Zinc in PDB 8cnl: Lymphocytic Choriomeningitis Virus 3'-5' Exonuclease Domain of Nucleoprotein

The structure of Lymphocytic Choriomeningitis Virus 3'-5' Exonuclease Domain of Nucleoprotein, PDB code: 8cnl was solved by M.Spiliopoulou, N.Papageorgiou, F.Ferron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	81.15 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	95.076, 95.066, 129.13, 90, 97.54, 90
R / Rfree (%)	27.3 / 28

The binding sites of Zinc atom in the Lymphocytic Choriomeningitis Virus 3'-5' Exonuclease Domain of Nucleoprotein (pdb code 8cnl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Lymphocytic Choriomeningitis Virus 3'-5' Exonuclease Domain of Nucleoprotein, PDB code: 8cnl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Lymphocytic Choriomeningitis Virus 3'-5' Exonuclease Domain of Nucleoprotein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Lymphocytic Choriomeningitis Virus 3'-5' Exonuclease Domain of Nucleoprotein within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn900 b:55.6 occ:1.00 NE2 B:HIS502 1.9 59.9 1.0 OE2 B:GLU392 2.0 52.9 1.0 SG B:CYS518 2.3 54.3 1.0 SG B:CYS499 2.4 44.2 1.0 CE1 B:HIS502 2.8 60.0 1.0 CD B:GLU392 2.9 52.2 1.0 O B:CYS518 2.9 69.4 1.0 CD2 B:HIS502 3.0 63.7 1.0 OE1 B:GLU392 3.1 52.4 1.0 CB B:CYS518 3.3 54.8 1.0 CA B:CYS518 3.4 51.4 1.0 CB B:CYS499 3.5 47.3 1.0 C B:CYS518 3.6 57.1 1.0 ND1 B:HIS502 3.9 60.4 1.0 CG B:HIS502 4.0 61.4 1.0 CE1 B:HIS405 4.1 44.1 1.0 CE B:MET426 4.4 51.2 1.0 CG B:GLU392 4.4 48.0 1.0 NE2 B:HIS405 4.5 42.2 1.0 CB B:MET501 4.7 56.8 1.0 CE1 B:TYR407 4.7 51.2 1.0 OH B:TYR407 4.7 52.1 1.0 N B:CYS518 4.8 52.2 1.0 CA B:CYS499 4.9 54.3 1.0 N B:ALA519 4.9 46.2 1.0 O B:HIS517 5.0 60.0 1.0

Zinc binding site 2 out of 8 in the Lymphocytic Choriomeningitis Virus 3'-5' Exonuclease Domain of Nucleoprotein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Lymphocytic Choriomeningitis Virus 3'-5' Exonuclease Domain of Nucleoprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn900 b:48.6 occ:1.00 NE2 A:HIS502 1.9 61.7 1.0 OE2 A:GLU392 2.1 50.9 1.0 SG A:CYS518 2.3 42.5 1.0 SG A:CYS499 2.4 39.8 1.0 CE1 A:HIS502 2.8 56.8 1.0 CD A:GLU392 3.0 48.7 1.0 CD2 A:HIS502 3.0 64.9 1.0 O A:CYS518 3.0 66.2 1.0 OE1 A:GLU392 3.2 50.8 1.0 CB A:CYS518 3.3 54.0 1.0 CA A:CYS518 3.5 51.5 1.0 CB A:CYS499 3.5 43.3 1.0 C A:CYS518 3.7 56.4 1.0 ND1 A:HIS502 3.9 60.0 1.0 CG A:HIS502 4.0 62.1 1.0 CE1 A:HIS405 4.1 49.2 1.0 CE A:MET426 4.4 56.7 1.0 CG A:GLU392 4.4 45.5 1.0 NE2 A:HIS405 4.5 46.7 1.0 CB A:MET501 4.6 47.4 1.0 CE1 A:TYR407 4.6 47.8 1.0 OH A:TYR407 4.7 49.5 1.0 N A:CYS518 4.9 51.8 1.0 CA A:CYS499 4.9 44.8 1.0 N A:ALA519 5.0 45.0 1.0

