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Zinc in PDB 5lww: Crystal Structure of A Laccase-Like Multicopper Oxidase Mcog From Aspergillus Niger Bound to Zinc

Enzymatic activity of Crystal Structure of A Laccase-Like Multicopper Oxidase Mcog From Aspergillus Niger Bound to Zinc

All present enzymatic activity of Crystal Structure of A Laccase-Like Multicopper Oxidase Mcog From Aspergillus Niger Bound to Zinc:
1.10.3.2;

Protein crystallography data

The structure of Crystal Structure of A Laccase-Like Multicopper Oxidase Mcog From Aspergillus Niger Bound to Zinc, PDB code: 5lww was solved by M.Ferraroni, F.Briganti, J.A.Tamayo-Ramos, W.J.H.Van Berkel, A.H.Westphal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.65
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 88.446, 128.158, 134.676, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 26.7

Other elements in 5lww:

The structure of Crystal Structure of A Laccase-Like Multicopper Oxidase Mcog From Aspergillus Niger Bound to Zinc also contains other interesting chemical elements:

Potassium (K) 1 atom
Chlorine (Cl) 1 atom
Copper (Cu) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Laccase-Like Multicopper Oxidase Mcog From Aspergillus Niger Bound to Zinc (pdb code 5lww). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of A Laccase-Like Multicopper Oxidase Mcog From Aspergillus Niger Bound to Zinc, PDB code: 5lww:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5lww

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Zinc binding site 1 out of 8 in the Crystal Structure of A Laccase-Like Multicopper Oxidase Mcog From Aspergillus Niger Bound to Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Laccase-Like Multicopper Oxidase Mcog From Aspergillus Niger Bound to Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn616

b:39.5
occ:1.00
 NE2 A:HIS253 2.1 41.3 1.0
NE2 A:HIS521 2.1 29.7 1.0
O A:HOH884 2.1 10.2 1.0
CL A:CL625 2.9 48.3 1.0
CD2 A:HIS253 2.9 41.6 1.0
CD2 A:HIS521 3.1 31.1 1.0
CE1 A:HIS521 3.1 31.6 1.0
CE1 A:HIS253 3.1 41.4 1.0
CD A:PRO208 4.0 38.3 1.0
CG A:HIS253 4.1 37.3 1.0
ND1 A:HIS253 4.2 39.9 1.0
ND1 A:HIS521 4.2 31.9 1.0
CG A:HIS521 4.2 32.8 1.0
NE1 A:TRP392 4.5 31.7 1.0
CG2 A:ILE518 4.7 29.0 1.0
CG A:PRO208 4.8 39.4 1.0
CA A:PRO207 4.8 42.5 1.0
O A:HOH905 4.9 38.8 1.0
O A:HOH823 5.0 34.1 1.0
CZ2 A:TRP392 5.0 31.7 1.0

Zinc binding site 2 out of 8 in 5lww

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Zinc binding site 2 out of 8 in the Crystal Structure of A Laccase-Like Multicopper Oxidase Mcog From Aspergillus Niger Bound to Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Laccase-Like Multicopper Oxidase Mcog From Aspergillus Niger Bound to Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn617

b:54.4
occ:1.00
 O A:HOH715 1.8 37.7 1.0
OD2 A:ASP366 2.0 34.0 1.0
ND1 A:HIS477 2.2 41.6 1.0
O A:HOH904 2.4 25.7 1.0
CG A:HIS477 3.0 41.3 1.0
CB A:HIS477 3.2 38.2 1.0
CG A:ASP366 3.3 41.5 1.0
CE1 A:HIS477 3.3 41.6 1.0
CA A:HIS477 3.6 37.6 1.0
CB A:ASP366 4.0 41.5 1.0
CD2 A:HIS477 4.2 41.6 1.0
OD1 A:ASP366 4.2 46.3 1.0
NE2 A:HIS477 4.3 42.6 1.0
C A:HIS477 4.5 41.7 1.0
N A:ASN478 4.5 40.8 1.0
N A:HIS477 4.7 35.2 1.0
O A:THR476 5.0 33.7 1.0

Zinc binding site 3 out of 8 in 5lww

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Zinc binding site 3 out of 8 in the Crystal Structure of A Laccase-Like Multicopper Oxidase Mcog From Aspergillus Niger Bound to Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Laccase-Like Multicopper Oxidase Mcog From Aspergillus Niger Bound to Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn618

b:44.2
occ:1.00
 OD2 A:ASP368 2.1 53.6 1.0
CG A:ASP368 2.9 49.8 1.0
OD1 A:ASP368 3.0 54.2 1.0
CB A:ASP368 4.4 43.3 1.0
O A:HOH764 4.6 40.6 1.0
O A:ASP368 4.8 40.6 1.0

