:LEU467 4.5 25.6 1.0 HA A:LEU467 4.6 26.6 1.0 CB A:ASP464 4.6 27.1 1.0 CA A:SER518 4.6 28.9 1.0 O A:HOH850 4.7 35.5 1.0 HE21 A:GLN519 4.7 40.8 1.0 HA3 A:GLY466 4.7 25.0 1.0 HA A:ASP464 4.8 25.5 1.0 CG A:GLN519 4.9 43.7 1.0 C A:SER518 5.0 34.0 1.0 HB2 A:ASP464 5.0 27.5 1.0 HG3 A:GLN519 5.0 42.7 1.0 CA A:LEU467 5.0 26.8 1.0

Sodium binding site 2 out of 35 in the CJGH35 with A Galactosidase Activity-Based Probe


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of CJGH35 with A Galactosidase Activity-Based Probe within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:27.3 occ:1.00 OE1 A:GLU544 2.5 28.1 1.0 O A:HOH916 2.5 23.9 1.0 OE2 A:GLU533 2.6 22.1 1.0 O A:HOH837 2.6 36.2 1.0 O A:HOH812 2.8 34.7 1.0 O A:HOH1140 3.1 55.0 1.0 HG2 A:GLU533 3.1 19.7 1.0 CD A:GLU533 3.5 21.4 1.0 CD A:GLU544 3.5 27.4 1.0 CG A:GLU533 3.6 19.7 1.0 HG3 A:GLU533 3.7 19.7 1.0 OE2 A:GLU544 3.8 31.0 1.0 O A:HOH988 3.8 26.0 1.0 HA A:HIS563 3.8 19.9 1.0 HD1 A:HIS563 3.9 20.3 0.0 O A:HOH1020 4.0 36.6 1.0 O B:HOH798 4.1 44.6 1.0 H A:LEU564 4.1 18.9 1.0 O A:PRO562 4.4 21.5 1.0 O A:GLY534 4.4 22.4 1.0 OE1 A:GLU533 4.6 20.6 1.0 ND1 A:HIS563 4.7 20.2 1.0 O A:HOH1108 4.7 28.7 1.0 O A:HOH1152 4.7 28.2 1.0 CA A:HIS563 4.8 19.8 1.0 O A:HOH1157 4.8 30.1 1.0 H A:GLY534 4.8 19.9 1.0 HB2 A:GLU544 4.8 22.4 1.0 HA2 A:GLY534 4.9 21.4 1.0 CG A:GLU544 4.9 24.2 1.0 N A:GLY534 5.0 19.6 1.0 O A:HOH950 5.0 32.4 1.0

Sodium binding site 3 out of 35 in the CJGH35 with A Galactosidase Activity-Based Probe


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of CJGH35 with A Galactosidase Activity-Based Probe within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:34.3 occ:1.00 O A:HOH850 2.3 35.5 1.0 O A:HOH1102 2.3 48.5 1.0 OG A:SER518 2.4 31.0 1.0 O A:HOH744 2.4 35.6 1.0 O A:SER518 2.5 33.5 1.0 OE1 A:GLN519 2.6 36.6 1.0 HG A:SER518 2.8 30.8 0.0 C A:SER518 3.2 34.0 1.0 NA A:NA601 3.4 29.8 1.0 HG3 A:GLN519 3.4 42.7 1.0 CB A:SER518 3.4 29.8 1.0 CD A:GLN519 3.5 44.2 1.0 CA A:SER518 3.7 28.9 1.0 HB3 A:SER518 3.7 29.8 1.0 HA A:SER518 3.7 29.2 1.0 CG A:GLN519 4.0 43.7 1.0 N A:GLN519 4.1 36.9 1.0 HA A:GLN519 4.1 39.0 1.0 HB2 A:SER518 4.2 29.8 1.0 OD1 A:ASP469 4.3 27.4 1.0 OD2 A:ASP469 4.3 31.2 1.0 CA A:GLN519 4.6 39.0 1.0 OD2 A:ASP464 4.6 37.8 1.0 NE2 A:GLN519 4.6 39.4 1.0 OD1 A:ASP464 4.6 30.1 1.0 HG2 A:GLN519 4.7 42.8 1.0 CG A:ASP464 4.7 31.4 1.0 CG A:ASP469 4.7 27.1 1.0 HE22 A:GLN519 4.8 40.7 1.0 H A:GLN519 4.8 36.5 1.0 CB A:GLN519 4.8 39.4 1.0 O A:HOH754 4.9 35.5 1.0 O A:GLY466 5.0 25.6 1.0

