Iodine in PDB 6pkg: Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide

The structure of Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide, PDB code: 6pkg 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)	35.66 / 2.80
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	124.356, 124.356, 278.792, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 20.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 78;

Binding sites:

The binding sites of Iodine atom in the Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide (pdb code 6pkg). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 78 binding sites of Iodine where determined in the Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide, PDB code: 6pkg:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 78 in the Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:I408 b:74.9 occ:1.00 HH21 A:ARG169 2.6 84.9 1.0 H A:GLY159 2.8 56.8 1.0 HG13 A:ILE174 3.1 54.5 1.0 HB2 A:SER171 3.3 65.7 1.0 NH2 A:ARG169 3.4 70.3 1.0 HD22 A:LEU158 3.4 49.6 1.0 N A:GLY159 3.7 46.9 1.0 HE A:ARG169 3.8 80.6 1.0 HH22 A:ARG169 3.8 84.9 1.0 HD2 A:HIS44 3.8 62.5 1.0 HA A:LEU158 3.8 46.9 1.0 HB3 A:HIS44 3.8 58.9 1.0 HB3 A:LEU158 4.0 45.5 1.0 HA2 A:GLY159 4.0 49.3 1.0 HD23 A:LEU158 4.0 49.6 1.0 HG21 A:ILE174 4.1 79.7 1.0 HA A:SER171 4.1 60.4 1.0 CG1 A:ILE174 4.1 45.0 1.0 CB A:SER171 4.1 54.4 1.0 CD2 A:LEU158 4.2 43.4 1.0 HB3 A:SER171 4.2 65.7 1.0 CZ A:ARG169 4.4 80.0 1.0 CA A:GLY159 4.4 40.6 1.0 HG12 A:ILE174 4.4 54.5 1.0 NE A:ARG169 4.4 66.8 1.0 O A:HOH623 4.4 53.4 1.0 HB A:ILE174 4.4 70.0 1.0 CA A:LEU158 4.5 41.1 1.0 CD2 A:HIS44 4.5 51.7 1.0 C A:LEU158 4.6 42.4 1.0 CA A:SER171 4.6 49.9 1.0 CB A:LEU158 4.6 39.9 1.0 CB A:ILE174 4.7 58.0 1.0 CB A:HIS44 4.7 48.7 1.0 O A:SER171 4.8 48.9 1.0 HD21 A:LEU158 4.8 49.6 1.0 CG2 A:ILE174 4.8 66.0 1.0 O A:HIS44 4.8 64.2 1.0 HD11 A:ILE174 4.9 63.4 1.0 CG A:HIS44 4.9 35.9 1.0

Iodine binding site 2 out of 78 in the Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:I409 b:64.9 occ:0.87 HB2 A:SER49 3.0 82.8 1.0 H A:ARG51 3.2 50.8 1.0 HB3 A:HIS50 3.3 47.9 1.0 HB2 A:ARG51 3.5 64.9 1.0 H A:HIS50 3.6 53.4 1.0 O A:HOH592 3.7 54.3 1.0 HH21 A:ARG51 3.8 89.2 1.0 N A:ARG51 3.9 43.5 1.0 O A:HOH598 4.0 50.4 1.0 CB A:SER49 4.0 68.6 1.0 N A:HIS50 4.1 44.1 1.0 NH2 A:ARG51 4.1 73.9 1.0 CB A:HIS50 4.2 41.9 1.0 CB A:ARG51 4.3 53.7 1.0 HB3 A:ARG51 4.3 64.9 1.0 HD1 A:HIS50 4.4 71.9 1.0 HG A:SER49 4.4 56.2 1.0 HH22 A:ARG51 4.4 89.2 1.0 HB3 A:SER49 4.4 82.8 1.0 HE A:ARG51 4.5 0.9 1.0 OG A:SER49 4.5 46.4 1.0 CA A:HIS50 4.6 42.4 1.0 HB2 A:SER193 4.6 59.5 1.0 CZ A:ARG51 4.6 98.5 1.0 C A:HIS50 4.7 43.7 1.0 HB2 A:HIS50 4.7 47.9 1.0 CA A:ARG51 4.7 50.6 1.0 NE A:ARG51 4.7 0.4 1.0 C A:SER49 4.9 49.3 1.0 HA A:SER49 4.9 64.6 1.0 CA A:SER49 4.9 53.4 1.0

