Zinc in PDB 6tc4: AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Measured with Ssx

Protein crystallography data

The structure of AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Measured with Ssx, PDB code: 6tc4 was solved by T.Tandrup, S.J.Muderspach, K.E.H.Frandsen, G.Santoni, J.C.N.Poulsen, L.Loleggio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.21 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.720, 61.430, 73.780, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 22.3

Other elements in 6tc4:

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

Chlorine (Cl) 1 atom

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Zinc atom in the AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Measured with Ssx (pdb code 6tc4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 13 binding sites of Zinc where determined in the AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Measured with Ssx, PDB code: 6tc4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 13 in 6tc4

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Zinc binding site 1 out of 13 in the AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Measured with Ssx


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 Measured with Ssx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:15.5
occ:1.00
ND1 A:HIC1 1.8 20.7 1.0
OH A:TYR224 2.0 14.8 1.0
NE2 A:HIS91 2.1 14.6 1.0
N A:HIC1 2.3 14.1 1.0
O A:HOH463 2.3 9.7 1.0
CE1 A:HIC1 2.8 22.2 1.0
CG A:HIC1 2.9 20.2 1.0
CZ A:TYR224 3.0 13.1 1.0
CD2 A:HIS91 3.1 13.3 1.0
CE1 A:HIS91 3.1 13.5 1.0
CA A:HIC1 3.1 14.6 1.0
CB A:HIC1 3.5 17.1 1.0
CE1 A:TYR224 3.6 12.5 1.0
CE2 A:TYR224 3.9 11.9 1.0
OE1 A:GLN222 3.9 14.1 1.0
NE2 A:HIC1 4.0 23.1 1.0
CD2 A:HIC1 4.0 22.9 1.0
O A:GLY89 4.1 11.1 1.0
ND1 A:HIS91 4.2 13.4 1.0
CG A:HIS91 4.2 13.5 1.0
CA A:GLY89 4.4 12.2 1.0
C A:HIC1 4.5 13.2 1.0
O A:HOH565 4.6 35.8 1.0
C A:GLY89 4.7 11.2 1.0
CD A:GLN222 4.8 13.0 1.0
CD1 A:TYR224 4.9 11.2 1.0

Zinc binding site 2 out of 13 in 6tc4

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Zinc binding site 2 out of 13 in the AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Measured with Ssx


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

b:34.7
occ:1.00
O A:GLN233 2.0 21.9 1.0
O A:HOH480 2.3 21.7 1.0
O A:HOH555 2.8 36.4 1.0
O A:HOH496 2.8 28.1 1.0
C A:GLN233 2.9 21.5 1.0
OG A:SER74 3.0 17.6 1.0
OXT A:GLN233 3.0 21.6 1.0
CB A:SER74 3.9 16.5 1.0
CA A:SER74 3.9 15.7 1.0
CA A:GLN233 4.2 20.2 1.0
O A:TYR73 4.3 13.4 1.0
CD A:PRO75 4.3 14.2 1.0
N A:GLN233 4.6 16.8 1.0
N A:SER74 4.6 15.2 1.0
C A:TYR73 4.7 14.3 1.0
O A:HOH446 4.7 23.1 1.0
CG A:GLN233 4.9 25.5 1.0
CB A:GLN233 4.9 22.4 1.0

Zinc binding site 3 out of 13 in 6tc4

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Zinc binding site 3 out of 13 in the AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Measured with Ssx


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

b:18.7
occ:0.50
OD2 A:ASP119 1.8 14.4 1.0
CG A:ASP119 2.9 12.5 1.0
CB A:ASP119 3.3 11.6 1.0
OD1 A:ASP119 4.0 13.6 1.0
O A:HOH478 4.0 11.0 1.0
CA A:ASP119 4.8 11.0 1.0

Zinc binding site 4 out of 13 in 6tc4

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Zinc binding site 4 out of 13 in the AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Measured with Ssx


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

b:25.9
occ:1.00
O A:HOH556 1.9 24.2 1.0
O A:HOH527 1.9 21.6 1.0
ND1 A:HIS208 2.0 13.6 1.0
O A:HOH558 2.1 34.1 1.0
CE1 A:HIS208 2.9 13.7 1.0
CG A:HIS208 3.0 12.9 1.0
CB A:HIS208 3.4 13.1 1.0
O A:SER67 3.6 33.3 1.0
O A:HOH535 3.7 37.5 1.0
NE2 A:HIS208 4.1 13.2 1.0
CD2 A:HIS208 4.1 13.3 1.0
O A:HOH408 4.3 25.1 1.0
C A:SER67 4.6 27.6 1.0
O A:HOH511 4.6 29.4 1.0
CA A:ASP68 4.7 27.5 1.0
CA A:HIS208 4.9 13.2 1.0

Zinc binding site 5 out of 13 in 6tc4

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Zinc binding site 5 out of 13 in the AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Measured with Ssx


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

b:35.5
occ:0.50
OE2 A:GLU77 2.0 21.5 1.0
CD A:GLU77 2.8 17.5 1.0
OE1 A:GLU77 2.9 17.0 1.0
CG A:GLU77 4.2 16.1 1.0
O A:HOH473 4.3 36.6 1.0
CD1 A:TYR73 4.7 14.6 1.0
O A:SER72 4.7 17.0 1.0
CA A:TYR73 4.8 14.7 1.0

