Zinc in PDB 8pn5: Crystal Structure of the HC7-GLU200ALA Mutant Complexed to A Triglycopeptide

The structure of Crystal Structure of the HC7-GLU200ALA Mutant Complexed to A Triglycopeptide, PDB code: 8pn5 was solved by V.Taleb, R.Hurtado-Guerrero, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 1.72
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	163.331, 260.637, 82.626, 90, 90, 90
R / Rfree (%)	20.8 / 23.5

The binding sites of Zinc atom in the Crystal Structure of the HC7-GLU200ALA Mutant Complexed to A Triglycopeptide (pdb code 8pn5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the HC7-GLU200ALA Mutant Complexed to A Triglycopeptide, PDB code: 8pn5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of the HC7-GLU200ALA Mutant Complexed to A Triglycopeptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the HC7-GLU200ALA Mutant Complexed to A Triglycopeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:27.8 occ:1.00 OE1 B:GLU318 1.9 23.5 1.0 OE1 A:GLU112 1.9 40.5 1.0 NE2 A:HIS161 2.1 23.5 1.0 CD B:GLU318 2.7 26.5 1.0 CD A:GLU112 2.7 30.5 1.0 OE2 B:GLU318 2.8 25.1 1.0 OE2 A:GLU112 2.9 28.6 1.0 CE1 A:HIS161 2.9 22.6 1.0 CD2 A:HIS161 3.2 25.2 1.0 NZ B:LYS316 3.7 32.3 1.0 NZ B:LYS356 3.9 39.1 1.0 O A:HOH1192 4.0 34.4 1.0 ND1 A:HIS161 4.1 23.1 1.0 CG A:GLU112 4.1 33.6 1.0 CG B:GLU318 4.1 26.1 1.0 O A:HOH1154 4.1 34.5 1.0 CE B:LYS316 4.2 36.4 1.0 CB A:PRO185 4.2 23.9 1.0 CG A:HIS161 4.2 22.6 1.0 OH B:TYR320 4.4 27.7 1.0 O B:HOH1115 4.4 35.6 1.0 CB A:GLU112 4.6 31.9 1.0 O A:PRO185 4.6 33.7 1.0 CA A:PRO185 4.6 26.4 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of the HC7-GLU200ALA Mutant Complexed to A Triglycopeptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the HC7-GLU200ALA Mutant Complexed to A Triglycopeptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:25.2 occ:1.00 OE1 A:GLU318 1.8 16.8 1.0 OE1 B:GLU112 2.0 29.9 1.0 NE2 B:HIS161 2.0 22.1 1.0 CD A:GLU318 2.7 18.9 1.0 CD B:GLU112 2.8 25.8 1.0 OE2 A:GLU318 2.8 21.0 1.0 CE1 B:HIS161 2.9 19.9 1.0 OE2 B:GLU112 3.0 28.2 1.0 CD2 B:HIS161 3.1 22.7 1.0 NZ A:LYS316 3.6 29.0 1.0 NZ A:LYS356 4.0 28.9 1.0 ND1 B:HIS161 4.1 20.6 1.0 CG A:GLU318 4.1 21.4 1.0 CB B:PRO185 4.2 24.0 1.0 CG B:GLU112 4.2 29.9 1.0 CE A:LYS316 4.2 36.0 1.0 CG B:HIS161 4.2 21.4 1.0 OH A:TYR320 4.3 25.4 1.0 O A:HOH1217 4.4 29.2 1.0 O B:PRO185 4.5 27.4 1.0 CA B:PRO185 4.5 23.3 1.0 CB B:GLU112 4.7 27.6 1.0 C B:PRO185 4.9 26.5 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of the HC7-GLU200ALA Mutant Complexed to A Triglycopeptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the HC7-GLU200ALA Mutant Complexed to A Triglycopeptide within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn702 b:30.0 occ:1.00 OE2 H:GLU318 1.8 21.3 1.0 OE1 E:GLU112 1.9 41.3 1.0 NE2 E:HIS161 2.1 26.4 1.0 CD H:GLU318 2.6 26.5 1.0 CD E:GLU112 2.8 34.9 1.0 OE1 H:GLU318 2.8 28.5 1.0 CE1 E:HIS161 2.9 23.9 1.0 OE2 E:GLU112 3.0 33.6 1.0 CD2 E:HIS161 3.1 26.4 1.0 NZ H:LYS316 3.7 32.5 1.0 NZ H:LYS356 4.0 33.9 1.0 CG H:GLU318 4.1 26.9 1.0 ND1 E:HIS161 4.1 23.6 1.0 CB E:PRO185 4.1 30.5 1.0 CG E:GLU112 4.2 37.1 1.0 O E:HOH883 4.2 34.0 1.0 CG E:HIS161 4.2 23.6 1.0 CE H:LYS316 4.2 41.5 1.0 OH H:TYR320 4.2 32.0 1.0 O E:PRO185 4.5 32.1 1.0 CA E:PRO185 4.5 32.1 1.0 CB E:GLU112 4.6 36.4 1.0 O H:HOH915 4.7 32.9 1.0 C E:PRO185 4.8 31.4 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of the HC7-GLU200ALA Mutant Complexed to A Triglycopeptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the