Zinc in PDB 5ccv: Crystal Structure of Full-Length NS5 From Dengue Virus Type 3

All present enzymatic activity of Crystal Structure of Full-Length NS5 From Dengue Virus Type 3:
2.1.1.56; 2.1.1.57; 2.7.7.48;

The structure of Crystal Structure of Full-Length NS5 From Dengue Virus Type 3, PDB code: 5ccv was solved by V.J.Klema, K.H.Choi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.22 / 3.60
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	215.314, 215.314, 480.683, 90.00, 90.00, 120.00
R / Rfree (%)	23.8 / 27.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Full-Length NS5 From Dengue Virus Type 3 (pdb code 5ccv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Crystal Structure of Full-Length NS5 From Dengue Virus Type 3, PDB code: 5ccv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the Crystal Structure of Full-Length NS5 From Dengue Virus Type 3


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 Full-Length NS5 From Dengue Virus Type 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:76.0 occ:1.00 NE2 A:HIS712 2.0 76.1 1.0 NE2 A:HIS714 2.1 76.1 1.0 SG A:CYS728 2.3 76.3 1.0 SG A:CYS847 2.4 0.8 1.0 CD2 A:HIS712 2.8 76.3 1.0 CD2 A:HIS714 3.0 76.4 1.0 CE1 A:HIS712 3.1 77.6 1.0 CE1 A:HIS714 3.2 75.9 1.0 CB A:CYS728 3.3 76.8 1.0 CB A:CYS847 3.6 75.3 1.0 CG A:HIS712 4.0 76.4 1.0 ND1 A:HIS712 4.1 76.3 1.0 CG A:HIS714 4.2 76.5 1.0 ND1 A:HIS714 4.3 76.1 1.0 CD2 A:LEU839 4.4 75.9 1.0 CA A:CYS728 4.6 77.0 1.0 N A:ARG729 4.7 76.7 1.0 C A:CYS728 4.7 76.9 1.0 CA A:CYS847 4.9 75.1 1.0

Zinc binding site 2 out of 16 in the Crystal Structure of Full-Length NS5 From Dengue Virus Type 3


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 Full-Length NS5 From Dengue Virus Type 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:0.7 occ:1.00 OE1 A:GLU437 2.1 89.3 1.0 NE2 A:HIS441 2.1 88.9 1.0 SG A:CYS449 2.4 87.8 1.0 SG A:CYS446 2.4 0.4 1.0 CE1 A:HIS441 3.0 88.7 1.0 CD A:GLU437 3.1 89.6 1.0 CD2 A:HIS441 3.2 89.4 1.0 CG A:GLU437 3.4 89.7 1.0 CB A:CYS449 3.5 0.0 1.0 N A:GLY447 3.5 89.2 1.0 CB A:CYS446 3.5 88.8 1.0 CA A:CYS446 3.6 90.8 1.0 N A:CYS449 3.7 0.1 1.0 N A:SER448 4.0 88.8 1.0 C A:CYS446 4.0 91.8 1.0 ND1 A:HIS441 4.2 89.0 1.0 OE2 A:GLU437 4.2 90.0 1.0 CA A:CYS449 4.2 0.2 1.0 CG A:HIS441 4.3 89.5 1.0 CA A:GLY447 4.6 92.6 1.0 C A:SER448 4.6 89.8 1.0 O A:LYS445 4.7 90.5 1.0 C A:GLY447 4.7 91.9 1.0 CA A:SER448 4.8 88.6 1.0 O A:GLU437 4.8 0.7 1.0 N A:CYS446 4.9 89.4 1.0 CB A:GLU437 4.9 92.8 1.0

Zinc binding site 3 out of 16 in the Crystal Structure of Full-Length NS5 From Dengue Virus Type 3


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 Full-Length NS5 From Dengue Virus Type 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:90.4 occ:1.00 OE1 B:GLU437 2.0 91.3 1.0 NE2 B:HIS441 2.2 90.9 1.0 SG B:CYS449 2.3 89.6 1.0 SG B:CYS446 2.3 90.1 1.0 CE1 B:HIS441 3.0 90.7 1.0 CD B:GLU437 3.1 91.8 1.0 CD2 B:HIS441 3.3 91.5 1.0 CB B:CYS449 3.4 89.0 1.0 CB B:CYS446 3.4 90.6 1.0 CG B:GLU437 3.7 91.8 1.0 N B:CYS449 3.8 89.7 1.0 CA B:CYS446 3.8 91.3 1.0 N B:GLY447 4.0 91.5 1.0 OE2 B:GLU437 4.2 92.2 1.0 N B:SER448 4.2 91.0 1.0 CA B:CYS449 4.2 89.1 1.0 ND1 B:HIS441 4.2 91.1 1.0 CG B:HIS441 4.4 91.5 1.0 C B:CYS446 4.4 91.5 1.0 C B:SER448 4.6 0.8 1.0 OG1 B:THR571 4.8 88.5 1.0 CA B:SER448 4.9 95.2 1.0 O B:LYS445 4.9 0.7 1.0