Zinc binding site 6 out of 13 in 6tc4

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Zinc binding site 6 out of 13 in the AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Measured with Ssx


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Measured with Ssx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn307

b:42.2
occ:0.50
O A:HOH532 1.8 30.9 1.0
OD2 A:ASP107 2.3 18.9 1.0
CG A:ASP107 3.3 15.4 1.0
OD1 A:ASP107 3.6 15.9 1.0
CG A:GLN103 3.9 16.4 1.0
CB A:ASP107 4.7 14.9 1.0
CD A:GLN103 4.8 16.8 1.0
NE2 A:GLN103 4.9 16.6 1.0

Zinc binding site 7 out of 13 in 6tc4

Go back to Zinc Binding Sites List in 6tc4
Zinc binding site 7 out of 13 in the AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Measured with Ssx


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Measured with Ssx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn308

b:33.7
occ:0.50
O A:HOH462 2.0 26.8 1.0
O A:HOH554 2.0 38.6 1.0
OE2 A:GLU153 2.6 39.1 1.0
OE1 A:GLU153 3.1 35.0 1.0
CD A:GLU153 3.3 34.3 1.0
O A:HOH495 3.9 22.5 1.0
NE1 A:TRP34 4.5 11.9 1.0
O A:ASP148 4.6 12.4 1.0
CB A:PRO35 4.7 14.2 1.0
CD1 A:TRP34 4.7 12.1 1.0
CG A:GLU153 4.8 30.2 1.0
CG A:PRO35 5.0 14.1 1.0

Zinc binding site 8 out of 13 in 6tc4

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Zinc binding site 8 out of 13 in the AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Measured with Ssx


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Measured with Ssx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn309

b:43.5
occ:0.50
ZN A:ZN309 0.0 43.5 0.5
O A:HOH561 1.8 33.1 1.0
OD2 A:ASP126 2.2 15.4 1.0
ZN A:ZN309 3.1 36.1 0.5
CG A:ASP126 3.1 13.1 1.0
OD1 A:ASP126 3.5 13.6 1.0
CG A:GLN122 4.4 9.6 1.0
CB A:ASP126 4.5 12.5 1.0
NE2 A:GLN122 4.9 9.0 1.0

Zinc binding site 9 out of 13 in 6tc4

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Zinc binding site 9 out of 13 in the AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Measured with Ssx


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Measured with Ssx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn309

b:36.1
occ:0.50
ZN A:ZN309 0.0 36.1 0.5
OD2 A:ASP126 2.2 15.4 1.0
ZN A:ZN309 3.1 43.5 0.5
O A:HOH489 3.1 28.5 1.0
CG A:ASP126 3.2 13.1 1.0
CB A:ASP126 3.5 12.5 1.0
CA A:ALA123 4.1 11.9 1.0
OD1 A:ASP126 4.3 13.6 1.0
O A:ALA123 4.6 12.9 1.0
CB A:ALA123 4.7 12.7 1.0
O A:HOH561 4.8 33.1 1.0
N A:ALA123 4.8 10.9 1.0
O A:GLN122 4.8 10.8 1.0
C A:ALA123 4.9 12.0 1.0

Zinc binding site 10 out of 13 in 6tc4

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Zinc binding site 10 out of 13 in the AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Measured with Ssx


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of AA13 Lytic Polysaccharide Monooxygenase From Aspergillus Oryzae Measured with Ssx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn310

b:13.4
occ:1.00
O A:HOH485 1.9 10.5 1.0
OE2 A:GLU125 2.0 11.1 1.0
OD2 A:ASP129 2.0 15.1 1.0
CL A:CL314 2.2 11.5 1.0
OD1 A:ASP129 2.5 15.9 1.0
CG A:ASP129 2.5 14.5 1.0
CD A:GLU125 3.0 11.8 1.0
CG A:GLU125 3.4 11.7 1.0
O A:HOH410 3.5 31.9 1.0
NH1 A:ARG98 3.9 8.3 1.0
CB A:ASP129 4.0 13.1 1.0
CE A:LYS214 4.1 9.4 1.0
CB A:ASP38 4.1 15.5 1.0
OE1 A:GLU125 4.1 12.3 1.0
O A:HOH474 4.1 14.4 1.0
O A:HOH488 4.2 24.5 1.0
NZ A:LYS214 4.3 9.9 1.0
CA A:ASP38 4.3 14.2 1.0
CD A:LYS214 4.3 9.0 1.0
O A:GLU125 4.3 11.9 1.0
O A:ASP38 4.4 12.9 1.0
O A:HOH562 4.6 19.7 1.0
O A:HOH503 4.8 12.8 1.0
CB A:GLU125 4.8 11.9 1.0
C A:ASP38 4.9 13.1 1.0
C A:GLU125 4.9 12.2 1.0
CA A:ASP129 4.9 12.2 1.0

Reference:

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
Page generated: Wed Dec 16 12:52:36 2020

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