Chlorine in PDB 6pki: Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain (C56S C230S) in Complex with N-Acetyl-Alpha-D-Glucosamine (Alpha-Glcnac) and Mannose 6-Phosphate (M6P)

The structure of Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain (C56S C230S) in Complex with N-Acetyl-Alpha-D-Glucosamine (Alpha-Glcnac) and Mannose 6-Phosphate (M6P), PDB code: 6pki 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)	22.66 / 2.29
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	124.170, 124.170, 276.989, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 20.4

The binding sites of Chlorine atom in the Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain (C56S C230S) in Complex with N-Acetyl-Alpha-D-Glucosamine (Alpha-Glcnac) and Mannose 6-Phosphate (M6P) (pdb code 6pki). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain (C56S C230S) in Complex with N-Acetyl-Alpha-D-Glucosamine (Alpha-Glcnac) and Mannose 6-Phosphate (M6P), PDB code: 6pki:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain (C56S C230S) in Complex with N-Acetyl-Alpha-D-Glucosamine (Alpha-Glcnac) and Mannose 6-Phosphate (M6P)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain (C56S C230S) in Complex with N-Acetyl-Alpha-D-Glucosamine (Alpha-Glcnac) and Mannose 6-Phosphate (M6P) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl406 b:70.6 occ:1.00 HD2 A:ARG51 3.0 78.7 1.0 CD A:ARG51 3.8 65.6 1.0 HE A:ARG51 3.9 78.1 1.0 HD3 A:ARG51 4.0 78.7 1.0 NE A:ARG51 4.1 65.0 1.0 HB3 A:ARG51 4.5 32.5 1.0 HH12 A:ARG54 4.5 99.1 1.0 O A:HOH688 4.6 86.7 1.0 CG A:ARG51 5.0 53.1 1.0

Chlorine binding site 2 out of 4 in the Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain (C56S C230S) in Complex with N-Acetyl-Alpha-D-Glucosamine (Alpha-Glcnac) and Mannose 6-Phosphate (M6P)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain (C56S C230S) in Complex with N-Acetyl-Alpha-D-Glucosamine (Alpha-Glcnac) and Mannose 6-Phosphate (M6P) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl405 b:75.4 occ:1.00 HG B:SER49 2.9 44.1 1.0 HB2 B:TYR52 3.3 46.1 1.0 OG B:SER49 3.6 36.7 1.0 H B:SER49 3.7 45.9 1.0 HD2 B:TYR52 4.1 59.3 1.0 HB2 B:HIS48 4.2 48.0 1.0 H B:TYR52 4.3 41.3 1.0 CB B:TYR52 4.3 38.4 1.0 HB3 B:SER49 4.4 39.0 1.0 HB2 B:ARG51 4.5 44.2 1.0 N B:SER49 4.5 38.2 1.0 CB B:SER49 4.6 32.7 1.0 O B:HOH628 4.7 38.3 1.0 N B:TYR52 4.7 34.4 1.0 HB3 B:TYR52 4.7 46.1 1.0 HA B:HIS48 4.7 53.1 1.0 HA B:TYR52 4.8 38.6 1.0 CD2 B:TYR52 4.9 49.4 1.0 CA B:TYR52 4.9 32.2 1.0 CB B:HIS48 5.0 40.0 1.0 HB3 B:HIS48 5.0 48.0 1.0

Chlorine binding site 3 out of 4 in the Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain (C56S C230S) in Complex with N-Acetyl-Alpha-D-Glucosamine (Alpha-Glcnac) and Mannose 6-Phosphate (M6P)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain (C56S C230S) in Complex with N-Acetyl-Alpha-D-Glucosamine (Alpha-Glcnac) and Mannose 6-Phosphate (M6P) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl406 b:81.5 occ:1.00 HA B:VAL245 3.4 33.0 1.0 HD2 B:HIS241 3.7 62.8 1.0 HB3 B:ASP244 3.9 37.4 1.0 O B:HOH609 4.0 34.0 1.0 HG23 B:VAL245 4.0 43.3 1.0 HE2 B:HIS241 4.0 73.3 1.0 HB2 B:ASP244 4.1 37.4 1.0 CD2 B:HIS241 4.2 52.2 1.0 CA B:VAL245 4.2 27.4 1.0 HB B:VAL245 4.2 33.6 1.0 N B:VAL245 4.3 31.7 1.0 O B:ASP244 4.4 32.4 1.0 NE2 B:HIS241 4.4 61.1 1.0 C B:ASP244 4.4 28.4 1.0 CB B:ASP244 4.5 31.1 1.0 CB B:VAL245 4.6 28.0 1.0 H B:VAL245 4.7 38.1 1.0 OD1 B:ASP270 4.8 65.1 1.0 CG2 B:VAL245 4.8 36.0 1.0

Chlorine binding site 4 out of 4 in the Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain (C56S C230S) in Complex with N-Acetyl-Alpha-D-Glucosamine (Alpha-Glcnac) and Mannose 6-Phosphate (M6P)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain (C56S C230S) in Complex with N-Acetyl-Alpha-D-Glucosamine (Alpha-Glcnac) and Mannose 6-Phosphate (M6P) within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl406 b:86.3 occ:1.00 O C:HOH613 3.5 80.7 1.0 HA2 C:GLY123 3.6 73.9 1.0 HA3 C:GLY119 4.1 68.6 1.0 HD2 C:HIS128 4.1 82.3 1.0 CA C:GLY123 4.3 61.5 1.0 HA3 C:GLY123 4.4 73.9 1.0 O C:PRO118 4.4 66.2 1.0 O C:PRO121 4.4 58.9 1.0 O C:GLY120 4.4 67.4 1.0 CD2 C:HIS128 4.4 68.5 1.0 C C:GLY119 4.4 57.5 1.0 N C:GLY123 4.5 59.3 1.0 O C:GLY119 4.5 65.3 1.0 H C:GLY123 4.7 71.2 1.0 N C:GLY120 4.7 62.3 1.0 HA3 C:GLY120 4.8 74.8 1.0 CA C:GLY119 4.8 57.1 1.0 C C:GLY122 4.8 66.2 1.0 C C:GLY120 4.9 58.9 1.0 HB2 C:HIS128 4.9 71.9 1.0 CG C:HIS128 4.9 66.0 1.0 ND1 C:HIS126 4.9 95.7 1.0 O C:GLY122 5.0 61.6 1.0

A.Gorelik, K.Illes, B.Nagar. Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N-Acetylglucosaminidase (Nagpa) Catalytic Domain (C56S C230S) in Complex with N-Acetyl-Alpha-D-Glucosamine (Alpha-Glcnac) and Mannose 6-Phosphate (M6P) To Be Published.