Zinc in PDB 5t7j: X-Ray Crystal Structure of AA13 Lpmo

The structure of X-Ray Crystal Structure of AA13 Lpmo, PDB code: 5t7j 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 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.040, 61.490, 73.790, 90.00, 90.00, 90.00
R / Rfree (%)	12.3 / 19.9

The binding sites of Zinc atom in the X-Ray Crystal Structure of AA13 Lpmo (pdb code 5t7j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the X-Ray Crystal Structure of AA13 Lpmo, PDB code: 5t7j:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 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:Zn402 b:15.3 occ:1.00 ND1 A:HIC1 2.0 15.3 1.0 NE2 A:HIS91 2.1 12.7 1.0 N A:HIC1 2.2 11.8 1.0 O A:HOH663 2.3 19.3 1.0 OH A:TYR224 2.4 15.8 1.0 O A:HOH539 2.4 30.1 1.0 CE1 A:HIC1 2.9 18.6 1.0 CG A:HIC1 3.0 14.2 1.0 CE1 A:HIS91 3.0 16.6 1.0 CD2 A:HIS91 3.1 13.4 1.0 CA A:HIC1 3.1 9.3 1.0 CB A:HIC1 3.4 10.9 1.0 CZ A:TYR224 3.5 13.3 1.0 NE2 A:GLN222 3.9 11.4 1.0 O A:GLY89 4.0 13.0 1.0 CA A:GLY89 4.0 15.6 1.0 CE2 A:TYR224 4.1 12.6 1.0 NE2 A:HIC1 4.1 16.9 1.0 CD2 A:HIC1 4.1 15.8 1.0 ND1 A:HIS91 4.1 18.2 1.0 CG A:HIS91 4.2 15.2 1.0 CE1 A:TYR224 4.4 13.2 1.0 C A:GLY89 4.4 13.3 1.0 C A:HIC1 4.5 8.6 1.0 O A:HOH630 4.6 18.3 1.0 CD1 A:ILE27 4.7 10.2 0.5 CD A:GLN222 4.8 15.2 1.0 OE1 A:GLN222 4.8 26.8 1.0

Zinc binding site 2 out of 9 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:Zn403 b:14.4 occ:0.50 NE2 A:HIS15 2.2 19.0 1.0 CD2 A:HIS15 3.2 14.7 1.0 CE1 A:HIS15 3.2 15.3 1.0 O A:HOH583 4.0 20.9 1.0 CE1 A:TYR186 4.1 15.8 1.0 CD1 A:TYR186 4.1 16.9 1.0 CZ A:TYR186 4.2 16.2 1.0 CG A:TYR186 4.3 10.9 1.0 CE2 A:TYR186 4.3 17.0 1.0 ND1 A:HIS15 4.3 18.0 1.0 CG A:HIS15 4.3 15.7 1.0 CD2 A:TYR186 4.4 15.1 1.0 OH A:TYR186 4.8 16.3 1.0 O A:HOH598 4.9 19.6 1.0

Zinc binding site 3 out of 9 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:Zn404 b:35.1 occ:0.80 NE2 A:HIS87 2.2 21.9 1.0 O A:HOH763 2.5 29.5 1.0 CE1 A:HIS87 3.1 19.8 1.0 CD2 A:HIS87 3.1 19.2 1.0 O A:HOH749 3.9 24.7 1.0 ND1 A:HIS87 4.2 18.2 1.0 CG A:HIS87 4.3 14.1 1.0 OH A:TYR193 4.5 16.7 1.0

Zinc binding site 4 out of 9 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:Zn405 b:14.1 occ:0.75 OD1 A:ASP38 1.8 15.0 0.8 OD1 A:ASP36 1.9 17.2 1.0 O A:HOH732 1.9 21.8 1.0 CG A:ASP36 2.6 19.5 1.0 OD2 A:ASP36 2.6 21.2 1.0 CG A:ASP38 3.0 16.0 0.8 OD2 A:ASP38 3.5 26.1 0.8 CB A:ASP38 3.7 16.1 0.2 N A:ALA39 3.9 11.7 1.0 O A:HOH506 3.9 27.4 0.5 OD2 A:ASP38 4.0 13.7 0.2 CB A:ASP36 4.1 13.2 1.0 N A:ASP38 4.1 13.5 1.0 C A:ASP38 4.1 11.7 1.0 CA A:ASP38 4.2 12.8 0.2 CB A:ASP38 4.2 16.4 0.8 CA A:ALA39 4.3 10.7 1.0 CG A:ASP38 4.3 15.3 0.2 CA A:ASP38 4.3 14.2 0.8 CB A:ALA39 4.4 16.7 1.0 O A:HOH700 4.6 37.8 1.0 O A:HOH576 4.6 24.0 0.8 O A:ASP38 4.7 17.3 1.0 C A:ASP36 4.7 15.5 1.0 CA A:ASP36 4.7 13.2 1.0 N A:LEU37 4.8 13.0 1.0

