Potassium in PDB 6u11: Xenopus Laevis N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) (C46S C219S C453S C480S C486S) with Ctd Mostly Flexible

The structure of Xenopus Laevis N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) (C46S C219S C453S C480S C486S) with Ctd Mostly Flexible, PDB code: 6u11 was solved by A.Gorelik, K.Illes, B.Nagar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.45 / 2.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	67.019, 383.969, 96.767, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 22.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Potassium atom in the Xenopus Laevis N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) (C46S C219S C453S C480S C486S) with Ctd Mostly Flexible (pdb code 6u11). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 11 binding sites of Potassium where determined in the Xenopus Laevis N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) (C46S C219S C453S C480S C486S) with Ctd Mostly Flexible, PDB code: 6u11:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 11 in the Xenopus Laevis N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) (C46S C219S C453S C480S C486S) with Ctd Mostly Flexible


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Xenopus Laevis N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) (C46S C219S C453S C480S C486S) with Ctd Mostly Flexible within 5.0Å range: probe atom residue distance (Å) B Occ A:K607 b:45.9 occ:1.00 O A:HOH806 2.7 44.7 1.0 HE2 A:MET141 3.2 73.4 1.0 HE1 A:MET141 3.3 73.4 1.0 OD1 A:ASP284 3.4 31.6 1.0 OD2 A:ASP284 3.5 35.5 1.0 CE A:MET141 3.6 60.8 1.0 HG A:SER288 3.7 49.1 1.0 O A:HOH773 3.7 32.3 1.0 CG A:ASP284 3.8 35.1 1.0 HE3 A:MET141 3.9 73.4 1.0 HD1 A:TYR138 3.9 45.9 1.0 HH12 A:ARG315 3.9 39.8 1.0 HH11 A:ARG315 4.0 39.8 1.0 H A:PHE139 4.1 63.3 1.0 O A:PHE139 4.3 64.9 1.0 OG A:SER288 4.3 40.5 1.0 NH1 A:ARG315 4.3 32.7 1.0 HD12 A:LEU24 4.3 71.8 1.0 HD11 A:LEU24 4.3 71.8 1.0 CD1 A:TYR138 4.5 37.8 1.0 HA A:TYR138 4.5 45.7 1.0 CE2 A:PHE139 4.8 52.1 1.0 HB3 A:TYR138 4.8 48.8 1.0 O A:LEU25 4.8 50.2 1.0 CD1 A:LEU24 4.8 59.4 1.0 HA A:SER26 4.8 61.9 1.0 HE2 A:PHE139 4.8 63.0 1.0 HE1 A:TYR138 4.9 37.5 1.0 CZ A:PHE139 4.9 40.6 1.0 N A:PHE139 4.9 52.3 1.0 HB2 A:MET141 4.9 85.1 1.0

Potassium binding site 2 out of 11 in the Xenopus Laevis N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) (C46S C219S C453S C480S C486S) with Ctd Mostly Flexible


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Xenopus Laevis N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) (C46S C219S C453S C480S C486S) with Ctd Mostly Flexible within 5.0Å range: probe atom residue distance (Å) B Occ A:K608 b:60.8 occ:1.00 HG2 A:PRO48 2.9 53.9 1.0 HE21 A:GLN213 2.9 52.4 1.0 NE2 A:HIS51 3.0 43.2 1.0 O A:HOH841 3.2 47.4 1.0 HE1 A:TYR210 3.3 43.0 1.0 O A:HOH801 3.5 28.7 1.0 O A:HOH836 3.5 37.4 1.0 HB2 A:PRO48 3.5 63.3 1.0 NE2 A:GLN213 3.6 43.3 1.0 CG A:PRO48 3.7 44.4 1.0 O A:HOH831 3.7 36.0 1.0 CE1 A:HIS51 3.7 43.4 1.0 HB3 A:PRO48 3.8 63.3 1.0 HE1 A:HIS51 3.8 52.6 1.0 CB A:PRO48 3.8 52.3 1.0 HE22 A:GLN213 3.9 52.4 1.0 CD2 A:HIS51 3.9 47.7 1.0 HG3 A:PRO48 4.0 53.9 1.0 HG2 A:GLN213 4.1 39.5 1.0 HD2 A:HIS51 4.1 57.8 1.0 CE1 A:TYR210 4.1 35.4 1.0 HD1 A:TYR210 4.2 37.0 1.0 HB A:ILE50 4.4 68.3 1.0 CD A:GLN213 4.6 41.7 1.0 CD1 A:TYR210 4.6 30.4 1.0 HH A:TYR210 4.7 43.1 1.0 HD2 A:PRO48 4.7 56.1 1.0 CG A:GLN213 4.8 32.5 1.0 ND1 A:HIS51 4.8 41.6 1.0 CD A:PRO48 4.8 46.3 1.0 O A:HOH771 4.9 41.8 1.0 CG A:HIS51 4.9 47.3 1.0