Iodine binding site 3 out of 78 in the Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:I410 b:63.2 occ:0.79 HN2 A:NAG401 2.7 76.9 1.0 HZ3 A:TRP277 3.1 73.0 1.0 H81 A:NAG401 3.4 64.3 1.0 HG21 A:ILE220 3.6 28.6 1.0 N2 A:NAG401 3.6 63.7 1.0 HB A:ILE220 3.7 34.7 1.0 O A:HOH556 3.7 28.9 1.0 H1 A:NAG401 3.8 55.3 1.0 H3 A:NAG401 3.8 61.0 1.0 CZ3 A:TRP277 3.8 60.5 1.0 HD12 A:ILE220 3.8 35.9 1.0 HE3 A:TRP277 3.9 59.1 1.0 HG22 A:ILE220 3.9 28.6 1.0 CG2 A:ILE220 4.1 23.4 1.0 CE3 A:TRP277 4.3 48.8 1.0 C8 A:NAG401 4.3 53.2 1.0 CB A:ILE220 4.4 28.5 1.0 C2 A:NAG401 4.4 55.2 1.0 C1 A:NAG401 4.5 45.6 1.0 C7 A:NAG401 4.5 64.7 1.0 HD13 A:ILE220 4.5 35.9 1.0 C3 A:NAG401 4.6 50.4 1.0 CD1 A:ILE220 4.6 29.6 1.0 O A:HOH620 4.8 44.6 1.0 H82 A:NAG401 4.8 64.3 1.0 ND2 A:ASN223 4.8 49.3 1.0 CH2 A:TRP277 4.9 58.9 1.0 HD21 A:ASN223 4.9 59.7 1.0 H83 A:NAG401 4.9 64.3 1.0 O A:HOH607 4.9 41.7 1.0 HH2 A:TRP277 5.0 71.2 1.0

Iodine binding site 4 out of 78 in the Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:I411 b:54.6 occ:0.62 HD21 A:ASN275 2.9 39.1 1.0 H A:ASP92 3.1 91.1 1.0 HE21 A:GLN278 3.2 74.0 1.0 HA A:ASP91 3.4 81.6 1.0 HB2 A:ASP91 3.5 0.8 1.0 O A:HOH632 3.6 36.4 1.0 HG3 A:GLN278 3.6 29.1 1.0 ND2 A:ASN275 3.8 32.2 1.0 HB2 A:TRP277 3.8 37.5 1.0 N A:ASP92 3.8 75.5 1.0 NE2 A:GLN278 3.9 61.2 1.0 O A:HOH630 4.0 59.6 1.0 HB3 A:ASP92 4.0 91.7 1.0 CA A:ASP91 4.1 67.6 1.0 CB A:ASP91 4.1 84.4 1.0 HD22 A:ASN275 4.2 39.1 1.0 HB3 A:ASP91 4.2 0.8 1.0 OD1 A:ASP92 4.3 0.6 1.0 HE22 A:GLN278 4.4 74.0 1.0 CG A:GLN278 4.4 23.8 1.0 CG A:ASP92 4.4 0.4 1.0 HB3 A:TRP277 4.4 37.5 1.0 HG2 A:GLN278 4.5 29.1 1.0 C A:ASP91 4.5 67.9 1.0 CB A:TRP277 4.5 30.9 1.0 OD1 A:ASN275 4.5 53.7 1.0 CB A:ASP92 4.6 76.0 1.0 CD A:GLN278 4.6 35.5 1.0 CG A:ASN275 4.6 30.0 1.0 O A:HOH626 4.8 30.7 1.0 CA A:ASP92 4.8 74.6 1.0 HD1 A:TRP277 4.8 57.3 1.0 OD2 A:ASP92 5.0 0.1 1.0