Zinc binding site 5 out of 9 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 5 of X-Ray Crystal Structure of AA13 Lpmo within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:19.2 occ:0.50 OD1 A:ASP148 1.9 12.5 1.0 O A:HOH535 2.2 23.6 1.0 O A:HOH750 2.3 15.2 0.8 CG A:ASP148 2.5 15.3 1.0 OD2 A:ASP148 2.5 15.3 1.0 CD1 A:PHE166 2.6 20.9 0.2 CE1 A:PHE166 3.0 21.3 0.2 CG A:PHE166 3.4 21.0 0.2 CE2 A:PHE218 3.6 19.2 1.0 N A:PHE166 3.7 20.6 0.2 N A:PHE166 3.8 23.6 0.8 CZ A:PHE166 3.8 22.4 0.2 OE1 A:GLU167 3.9 29.5 1.0 CD2 A:PHE218 3.9 17.4 1.0 CB A:ASP148 4.0 13.9 1.0 CB A:PHE166 4.0 21.2 0.2 O A:HOH787 4.0 20.0 1.0 O A:HOH590 4.1 14.5 1.0 CB A:PHE166 4.1 19.2 0.8 CD2 A:PHE166 4.1 21.0 0.2 CZ A:PHE218 4.3 17.0 1.0 CE2 A:PHE166 4.4 18.6 0.2 CA A:PHE166 4.5 22.3 0.2 CA A:GLY165 4.5 15.6 0.2 CA A:PHE166 4.6 27.4 0.8 CA A:GLY165 4.6 16.2 0.8 C A:GLY165 4.6 16.7 0.2 CA A:ASP148 4.7 13.6 1.0 C A:GLY165 4.7 18.8 0.8 O A:HOH609 4.7 15.5 1.0 CG A:PHE218 4.8 11.8 1.0 N A:ASP148 5.0 13.1 1.0

Zinc binding site 6 out of 9 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 6 of X-Ray Crystal Structure of AA13 Lpmo within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn407 b:22.6 occ:0.50 OXT A:GLN233 2.0 18.0 1.0 O A:HOH687 2.1 13.8 0.5 OG A:SER74 2.5 26.4 1.0 C A:GLN233 3.0 18.5 1.0 O A:HOH706 3.0 27.9 1.0 O A:GLN233 3.3 23.0 1.0 CB A:SER74 3.6 21.5 1.0 CA A:SER74 3.8 15.0 1.0 O A:TYR73 4.3 17.9 1.0 CA A:GLN233 4.3 17.9 1.0 CD A:PRO75 4.4 15.2 1.0 N A:SER74 4.4 18.1 1.0 C A:TYR73 4.6 15.9 1.0 N A:GLN233 4.7 15.2 1.0 CB A:GLN233 4.7 24.5 1.0

Zinc binding site 7 out of 9 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 7 of X-Ray Crystal Structure of AA13 Lpmo within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn408 b:18.5 occ:0.20 O A:HOH548 1.7 39.3 1.0 O A:HOH581 1.9 28.0 1.0 OD1 A:ASP102 2.1 17.8 1.0 OG A:SER104 2.1 21.3 1.0 CG A:ASP102 3.0 14.8 1.0 CB A:SER104 3.0 18.2 1.0 OD2 A:ASP102 3.2 22.0 1.0 N A:SER104 3.7 13.3 1.0 CA A:SER104 3.9 15.9 1.0 O A:HOH753 4.1 34.0 1.0 CB A:ASP102 4.4 16.7 1.0 N A:ILE105 4.7 14.4 1.0 C A:ASP102 4.7 13.0 1.0 CA A:ASP102 4.7 16.7 1.0 O A:HOH677 4.7 30.0 1.0 N A:GLN103 4.7 15.8 1.0 C A:SER104 4.7 15.0 1.0 C A:GLN103 4.9 13.4 1.0

Zinc binding site 8 out of 9 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 8 of X-Ray Crystal Structure of AA13 Lpmo within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn409 b:28.3 occ:0.50 OD2 A:ASP129 2.2 16.5 0.5 OE2 A:GLU125 2.3 13.3 1.0 O A:HOH618 2.6 8.8 1.0 OD1 A:ASP129 2.6 13.0 0.5 CG A:ASP129 2.7 17.0 0.5 O A:HOH501 3.1 12.8 0.5 CD A:GLU125 3.3 13.5 1.0 CG A:GLU125 3.5 13.6 1.0 O A:HOH642 3.5 15.6 1.0 CB A:ASP38 3.8 16.4 0.8 CE A:LYS214 4.0 18.6 1.0 CB A:ASP129 4.1 14.6 0.5 NZ A:LYS214 4.1 19.3 1.0 NH1 A:ARG98 4.2 11.7 1.0 CB A:ASP129 4.2 14.9 0.5 CA A:ASP38 4.2 14.2 0.8 CA A:ASP38 4.3 12.8 0.2 CB A:ASP38 4.3 16.1 0.2 OD1 A:ASP38 4.4 14.5 0.2 O A:HOH610 4.4 15.0 1.0 O A:HOH537 4.4 14.7 0.5 CG A:ASP129 4.4 17.4 0.5 O A:GLU125 4.4 11.4 1.0 CD A:LYS214 4.4 13.4 1.0 OE1 A:GLU125 4.5 15.4 1.0 O A:ASP38 4.5 17.3 1.0 O A:HOH661 4.5 12.0 1.0 OD1 A:ASP129 4.6 17.8 0.5 CG A:ASP38 4.7 15.3 0.2 C A:ASP38 4.8 11.7 1.0 CB A:GLU125 4.9 11.5 1.0 C A:GLU125 4.9 11.1 1.0

Zinc binding site 9 out of 9 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 9 of X-Ray Crystal Structure of AA13 Lpmo within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn410 b:45.2 occ:0.50 O A:HOH764 1.8 20.1 0.5 O A:HOH697 1.9 22.8 0.5 O A:HOH514 2.2 27.6 1.0 OE2 A:GLU153 2.9 26.9 0.7 OE1 A:GLU153 3.6 21.5 0.7 CD A:GLU153 3.6 25.0 0.7 O A:HOH554 4.4 21.1 1.0 NE1 A:TRP34 4.6 14.5 1.0 CD1 A:TRP34 4.7 13.9 1.0 O A:ASP148 4.8 13.9 1.0 CB A:PRO35 4.8 14.2 1.0 CG A:PRO35 4.9 15.5 1.0

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