Chlorine in PDB 7s69: N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Gamma Subunit (Gnptg), From Clawed Frog

Protein crystallography data

The structure of N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Gamma Subunit (Gnptg), From Clawed Frog, PDB code: 7s69 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) 49.19 / 3.04
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.317, 61.684, 163.029, 90, 90, 90
R / Rfree (%) 19.1 / 24.2

Chlorine Binding Sites:

The binding sites of Chlorine atom in the N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Gamma Subunit (Gnptg), From Clawed Frog (pdb code 7s69). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Gamma Subunit (Gnptg), From Clawed Frog, PDB code: 7s69:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 7s69

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Chlorine binding site 1 out of 10 in the N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Gamma Subunit (Gnptg), From Clawed Frog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Gamma Subunit (Gnptg), From Clawed Frog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:53.3
occ:1.00
 H A:SER61 2.6 49.4 1.0
HA A:PRO60 3.2 53.1 1.0
N A:SER61 3.4 41.2 1.0
HG22 A:THR178 3.4 49.5 1.0
HB2 A:SER61 3.6 77.7 1.0
HB3 A:PRO60 3.7 50.0 1.0
OG A:SER61 3.8 67.7 1.0
H A:HIS62 3.9 57.3 1.0
CA A:PRO60 3.9 44.3 1.0
HG A:SER61 4.0 81.3 1.0
ND1 A:HIS62 4.0 48.9 1.0
CB A:SER61 4.1 64.8 1.0
HE1 A:HIS62 4.1 61.9 1.0
HA A:THR178 4.1 52.2 1.0
C A:PRO60 4.1 44.4 1.0
CA A:SER61 4.3 41.4 1.0
CB A:PRO60 4.3 41.7 1.0
CG2 A:THR178 4.3 41.2 1.0
HB2 A:PRO177 4.4 46.3 1.0
CE1 A:HIS62 4.4 51.6 1.0
HE22 B:GLN184 4.5 58.1 1.0
N A:HIS62 4.6 47.8 1.0
HG23 A:THR178 4.6 49.5 1.0
HB3 B:PRO177 4.7 40.2 1.0
HG21 A:THR178 4.8 49.5 1.0
HB2 A:PRO60 4.8 50.0 1.0
CA A:THR178 4.9 43.5 1.0
O A:PRO177 5.0 38.2 1.0
HB3 A:SER61 5.0 77.7 1.0

Chlorine binding site 2 out of 10 in 7s69

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Chlorine binding site 2 out of 10 in the N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Gamma Subunit (Gnptg), From Clawed Frog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Gamma Subunit (Gnptg), From Clawed Frog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:56.2
occ:1.00
 O B:HOH515 3.2 31.2 1.0
HE2 B:HIS171 3.5 44.4 1.0
O A:HOH509 3.5 37.0 1.0
HE1 B:HIS171 3.7 56.4 1.0
HB2 A:ASN115 4.0 57.1 1.0
HD22 A:ASN115 4.0 66.3 1.0
NE2 B:HIS171 4.1 37.0 1.0
O A:ASN114 4.2 49.9 1.0
CE1 B:HIS171 4.2 47.0 1.0
HD21 A:LEU174 4.3 40.8 1.0
HD22 A:LEU174 4.7 40.8 1.0
HG23 A:THR116 4.7 51.5 1.0
ND2 A:ASN115 4.8 55.3 1.0
CB A:ASN115 4.9 47.6 1.0
HG22 A:THR116 4.9 51.5 1.0
CD2 A:LEU174 4.9 34.0 1.0

Chlorine binding site 3 out of 10 in 7s69

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Chlorine binding site 3 out of 10 in the N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Gamma Subunit (Gnptg), From Clawed Frog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Gamma Subunit (Gnptg), From Clawed Frog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:74.0
occ:1.00
 HH22 A:ARG133 2.6 88.0 1.0
NH2 A:ARG133 3.5 73.3 1.0
HE1 A:TYR100 3.6 95.2 1.0
HH21 A:ARG133 3.8 88.0 1.0
HA A:CYS128 3.9 103.8 1.0
HH12 A:ARG133 4.0 93.7 1.0
CE1 A:TYR100 4.2 79.3 1.0
O A:SER127 4.4 77.8 1.0
CZ A:ARG133 4.5 73.9 1.0
HH A:TYR100 4.5 70.7 1.0
NH1 A:ARG133 4.6 78.1 1.0
HD1 A:TYR100 4.7 90.5 1.0
CD1 A:TYR100 4.8 75.4 1.0
CA A:CYS128 4.9 86.5 1.0
CZ A:TYR100 4.9 69.0 1.0
OH A:TYR100 4.9 58.9 1.0