Iodine binding site 5 out of 78 in the Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:I412 b:53.0 occ:0.55 HE22 A:GLN268 2.8 0.2 1.0 HH22 A:ARG322 3.0 69.1 1.0 HE1 A:HIS315 3.1 93.1 1.0 HH2 B:TRP98 3.4 67.8 1.0 O A:HOH629 3.5 48.1 1.0 NE2 A:GLN268 3.7 90.6 1.0 NH2 A:ARG322 3.7 57.1 1.0 CE1 A:HIS315 3.9 77.2 1.0 OE1 A:GLN268 4.0 48.5 1.0 HH21 A:ARG322 4.1 69.1 1.0 HH12 A:ARG322 4.1 48.6 1.0 CH2 B:TRP98 4.2 56.1 1.0 HE21 A:GLN268 4.3 0.2 1.0 NE2 A:HIS315 4.3 71.7 1.0 CD A:GLN268 4.3 56.0 1.0 HZ3 B:TRP98 4.5 79.7 1.0 CZ A:ARG322 4.6 37.6 1.0 NH1 A:ARG322 4.7 40.1 1.0 HH12 A:ARG272 4.7 57.4 1.0 CZ3 B:TRP98 4.8 66.0 1.0 O A:HOH579 4.9 46.6 1.0 HZ2 B:TRP98 5.0 39.0 1.0

Iodine binding site 6 out of 78 in the Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:I413 b:52.5 occ:0.50 HE A:ARG240 2.8 0.9 1.0 HH21 A:ARG240 2.9 90.3 1.0 HG22 A:THR236 3.5 82.2 1.0 HA2 A:GLY237 3.5 54.2 1.0 NE A:ARG240 3.6 0.1 1.0 NH2 A:ARG240 3.7 74.8 1.0 HB A:THR236 3.8 83.8 1.0 N A:GLY237 4.0 72.6 1.0 CA A:GLY237 4.1 45.1 1.0 CZ A:ARG240 4.1 81.8 1.0 H A:GLY237 4.1 87.6 1.0 CG2 A:THR236 4.2 68.1 1.0 HA3 A:GLY237 4.2 54.2 1.0 HG21 A:THR236 4.3 82.2 1.0 C A:THR236 4.3 48.5 1.0 HH22 A:ARG240 4.4 90.3 1.0 CB A:THR236 4.4 69.4 1.0 O A:THR236 4.6 43.0 1.0 HG3 A:ARG240 4.6 63.1 1.0 HD3 A:ARG240 4.7 91.0 1.0 CD A:ARG240 4.7 75.4 1.0

Iodine binding site 7 out of 78 in the Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:I414 b:0.2 occ:0.64 HG23 A:ILE89 2.9 73.5 1.0 HD3 A:LYS281 3.0 86.1 1.0 HD12 A:ILE89 3.3 61.8 1.0 HZ3 A:LYS281 3.4 85.4 1.0 O A:HOH600 3.4 37.4 1.0 HG2 A:GLN278 3.4 29.1 1.0 H A:THR90 3.4 76.4 1.0 O A:THR90 3.5 73.0 1.0 I A:IOD422 3.8 0.4 0.6 CG2 A:ILE89 3.8 60.8 1.0 CD A:LYS281 3.9 71.3 1.0 O A:HOH632 3.9 36.4 1.0 HA A:ILE89 4.0 47.4 1.0 HA A:GLN278 4.0 32.8 1.0 HB3 A:LYS281 4.1 28.2 1.0 NZ A:LYS281 4.2 70.7 1.0 N A:THR90 4.2 63.3 1.0 HB3 A:GLN278 4.2 37.0 1.0 HE2 A:LYS281 4.2 87.2 1.0 HG21 A:ILE89 4.2 73.5 1.0 HG22 A:ILE89 4.2 73.5 1.0 CD1 A:ILE89 4.3 51.1 1.0 CG A:GLN278 4.3 23.8 1.0 CE A:LYS281 4.3 72.3 1.0 HD2 A:LYS281 4.4 86.1 1.0 HD13 A:ILE89 4.5 61.8 1.0 HZ2 A:LYS281 4.5 85.4 1.0 C A:THR90 4.6 57.2 1.0 CB A:GLN278 4.6 30.4 1.0 CA A:ILE89 4.7 41.5 1.0 CB A:ILE89 4.7 40.2 1.0 HG3 A:GLN278 4.7 29.1 1.0 CA A:GLN278 4.7 26.9 1.0 HZ1 A:LYS281 4.8 85.4 1.0 HG2 A:LYS281 4.8 57.3 1.0 CG A:LYS281 4.8 47.3 1.0 HD11 A:ILE89 4.8 61.8 1.0 HB A:THR90 4.9 64.7 1.0 CB A:LYS281 4.9 23.9 1.0 C A:ILE89 4.9 44.8 1.0 O A:GLN278 4.9 37.8 1.0 CA A:THR90 4.9 69.1 1.0