Zinc binding site 3 out of 8 in the Lymphocytic Choriomeningitis Virus 3'-5' Exonuclease Domain of Nucleoprotein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Lymphocytic Choriomeningitis Virus 3'-5' Exonuclease Domain of Nucleoprotein within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn900 b:42.6 occ:1.00 NE2 C:HIS502 1.9 59.8 1.0 OE2 C:GLU392 2.0 51.0 1.0 SG C:CYS518 2.3 50.0 1.0 SG C:CYS499 2.4 42.9 1.0 CE1 C:HIS502 2.8 55.6 1.0 CD C:GLU392 2.9 51.0 1.0 O C:CYS518 3.0 67.9 1.0 CD2 C:HIS502 3.0 64.4 1.0 OE1 C:GLU392 3.1 52.9 1.0 CB C:CYS518 3.3 51.1 1.0 CA C:CYS518 3.5 49.3 1.0 CB C:CYS499 3.6 46.4 1.0 C C:CYS518 3.7 58.5 1.0 ND1 C:HIS502 3.9 58.2 1.0 CG C:HIS502 4.1 60.4 1.0 CE1 C:HIS405 4.1 46.9 1.0 CG C:GLU392 4.4 47.5 1.0 CE C:MET426 4.4 54.5 1.0 NE2 C:HIS405 4.5 46.6 1.0 CB C:MET501 4.6 49.8 1.0 CE1 C:TYR407 4.6 51.2 1.0 OH C:TYR407 4.7 47.8 1.0 N C:CYS518 4.9 52.7 1.0 CA C:CYS499 4.9 44.3 1.0 N C:ALA519 5.0 49.6 1.0

Zinc binding site 4 out of 8 in the Lymphocytic Choriomeningitis Virus 3'-5' Exonuclease Domain of Nucleoprotein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Lymphocytic Choriomeningitis Virus 3'-5' Exonuclease Domain of Nucleoprotein within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn900 b:49.7 occ:1.00 NE2 D:HIS502 1.9 65.4 1.0 OE2 D:GLU392 2.1 54.6 1.0 SG D:CYS518 2.3 46.7 1.0 SG D:CYS499 2.3 42.7 1.0 CE1 D:HIS502 2.8 59.9 1.0 CD2 D:HIS502 2.9 64.6 1.0 CD D:GLU392 3.0 52.5 1.0 O D:CYS518 3.0 66.8 1.0 OE1 D:GLU392 3.2 53.2 1.0 CB D:CYS518 3.3 60.0 1.0 CA D:CYS518 3.4 53.7 1.0 CB D:CYS499 3.5 49.6 1.0 C D:CYS518 3.7 57.0 1.0 ND1 D:HIS502 3.9 63.4 1.0 CG D:HIS502 4.0 63.0 1.0 CE1 D:HIS405 4.1 50.0 1.0 CE D:MET426 4.4 49.5 1.0 CG D:GLU392 4.4 45.4 1.0 NE2 D:HIS405 4.5 47.9 1.0 CB D:MET501 4.6 57.6 1.0 CE1 D:TYR407 4.7 49.7 1.0 OH D:TYR407 4.7 54.6 1.0 N D:CYS518 4.8 56.0 1.0 CA D:CYS499 4.9 51.1 1.0 N D:ALA519 5.0 54.8 1.0 O D:HIS517 5.0 67.0 1.0

Zinc binding site 5 out of 8 in the Lymphocytic Choriomeningitis Virus 3'-5' Exonuclease Domain of Nucleoprotein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Lymphocytic Choriomeningitis Virus 3'-5' Exonuclease Domain of Nucleoprotein within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn900 b:56.9 occ:1.00 NE2 E:HIS502 1.9 58.7 1.0 OE2 E:GLU392 2.1 52.1 1.0 SG E:CYS518 2.3 54.1 1.0 SG E:CYS499 2.4 56.0 1.0 CE1 E:HIS502 2.8 61.8 1.0 CD E:GLU392 2.9 48.1 1.0 O E:CYS518 3.0 70.7 1.0 CD2 E:HIS502 3.0 57.3 1.0 OE1 E:GLU392 3.1 46.6 1.0 CB E:CYS518 3.3 52.5 1.0 CA E:CYS518 3.4 58.1 1.0 CB E:CYS499 3.6 55.6 1.0 C E:CYS518 3.6 59.7 1.0 ND1 E:HIS502 3.9 67.6 1.0 CG E:HIS502 4.1 65.0 1.0 CE1 E:HIS405 4.1 44.9 1.0 CE E:MET426 4.4 65.1 1.0 CG E:GLU392 4.4 49.2 1.0 NE2 E:HIS405 4.5 45.1 1.0 CB E:MET501 4.6 61.8 1.0 CE1 E:TYR407 4.7 48.2 1.0 OH E:TYR407 4.7 46.1 1.0 N E:CYS518 4.9 58.0 1.0 CA E:CYS499 4.9 64.0 1.0 N E:ALA519 4.9 51.7 1.0 O E:HIS517 5.0 68.4 1.0

