Zinc in PDB 6tbr: Glycosylated AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae in P1 Space Group

The structure of Glycosylated AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae in P1 Space Group, PDB code: 6tbr was solved by K.E.H.Frandsen, S.J.Muderspach, T.Tandrup, J.C.N.Poulsen, L.Lo Leggio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.84 / 1.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.060, 49.760, 57.100, 109.37, 90.07, 95.46
R / Rfree (%)	19.2 / 24.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Glycosylated AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae in P1 Space Group (pdb code 6tbr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Glycosylated AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae in P1 Space Group, PDB code: 6tbr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Glycosylated AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae in P1 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Glycosylated AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae in P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:19.2 occ:1.00 ND1 A:HIC1 2.0 18.2 1.0 NE2 A:HIS91 2.1 18.3 1.0 O A:HOH518 2.2 20.4 1.0 O A:HOH519 2.2 14.2 1.0 N A:HIC1 2.4 16.9 1.0 OH A:TYR224 2.4 14.8 1.0 CG A:HIC1 2.9 18.4 1.0 CE1 A:HIS91 3.0 18.4 1.0 CE1 A:HIC1 3.0 18.0 1.0 CA A:HIC1 3.2 17.1 1.0 CD2 A:HIS91 3.3 18.2 1.0 CB A:HIC1 3.3 18.0 1.0 CZ A:TYR224 3.5 14.5 1.0 O A:HOH603 3.9 37.6 1.0 OE1 A:GLN222 4.0 16.9 1.0 CE2 A:TYR224 4.0 15.8 1.0 NE2 A:HIC1 4.1 18.9 1.0 O A:GLY89 4.1 18.1 1.0 CD2 A:HIC1 4.1 18.3 1.0 CA A:GLY89 4.1 19.2 1.0 ND1 A:HIS91 4.1 18.6 1.0 O A:HOH544 4.3 23.4 1.0 CG A:HIS91 4.3 18.0 1.0 CE1 A:TYR224 4.5 14.8 1.0 C A:HIC1 4.5 14.9 1.0 C A:GLY89 4.6 18.0 1.0 CD A:GLN222 4.8 16.6 1.0 NE2 A:GLN222 4.9 17.9 1.0 CD1 A:ILE27 4.9 17.5 1.0

Zinc binding site 2 out of 12 in the Glycosylated AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae in P1 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Glycosylated AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae in P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:13.4 occ:0.80 OD1 A:ASP36 1.9 17.8 1.0 OE2 B:GLU203 2.0 15.6 1.0 OD1 A:ASP38 2.0 18.5 1.0 O A:HOH549 2.1 18.0 1.0 OD2 A:ASP36 2.6 17.6 1.0 CG A:ASP36 2.6 18.9 1.0 CD B:GLU203 2.6 17.6 1.0 OE1 B:GLU203 2.6 18.7 1.0 CG A:ASP38 3.0 19.4 1.0 OD2 A:ASP38 3.4 25.3 1.0 N A:ALA39 3.9 13.8 1.0 CG B:GLU203 4.1 16.1 1.0 CB A:ASP36 4.1 17.9 1.0 N A:ASP38 4.1 13.8 1.0 O A:HOH448 4.1 29.1 1.0 C A:ASP38 4.2 15.2 1.0 CB A:ASP38 4.3 17.7 1.0 CA A:ALA39 4.3 16.6 1.0 CB A:ALA39 4.3 18.1 1.0 CA A:ASP38 4.4 15.1 1.0 O A:HOH580 4.5 34.8 1.0 C A:ASP36 4.7 13.9 1.0 NZ B:LYS200 4.7 25.4 1.0 CA A:ASP36 4.7 15.3 1.0 O B:HOH426 4.7 14.9 1.0 N A:LEU37 4.8 12.8 1.0 O A:ASP38 4.8 16.8 1.0 O A:HOH408 5.0 30.2 1.0

Zinc binding site 3 out of 12 in the Glycosylated AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae in P1 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Glycosylated AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae in P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:16.8 occ:0.60 O A:HOH428 1.9 27.9 1.0 OD1 A:ASP102 2.0 16.6 1.0 O A:HOH571 2.1 23.3 1.0 OG A:SER104 2.2 17.8 1.0 CG A:ASP102 3.0 18.7 1.0 CB A:SER104 3.2 17.1 1.0 OD2 A:ASP102 3.3 18.5 1.0 N A:SER104 3.8 15.2 1.0 CA A:SER104 4.0 16.6 1.0 CB A:ASP102 4.3 16.2 1.0 O A:HOH455 4.4 29.8 1.0 CA A:ASP102 4.5 15.8 1.0 C A:ASP102 4.5 15.4 1.0 N A:GLN103 4.5 15.6 1.0 N A:ILE105 4.7 17.2 1.0 C A:SER104 4.8 18.6 1.0 C A:GLN103 5.0 15.6 1.0 O A:ASP102 5.0 15.6 1.0

