Zinc in PDB 5i72: Crystal Structure of the Oligomeric Form of the Lassa Virus Matrix Protein Z

The structure of Crystal Structure of the Oligomeric Form of the Lassa Virus Matrix Protein Z, PDB code: 5i72 was solved by K.Hastie, M.Zandonatti, T.Liu, S.Li, V.Woods Jr, E.O.Saphire, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.22 / 2.90
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	116.961, 116.961, 82.544, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 20.9

The binding sites of Zinc atom in the Crystal Structure of the Oligomeric Form of the Lassa Virus Matrix Protein Z (pdb code 5i72). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Oligomeric Form of the Lassa Virus Matrix Protein Z, PDB code: 5i72:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Oligomeric Form of the Lassa Virus Matrix Protein Z


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 the Oligomeric Form of the Lassa Virus Matrix Protein Z within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:98.0 occ:1.00 SG A:CYS34 2.3 87.4 1.0 SG A:CYS53 2.3 76.5 1.0 SG A:CYS50 2.4 87.0 1.0 SG A:CYS31 2.4 79.6 1.0 CB A:CYS34 2.9 77.4 1.0 CB A:CYS31 3.1 61.7 1.0 CB A:CYS53 3.3 75.8 1.0 CB A:CYS50 3.6 64.9 1.0 N A:CYS34 3.7 66.3 1.0 CA A:CYS34 3.9 69.9 1.0 N A:CYS50 4.2 84.3 1.0 CA A:CYS50 4.4 78.4 1.0 CA A:CYS53 4.5 75.9 1.0 N A:CYS53 4.5 90.7 1.0 CA A:CYS31 4.6 78.0 1.0 CB A:SER33 4.6 69.5 1.0 CB A:GLU37 4.7 90.0 1.0 C A:SER33 4.7 75.1 1.0 C A:CYS34 4.7 65.7 1.0 OG A:SER33 4.8 70.0 1.0 O A:CYS31 4.9 70.9 1.0 C A:CYS31 5.0 74.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Oligomeric Form of the Lassa Virus Matrix Protein Z


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 the Oligomeric Form of the Lassa Virus Matrix Protein Z within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:97.4 occ:1.00 NE2 A:HIS47 2.1 72.5 1.0 SG A:CYS67 2.3 74.8 1.0 SG A:CYS44 2.4 83.1 1.0 SG A:CYS64 2.4 73.8 1.0 CD2 A:HIS47 3.0 72.7 1.0 CE1 A:HIS47 3.0 68.1 1.0 CB A:CYS64 3.2 67.8 1.0 CB A:CYS67 3.4 58.6 1.0 CB A:CYS44 3.5 83.7 1.0 N A:CYS67 4.0 59.7 1.0 ND1 A:HIS47 4.1 70.5 1.0 CG A:HIS47 4.1 63.2 1.0 ND2 A:ASN45 4.3 86.6 1.0 CA A:CYS67 4.3 61.5 1.0 N A:ASN45 4.3 75.4 1.0 CB A:ILE66 4.6 60.5 1.0 CA A:CYS64 4.7 61.9 1.0 CA A:CYS44 4.8 79.3 1.0 CD1 A:LEU49 4.9 63.5 1.0 C A:ILE66 4.9 58.3 1.0 O A:MET69 4.9 86.5 1.0 C A:CYS44 5.0 98.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Oligomeric Form of the Lassa Virus Matrix Protein Z


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 the Oligomeric Form of the Lassa Virus Matrix Protein Z within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:92.7 occ:1.00 SG B:CYS53 2.3 72.8 1.0 SG B:CYS34 2.3 83.2 1.0 SG B:CYS31 2.4 76.0 1.0 SG B:CYS50 2.4 84.9 1.0 CB B:CYS34 3.1 80.2 1.0 CB B:CYS31 3.1 55.8 1.0 CB B:CYS53 3.3 75.8 1.0 CB B:CYS50 3.6 64.0 1.0 N B:CYS34 3.7 64.8 1.0 CA B:CYS34 4.0 68.3 1.0 N B:CYS50 4.2 78.0 1.0 CA B:CYS50 4.5 73.5 1.0 CA B:CYS53 4.5 74.7 1.0 CB B:GLU37 4.5 87.3 1.0 CB B:SER33 4.5 67.6 1.0 CA B:CYS31 4.5 75.4 1.0 N B:CYS53 4.5 91.0 1.0 C B:SER33 4.7 74.6 1.0 OG B:SER33 4.8 71.9 1.0 O B:CYS31 4.8 72.1 1.0 C B:CYS34 4.8 67.3 1.0 C B:CYS31 4.9 76.8 1.0 CA B:SER33 5.0 74.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Oligomeric Form of the Lassa Virus Matrix Protein Z


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 the Oligomeric Form of the Lassa Virus Matrix Protein Z within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:91.0 occ:1.00 NE2 B:HIS47 2.0 66.1 1.0 SG B:CYS67 2.3 77.0 1.0 SG B:CYS44 2.4 85.4 1.0 SG B:CYS64 2.4 70.6 1.0 CE1 B:HIS47 3.0 69.5 1.0 CD2 B:HIS47 3.1 71.8 1.0 CB B:CYS64 3.1 65.7 1.0 CB B:CYS67 3.4 60.0 1.0 CB B:CYS44 3.5 84.3 1.0 N B:CYS67 3.9 64.4 1.0 ND1 B:HIS47 4.1 67.9 1.0 CG B:HIS47 4.2 64.4 1.0 CA B:CYS67 4.2 61.9 1.0 ND2 B:ASN45 4.3 89.3 1.0 N B:ASN45 4.4 73.0 1.0 CB B:ILE66 4.6 59.9 1.0 CA B:CYS64 4.6 56.7 1.0 CA B:CYS44 4.7 80.0 1.0 C B:ILE66 4.8 60.4 1.0 C B:CYS67 4.9 62.9 1.0 CD1 B:LEU49 5.0 63.1 1.0 O B:MET69 5.0 81.6 1.0 C B:CYS44 5.0 94.1 1.0

K.M.Hastie, M.Zandonatti, T.Liu, S.Li, V.L.Woods, E.O.Saphire. Crystal Structure of the Oligomeric Form of Lassa Virus Matrix Protein Z. J.Virol. V. 90 4556 2016.
ISSN: ESSN 1098-5514
PubMed: 26912609
DOI: 10.1128/JVI.02896-15