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Zinc in PDB 4opb: AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae

Protein crystallography data

The structure of AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae, PDB code: 4opb was solved by L.Lo Leggio, K.H.Frandsen, G.J.Davies, P.Dupree, P.Walton, B.Henrissat, M.Stringer, M.Tovborg, L.De Maria, K.S.Johansen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.560, 61.600, 73.160, 90.00, 90.00, 90.00
R / Rfree (%) 11.9 / 17

Other elements in 4opb:

The structure of AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae also contains other interesting chemical elements:

Copper (Cu) 1 atom

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 4opb

Go back to Zinc Binding Sites List in 4opb
Zinc binding site 1 out of 4 in the AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:10.6
occ:0.85
O A:HOH451 2.0 17.4 1.0
OE2 A:GLU125 2.0 10.4 1.0
OD2 A:ASP129 2.1 20.0 1.0
O A:HOH603 2.2 10.3 1.0
OD1 A:ASP129 2.3 16.6 1.0
CG A:ASP129 2.6 12.1 1.0
CD A:GLU125 3.0 10.9 1.0
CG A:GLU125 3.4 9.2 1.0
NH1 A:ARG98 3.8 10.5 1.0
CB A:ASP129 4.1 12.2 1.0
O A:HOH454 4.1 26.6 1.0
CB A:ASP38 4.1 14.7 1.0
CE A:LYS214 4.1 9.9 1.0
OE1 A:GLU125 4.2 12.3 1.0
O A:HOH450 4.3 14.6 1.0
O A:GLU125 4.3 8.6 1.0
O A:HOH490 4.3 30.0 1.0
NZ A:LYS214 4.4 8.7 1.0
CA A:ASP38 4.4 12.9 1.0
CD A:LYS214 4.4 8.2 1.0
O A:ASP38 4.5 15.3 1.0
O A:HOH456 4.7 16.6 1.0
C A:GLU125 4.8 9.1 1.0
CB A:GLU125 4.8 10.0 1.0
O A:HOH452 4.9 12.0 1.0
CA A:ASP129 4.9 9.8 1.0
C A:ASP38 5.0 11.3 1.0

Zinc binding site 2 out of 4 in 4opb

Go back to Zinc Binding Sites List in 4opb
Zinc binding site 2 out of 4 in the AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:16.7
occ:0.60
NE2 A:HIS15 2.3 22.9 1.0
O A:HOH404 2.3 20.1 1.0
CE1 A:HIS15 3.2 17.7 1.0
CD2 A:HIS15 3.2 18.4 1.0
O A:HOH595 3.6 35.2 1.0
ND1 A:HIS15 4.3 16.4 1.0
CE1 A:TYR186 4.3 15.4 1.0
CG A:HIS15 4.3 12.0 1.0
CZ A:TYR186 4.4 14.4 1.0
CD1 A:TYR186 4.4 16.1 1.0
CE2 A:TYR186 4.6 15.6 1.0
CG A:TYR186 4.7 12.9 1.0
CD2 A:TYR186 4.7 12.1 1.0
OH A:TYR186 4.9 18.6 1.0

Zinc binding site 3 out of 4 in 4opb

Go back to Zinc Binding Sites List in 4opb
Zinc binding site 3 out of 4 in the AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:15.5
occ:0.95
OD1 A:ASP38 2.0 16.1 1.0
OD1 A:ASP36 2.0 19.4 1.0
O A:HOH458 2.1 14.4 1.0
OD2 A:ASP36 2.7 28.3 1.0
CG A:ASP36 2.7 15.8 1.0
CG A:ASP38 3.1 19.8 1.0
OD2 A:ASP38 3.5 28.2 1.0
N A:ALA39 4.0 10.2 1.0
O A:HOH553 4.1 32.4 1.0
CB A:ASP36 4.2 15.0 1.0
N A:ASP38 4.2 11.4 1.0
C A:ASP38 4.3 11.3 1.0
CB A:ALA39 4.3 13.7 1.0
CB A:ASP38 4.3 14.7 1.0
CA A:ALA39 4.4 12.9 1.0
O A:HOH457 4.4 15.4 1.0
CA A:ASP38 4.5 12.9 1.0
C A:ASP36 4.7 11.8 1.0
CA A:ASP36 4.7 13.3 1.0
O A:ASP38 4.9 15.3 1.0
N A:LEU37 4.9 12.2 1.0

Zinc binding site 4 out of 4 in 4opb

Go back to Zinc Binding Sites List in 4opb
Zinc binding site 4 out of 4 in the AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn306

b:25.7
occ:0.80
O A:HOH578 1.9 19.5 0.5
OE1 A:GLU142 2.0 21.9 1.0
O A:HOH579 2.2 15.8 1.0
CD A:GLU142 2.7 19.3 1.0
OE2 A:GLU142 2.7 30.5 1.0
CG A:GLU142 4.2 16.5 1.0
O A:HOH496 4.7 32.2 1.0
CB A:GLU142 4.8 12.4 1.0

Reference:

L.Lo Leggio, T.J.Simmons, J.C.N.Poulsen, K.E.H.Frandsen, G.R.Hemsworth, M.A.Stringer, P.Von Freiesleben, M.Tovborg, K.S.Johansen, L.De Maria, P.V.Harris, C.L.Soong, P.Dupree, T.Tryfona, N.Lenfant, B.Henrissat, G.J.Davies, P.H.Walton. Structure and Boosting Activity of A Starch-Degrading Lytic Polysaccharide Monooxygenase. Nat Commun 2015.
ISSN: ESSN 2041-1723
DOI: NCOMMS6961
Page generated: Wed Dec 16 05:39:23 2020

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