Sodium binding site 4 out of 35 in the CJGH35 with A Galactosidase Activity-Based Probe


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of CJGH35 with A Galactosidase Activity-Based Probe within 5.0Å range: probe atom residue distance (Å) B Occ A:Na606 b:32.0 occ:1.00 O A:HIS49 2.5 22.8 1.0 O A:GLY367 2.6 22.6 1.0 O A:HOH1031 2.9 31.0 1.0 OG A:SER417 2.9 34.5 1.0 O A:HOH930 3.2 27.7 1.0 HA3 A:GLY367 3.4 22.0 1.0 HA2 A:GLY367 3.4 22.0 1.0 C A:GLY367 3.5 22.2 1.0 HB3 A:SER417 3.5 27.9 1.0 HG A:SER417 3.6 34.1 0.0 H A:HIS49 3.6 25.8 1.0 HA A:TYR418 3.6 26.6 1.0 C A:HIS49 3.6 22.2 1.0 CA A:GLY367 3.7 22.2 1.0 CB A:SER417 3.7 26.6 1.0 HA A:ALA50 3.9 24.4 1.0 C A:SER417 3.9 30.2 1.0 HG22 A:ILE369 3.9 24.3 1.0 HB2 A:TYR418 4.0 24.9 1.0 N A:TYR418 4.0 25.2 1.0 O A:SER417 4.1 31.1 1.0 HB2 A:HIS49 4.1 23.8 1.0 CA A:TYR418 4.2 26.5 1.0 O A:HOH924 4.3 36.1 1.0 N A:HIS49 4.3 25.0 1.0 H A:TYR418 4.4 26.6 1.0 CA A:SER417 4.4 24.9 1.0 HD1 A:TYR418 4.5 25.8 1.0 CA A:HIS49 4.5 24.8 1.0 HB2 A:SER417 4.5 27.9 1.0 HB2 A:ALA50 4.6 25.1 1.0 O A:HOH962 4.6 25.2 1.0 HG21 A:ILE369 4.6 24.3 1.0 N A:ALA50 4.6 22.7 1.0 O A:HOH910 4.6 21.3 1.0 CB A:TYR418 4.6 24.1 1.0 CA A:ALA50 4.6 24.9 1.0 O A:GLY368 4.7 23.3 1.0 N A:GLY368 4.7 20.6 1.0 CG2 A:ILE369 4.7 25.5 1.0 O A:HOH848 4.8 26.9 1.0 HB3 A:LYS48 4.8 34.4 1.0 O A:HOH846 4.8 29.5 1.0 CB A:HIS49 4.8 24.0 1.0 C A:GLY368 4.8 21.2 1.0 HA A:SER417 5.0 25.6 1.0 HA A:ILE369 5.0 20.0 1.0

Sodium binding site 5 out of 35 in the CJGH35 with A Galactosidase Activity-Based Probe