Zinc binding site 6 out of 8 in the Lymphocytic Choriomeningitis Virus 3'-5' Exonuclease Domain of Nucleoprotein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Lymphocytic Choriomeningitis Virus 3'-5' Exonuclease Domain of Nucleoprotein within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn900 b:57.2 occ:1.00 NE2 F:HIS502 1.9 63.5 1.0 OE2 F:GLU392 2.1 52.1 1.0 SG F:CYS518 2.3 59.2 1.0 SG F:CYS499 2.4 62.2 1.0 CE1 F:HIS502 2.8 63.1 1.0 CD2 F:HIS502 3.0 62.9 1.0 CD F:GLU392 3.0 52.6 1.0 O F:CYS518 3.0 70.4 1.0 OE1 F:GLU392 3.2 47.5 1.0 CB F:CYS518 3.3 56.5 1.0 CA F:CYS518 3.5 59.4 1.0 CB F:CYS499 3.5 61.9 1.0 C F:CYS518 3.7 63.8 1.0 ND1 F:HIS502 3.9 69.1 1.0 CG F:HIS502 4.0 67.2 1.0 CE1 F:HIS405 4.1 43.5 1.0 CE F:MET426 4.4 69.4 1.0 CG F:GLU392 4.4 51.0 1.0 NE2 F:HIS405 4.5 45.6 1.0 CB F:MET501 4.6 63.2 1.0 CE1 F:TYR407 4.7 50.1 1.0 OH F:TYR407 4.7 53.8 1.0 N F:CYS518 4.9 61.3 1.0 CA F:CYS499 4.9 67.8 1.0 N F:ALA519 5.0 57.8 1.0 O F:HIS517 5.0 65.0 1.0

Zinc binding site 7 out of 8 in the Lymphocytic Choriomeningitis Virus 3'-5' Exonuclease Domain of Nucleoprotein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Lymphocytic Choriomeningitis Virus 3'-5' Exonuclease Domain of Nucleoprotein within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn900 b:79.9 occ:1.00 NE2 G:HIS502 1.9 69.9 1.0 OE2 G:GLU392 2.0 58.8 1.0 SG G:CYS518 2.4 64.9 1.0 SG G:CYS499 2.4 68.7 1.0 CE1 G:HIS502 2.8 70.3 1.0 CD G:GLU392 3.0 59.6 1.0 CD2 G:HIS502 3.0 74.5 1.0 O G:CYS518 3.0 72.9 1.0 OE1 G:GLU392 3.2 54.7 1.0 CB G:CYS518 3.3 63.2 1.0 CA G:CYS518 3.5 64.1 1.0 CB G:CYS499 3.5 61.2 1.0 C G:CYS518 3.7 63.1 1.0 ND1 G:HIS502 3.9 75.7 1.0 CG G:HIS502 4.1 75.8 1.0 CE1 G:HIS405 4.1 48.3 1.0 CE G:MET426 4.4 80.8 1.0 CG G:GLU392 4.4 53.8 1.0 NE2 G:HIS405 4.4 50.2 1.0 CB G:MET501 4.6 73.0 1.0 CE1 G:TYR407 4.6 50.6 1.0 OH G:TYR407 4.6 51.6 1.0 CA G:CYS499 4.9 72.0 1.0 N G:CYS518 4.9 70.2 1.0

Zinc binding site 8 out of 8 in the Lymphocytic Choriomeningitis Virus 3'-5' Exonuclease Domain of Nucleoprotein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Lymphocytic Choriomeningitis Virus 3'-5' Exonuclease Domain of Nucleoprotein within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn900 b:75.5 occ:1.00 NE2 H:HIS502 1.9 67.7 1.0 OE2 H:GLU392 2.0 63.4 1.0 SG H:CYS518 2.4 65.0 1.0 SG H:CYS499 2.4 61.2 1.0 CE1 H:HIS502 2.8 69.2 1.0 CD H:GLU392 2.9 58.0 1.0 O H:CYS518 3.0 74.9 1.0 CD2 H:HIS502 3.0 68.9 1.0 OE1 H:GLU392 3.1 49.2 1.0 CB H:CYS518 3.3 60.4 1.0 CA H:CYS518 3.5 63.2 1.0 CB H:CYS499 3.6 58.7 1.0 C H:CYS518 3.7 64.4 1.0 ND1 H:HIS502 3.9 75.9 1.0 CE1 H:HIS405 4.1 49.2 1.0 CG H:HIS502 4.1 72.2 1.0 CG H:GLU392 4.4 52.1 1.0 CE H:MET426 4.4 76.4 1.0 NE2 H:HIS405 4.4 53.8 1.0 CB H:MET501 4.6 65.6 1.0 CE1 H:TYR407 4.6 50.8 1.0 OH H:TYR407 4.6 52.8 1.0 N H:CYS518 4.9 65.7 1.0 CA H:CYS499 4.9 68.1 1.0 N H:ALA519 5.0 59.6 1.0

M.Spiliopoulou, N.Papageorgiou, F.Ferron. Lymphocytic Choriomeningitis Virus 3'-5' Exonuclease Domain of Nucleoprotein To Be Published.