Zinc binding site 4 out of 8 in 5lww

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Zinc binding site 4 out of 8 in the Crystal Structure of A Laccase-Like Multicopper Oxidase Mcog From Aspergillus Niger Bound to Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A Laccase-Like Multicopper Oxidase Mcog From Aspergillus Niger Bound to Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn619

b:54.6
occ:1.00
 ND1 A:HIS170 2.2 41.6 1.0
O A:HOH886 2.2 19.5 1.0
O A:HOH911 2.7 28.7 1.0
CE1 A:HIS170 3.0 41.7 1.0
CG A:HIS170 3.3 40.7 1.0
CB A:HIS170 3.7 40.1 1.0
OD2 A:ASP180 3.9 38.6 1.0
NE2 A:HIS170 4.1 41.4 1.0
OH A:TYR177 4.2 45.1 1.0
NH2 A:ARG246 4.3 42.9 1.0
CD2 A:HIS170 4.3 42.2 1.0
CA A:HIS170 4.3 36.3 1.0
CG A:ASP180 4.9 38.5 1.0
N A:GLY171 5.0 35.1 1.0

Zinc binding site 5 out of 8 in 5lww

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Zinc binding site 5 out of 8 in the Crystal Structure of A Laccase-Like Multicopper Oxidase Mcog From Aspergillus Niger Bound to Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of A Laccase-Like Multicopper Oxidase Mcog From Aspergillus Niger Bound to Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn620

b:56.5
occ:1.00
 O A:HOH801 2.0 33.0 1.0
OD1 A:ASP334 2.2 64.7 1.0
NE2 A:HIS328 2.2 46.4 1.0
CG A:ASP334 3.0 65.8 1.0
CE1 A:HIS328 3.2 50.0 1.0
OD2 A:ASP334 3.2 64.7 1.0
CD2 A:HIS328 3.2 48.1 1.0
CB A:ALA332 3.3 75.9 1.0
CA A:ALA332 3.7 69.5 1.0
OE1 A:GLU236 3.8 63.0 1.0
O A:GLU330 4.0 62.1 1.0
ND1 A:HIS328 4.3 47.2 1.0
N A:ALA332 4.3 65.9 1.0
CG A:HIS328 4.3 49.3 1.0
CB A:ASP334 4.5 57.8 1.0
C A:ALA332 4.8 66.9 1.0
CA A:ASP334 4.9 59.7 1.0
O A:TYR329 4.9 53.5 1.0
CD A:GLU236 4.9 64.3 1.0
C A:GLU330 4.9 59.2 1.0
N A:ASP334 4.9 65.7 1.0

Zinc binding site 6 out of 8 in 5lww

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Zinc binding site 6 out of 8 in the Crystal Structure of A Laccase-Like Multicopper Oxidase Mcog From Aspergillus Niger Bound to Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of A Laccase-Like Multicopper Oxidase Mcog From Aspergillus Niger Bound to Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn621

b:77.6
occ:1.00
 OD1 A:ASP414 2.2 75.6 1.0
OD1 A:ASP416 2.2 55.8 1.0
CG A:ASP414 3.1 64.2 1.0
CG A:ASP416 3.3 59.7 1.0
OD2 A:ASP414 3.4 69.8 1.0
OD2 A:ASP416 3.7 64.5 1.0
CB A:ASP414 4.5 52.4 1.0
C A:ASP416 4.7 57.8 1.0
N A:ASP416 4.7 54.7 1.0
CB A:ASP416 4.7 57.1 1.0
N A:LYS417 4.8 53.4 1.0
O A:ASP416 4.9 56.7 1.0
CA A:ASP416 4.9 58.0 1.0
CA A:ASP414 5.0 50.5 1.0

Zinc binding site 7 out of 8 in 5lww

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Zinc binding site 7 out of 8 in the Crystal Structure of A Laccase-Like Multicopper Oxidase Mcog From Aspergillus Niger Bound to Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of A Laccase-Like Multicopper Oxidase Mcog From Aspergillus Niger Bound to Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn622

b:65.4
occ:0.50
 OXT A:ACT626 2.0 28.2 0.5
OE1 A:GLU555 2.2 67.5 1.0
CD A:GLU555 3.0 63.7 1.0
C A:ACT626 3.1 27.4 0.5
CG A:GLU555 3.2 51.4 1.0
O A:ACT626 3.5 25.6 0.5
OE2 A:GLU555 4.2 70.5 1.0
CH3 A:ACT626 4.4 25.9 0.5
CB A:GLU555 4.7 44.5 1.0
O A:ASP551 4.8 34.9 1.0
CB A:ASP551 4.9 43.1 1.0

Zinc binding site 8 out of 8 in 5lww

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Zinc binding site 8 out of 8 in the Crystal Structure of A Laccase-Like Multicopper Oxidase Mcog From Aspergillus Niger Bound to Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of A Laccase-Like Multicopper Oxidase Mcog From Aspergillus Niger Bound to Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn623

b:66.9
occ:0.50
 OE2 A:GLU330 1.9 71.5 1.0
CD A:GLU330 3.0 75.8 1.0
OE1 A:GLU330 3.7 68.9 1.0
CG A:GLU330 3.9 69.2 1.0

Reference:

M.Ferraroni, A.H.Westphal, M.Borsari, J.A.Tamayo-Ramos, F.Briganti, L.H.De Graaff, W.J.H.Van Berkel. Structure and Function of Aspergillus Niger Laccase Mcog Biocatalysis 2017.
ISSN: ESSN 2353-1746
DOI: 10.1515/BOCA-2017-0001
Page generated: Sun Oct 27 21:32:28 2024

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