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of CJGH35 with A Galactosidase Activity-Based Probe within 5.0Å range: probe atom residue distance (Å) B Occ B:Na601 b:31.5 occ:1.00 O B:GLY466 2.3 25.1 1.0 O B:HOH1067 2.4 35.8 1.0 OD1 B:ASP464 2.4 28.5 1.0 O B:HOH1170 2.5 46.0 1.0 OG B:SER518 2.5 31.0 1.0 O B:HOH1127 2.6 36.0 1.0 HG B:SER518 2.9 31.0 0.0 HB3 B:SER518 3.2 29.9 1.0 CG B:ASP464 3.2 34.0 1.0 CB B:SER518 3.3 29.7 1.0 O B:HOH705 3.4 27.9 1.0 C B:GLY466 3.4 25.2 1.0 H B:GLY466 3.4 25.8 1.0 OD2 B:ASP464 3.4 36.3 1.0 HA2 B:GLY466 3.5 26.7 1.0 HB2 B:SER518 3.7 29.9 1.0 CA B:GLY466 3.8 27.6 1.0 N B:GLY466 3.9 26.1 1.0 O B:HOH1175 4.0 43.1 1.0 OD1 B:ASP469 4.3 27.1 1.0 N B:LEU467 4.6 26.0 1.0 CB B:ASP464 4.6 25.9 1.0 HA B:LEU467 4.6 25.1 1.0 CA B:SER518 4.6 29.4 1.0 HA3 B:GLY466 4.7 26.7 1.0 HA B:ASP464 4.8 25.6 1.0 O B:HOH718 4.8 41.5 1.0 HB2 B:ASP464 4.9 27.5 1.0 C B:SER518 4.9 32.9 1.0 O B:SER518 5.0 33.7 1.0 H B:LEU465 5.0 24.2 1.0 HA B:SER518 5.0 29.4 1.0

Sodium binding site 6 out of 35 in the CJGH35 with A Galactosidase Activity-Based Probe


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of CJGH35 with A Galactosidase Activity-Based Probe within 5.0Å range: probe atom residue distance (Å) B Occ B:Na603 b:27.3 occ:1.00 O B:HOH759 2.5 34.0 1.0 O B:HOH1001 2.6 23.9 1.0 OE2 B:GLU533 2.6 22.7 1.0 OE1 B:GLU544 2.6 26.5 1.0 O B:HOH753 2.8 37.4 1.0 HG2 B:GLU533 3.2 20.0 1.0 CD B:GLU533 3.5 22.4 1.0 CD B:GLU544 3.6 26.9 1.0 CG B:GLU533 3.7 19.7 1.0 HA B:HIS563 3.7 19.0 1.0 O B:HOH1033 3.8 24.6 1.0 HG3 B:GLU533 3.8 19.9 1.0 OE2 B:GLU544 3.8 29.7 1.0 HD1 B:HIS563 3.9 21.9 0.0 O B:HOH1147 4.0 40.4 1.0 O H:HOH749 4.1 47.1 1.0 H B:LEU564 4.1 18.8 1.0 O B:PRO562 4.3 22.2 1.0 O B:GLY534 4.5 21.3 1.0 OE1 B:GLU533 4.6 21.4 1.0 O B:HOH1169 4.6 28.9 1.0 ND1 B:HIS563 4.7 21.9 1.0 O B:HOH1231 4.7 29.1 1.0 CA B:HIS563 4.7 18.3 1.0 O B:HOH1240 4.8 28.9 1.0 O B:HOH866 4.8 31.1 1.0 HB2 B:GLU544 4.9 23.1 1.0 HA2 B:GLY534 4.9 21.1 1.0 CG B:GLU544 5.0 22.1 1.0 H B:GLY534 5.0 20.4 1.0 N B:LEU564 5.0 18.1 1.0

Sodium binding site 7 out of 35 in the CJGH35 with A Galactosidase Activity-Based Probe


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of CJGH35 with A Galactosidase Activity-Based Probe within 5.0Å range: probe atom residue distance (Å) B Occ C:Na601 b:45.8 occ:1.00 O C:HOH1107 2.1 31.8 0.5 O C:HOH982 2.2 42.1 1.0 O C:HOH818 2.3 44.7 1.0 OG C:SER518 2.6 40.7 1.0 O C:SER518 2.6 39.9 1.0 O C:HOH1067 2.7 45.5 1.0 HG C:SER518 3.0 40.2 0.0 C C:SER518 3.3 36.6 1.0 NA C:NA602 3.4 38.7 1.0 CB C:SER518 3.6 35.4 1.0 HB3 C:SER518 3.7 36.2 1.0 CA C:SER518 3.8 34.0 1.0 HA C:SER518 3.9 34.0 1.0 N C:GLN519 4.2 39.8 1.0 HB3 C:GLN519 4.2 42.6 0.0 HA C:GLN519 4.3 45.7 1.0 HB2 C:SER518 4.4 36.2 1.0 OD1 C:ASP469 4.5 31.0 1.0 OD2 C:ASP469 4.5 37.5 1.0 OD2 C:ASP464 4.6 42.1 1.0 CA C:GLN519 4.7 48.1 1.0 CG C:ASP464 4.8 34.5 1.0 OD1 C:ASP464 4.8 30.7 1.0 H C:GLN519 4.9 40.5 1.0 CG C:ASP469 4.9 32.9 1.0