Chlorine binding site 4 out of 10 in 7s69

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Chlorine binding site 4 out of 10 in the N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Gamma Subunit (Gnptg), From Clawed Frog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Gamma Subunit (Gnptg), From Clawed Frog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:65.9
occ:1.00
 HG2 A:GLU189 3.0 87.6 1.0
HA A:GLU189 3.3 56.8 1.0
HB3 A:GLU189 3.8 72.5 1.0
CG A:GLU189 3.9 73.0 1.0
HB3 A:GLN192 4.0 59.4 1.0
CB A:GLU189 4.1 60.4 1.0
CA A:GLU189 4.1 47.3 1.0
HG3 A:GLU189 4.5 87.6 1.0
HG2 A:GLN192 4.5 68.5 1.0
O A:GLU189 4.6 55.3 1.0
CD A:GLU189 4.7 72.7 1.0
CB A:GLN192 4.8 49.5 1.0
C A:GLU189 4.9 46.9 1.0

Chlorine binding site 5 out of 10 in 7s69

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Chlorine binding site 5 out of 10 in the N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Gamma Subunit (Gnptg), From Clawed Frog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Gamma Subunit (Gnptg), From Clawed Frog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:71.8
occ:1.00
 HG3 A:LYS219 3.0 92.0 1.0
HA A:LYS219 3.0 85.7 1.0
HB2 A:LYS219 3.7 83.0 1.0
HA2 A:GLY216 3.7 54.9 1.0
O A:GLY216 3.8 49.0 1.0
HD2 A:PRO56 3.9 45.4 1.0
CA A:LYS219 3.9 71.4 1.0
CG A:LYS219 3.9 76.7 1.0
HG A:SER55 3.9 50.5 1.0
HB3 A:SER55 3.9 43.5 1.0
CB A:LYS219 4.0 69.1 1.0
OG A:SER55 4.3 42.1 1.0
HD2 A:LYS219 4.3 98.7 1.0
HA3 A:GLY216 4.4 54.9 1.0
CA A:GLY216 4.4 45.8 1.0
N A:LYS219 4.4 63.6 1.0
O A:LEU218 4.4 61.1 1.0
C A:GLY216 4.5 45.0 1.0
O A:HOH504 4.5 39.2 1.0
HD3 A:PRO56 4.5 45.4 1.0
HG2 A:LYS219 4.5 92.0 1.0
O A:GLN108 4.6 49.8 1.0
CB A:SER55 4.6 36.3 1.0
CD A:PRO56 4.6 37.9 1.0
H A:THR220 4.6 109.2 1.0
C A:LEU218 4.6 61.2 1.0
CD A:LYS219 4.7 82.3 1.0
H A:LYS219 4.8 76.4 1.0
HB3 A:LYS219 5.0 83.0 1.0

Chlorine binding site 6 out of 10 in 7s69

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Chlorine binding site 6 out of 10 in the N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Gamma Subunit (Gnptg), From Clawed Frog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Gamma Subunit (Gnptg), From Clawed Frog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:75.5
occ:1.00
 HB3 A:PHE64 3.2 49.9 1.0
O A:PHE64 3.9 35.5 1.0
HB3 A:ALA67 3.9 56.2 1.0
CB A:PHE64 4.2 41.6 1.0
HG11 A:VAL57 4.3 43.8 1.0
HG21 A:VAL57 4.4 45.1 1.0
HB2 A:PHE64 4.5 49.9 1.0
C A:PHE64 4.5 41.4 1.0
HD2 A:PHE64 4.7 47.8 1.0
CB A:ALA67 4.8 46.8 1.0
CA A:PHE64 4.9 39.3 1.0
HA A:ARG65 4.9 61.4 1.0
HB A:VAL57 5.0 49.5 1.0
HB2 A:ALA67 5.0 56.2 1.0
HA A:PHE64 5.0 47.2 1.0

