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Zinc in PDB 4fvk: Structural and Functional Characterization of Neuraminidase-Like Molecule N10 Derived From Bat Influenza A Virus

Enzymatic activity of Structural and Functional Characterization of Neuraminidase-Like Molecule N10 Derived From Bat Influenza A Virus

All present enzymatic activity of Structural and Functional Characterization of Neuraminidase-Like Molecule N10 Derived From Bat Influenza A Virus:
3.2.1.18;

Protein crystallography data

The structure of Structural and Functional Characterization of Neuraminidase-Like Molecule N10 Derived From Bat Influenza A Virus, PDB code: 4fvk was solved by Q.Li, X.M.Sun, Z.X.Li, Y.Liu, C.J.Vavricka, J.X.Qi, G.F.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.03 / 2.20
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 122.496, 122.496, 110.504, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 24.6

Other elements in 4fvk:

The structure of Structural and Functional Characterization of Neuraminidase-Like Molecule N10 Derived From Bat Influenza A Virus also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural and Functional Characterization of Neuraminidase-Like Molecule N10 Derived From Bat Influenza A Virus (pdb code 4fvk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structural and Functional Characterization of Neuraminidase-Like Molecule N10 Derived From Bat Influenza A Virus, PDB code: 4fvk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4fvk

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Zinc binding site 1 out of 6 in the Structural and Functional Characterization of Neuraminidase-Like Molecule N10 Derived From Bat Influenza A Virus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural and Functional Characterization of Neuraminidase-Like Molecule N10 Derived From Bat Influenza A Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:14.4
occ:1.00
 OE1 A:GLU442 2.0 23.4 1.0
O A:HOH784 2.0 30.0 1.0
O A:HOH601 2.1 40.5 1.0
O A:HOH662 2.1 40.5 1.0
OG A:SER166 2.7 20.1 1.0
CD A:GLU442 2.7 26.8 1.0
OE2 A:GLU442 2.8 27.4 1.0
CB A:SER166 3.7 21.9 1.0
O A:HOH673 3.8 40.5 1.0
CG A:GLU442 4.2 26.1 1.0
N A:SER166 4.2 19.1 1.0
O A:ILE115 4.3 20.8 1.0
NE1 A:TRP106 4.3 21.3 1.0
CD2 A:LEU114 4.5 25.2 1.0
NZ A:LYS131 4.6 21.9 1.0
CA A:SER166 4.6 21.1 1.0
CD1 A:TRP106 4.7 21.1 1.0
CG A:LEU114 4.8 25.7 1.0
OG A:SER117 4.8 20.4 1.0
O A:HOH642 4.8 40.5 1.0

Zinc binding site 2 out of 6 in 4fvk

Go back to Zinc Binding Sites List in 4fvk
Zinc binding site 2 out of 6 in the Structural and Functional Characterization of Neuraminidase-Like Molecule N10 Derived From Bat Influenza A Virus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural and Functional Characterization of Neuraminidase-Like Molecule N10 Derived From Bat Influenza A Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:53.3
occ:1.00
 OE1 A:GLU386 2.0 46.1 1.0
O A:HOH613 2.1 40.5 1.0
O A:HOH732 2.1 40.5 1.0
OG1 A:THR388 2.6 42.6 1.0
CD A:GLU386 3.0 49.8 1.0
CB A:THR388 3.4 38.9 1.0
CG A:GLU386 3.5 44.6 1.0
ND2 A:ASN381 4.0 37.7 1.0
OE2 A:GLU386 4.1 50.0 1.0
CG2 A:THR388 4.1 40.5 1.0
O A:HOH686 4.5 40.5 1.0
O A:HOH781 4.5 40.9 1.0
CA A:THR388 4.6 40.5 1.0
N A:THR388 4.7 36.5 1.0
O A:HOH709 4.7 40.5 1.0
CB A:GLU386 5.0 43.5 1.0

Zinc binding site 3 out of 6 in 4fvk

Go back to Zinc Binding Sites List in 4fvk
Zinc binding site 3 out of 6 in the Structural and Functional Characterization of Neuraminidase-Like Molecule N10 Derived From Bat Influenza A Virus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural and Functional Characterization of Neuraminidase-Like Molecule N10 Derived From Bat Influenza A Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:49.7
occ:1.00
 O A:HOH688 2.0 40.5 1.0
O A:HOH643 2.1 40.5 1.0
O A:TRP154 2.4 33.2 1.0
OE2 A:GLU156 2.7 37.3 1.0
OE1 A:GLU156 3.2 43.9 1.0
CD A:GLU156 3.3 37.7 1.0
C A:TRP154 3.4 33.0 1.0
CA A:TRP154 3.8 33.8 1.0
CB A:TRP154 4.0 35.5 1.0
NH2 A:ARG178 4.4 51.8 1.0
N A:GLU155 4.5 28.8 1.0
CG A:GLU156 4.7 30.8 1.0
O A:HOH744 4.7 40.9 1.0
CA A:GLU155 4.8 28.6 1.0

