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Zinc in PDB 4d7v: The Structure of the Catalytic Domain of NCLPMO9C From the Filamentous Fungus Neurospora Crassa

Protein crystallography data

The structure of The Structure of the Catalytic Domain of NCLPMO9C From the Filamentous Fungus Neurospora Crassa, PDB code: 4d7v was solved by A.S.Borisova, T.Isaksen, M.Sandgren, M.Sorlie, V.G.H.Eijsink, M.Dimarogona, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.41 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.308, 67.528, 65.592, 90.00, 100.91, 90.00
R / Rfree (%) 21.2 / 26.7

Zinc Binding Sites:

The binding sites of Zinc atom in the The Structure of the Catalytic Domain of NCLPMO9C From the Filamentous Fungus Neurospora Crassa (pdb code 4d7v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the The Structure of the Catalytic Domain of NCLPMO9C From the Filamentous Fungus Neurospora Crassa, PDB code: 4d7v:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4d7v

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Zinc binding site 1 out of 6 in the The Structure of the Catalytic Domain of NCLPMO9C From the Filamentous Fungus Neurospora Crassa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of the Catalytic Domain of NCLPMO9C From the Filamentous Fungus Neurospora Crassa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1228

b:11.0
occ:1.00
ND1 A:HIS1 2.1 3.5 1.0
NE2 A:HIS83 2.1 4.2 1.0
N A:HIS1 2.2 3.4 1.0
O A:ACT1232 2.3 3.8 0.4
OXT A:ACT1231 2.3 8.8 1.0
O A:HOH2001 2.6 2.1 0.5
CG A:HIS1 3.0 3.5 1.0
C A:ACT1232 3.0 3.8 0.4
CD2 A:HIS83 3.0 4.2 1.0
CE1 A:HIS83 3.1 4.2 1.0
C A:ACT1231 3.1 9.1 1.0
CB A:HIS1 3.1 3.4 1.0
CA A:HIS1 3.2 3.4 1.0
O A:ACT1231 3.2 9.1 1.0
CE1 A:HIS1 3.2 3.5 1.0
OXT A:ACT1232 3.6 3.9 0.4
OH A:TYR166 3.8 3.1 1.0
CH3 A:ACT1232 3.9 3.8 0.4
ND1 A:HIS83 4.1 4.2 1.0
CG A:HIS83 4.1 4.2 1.0
CD2 A:HIS1 4.2 3.5 1.0
NE2 A:HIS1 4.3 3.5 1.0
OE1 A:GLN164 4.3 3.5 1.0
C A:HIS1 4.4 3.4 1.0
CH3 A:ACT1231 4.5 8.9 1.0
CZ A:TYR166 4.6 3.0 1.0
O A:HIS1 4.7 3.5 1.0

Zinc binding site 2 out of 6 in 4d7v

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Zinc binding site 2 out of 6 in the The Structure of the Catalytic Domain of NCLPMO9C From the Filamentous Fungus Neurospora Crassa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of the Catalytic Domain of NCLPMO9C From the Filamentous Fungus Neurospora Crassa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1229

b:15.9
occ:0.75
O A:HOH2092 1.7 4.5 0.2
O A:HOH2091 2.0 31.1 1.0
NE2 A:HIS64 2.1 8.1 1.0
CE1 A:HIS64 2.9 8.1 1.0
CD2 A:HIS64 3.2 7.8 1.0
O A:HOH2021 3.8 33.4 1.0
OE2 A:GLU65 3.9 14.3 1.0
ND1 A:HIS64 4.1 7.9 1.0
CG A:HIS64 4.2 7.8 1.0
O A:HOH2097 4.6 24.5 1.0
OD2 A:ASP76 4.6 25.5 1.0
CH3 A:ACT1231 4.9 8.9 1.0
CD A:GLU65 4.9 12.9 1.0

Zinc binding site 3 out of 6 in 4d7v

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Zinc binding site 3 out of 6 in the The Structure of the Catalytic Domain of NCLPMO9C From the Filamentous Fungus Neurospora Crassa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structure of the Catalytic Domain of NCLPMO9C From the Filamentous Fungus Neurospora Crassa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1230

b:9.1
occ:0.50
O A:HOH2104 2.0 22.6 1.0
OD2 A:ASP74 2.0 21.0 1.0
O A:HOH2098 2.2 31.9 1.0
O A:HOH2099 2.2 16.7 1.0
O A:HOH2103 2.6 30.0 1.0
OD1 A:ASP74 2.7 20.5 1.0
CG A:ASP74 2.7 20.9 1.0
O A:PRO72 4.1 21.2 1.0
O A:ALA70 4.1 18.5 1.0
CB A:ASP74 4.2 21.0 1.0
OD2 A:ASP76 4.2 25.5 1.0
CG A:ASP76 4.3 21.2 1.0
CB A:ASP76 4.3 19.2 1.0
CB A:ASN77 4.5 10.2 1.0
O A:HOH2105 4.5 31.6 1.0
O A:HOH2097 4.5 24.5 1.0
N A:ASP76 4.7 17.5 1.0
CD A:PRO72 4.8 21.8 1.0
N A:ASN77 4.8 11.9 1.0
OD1 A:ASP76 4.9 25.7 1.0
CA A:ASP76 4.9 16.7 1.0
O A:HOH2108 5.0 35.0 1.0