Potassium binding site 3 out of 11 in the Xenopus Laevis N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) (C46S C219S C453S C480S C486S) with Ctd Mostly Flexible


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Xenopus Laevis N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) (C46S C219S C453S C480S C486S) with Ctd Mostly Flexible within 5.0Å range: probe atom residue distance (Å) B Occ A:K609 b:48.3 occ:1.00 O A:GLN47 3.0 58.2 1.0 O A:ARG44 3.1 52.3 1.0 O A:ASP45 3.1 59.7 1.0 O A:HOH827 3.3 37.1 1.0 HA A:VAL49 3.4 55.9 1.0 HG2 A:GLN47 3.7 49.2 1.0 HA A:ASP45 3.7 61.1 1.0 C A:ASP45 3.7 48.7 1.0 O A:HOH759 3.7 47.3 1.0 HG3 A:GLN47 3.8 49.2 1.0 H A:GLN47 3.9 58.1 1.0 C A:GLN47 4.0 52.2 1.0 O A:GLY52 4.1 41.1 1.0 CG A:GLN47 4.2 40.6 1.0 CA A:ASP45 4.2 50.5 1.0 C A:ARG44 4.2 45.4 1.0 N A:GLN47 4.2 48.0 1.0 CA A:VAL49 4.2 46.1 1.0 HB A:VAL49 4.4 56.0 1.0 O A:PRO48 4.4 51.9 1.0 N A:VAL49 4.4 49.0 1.0 C A:PRO48 4.4 50.5 1.0 N A:SER46 4.6 49.6 1.0 HE21 A:GLN47 4.6 48.9 1.0 CA A:GLN47 4.6 47.2 1.0 N A:ASP45 4.7 49.9 1.0 H A:VAL49 4.8 59.4 1.0 CB A:VAL49 4.8 46.2 1.0 HG23 A:VAL49 4.8 60.9 1.0 C A:SER46 4.9 49.2 1.0 HA A:SER46 4.9 66.2 1.0 HA2 A:GLY52 5.0 60.5 1.0

Potassium binding site 4 out of 11 in the Xenopus Laevis N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) (C46S C219S C453S C480S C486S) with Ctd Mostly Flexible