Zinc binding site 4 out of 6 in 4fvk

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Zinc binding site 4 out of 6 in the Structural and Functional Characterization of Neuraminidase-Like Molecule N10 Derived From Bat Influenza A Virus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural and Functional Characterization of Neuraminidase-Like Molecule N10 Derived From Bat Influenza A Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:25.3
occ:1.00
 O B:HOH605 2.0 40.5 1.0
O B:HOH663 2.0 40.9 1.0
OE1 B:GLU442 2.1 37.4 1.0
O B:HOH601 2.1 40.5 1.0
OG B:SER166 2.7 32.5 1.0
OE2 B:GLU442 2.7 39.6 1.0
CD B:GLU442 2.7 40.4 1.0
O B:HOH616 3.7 40.5 1.0
CB B:SER166 3.8 33.3 1.0
O B:HOH680 3.9 40.9 1.0
CG B:GLU442 4.2 40.4 1.0
N B:SER166 4.3 32.4 1.0
O B:ILE115 4.4 32.6 1.0
NE1 B:TRP106 4.5 41.7 1.0
OG B:SER117 4.6 33.8 1.0
CA B:SER166 4.7 32.9 1.0
NZ B:LYS131 4.7 37.8 1.0
CD1 B:LEU114 4.7 37.4 1.0
CD2 B:LEU114 4.7 36.3 1.0
CG B:LEU114 4.8 33.6 1.0
CD1 B:TRP106 4.9 41.5 1.0

Zinc binding site 5 out of 6 in 4fvk

Go back to Zinc Binding Sites List in 4fvk
Zinc binding site 5 out of 6 in the Structural and Functional Characterization of Neuraminidase-Like Molecule N10 Derived From Bat Influenza A Virus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structural and Functional Characterization of Neuraminidase-Like Molecule N10 Derived From Bat Influenza A Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:86.2
occ:1.00
 OE1 B:GLU386 2.0 96.8 1.0
O B:HOH696 2.1 30.0 1.0
O B:HOH635 2.1 40.5 1.0
OG1 B:THR388 2.6 92.8 1.0
CD B:GLU386 2.9 96.9 1.0
CG B:GLU386 3.3 92.3 1.0
CB B:THR388 3.4 87.4 1.0
OE2 B:GLU386 3.9 100.0 1.0
O B:HOH692 4.2 40.9 1.0
ND2 B:ASN381 4.2 79.4 1.0
CG2 B:THR388 4.3 85.5 1.0
CA B:THR388 4.7 85.7 1.0
N B:THR388 4.7 84.2 1.0
CB B:GLU386 4.8 91.4 1.0

Zinc binding site 6 out of 6 in 4fvk

Go back to Zinc Binding Sites List in 4fvk
Zinc binding site 6 out of 6 in the Structural and Functional Characterization of Neuraminidase-Like Molecule N10 Derived From Bat Influenza A Virus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structural and Functional Characterization of Neuraminidase-Like Molecule N10 Derived From Bat Influenza A Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:61.1
occ:1.00
 O B:HOH660 2.1 40.5 1.0
O B:TRP154 2.4 53.1 1.0
OE2 B:GLU156 2.8 61.0 1.0
OE1 B:GLU156 3.0 65.9 1.0
CD B:GLU156 3.3 61.8 1.0
C B:TRP154 3.5 53.4 1.0
CA B:TRP154 4.0 54.7 1.0
CB B:TRP154 4.2 54.7 1.0
N B:GLU155 4.6 49.7 1.0
CG B:GLU156 4.7 55.1 1.0
NH2 B:ARG178 4.8 68.6 1.0
CA B:GLU155 4.9 50.0 1.0
N B:GLU156 5.0 53.5 1.0

Reference:

Q.Li, X.M.Sun, Z.X.Li, Y.Liu, C.J.Vavricka, J.X.Qi, G.F.Gao. Structural and Functional Characterization of Neuraminidase-Like Molecule N10 Derived From Bat Influenza A Virus Proc.Natl.Acad.Sci.Usa V. 109 18897 2012.
ISSN: ISSN 0027-8424
PubMed: 23012237
DOI: 10.1073/PNAS.1211037109
Page generated: Sat Oct 26 22:56:44 2024

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