Sodium binding site 8 out of 35 in the CJGH35 with A Galactosidase Activity-Based Probe


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of CJGH35 with A Galactosidase Activity-Based Probe within 5.0Å range: probe atom residue distance (Å) B Occ C:Na602 b:38.7 occ:1.00 O C:HOH818 2.3 44.7 1.0 O C:GLY466 2.4 30.2 1.0 OD1 C:ASP464 2.5 30.7 1.0 OG C:SER518 2.5 40.7 1.0 O C:HOH1067 2.5 45.5 1.0 HG C:SER518 2.9 40.2 0.0 CG C:ASP464 3.2 34.5 1.0 HB3 C:SER518 3.2 36.2 1.0 OD2 C:ASP464 3.3 42.1 1.0 CB C:SER518 3.4 35.4 1.0 NA C:NA601 3.4 45.8 1.0 C C:GLY466 3.4 28.1 1.0 H C:GLY466 3.4 28.1 1.0 HA2 C:GLY466 3.5 28.1 1.0 HB2 C:SER518 3.7 36.2 1.0 CA C:GLY466 3.8 27.8 1.0 N C:GLY466 4.0 28.7 1.0 OD1 C:ASP469 4.3 31.0 1.0 O C:HOH1118 4.4 50.0 1.0 CB C:ASP464 4.5 28.3 1.0 O C:HOH982 4.5 42.1 1.0 N C:LEU467 4.6 30.3 1.0 CA C:SER518 4.7 34.0 1.0 HA C:LEU467 4.8 30.7 1.0 HA3 C:GLY466 4.8 28.1 1.0 HB2 C:ASP464 4.8 29.3 1.0 HA C:ASP464 4.8 27.0 1.0 O C:HOH1107 5.0 31.8 0.5

Sodium binding site 9 out of 35 in the CJGH35 with A Galactosidase Activity-Based Probe


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of CJGH35 with A Galactosidase Activity-Based Probe within 5.0Å range: probe atom residue distance (Å) B Occ C:Na604 b:28.3 occ:1.00 O C:HOH1105 2.2 51.8 1.0 O C:HOH913 2.6 21.2 1.0 OE2 C:GLU533 2.6 21.2 1.0 O C:HOH815 2.6 36.2 1.0 OE1 C:GLU544 2.6 26.9 1.0 O C:HOH735 3.0 34.1 1.0 HG2 C:GLU533 3.1 20.6 1.0 CD C:GLU533 3.5 22.7 1.0 CD C:GLU544 3.6 24.9 1.0 O C:HOH1133 3.7 40.7 1.0 O C:HOH1153 3.7 49.7 1.0 CG C:GLU533 3.7 20.3 1.0 HA C:HIS563 3.8 18.7 1.0 OE2 C:GLU544 3.8 28.9 1.0 O C:HOH990 3.8 25.4 1.0 HG3 C:GLU533 3.8 20.5 1.0 HD1 C:HIS563 3.8 21.8 0.0 O C:HOH1088 4.0 34.5 1.0 H C:LEU564 4.1 18.7 1.0 O A:HOH813 4.2 52.7 1.0 O C:PRO562 4.4 21.0 1.0 OE1 C:GLU533 4.6 22.1 1.0 O C:GLY534 4.6 21.8 1.0 O C:HOH1109 4.6 30.5 1.0 ND1 C:HIS563 4.7 21.8 1.0 O C:HOH1148 4.7 28.4 1.0 O C:HOH1158 4.7 29.7 1.0 CA C:HIS563 4.8 18.1 1.0 HB2 C:GLU544 4.8 21.5 1.0 HA2 C:GLY534 4.9 20.0 1.0 O C:HOH870 4.9 30.4 1.0 CG C:GLU544 5.0 22.5 1.0