HC7-GLU200ALA Mutant Complexed to A Triglycopeptide within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn703 b:31.4 occ:1.00 OE1 F:GLU112 2.0 41.2 1.0 NE2 F:HIS161 2.1 28.8 1.0 CD F:GLU112 2.8 35.8 1.0 CE1 F:HIS161 3.0 27.7 1.0 OE2 F:GLU112 3.0 35.8 1.0 CD2 F:HIS161 3.2 30.3 1.0 O F:HOH859 4.0 37.4 1.0 ND1 F:HIS161 4.1 28.6 1.0 CG F:GLU112 4.3 41.4 1.0 CG F:HIS161 4.3 31.0 1.0 CB F:PRO185 4.3 32.1 1.0 CA F:PRO185 4.7 32.8 1.0 O F:PRO185 4.7 28.2 1.0 CB F:GLU112 4.7 42.0 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of the HC7-GLU200ALA Mutant Complexed to A Triglycopeptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the HC7-GLU200ALA Mutant Complexed to A Triglycopeptide within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn704 b:26.1 occ:1.00 OE2 F:GLU318 1.9 18.8 1.0 CD F:GLU318 2.7 21.8 1.0 OE1 F:GLU318 2.9 24.1 1.0 NZ F:LYS316 3.7 31.1 1.0 NZ F:LYS356 4.0 36.2 1.0 CG F:GLU318 4.2 24.8 1.0 CE F:LYS316 4.2 38.6 1.0 OH F:TYR320 4.3 27.1 1.0 O F:HOH841 4.3 31.6 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of the HC7-GLU200ALA Mutant Complexed to A Triglycopeptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the HC7-GLU200ALA Mutant Complexed to A Triglycopeptide within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn702 b:29.9 occ:1.00 OE1 G:GLU112 1.9 33.0 1.0 NE2 G:HIS161 2.0 24.9 1.0 CD G:GLU112 2.7 29.6 1.0 OE2 G:GLU112 2.9 28.1 1.0 CE1 G:HIS161 2.9 26.2 1.0 CD2 G:HIS161 3.1 24.7 1.0 ND1 G:HIS161 4.1 25.3 1.0 CG G:GLU112 4.1 31.8 1.0 CB G:PRO185 4.1 29.0 1.0 O G:HOH844 4.2 28.6 1.0 CG G:HIS161 4.2 26.1 1.0 CA G:PRO185 4.5 30.2 1.0 O G:PRO185 4.6 34.6 1.0 CB G:GLU112 4.6 30.7 1.0 C G:PRO185 4.9 33.8 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of the HC7-GLU200ALA Mutant Complexed to A Triglycopeptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the HC7-GLU200ALA Mutant Complexed to A Triglycopeptide within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn703 b:31.3 occ:1.00 OE2 G:GLU318 1.7 19.6 1.0 CD G:GLU318 2.6 28.6 1.0 OE1 G:GLU318 2.8 27.9 1.0 NZ G:LYS316 3.8 34.6 1.0 NZ G:LYS356 3.9 45.6 1.0 CG G:GLU318 4.1 28.3 1.0 OH G:TYR320 4.2 39.5 1.0 CE G:LYS316 4.3 41.8 1.0 O G:HOH876 4.6 35.5 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of the HC7-GLU200ALA Mutant Complexed to A Triglycopeptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the HC7-GLU200ALA Mutant Complexed to A Triglycopeptide within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn704 b:29.6 occ:1.00 OE2 E:GLU318 1.8 20.6 1.0 OE2 H:GLU112 1.9 40.4 1.0 NE2 H:HIS161 2.1 24.2 1.0 CD E:GLU318 2.6 25.9 1.0 CD H:GLU112 2.6 27.9 1.0 OE1 H:GLU112 2.7 28.4 1.0 OE1 E:GLU318 2.8 26.2 1.0 CE1 H:HIS161 2.9 22.9 1.0 CD2 H:HIS161 3.2 25.8 1.0 NZ E:LYS316 3.7 39.3 1.0 NZ E:LYS356 3.9 39.2 1.0 CG H:GLU112 4.1 31.8 1.0 CG E:GLU318 4.1 25.9 1.0 O H:HOH850 4.1 32.3 1.0 ND1 H:HIS161 4.1 22.6 1.0 CB H:PRO185 4.2 24.1 1.0 CE E:LYS316 4.2 44.9 1.0 OH E:TYR320 4.2 30.8 1.0 CG H:HIS161 4.3 23.4 1.0 O E:HOH867 4.5 35.8 1.0 O H:PRO185 4.6 28.9 1.0 CB H:GLU112 4.6 30.7 1.0 CA H:PRO185 4.6 27.4 1.0 C H:PRO185 5.0 28.4 1.0

Y.Narimatsu, C.Bull, V.Taleb, Q.Liao, I.Companon, D.Sanchez-Navarro, F.Durbesson, R.Vincentelli, L.Hansen, F.Corzana, C.Rovira, B.Henrissat, H.Clausen, H.J.Joshi, R.Hurtado-Guerrero. A Family of Di-Glutamate Mucin-Degrading Enzymes That Bridges Glycan Hydrolases and Peptidases Nat Catal 2024.
ISSN: ESSN 2520-1158
DOI: 10.1038/S41929-024-01116-5