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Xenopus Laevis N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) (C46S C219S C453S C480S C486S) with Ctd Mostly Flexible within 5.0Å range: probe atom residue distance (Å) B Occ A:K610 b:94.8 occ:1.00 HB A:THR224 2.6 0.0 1.0 H A:ASP227 3.1 91.0 1.0 HB2 A:ASP227 3.3 0.3 1.0 OE1 A:GLN223 3.3 90.6 1.0 CB A:THR224 3.5 88.8 1.0 HG3 A:GLN223 3.5 0.2 1.0 O A:THR224 3.7 93.8 1.0 O A:HOH820 3.8 72.1 1.0 CD A:GLN223 3.8 97.2 1.0 OD2 A:ASP227 3.8 88.2 1.0 N A:ASP227 3.8 75.4 1.0 H A:GLY226 3.8 0.9 1.0 H A:THR224 3.9 0.3 1.0 CB A:ASP227 4.0 89.8 1.0 CG A:GLN223 4.1 83.8 1.0 HA3 A:GLY226 4.1 82.0 1.0 HG22 A:THR224 4.1 0.0 1.0 CG A:ASP227 4.2 95.2 1.0 OG1 A:THR224 4.3 93.2 1.0 HG1 A:THR224 4.3 0.3 1.0 CG2 A:THR224 4.3 87.9 1.0 C A:THR224 4.3 98.2 1.0 HG2 A:GLN223 4.3 0.2 1.0 CA A:THR224 4.3 94.8 1.0 HG21 A:THR224 4.3 0.0 1.0 N A:THR224 4.4 88.2 1.0 N A:GLY226 4.5 87.0 1.0 CA A:ASP227 4.6 73.5 1.0 CA A:GLY226 4.6 67.9 1.0 C A:GLY226 4.7 57.9 1.0 NE2 A:GLN223 4.7 0.8 1.0 HB3 A:ASP227 4.8 0.3 1.0 HE22 A:GLN223 4.9 0.7 1.0 HA A:ASP227 5.0 88.7 1.0

Potassium binding site 5 out of 11 in the Xenopus Laevis N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) (C46S C219S C453S C480S C486S) with Ctd Mostly Flexible


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Xenopus Laevis N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) (C46S C219S C453S C480S C486S) with Ctd Mostly Flexible within 5.0Å range: probe atom residue distance (Å) B Occ A:K611 b:99.8 occ:1.00 O A:THR118 2.8 58.9 1.0 HB3 A:SER16 2.9 0.1 1.0 OG1 A:THR118 3.2 82.2 1.0 H A:THR118 3.4 81.3 1.0 O A:HOH839 3.4 56.9 1.0 N A:SER16 3.6 0.7 1.0 O A:HOH808 3.6 49.9 1.0 HG1 A:THR118 3.7 99.2 1.0 CB A:SER16 3.8 0.7 1.0 C A:THR118 3.8 56.2 1.0 O A:HOH715 3.9 61.2 1.0 CA A:SER16 4.0 0.8 1.0 N A:THR118 4.2 67.3 1.0 O A:SER16 4.2 0.3 1.0 C A:SER16 4.2 0.5 1.0 HB2 A:SER16 4.2 0.1 1.0 CA A:THR118 4.4 60.0 1.0 CB A:THR118 4.4 58.3 1.0 HB3 A:SER316 4.4 65.7 1.0 HG A:SER316 4.5 81.5 1.0 HG A:SER16 4.5 0.1 1.0 OG A:SER16 4.7 98.8 1.0 HA A:ALA119 4.7 60.8 1.0 HB A:THR118 4.8 70.4 1.0 N A:ARG17 4.9 0.2 1.0 HA A:LEU117 4.9 81.2 1.0 N A:ALA119 5.0 56.3 1.0 HA A:SER16 5.0 0.1 1.0

Potassium binding site 6 out of 11 in the Xenopus Laevis N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) (C46S C219S C453S C480S C486S) with Ctd Mostly Flexible


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Xenopus Laevis N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) (C46S C219S C453S C480S C486S) with Ctd Mostly Flexible within 5.0Å range: probe atom residue distance (Å) B Occ A:K612 b:93.2 occ:1.00 O A:HOH840 3.0 84.8 1.0 HD13 A:ILE163 3.7 66.2 1.0 HA3 A:GLY162 3.8 71.7 1.0 O A:GLY162 3.8 48.8 1.0 O A:HOH786 3.8 40.1 1.0 O A:LYS161 3.9 67.0 1.0 C A:GLY162 4.0 53.1 1.0 HA A:SER39 4.1 53.0 1.0 HA A:ILE163 4.3 57.6 1.0 O A:HIS38 4.3 43.9 1.0 CA A:GLY162 4.4 59.3 1.0 CD1 A:ILE163 4.5 54.7 1.0 N A:ILE163 4.5 51.5 1.0 HD11 A:ILE163 4.6 66.2 1.0 O A:SER37 4.7 60.6 1.0 H A:TYR40 4.8 48.1 1.0 CA A:ILE163 4.9 47.5 1.0 HG12 A:ILE163 4.9 66.7 1.0 C A:LYS161 5.0 64.4 1.0 H A:ILE163 5.0 62.3 1.0