Zinc binding site 4 out of 16 in the Crystal Structure of Full-Length NS5 From Dengue Virus Type 3


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 Full-Length NS5 From Dengue Virus Type 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:77.5 occ:1.00 NE2 B:HIS712 2.0 77.4 1.0 NE2 B:HIS714 2.1 77.6 1.0 SG B:CYS728 2.2 77.9 1.0 SG B:CYS847 2.3 76.9 1.0 CD2 B:HIS714 2.8 78.0 1.0 CD2 B:HIS712 2.8 77.6 1.0 CE1 B:HIS712 3.0 77.4 1.0 CB B:CYS728 3.1 78.3 1.0 CE1 B:HIS714 3.2 77.4 1.0 CB B:CYS847 3.7 76.8 1.0 CG B:HIS712 4.0 77.7 1.0 ND1 B:HIS712 4.1 77.5 1.0 CG B:HIS714 4.1 78.0 1.0 ND1 B:HIS714 4.2 77.7 1.0 CD1 B:LEU839 4.4 77.9 1.0 CA B:CYS728 4.4 78.6 1.0 C B:CYS728 4.6 78.4 1.0 N B:ARG729 4.6 78.2 1.0 NH2 B:ARG769 4.8 77.7 1.0 O B:GLU843 4.9 76.5 1.0 CA B:CYS847 5.0 76.5 1.0

Zinc binding site 5 out of 16 in the Crystal Structure of Full-Length NS5 From Dengue Virus Type 3


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 Full-Length NS5 From Dengue Virus Type 3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1001 b:82.6 occ:1.00 NE2 C:HIS441 2.1 82.1 1.0 OE1 C:GLU437 2.1 83.4 1.0 SG C:CYS449 2.2 82.2 1.0 SG C:CYS446 2.2 83.0 1.0 CE1 C:HIS441 2.9 81.6 1.0 CD C:GLU437 3.1 83.6 1.0 CD2 C:HIS441 3.2 82.2 1.0 CB C:CYS449 3.2 82.5 1.0 CB C:CYS446 3.5 83.2 1.0 CG C:GLU437 3.5 83.1 1.0 N C:CYS449 3.6 83.5 1.0 CA C:CYS446 3.9 83.6 1.0 CA C:CYS449 4.0 83.0 1.0 N C:GLY447 4.1 84.3 1.0 ND1 C:HIS441 4.1 81.4 1.0 OE2 C:GLU437 4.2 84.1 1.0 N C:SER448 4.2 84.5 1.0 CG C:HIS441 4.3 81.7 1.0 C C:CYS446 4.5 84.2 1.0 CG2 C:THR571 4.6 81.1 1.0 C C:SER448 4.6 99.2 1.0 CA C:SER448 4.9 98.4 1.0 O C:LYS445 5.0 82.9 1.0

Zinc binding site 6 out of 16 in the Crystal Structure of Full-Length NS5 From Dengue Virus Type 3


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 Full-Length NS5 From Dengue Virus Type 3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1002 b:76.5 occ:1.00 NE2 C:HIS714 2.1 76.0 1.0 NE2 C:HIS712 2.1 76.3 1.0 SG C:CYS728 2.2 76.8 1.0 SG C:CYS847 2.4 77.0 1.0 CD2 C:HIS714 2.8 75.9 1.0 CD2 C:HIS712 2.9 75.9 1.0 CB C:CYS728 3.1 76.4 1.0 CE1 C:HIS712 3.2 76.4 1.0 CE1 C:HIS714 3.2 75.8 1.0 CB C:CYS847 3.8 77.5 1.0 CG C:HIS714 4.0 75.6 1.0 CG C:HIS712 4.1 75.8 1.0 ND1 C:HIS714 4.2 75.6 1.0 ND1 C:HIS712 4.2 76.2 1.0 CA C:CYS728 4.4 76.5 1.0 CD1 C:LEU839 4.4 92.2 1.0 C C:CYS728 4.6 76.6 1.0 N C:ARG729 4.6 77.0 1.0

Zinc binding site 7 out of 16 in the Crystal Structure of Full-Length NS5 From Dengue Virus Type 3


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 Full-Length NS5 From Dengue Virus Type 3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1001 b:83.1 occ:1.00 NE2 D:HIS441 2.0 83.7 1.0 OE1 D:GLU437 2.1 0.0 1.0 SG D:CYS449 2.3 82.7 1.0 SG D:CYS446 2.3 94.1 1.0 CD2 D:HIS441 3.0 84.1 1.0 CE1 D:HIS441 3.1 83.9 1.0 CD D:GLU437 3.2 0.8 1.0 CB D:CYS446 3.4 82.6 1.0 CB D:CYS449 3.5 81.9 1.0 CA D:CYS446 3.6 83.0 1.0 N D:GLY447 3.6 82.8 1.0 CG D:GLU437 3.6 0.5 1.0 N D:CYS449 3.8 81.9 1.0 N D:SER448 4.1 82.4 1.0 C D:CYS446 4.1 82.7 1.0 CG D:HIS441 4.1 84.6 1.0 ND1 D:HIS441 4.1 84.4 1.0 OE2 D:GLU437 4.2 0.9 1.0 CA D:CYS449 4.3 81.7 1.0 OG D:SER448 4.6 90.8 1.0 O D:LYS445 4.6 84.1 1.0 C D:SER448 4.7 82.0 1.0 CA D:GLY447 4.8 82.6 1.0 CG2 D:THR571 4.8 83.6 1.0 N D:CYS446 4.8 83.3 1.0 CA D:SER448 4.9 82.2 1.0 C D:GLY447 4.9 82.3 1.0 O D:GLU437 5.0 85.2 1.0