Chlorine binding site 7 out of 10 in 7s69

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Chlorine binding site 7 out of 10 in the N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Gamma Subunit (Gnptg), From Clawed Frog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Gamma Subunit (Gnptg), From Clawed Frog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:77.2
occ:1.00
 O B:TYR195 3.7 61.3 1.0
OE1 B:GLU197 3.9 69.0 1.0
CD B:GLU197 4.3 75.5 1.0
HA B:ASP196 4.4 65.8 1.0
HG3 B:GLU197 4.5 81.2 1.0
OE2 B:GLU197 4.8 66.3 1.0
C B:TYR195 4.9 58.1 1.0
CZ B:TYR195 4.9 57.6 1.0
CG B:GLU197 5.0 67.6 1.0

Chlorine binding site 8 out of 10 in 7s69

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Chlorine binding site 8 out of 10 in the N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Gamma Subunit (Gnptg), From Clawed Frog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Gamma Subunit (Gnptg), From Clawed Frog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:65.0
occ:1.00
 OE2 B:GLU201 3.5 63.1 1.0
HE1 B:HIS204 3.8 72.9 1.0
HD23 B:LEU194 3.9 57.7 1.0
HD21 B:LEU194 3.9 57.7 1.0
CD2 B:LEU194 4.3 48.1 1.0
OE2 B:GLU191 4.4 62.8 1.0
CE1 B:HIS204 4.4 60.7 1.0
CD B:GLU201 4.5 80.0 1.0
OE1 B:GLU191 4.5 53.5 1.0
ND1 B:HIS204 4.6 57.1 1.0
OE1 B:GLU201 4.7 92.0 1.0
HD22 B:LEU194 4.8 57.7 1.0
CD B:GLU191 4.9 51.9 1.0

Chlorine binding site 9 out of 10 in 7s69

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Chlorine binding site 9 out of 10 in the N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Gamma Subunit (Gnptg), From Clawed Frog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Gamma Subunit (Gnptg), From Clawed Frog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:79.2
occ:1.00
 HZ3 B:LYS79 2.7 119.0 1.0
NZ B:LYS79 3.4 99.1 1.0
HZ1 B:LYS79 3.4 119.0 1.0
HZ2 B:LYS79 3.5 119.0 1.0
OE2 B:GLU81 4.0 68.6 1.0
OE1 B:GLU81 4.0 59.5 1.0
HD2 B:HIS91 4.1 81.3 1.0
CD B:GLU81 4.2 64.0 1.0
NE2 B:HIS91 4.3 57.9 1.0
CD2 B:HIS91 4.5 67.8 1.0
CE B:LYS79 4.7 84.0 1.0
HE2 B:LYS79 4.7 100.8 1.0
HB2 B:GLU81 4.8 67.6 1.0
HD3 B:LYS79 5.0 96.6 1.0

Chlorine binding site 10 out of 10 in 7s69

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Chlorine binding site 10 out of 10 in the N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Gamma Subunit (Gnptg), From Clawed Frog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Gamma Subunit (Gnptg), From Clawed Frog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl404

b:62.7
occ:1.00
 HE22 B:GLN134 3.1 74.1 1.0
HH21 B:ARG123 3.4 63.5 1.0
OE1 B:GLN134 3.8 43.4 1.0
NE2 B:GLN134 3.8 61.8 1.0
NH2 B:ARG123 4.1 52.9 1.0
CD B:GLN134 4.2 52.1 1.0
HE B:ARG123 4.4 62.4 1.0
HH22 B:ARG123 4.5 63.5 1.0
HE21 B:GLN134 4.5 74.1 1.0
CZ B:ARG123 5.0 51.7 1.0
NE B:ARG123 5.0 52.0 1.0

Reference:

A.Gorelik, K.Illes, K.H.Bui, B.Nagar. Structures of the Mannose-6-Phosphate Pathway Enzyme, Glcnac-1-Phosphotransferase. Proc.Natl.Acad.Sci.Usa V. 119 18119 2022.
ISSN: ESSN 1091-6490
PubMed: 35939698
DOI: 10.1073/PNAS.2203518119
Page generated: Tue Jul 30 04:02:42 2024

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