Potassium binding site 7 out of 11 in the Xenopus Laevis N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) (C46S C219S C453S C480S C486S) with Ctd Mostly Flexible


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Xenopus Laevis N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) (C46S C219S C453S C480S C486S) with Ctd Mostly Flexible within 5.0Å range: probe atom residue distance (Å) B Occ A:K613 b:86.4 occ:1.00 O A:HOH795 3.5 48.5 1.0 O A:HOH726 3.6 38.4 1.0 OE1 A:GLU246 3.6 49.8 1.0 HB2 A:ASP244 3.9 56.2 1.0 HB2 A:ARG245 4.0 81.2 1.0 OE2 A:GLU246 4.2 52.7 1.0 HA3 A:GLY276 4.2 39.0 1.0 H A:ARG245 4.4 56.7 1.0 CD A:GLU246 4.4 52.3 1.0 HH21 A:ARG248 4.4 94.9 1.0 HH22 A:ARG248 4.7 94.9 1.0 O A:HOH761 4.7 37.0 1.0 OD2 A:ASP244 4.8 45.2 1.0 CB A:ASP244 4.8 46.4 1.0 HG3 A:ARG245 4.9 84.8 1.0 NH2 A:ARG248 4.9 78.6 1.0 CB A:ARG245 5.0 67.2 1.0

Potassium binding site 8 out of 11 in the Xenopus Laevis N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) (C46S C219S C453S C480S C486S) with Ctd Mostly Flexible


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Xenopus Laevis N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) (C46S C219S C453S C480S C486S) with Ctd Mostly Flexible within 5.0Å range: probe atom residue distance (Å) B Occ A:K614 b:84.5 occ:1.00 HH A:TYR307 3.3 0.8 1.0 O A:ARG312 3.6 39.8 1.0 O A:HOH838 3.8 49.2 1.0 SG A:CYS313 4.0 75.1 1.0 OH A:TYR307 4.0 0.2 1.0 HA A:CYS313 4.0 45.2 1.0 SG A:CYS305 4.2 87.1 1.0 HB3 A:TRP311 4.5 66.7 1.0 HE2 A:TYR307 4.6 0.7 1.0 C A:ARG312 4.7 36.9 1.0 HD2 A:PRO314 4.7 49.3 1.0 CA A:CYS313 4.8 37.3 1.0 HD3 A:PRO314 5.0 49.3 1.0

Potassium binding site 9 out of 11 in the Xenopus Laevis N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) (C46S C219S C453S C480S C486S) with Ctd Mostly Flexible