Zinc binding site 4 out of 12 in the Glycosylated AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae in P1 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Glycosylated AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae in P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:21.3 occ:0.50 ND1 A:HIS15 1.7 21.3 1.0 OD1 A:ASP20 2.0 21.1 1.0 O A:HOH554 2.3 26.4 1.0 CE1 A:HIS15 2.5 18.5 1.0 CG A:HIS15 2.9 19.4 1.0 CG A:ASP20 3.1 20.1 1.0 CB A:HIS15 3.5 17.8 1.0 OD2 A:ASP20 3.5 19.6 1.0 CA A:HIS15 3.6 17.6 1.0 NE2 A:HIS15 3.7 23.7 1.0 O A:HIS15 3.8 17.6 1.0 O A:ASP20 3.9 22.9 1.0 CD2 A:HIS15 3.9 20.6 1.0 C A:HIS15 4.1 17.8 1.0 C A:ASP20 4.1 22.9 1.0 CD A:PRO23 4.4 19.6 1.0 CB A:ASP20 4.4 18.6 1.0 N A:SER21 4.5 21.5 1.0 CA A:ASP20 4.6 21.9 1.0 N A:ASP20 4.6 19.4 1.0 C A:SER21 4.6 22.1 1.0 CA A:SER21 4.7 22.6 1.0 CE2 A:TYR186 4.7 21.8 1.0 O A:HOH510 4.8 35.9 1.0 OH A:TYR186 4.8 25.1 1.0 N A:HIS15 4.8 15.5 1.0 N A:CYS22 4.8 18.0 1.0 O A:SER21 4.9 23.4 1.0 CG A:PRO23 4.9 19.0 1.0

Zinc binding site 5 out of 12 in the Glycosylated AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae in P1 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Glycosylated AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae in P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:9.4 occ:0.60 OE2 A:GLU125 1.9 16.2 1.0 O A:HOH501 2.0 15.2 1.0 OD2 A:ASP129 2.1 18.5 1.0 O A:HOH578 2.2 2.3 1.0 OD1 A:ASP129 2.4 18.5 1.0 CG A:ASP129 2.6 18.9 1.0 CD A:GLU125 3.0 15.0 1.0 CG A:GLU125 3.4 13.9 1.0 NH1 A:ARG98 3.8 9.9 1.0 CB A:ASP129 4.0 17.0 1.0 O A:HOH402 4.0 18.1 1.0 CB A:ASP38 4.1 17.7 1.0 CE A:LYS214 4.1 12.3 1.0 OE1 A:GLU125 4.1 14.7 1.0 O A:HOH513 4.3 29.1 1.0 O A:GLU125 4.3 12.4 1.0 CD A:LYS214 4.3 11.7 1.0 CA A:ASP38 4.4 15.1 1.0 O A:HOH485 4.4 17.6 1.0 NZ A:LYS214 4.4 12.2 1.0 O A:ASP38 4.4 16.8 1.0 O A:HOH490 4.7 12.5 1.0 O A:HOH563 4.8 14.6 1.0 CB A:GLU125 4.9 14.8 1.0 CZ A:ARG98 4.9 10.9 1.0 C A:ASP38 4.9 15.2 1.0 CA A:ASP129 4.9 15.6 1.0 C A:GLU125 5.0 14.0 1.0

Zinc binding site 6 out of 12 in the Glycosylated AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae in P1 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Glycosylated AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae in P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn306 b:42.0 occ:0.50 NE2 A:HIS87 2.2 28.6 1.0 CE1 A:HIS87 3.0 25.8 1.0 CD2 A:HIS87 3.3 27.4 1.0 O A:HOH589 3.7 44.1 1.0 ND1 A:HIS87 4.2 26.3 1.0 CG A:HIS87 4.4 24.4 1.0 OH A:TYR193 4.6 25.0 1.0

Zinc binding site 7 out of 12 in the Glycosylated AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae in P1 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Glycosylated AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae in P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:19.2 occ:1.00 ND1 B:HIC1 2.1 18.7 1.0 NE2 B:HIS91 2.1 18.0 1.0 N B:HIC1 2.2 15.4 1.0 O B:HOH503 2.3 16.0 1.0 O B:HOH516 2.3 25.1 1.0 OH B:TYR224 2.4 16.0 1.0 CG B:HIC1 3.0 18.9 1.0 CE1 B:HIS91 3.0 19.2 1.0 CE1 B:HIC1 3.1 18.9 1.0 CA B:HIC1 3.2 16.0 1.0 CD2 B:HIS91 3.2 17.9 1.0 CB B:HIC1 3.3 17.5 1.0 CZ B:TYR224 3.5 13.7 1.0 OE1 B:GLN222 4.0 16.9 1.0 CE2 B:TYR224 4.0 14.9 1.0 O B:GLY89 4.1 17.6 1.0 CA B:GLY89 4.1 18.3 1.0 ND1 B:HIS91 4.2 19.1 1.0 NE2 B:HIC1 4.2 20.3 1.0 CD2 B:HIC1 4.2 19.4 1.0 O B:HOH565 4.3 22.4 1.0 CG B:HIS91 4.3 17.9 1.0 CE1 B:TYR224 4.5 14.9 1.0 C B:HIC1 4.5 13.6 1.0 C B:GLY89 4.5 16.8 1.0 O B:HOH608 4.6 33.6 1.0 CD B:GLN222 4.8 16.7 1.0 NE2 B:GLN222 4.8 18.5 1.0 O B:HIC1 5.0 13.8 1.0