Zinc binding site 4 out of 6 in 4d7v

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Zinc binding site 4 out of 6 in the The Structure of the Catalytic Domain of NCLPMO9C From the Filamentous Fungus Neurospora Crassa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structure of the Catalytic Domain of NCLPMO9C From the Filamentous Fungus Neurospora Crassa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1228

b:10.7
occ:1.00
NE2 B:HIS83 2.1 4.5 1.0
O B:ACT1231 2.1 11.1 1.0
ND1 B:HIS1 2.2 4.2 1.0
OXT B:ACT1232 2.2 5.0 0.5
N B:HIS1 2.3 4.0 1.0
O B:ACT1232 2.6 4.8 0.5
C B:ACT1232 2.6 5.0 0.5
CE1 B:HIS83 3.0 4.5 1.0
CG B:HIS1 3.0 4.2 1.0
CD2 B:HIS83 3.0 4.5 1.0
C B:ACT1231 3.1 12.0 1.0
CB B:HIS1 3.2 4.1 1.0
CA B:HIS1 3.2 4.1 1.0
CE1 B:HIS1 3.3 4.2 1.0
OXT B:ACT1231 3.5 11.7 1.0
OH B:TYR166 3.5 3.4 1.0
CH3 B:ACT1232 4.0 5.0 0.5
ND1 B:HIS83 4.0 4.5 1.0
CG B:HIS83 4.1 4.5 1.0
O B:HOH2141 4.2 2.0 0.5
OE1 B:GLN164 4.2 3.5 1.0
CD2 B:HIS1 4.2 4.2 1.0
NE2 B:HIS1 4.3 4.2 1.0
CH3 B:ACT1231 4.4 11.8 1.0
CZ B:TYR166 4.4 3.4 1.0
C B:HIS1 4.5 4.1 1.0
O B:HIS1 4.8 4.3 1.0
CE1 B:HIS155 5.0 4.7 1.0

Zinc binding site 5 out of 6 in 4d7v

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Zinc binding site 5 out of 6 in the The Structure of the Catalytic Domain of NCLPMO9C From the Filamentous Fungus Neurospora Crassa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Structure of the Catalytic Domain of NCLPMO9C From the Filamentous Fungus Neurospora Crassa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1229

b:23.1
occ:0.75
O B:HOH2076 1.8 7.9 0.2
NE2 B:HIS64 2.1 9.2 1.0
O B:HOH2187 2.5 30.4 1.0
CE1 B:HIS64 2.8 9.2 1.0
CD2 B:HIS64 3.2 9.2 1.0
O B:HOH2029 3.7 29.4 1.0
OE2 B:GLU65 4.0 16.0 1.0
ND1 B:HIS64 4.0 9.2 1.0
CG B:HIS64 4.2 9.1 1.0
CH3 B:ACT1231 4.7 11.8 1.0
OD2 B:ASP76 4.9 29.4 1.0
O B:HOH2079 5.0 18.2 1.0

Zinc binding site 6 out of 6 in 4d7v

Go back to Zinc Binding Sites List in 4d7v
Zinc binding site 6 out of 6 in the The Structure of the Catalytic Domain of NCLPMO9C From the Filamentous Fungus Neurospora Crassa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Structure of the Catalytic Domain of NCLPMO9C From the Filamentous Fungus Neurospora Crassa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1230

b:29.5
occ:0.50
OD2 B:ASP74 2.0 31.2 1.0
CG B:ASP74 2.7 32.7 1.0
OD1 B:ASP74 2.7 31.0 1.0
O B:HOH2079 3.2 18.2 1.0
OXT B:ACT1235 3.7 34.1 1.0
OD2 B:ASP76 3.8 29.4 1.0
CG B:ASP76 4.0 25.3 1.0
O B:ALA70 4.0 42.6 1.0
O B:PRO72 4.1 41.1 1.0
CB B:ASP74 4.2 33.9 1.0
CB B:ASP76 4.3 23.1 1.0
CB B:ASN77 4.5 13.3 1.0
C B:ACT1235 4.5 35.3 1.0
OD1 B:ASP76 4.6 28.9 1.0
CD B:PRO72 4.7 43.9 1.0
N B:ASP76 4.8 22.5 1.0
N B:ASN77 4.9 14.9 1.0
CA B:ASP76 5.0 20.2 1.0

Reference:

A.S.Borisova, T.Isaksen, M.Dimarogona, A.A.Kognole, G.Mathiesen, A.Varnai, A.K.Rohr, C.Payne, M.Sorlie, M.Sandgren, V.G.H.Eijsink, M.Sorlie. Structural and Functional Characterization of A Lytic Polysaccharide Monooxygenase with Broad Substrate Specificity J.Biol.Chem. V. 290 22955 2015.
ISSN: ISSN 0021-9258
PubMed: 26178376
DOI: 10.1074/JBC.M115.660183
Page generated: Wed Dec 16 05:10:48 2020

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