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Xenopus Laevis N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) (C46S C219S C453S C480S C486S) with Ctd Mostly Flexible within 5.0Å range: probe atom residue distance (Å) B Occ A:K615 b:94.6 occ:1.00 HA A:THR71 3.0 70.2 1.0 HG2 A:PRO68 3.2 0.1 1.0 O A:ALA70 3.2 62.2 1.0 O3 A:NAG605 3.4 0.9 1.0 HO3 A:NAG605 3.4 0.7 1.0 H82 A:NAG605 3.5 90.4 1.0 HO6 A:NAG606 3.8 0.5 1.0 H A:THR72 3.8 67.7 1.0 C7 A:NAG605 3.9 0.7 1.0 O6 A:NAG606 3.9 0.8 1.0 CA A:THR71 4.0 58.1 1.0 HG23 A:THR71 4.0 80.4 1.0 O7 A:NAG605 4.0 0.3 1.0 C8 A:NAG605 4.0 74.9 1.0 CG A:PRO68 4.1 0.4 1.0 O A:HOH824 4.2 64.9 1.0 HB2 A:PRO68 4.2 0.7 1.0 O A:HOH777 4.2 59.1 1.0 H81 A:NAG605 4.2 90.4 1.0 N2 A:NAG605 4.2 99.5 1.0 C A:ALA70 4.2 56.2 1.0 OG1 A:THR71 4.4 68.7 1.0 HN2 A:NAG605 4.5 0.9 1.0 N A:THR72 4.5 56.0 1.0 HG3 A:PRO68 4.6 0.1 1.0 C3 A:NAG605 4.6 0.2 1.0 N A:THR71 4.6 51.1 1.0 CB A:PRO68 4.6 92.7 1.0 CB A:THR71 4.7 54.8 1.0 HD2 A:PRO68 4.7 0.0 1.0 H2 A:NAG605 4.7 0.7 1.0 CG2 A:THR71 4.8 66.5 1.0 C2 A:NAG605 4.8 98.5 1.0 C A:THR71 4.9 57.1 1.0 H3 A:NAG605 4.9 0.1 1.0 O5 A:NAG606 4.9 0.4 1.0 HB3 A:PRO68 4.9 0.7 1.0 H83 A:NAG605 4.9 90.4 1.0

Potassium binding site 10 out of 11 in the Xenopus Laevis N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) (C46S C219S C453S C480S C486S) with Ctd Mostly Flexible


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Xenopus Laevis N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) (C46S C219S C453S C480S C486S) with Ctd Mostly Flexible within 5.0Å range: probe atom residue distance (Å) B Occ A:K616 b:69.8 occ:1.00 HH12 A:ARG312 3.0 38.3 1.0 HB2 A:ASP23 3.0 47.4 1.0 HG3 A:GLN257 3.2 34.9 1.0 O A:SER302 3.3 34.5 1.0 HE1 A:HIS304 3.5 41.5 1.0 NH1 A:ARG312 3.5 31.5 1.0 HH11 A:ARG312 3.6 38.3 1.0 OD2 A:ASP22 3.6 35.6 1.0 HD1 A:HIS304 3.7 42.5 1.0 CD A:GLN257 3.7 36.1 1.0 CG A:GLN257 3.7 28.6 1.0 HG2 A:GLN257 3.7 34.9 1.0 NE2 A:GLN257 3.9 49.8 1.0 CB A:ASP23 3.9 39.1 1.0 HE21 A:GLN257 3.9 60.3 1.0 HB2 A:SER302 4.1 37.5 1.0 HA A:ASP23 4.1 45.0 1.0 CE1 A:HIS304 4.1 34.1 1.0 OE1 A:GLN257 4.1 45.6 1.0 ND1 A:HIS304 4.2 35.0 1.0 CG A:ASP22 4.2 39.5 1.0 HE22 A:GLN257 4.3 60.3 1.0 CG A:ASP23 4.3 35.8 1.0 CA A:ASP23 4.4 37.0 1.0 O A:ASP22 4.4 46.4 1.0 N A:ASP23 4.4 41.6 1.0 OD1 A:ASP23 4.4 37.9 1.0 C A:SER302 4.4 29.7 1.0 HA A:ASP303 4.5 43.0 1.0 C A:ASP22 4.5 43.4 1.0 HB3 A:ASP23 4.6 47.4 1.0 OD1 A:ASP22 4.6 43.4 1.0 CZ A:ARG312 4.7 26.9 1.0 HB2 A:ASP22 4.7 51.5 1.0 HH22 A:ARG312 4.7 32.9 1.0 H A:ASP23 4.7 50.5 1.0 CB A:SER302 5.0 30.8 1.0 CB A:ASP22 5.0 42.5 1.0 OD2 A:ASP23 5.0 39.0 1.0

A.Gorelik, K.Illes, B.Nagar. Xenopus Laevis N-Acetylglucosamine-1-Phosphodiester Alpha-N-Acetylglucosaminidase (Nagpa) (C46S C219S C453S C480S C486S) with Ctd Mostly Flexible To Be Published.