Zinc in PDB 5t7n: X-Ray Crystal Structure of AA13 Lpmo

The structure of X-Ray Crystal Structure of AA13 Lpmo, PDB code: 5t7n was solved by K.E.H.Frandsen, J.-C.N.Poulsen, M.Tovborg, K.S.Johansen, L.Lo Leggio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.670, 59.000, 72.150, 90.00, 90.00, 90.00
R / Rfree (%)	10.6 / 17.2

The binding sites of Zinc atom in the X-Ray Crystal Structure of AA13 Lpmo (pdb code 5t7n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the X-Ray Crystal Structure of AA13 Lpmo, PDB code: 5t7n:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the X-Ray Crystal Structure of AA13 Lpmo


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Crystal Structure of AA13 Lpmo within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:12.8 occ:0.70 ND1 A:HIC1 1.6 17.5 0.3 ND1 A:HIC1 2.0 20.1 0.7 NE2 A:HIS91 2.1 16.7 0.7 N A:HIC1 2.1 12.1 0.7 OH A:TYR224 2.1 29.3 1.0 N A:HIC1 2.3 14.2 0.3 CE1 A:HIC1 2.4 18.5 0.3 CG A:HIC1 2.6 18.0 0.3 O A:HOH674 2.8 12.5 0.3 CG A:HIC1 3.0 20.8 0.7 CE1 A:HIS91 3.0 15.6 0.7 CE1 A:HIC1 3.0 35.8 0.7 CD2 A:HIS91 3.1 15.4 0.7 CA A:HIC1 3.1 12.4 0.7 CA A:HIC1 3.1 13.2 0.3 CZ A:TYR224 3.2 20.5 1.0 CB A:HIC1 3.3 14.3 0.3 NE2 A:HIC1 3.4 21.9 0.3 CB A:HIC1 3.4 13.5 0.7 CD2 A:HIC1 3.5 21.3 0.3 CE1 A:TYR224 3.9 14.1 1.0 OE1 A:GLN222 3.9 15.9 0.3 OE1 A:GLN222 3.9 17.4 0.7 O A:GLY89 4.0 14.6 0.7 CA A:GLY89 4.1 18.3 0.3 CD2 A:HIC1 4.1 28.7 0.7 ND1 A:HIS91 4.1 16.1 0.7 CE2 A:TYR224 4.1 15.8 1.0 NE2 A:HIC1 4.1 30.1 0.7 CA A:GLY89 4.2 17.6 0.7 O A:GLY89 4.2 12.1 0.3 NE2 A:GLN222 4.2 19.5 0.7 CG A:HIS91 4.2 15.3 0.7 CD A:GLN222 4.4 16.8 0.7 C A:GLY89 4.5 14.9 0.3 C A:HIC1 4.5 8.9 0.7 C A:HIC1 4.5 9.9 0.3 C A:GLY89 4.5 14.6 0.7 CZ A:HIC1 4.7 25.2 0.3 O A:HOH698 4.7 30.8 1.0 CD A:GLN222 4.8 14.8 0.3 O A:HOH522 4.8 38.7 0.7 NE2 A:GLN222 4.9 12.1 0.3

Zinc binding site 2 out of 4 in the X-Ray Crystal Structure of AA13 Lpmo


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Crystal Structure of AA13 Lpmo within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn407 b:12.2 occ:0.75 OD1 A:ASP36 2.0 11.0 1.0 OD1 A:ASP38 2.1 17.9 1.0 OD2 A:ASP36 2.6 14.9 1.0 CG A:ASP36 2.6 11.5 1.0 CG A:ASP38 3.1 14.4 1.0 OD2 A:ASP38 3.6 15.2 1.0 N A:ALA39 3.8 8.8 1.0 N A:ASP38 4.0 7.8 1.0 C A:ASP38 4.0 8.8 1.0 CB A:ASP36 4.1 8.7 1.0 CA A:ASP38 4.2 9.5 1.0 CB A:ASP38 4.2 14.0 1.0 CA A:ALA39 4.3 10.2 1.0 CB A:ALA39 4.3 14.8 1.0 O A:HOH685 4.4 19.3 1.0 O A:ASP38 4.7 10.0 1.0 N A:LEU37 4.7 7.1 1.0 CA A:ASP36 4.7 7.3 1.0 C A:ASP36 4.7 7.2 1.0

Zinc binding site 3 out of 4 in the X-Ray Crystal Structure of AA13 Lpmo


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Crystal Structure of AA13 Lpmo within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn408 b:13.9 occ:0.60 OD1 A:ASP102 2.1 13.5 1.0 OG A:SER104 2.1 17.8 1.0 O A:HOH600 2.2 34.4 1.0 CG A:ASP102 3.1 11.9 1.0 CB A:SER104 3.2 13.2 1.0 OD2 A:ASP102 3.4 13.0 1.0 N A:SER104 3.7 7.7 1.0 CA A:SER104 4.0 9.6 1.0 CB A:ASP102 4.3 9.7 1.0 O A:HOH586 4.3 27.0 1.0 O A:HOH797 4.5 23.4 1.0 C A:ASP102 4.6 8.3 1.0 N A:GLN103 4.6 7.7 1.0 CA A:ASP102 4.6 8.5 1.0 N A:ILE105 4.7 9.2 1.0 C A:SER104 4.8 8.0 1.0 C A:GLN103 4.9 8.6 1.0

Zinc binding site 4 out of 4 in the X-Ray Crystal Structure of AA13 Lpmo


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Crystal Structure of AA13 Lpmo within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn409 b:16.9 occ:0.50 OE2 A:GLU29 2.2 16.3 1.0 O A:HOH762 2.2 16.9 1.0 OE1 A:GLU29 2.8 17.9 1.0 CD A:GLU29 2.9 13.7 1.0 O A:HOH522 3.2 38.7 0.7 NE2 A:GLN222 3.8 12.1 0.3 CG A:GLU29 4.3 12.4 1.0 CD1 A:ILE27 4.7 20.3 1.0 O A:HOH535 4.8 17.1 0.5

K.E.Frandsen, J.C.Poulsen, M.Tovborg, K.S.Johansen, L.Lo Leggio. Learning From Oligosaccharide Soaks of Crystals of An AA13 Lytic Polysaccharide Monooxygenase: Crystal Packing, Ligand Binding and Active-Site Disorder. Acta Crystallogr D Struct V. 73 64 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 28045386
DOI: 10.1107/S2059798316019641