Zinc in PDB 6tbq: AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Partially in Cu(II) State

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

Resolution Low / High (Å)	46.90 / 1.72
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.305, 61.316, 72.982, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 26.3

The structure of AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Partially in Cu(II) State also contains other interesting chemical elements:

Copper

(Cu)

1 atom

The binding sites of Zinc atom in the AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Partially in Cu(II) State (pdb code 6tbq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Partially in Cu(II) State, PDB code: 6tbq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Partially in Cu(II) State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Partially in Cu(II) State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:45.0 occ:1.00 OD1 A:ASP36 2.1 32.3 1.0 CG A:ASP36 2.8 28.2 1.0 OD2 A:ASP36 2.9 27.6 1.0 OD1 A:ASP38 2.9 41.8 1.0 N A:ALA39 3.5 26.6 1.0 C A:ASP38 3.7 27.6 1.0 CG A:ASP38 3.8 38.0 1.0 CA A:ALA39 3.9 29.4 1.0 N A:ASP38 4.0 24.1 1.0 CA A:ASP38 4.1 28.0 1.0 O A:ASP38 4.2 28.6 1.0 CB A:ASP38 4.2 33.5 1.0 CB A:ASP36 4.3 26.2 1.0 CB A:ALA39 4.3 29.5 1.0 O A:HOH542 4.6 36.3 1.0 OD2 A:ASP38 4.8 41.5 1.0 C A:ASP36 4.9 24.1 1.0 O A:HOH401 4.9 29.4 1.0

Zinc binding site 2 out of 5 in the AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Partially in Cu(II) State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Partially in Cu(II) State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:62.4 occ:1.00 OH A:TYR97 2.7 17.1 1.0 O A:VAL195 2.8 16.2 1.0 O A:VAL81 3.0 16.1 1.0 CD1 A:TRP83 3.4 20.0 1.0 CE2 A:TYR97 3.4 15.9 1.0 CZ A:TYR97 3.5 15.6 1.0 C A:VAL81 3.6 18.7 1.0 C A:VAL195 3.6 16.4 1.0 CA A:GLN82 3.7 17.5 1.0 CE2 A:PHE95 3.7 14.5 1.0 N A:LYS197 3.7 17.6 1.0 N A:TRP83 3.7 18.8 1.0 N A:GLN82 3.9 17.6 1.0 CA A:THR196 3.9 17.4 1.0 C A:GLN82 4.0 17.3 1.0 N A:THR196 4.0 16.4 1.0 CB A:LYS197 4.1 17.7 1.0 C A:THR196 4.1 18.7 1.0 NE1 A:TRP83 4.1 19.2 1.0 CG A:LYS197 4.1 17.2 1.0 CZ A:PHE95 4.3 15.2 1.0 CG2 A:VAL81 4.4 18.8 1.0 CG A:TRP83 4.4 18.2 1.0 CD2 A:PHE95 4.4 14.9 1.0 CA A:LYS197 4.5 18.0 1.0 CB A:VAL81 4.6 18.3 1.0 CA A:VAL81 4.7 18.9 1.0 CD2 A:TYR97 4.7 15.9 1.0 CB A:VAL195 4.7 16.6 1.0 CB A:TRP83 4.7 18.7 1.0 CE1 A:TYR97 4.8 15.3 1.0 CA A:VAL195 4.8 17.0 1.0 CA A:TRP83 4.8 18.2 1.0 CG1 A:VAL195 4.8 16.6 1.0 O A:GLN82 4.9 16.5 1.0 O A:THR196 5.0 18.2 1.0

Zinc binding site 3 out of 5 in the AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Partially in Cu(II) State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Partially in Cu(II) State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:68.0 occ:1.00 OE2 A:GLU125 2.3 20.5 1.0 OD2 A:ASP129 2.5 28.7 1.0 O A:HOH523 2.7 17.3 1.0 OD1 A:ASP129 2.8 28.4 1.0 CG A:ASP129 3.0 27.9 1.0 CD A:GLU125 3.2 20.6 1.0 O A:HOH474 3.3 21.3 1.0 CG A:GLU125 3.3 20.9 1.0 CB A:ASP38 3.7 33.5 1.0 CE A:LYS214 4.0 19.5 1.0 NZ A:LYS214 4.1 19.2 1.0 NH1 A:ARG98 4.2 16.1 1.0 O A:HOH489 4.3 27.6 1.0 CA A:ASP38 4.4 28.0 1.0 OE1 A:GLU125 4.4 22.8 1.0 O A:HOH470 4.4 22.7 1.0 CD A:LYS214 4.4 17.9 1.0 CB A:ASP129 4.5 24.0 1.0 O A:GLU125 4.6 24.5 1.0 O A:ASP38 4.7 28.6 1.0 CB A:GLU125 4.8 20.2 1.0 CG A:ASP38 4.8 38.0 1.0 O A:ALA40 5.0 25.5 1.0 C A:GLU125 5.0 21.5 1.0 OD2 A:ASP38 5.0 41.5 1.0

Zinc binding site 4 out of 5 in the AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Partially in Cu(II) State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Partially in Cu(II) State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn306 b:40.9 occ:0.50 OE2 A:GLU120 3.7 27.7 1.0 CZ A:TYR114 3.9 35.5 1.0 OH A:TYR114 3.9 31.6 1.0 CE2 A:TYR114 4.1 32.8 1.0 CE A:LYS108 4.1 36.9 1.0 CE1 A:TYR114 4.3 35.0 1.0 CD A:LYS108 4.4 33.0 1.0 NZ A:LYS108 4.6 40.3 1.0 CG A:LYS108 4.7 30.6 1.0 CD A:GLU120 4.7 28.9 1.0 CD2 A:TYR114 4.7 32.1 1.0 CD1 A:TYR114 4.9 35.2 1.0 OE1 A:GLU120 5.0 29.1 1.0

Zinc binding site 5 out of 5 in the AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Partially in Cu(II) State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Partially in Cu(II) State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn307 b:48.3 occ:1.00 OE1 A:GLU142 2.4 43.6 1.0 OE2 A:GLU142 2.6 35.3 1.0 CD A:GLU142 2.8 38.6 1.0 O A:HOH510 4.0 33.6 1.0 CG A:GLU142 4.3 39.0 1.0 O A:HOH541 4.5 43.3 1.0 O A:HOH495 4.7 34.1 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