Sodium binding site 10 out of 35 in the CJGH35 with A Galactosidase Activity-Based Probe


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of CJGH35 with A Galactosidase Activity-Based Probe within 5.0Å range: probe atom residue distance (Å) B Occ C:Na605 b:30.5 occ:1.00 O C:HIS49 2.4 24.5 1.0 O C:SER417 2.4 28.4 0.5 O C:GLY367 2.5 23.1 1.0 O C:HOH1047 2.8 28.0 1.0 OG C:SER417 2.9 26.6 0.5 HG C:SER417 3.0 31.8 0.0 O C:HOH889 3.3 28.8 1.0 C C:SER417 3.4 27.1 0.5 HA3 C:GLY367 3.4 21.4 1.0 C C:GLY367 3.4 22.0 1.0 HG C:SER417 3.5 26.1 0.0 HA2 C:GLY367 3.5 21.4 1.0 H C:HIS49 3.5 25.4 1.0 HB3 C:SER417 3.5 26.1 0.5 C C:HIS49 3.6 23.1 1.0 HA C:TYR418 3.6 27.4 1.0 CA C:GLY367 3.7 20.7 1.0 CB C:SER417 3.7 26.1 0.5 OG C:SER417 3.8 31.7 0.5 HB2 C:SER417 3.9 26.7 0.5 HA C:ALA50 3.9 22.9 1.0 HG22 C:ILE369 4.0 25.2 1.0 C C:SER417 4.0 27.3 0.5 N C:TYR418 4.1 25.3 1.0 HB2 C:HIS49 4.2 24.1 1.0 HB2 C:TYR418 4.2 25.9 1.0 CB C:SER417 4.2 25.3 0.5 O C:HOH1076 4.2 31.6 1.0 N C:HIS49 4.2 25.2 1.0 O C:SER417 4.3 26.7 0.5 CA C:TYR418 4.3 27.8 1.0 CA C:SER417 4.4 25.4 0.5 CA C:HIS49 4.4 24.1 1.0 HD1 C:TYR418 4.5 27.9 1.0 CA C:SER417 4.5 25.7 0.5 O C:HOH967 4.5 23.9 1.0 HB2 C:SER417 4.5 26.1 0.5 HG21 C:ILE369 4.5 25.2 1.0 N C:ALA50 4.6 21.6 1.0 O C:HOH986 4.6 21.6 1.0 O C:GLY368 4.6 21.5 1.0 CA C:ALA50 4.6 23.0 1.0 N C:GLY368 4.6 20.1 1.0 H C:TYR418 4.7 26.4 1.0 HB3 C:LYS48 4.7 33.7 1.0 CG2 C:ILE369 4.7 25.9 1.0 CB C:TYR418 4.8 24.9 1.0 HB2 C:ALA50 4.8 23.5 1.0 O C:HOH809 4.8 25.1 1.0 CB C:HIS49 4.8 23.7 1.0 C C:GLY368 4.8 22.0 1.0 HA C:SER417 4.8 25.5 0.5 O C:HOH866 4.8 28.5 1.0 HA C:SER417 5.0 25.6 0.5

C.L.Kuo, Q.Su, A.M.C.H.Van Den Nieuwendijk, T.J.M.Beenakker, W.A.Offen, L.I.Willems, R.G.Boot, A.J.Sarris, A.R.A.Marques, J.D.C.Codee, G.A.Van Der Marel, B.I.Florea, G.J.Davies, H.S.Overkleeft, J.M.F.G.Aerts. The Development of A Broad-Spectrum Retaining Beta-Exo-Galactosidase Activity-Based Probe. Org.Biomol.Chem. 2023.
ISSN: ESSN 1477-0539
PubMed: 37724332
DOI: 10.1039/D3OB01261A