Iodine binding site 8 out of 78 in the Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:I415 b:93.1 occ:0.65 HG21 A:THR236 2.8 82.2 1.0 O A:HOH591 3.2 62.5 1.0 HD3 A:ARG240 3.4 91.0 1.0 CG2 A:THR236 3.6 68.1 1.0 HG23 A:THR236 3.6 82.2 1.0 HG22 A:THR236 3.7 82.2 1.0 HG22 A:ILE226 3.9 51.9 1.0 HG21 A:ILE226 4.3 51.9 1.0 CD A:ARG240 4.4 75.4 1.0 CG2 A:ILE226 4.5 42.8 1.0 HG23 A:ILE226 4.6 51.9 1.0 HG1 A:THR236 4.6 80.7 1.0 HE A:ARG240 4.7 0.9 1.0 HG3 A:ARG240 4.8 63.1 1.0 CB A:THR236 4.9 69.4 1.0 HD2 A:ARG240 4.9 91.0 1.0 NE A:ARG240 5.0 0.1 1.0 HG2 A:ARG240 5.0 63.1 1.0

Iodine binding site 9 out of 78 in the Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:I416 b:79.3 occ:0.66 HB2 A:LYS232 3.5 89.0 1.0 CB A:LYS232 4.4 73.8 1.0 HB3 A:LYS232 4.5 89.0 1.0 HD2 A:LYS232 4.6 0.4 1.0 O A:LYS232 4.7 80.6 1.0 HA A:LYS232 4.8 70.4 1.0

Iodine binding site 10 out of 78 in the Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:I417 b:0.5 occ:0.75 HG2 A:LYS137 3.2 60.5 1.0 HA A:LYS140 3.3 74.2 1.0 HG2 A:LYS140 3.3 89.4 1.0 HA A:LYS137 3.5 57.5 1.0 H4 B:NAG402 4.0 0.8 1.0 CG A:LYS137 4.1 50.0 1.0 HB3 A:LYS137 4.1 54.5 1.0 HO4 B:NAG402 4.1 99.6 1.0 CG A:LYS140 4.2 74.1 1.0 CA A:LYS140 4.2 61.4 1.0 CA A:LYS137 4.3 47.5 1.0 CB A:LYS137 4.4 47.4 1.0 HA3 A:GLY306 4.5 68.2 1.0 HG3 A:LYS140 4.5 89.4 1.0 O A:LYS137 4.5 60.8 1.0 HG3 A:LYS137 4.5 60.5 1.0 HB3 A:LYS140 4.6 64.6 1.0 CB A:LYS140 4.6 53.4 1.0 H A:LYS140 4.6 74.7 1.0 H61 B:NAG402 4.7 0.9 1.0 O4 B:NAG402 4.8 82.6 1.0 C4 B:NAG402 4.8 0.1 1.0 HD3 A:LYS137 4.9 80.2 1.0 HE2 A:LYS137 4.9 97.9 1.0 O A:ASN305 4.9 46.0 1.0 C A:LYS137 5.0 48.4 1.0 N A:LYS140 5.0 61.9 1.0

A.Gorelik, K.Illes, B.Nagar. Zebrafish N-Acetylglucosamine-1-Phosphodiester Alpha-N-Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro-Peptide To Be Published.