Zinc binding site 8 out of 16 in the Crystal Structure of Full-Length NS5 From Dengue Virus Type 3


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 Full-Length NS5 From Dengue Virus Type 3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1002 b:82.6 occ:1.00 NE2 D:HIS712 2.0 82.1 1.0 NE2 D:HIS714 2.1 83.3 1.0 SG D:CYS728 2.3 82.6 1.0 SG D:CYS847 2.4 82.2 1.0 CD2 D:HIS712 2.7 82.5 1.0 CD2 D:HIS714 3.0 83.8 1.0 CB D:CYS728 3.1 83.0 1.0 CE1 D:HIS712 3.1 81.7 1.0 CE1 D:HIS714 3.2 83.5 1.0 CB D:CYS847 3.8 81.8 1.0 CG D:HIS712 4.0 82.2 1.0 ND1 D:HIS712 4.1 81.7 1.0 CG D:HIS714 4.2 84.3 1.0 ND1 D:HIS714 4.2 84.1 1.0 CA D:CYS728 4.4 82.8 1.0 C D:CYS728 4.5 82.2 1.0 N D:ARG729 4.6 81.9 1.0 CD1 D:LEU839 4.6 91.0 1.0 NH2 D:ARG769 4.9 82.1 1.0 CA D:CYS847 5.0 81.4 1.0

Zinc binding site 9 out of 16 in the Crystal Structure of Full-Length NS5 From Dengue Virus Type 3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Full-Length NS5 From Dengue Virus Type 3 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1001 b:0.7 occ:1.00 NE2 E:HIS441 2.0 0.3 1.0 OE1 E:GLU437 2.1 0.7 1.0 SG E:CYS449 2.3 99.6 1.0 SG E:CYS446 2.4 0.4 1.0 CE1 E:HIS441 3.0 99.5 1.0 CD2 E:HIS441 3.0 0.8 1.0 CD E:GLU437 3.2 0.8 1.0 CB E:CYS446 3.4 0.7 1.0 CA E:CYS446 3.4 0.5 1.0 N E:GLY447 3.5 0.9 1.0 CB E:CYS449 3.6 99.5 1.0 CG E:GLU437 3.7 0.2 1.0 C E:CYS446 4.0 0.1 1.0 N E:CYS449 4.1 0.8 1.0 ND1 E:HIS441 4.1 99.5 1.0 CG E:HIS441 4.2 0.1 1.0 OE2 E:GLU437 4.2 0.6 1.0 N E:SER448 4.3 0.4 1.0 O E:LYS445 4.5 0.4 1.0 CA E:CYS449 4.5 99.9 1.0 CA E:GLY447 4.7 0.4 1.0 N E:CYS446 4.7 1.0 1.0 O E:GLU437 4.9 0.8 1.0 C E:GLY447 5.0 0.2 1.0

Zinc binding site 10 out of 16 in the Crystal Structure of Full-Length NS5 From Dengue Virus Type 3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Full-Length NS5 From Dengue Virus Type 3 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1002 b:79.5 occ:1.00 NE2 E:HIS714 2.1 92.0 1.0 NE2 E:HIS712 2.1 92.2 1.0 SG E:CYS728 2.4 80.1 1.0 SG E:CYS847 2.4 87.4 1.0 CD2 E:HIS712 3.0 93.0 1.0 CD2 E:HIS714 3.0 78.9 1.0 CE1 E:HIS714 3.1 0.6 1.0 CE1 E:HIS712 3.1 99.2 1.0 CB E:CYS728 3.3 80.1 1.0 CB E:CYS847 3.6 79.7 1.0 ND1 E:HIS714 4.2 94.6 1.0 CG E:HIS714 4.2 78.5 1.0 CG E:HIS712 4.2 97.7 1.0 ND1 E:HIS712 4.2 0.6 1.0 N E:ARG729 4.5 81.1 1.0 C E:CYS728 4.5 80.9 1.0 CA E:CYS728 4.5 80.6 1.0 CD1 E:LEU839 4.6 85.5 1.0 CA E:CYS847 4.8 79.8 1.0

V.J.Klema, M.Ye, A.Hindupur, T.Teramoto, K.Gottipati, R.Padmanabhan, K.H.Choi. Crystal Structure of Full-Length NS5 From Dengue Virus Type 3 To Be Published.