Zinc binding site 8 out of 12 in the Glycosylated AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae in P1 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Glycosylated AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae in P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:15.0 occ:0.85 OD1 B:ASP38 2.0 18.3 1.0 OD1 B:ASP36 2.1 17.9 1.0 O B:HOH570 2.2 20.5 1.0 OD2 B:ASP36 2.6 17.6 1.0 CG B:ASP36 2.7 17.7 1.0 CG B:ASP38 3.0 20.8 1.0 OD2 B:ASP38 3.4 27.6 1.0 N B:ALA39 3.9 13.3 1.0 N B:ASP38 4.2 15.2 1.0 CB B:ASP36 4.2 17.7 1.0 C B:ASP38 4.2 15.9 1.0 CB B:ASP38 4.3 18.0 1.0 CA B:ALA39 4.3 15.8 1.0 CB B:ALA39 4.4 17.3 1.0 CA B:ASP38 4.4 15.4 1.0 O B:HOH612 4.7 37.6 1.0 C B:ASP36 4.7 14.6 1.0 CA B:ASP36 4.8 16.0 1.0 N B:LEU37 4.8 14.3 1.0 O B:ASP38 4.9 15.5 1.0

Zinc binding site 9 out of 12 in the Glycosylated AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae in P1 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Glycosylated AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae in P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:19.8 occ:0.50 OD1 B:ASP102 2.0 19.1 1.0 OG B:SER104 2.2 16.7 1.0 O A:HOH456 2.3 14.8 1.0 CG B:ASP102 2.8 18.4 1.0 OD2 B:ASP102 3.2 18.9 1.0 CB B:SER104 3.2 15.0 1.0 OE1 A:GLU151 3.8 22.5 1.0 N B:SER104 3.8 15.1 1.0 CA B:SER104 4.0 15.5 1.0 CB B:ASP102 4.2 15.7 1.0 CA B:ASP102 4.4 15.1 1.0 C B:ASP102 4.4 14.7 1.0 N B:GLN103 4.5 15.0 1.0 N B:ILE105 4.7 15.7 1.0 C B:SER104 4.8 16.0 1.0 CD A:GLU151 4.8 18.8 1.0 O A:HOH565 4.8 27.7 1.0 O B:HOH553 4.8 38.1 1.0 C B:GLN103 4.9 14.8 1.0 O B:ASP102 5.0 14.8 1.0

Zinc binding site 10 out of 12 in the Glycosylated AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae in P1 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Glycosylated AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae in P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:14.9 occ:0.30 ND1 B:HIS15 1.6 22.0 1.0 OD1 B:ASP20 2.0 20.4 1.0 O B:HOH555 2.1 25.8 1.0 O B:HOH578 2.2 24.3 1.0 CE1 B:HIS15 2.2 23.6 1.0 CG B:HIS15 2.9 21.5 1.0 CG B:ASP20 3.1 23.3 1.0 NE2 B:HIS15 3.5 23.5 1.0 CB B:HIS15 3.5 18.2 1.0 OD2 B:ASP20 3.6 23.4 1.0 O B:HIS15 3.6 16.9 1.0 CA B:HIS15 3.6 18.0 1.0 CD2 B:HIS15 3.8 22.1 1.0 O B:ASP20 4.0 28.1 1.0 C B:HIS15 4.0 17.7 1.0 C B:ASP20 4.1 24.0 1.0 CB B:ASP20 4.4 21.4 1.0 N B:SER21 4.5 20.6 1.0 CD B:PRO23 4.5 18.4 1.0 CE2 B:TYR186 4.6 20.7 1.0 CA B:ASP20 4.6 22.7 1.0 C B:SER21 4.6 20.7 1.0 N B:ASP20 4.6 19.5 1.0 CA B:SER21 4.6 22.2 1.0 OH B:TYR186 4.8 24.8 1.0 N B:HIS15 4.8 14.4 1.0 O B:SER21 4.8 22.4 1.0 N B:CYS22 4.9 17.9 1.0

S.J.Muderspach, T.Tandrup, K.E.H.Frandsen, G.Santoni, J.C.N.Poulsen, L.Lo Leggio. Further Structural Studies of the Lytic Polysaccharide Monooxygenase AOAA13 Belonging to the Starch-Active AA13 Family Amylase V.3(1) 41 2019.
ISSN: ESSN 2450-9728
DOI: 10.1515/AMYLASE-2019-0004