Zinc in PDB 9bgl: Complex of Zinc Finger Antiviral Protein Rbd and Khnyn Ctd

The structure of Complex of Zinc Finger Antiviral Protein Rbd and Khnyn Ctd, PDB code: 9bgl was solved by J.L.Meagher, J.L.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.00 / 2.29
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.213, 88.001, 94.546, 90, 90, 90
R / Rfree (%)	20.6 / 24.5

The binding sites of Zinc atom in the Complex of Zinc Finger Antiviral Protein Rbd and Khnyn Ctd (pdb code 9bgl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Complex of Zinc Finger Antiviral Protein Rbd and Khnyn Ctd, PDB code: 9bgl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Complex of Zinc Finger Antiviral Protein Rbd and Khnyn Ctd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complex of Zinc Finger Antiviral Protein Rbd and Khnyn Ctd within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:36.8 occ:1.00 NE2 A:HIS86 2.1 39.0 1.0 SG A:CYS82 2.3 51.6 1.0 SG A:CYS73 2.3 34.9 1.0 SG A:CYS78 2.3 50.8 1.0 CD2 A:HIS86 3.1 37.8 1.0 CE1 A:HIS86 3.1 38.9 1.0 CB A:CYS82 3.2 53.2 1.0 CB A:CYS73 3.2 29.2 1.0 CB A:CYS78 3.3 52.0 1.0 CG A:HIS86 4.2 36.3 1.0 ND1 A:HIS86 4.2 38.0 1.0 O A:HOH652 4.2 41.6 1.0 O A:HOH630 4.4 32.5 1.0 CA A:CYS73 4.5 27.8 1.0 CG A:ARG75 4.6 46.1 1.0 CA A:CYS82 4.6 53.8 1.0 NH1 A:ARG80 4.7 64.7 1.0 CA A:CYS78 4.7 53.2 1.0 CZ A:ARG80 4.8 65.3 1.0 O A:HOH617 4.8 45.6 1.0 NE A:ARG80 4.9 64.9 1.0

Zinc binding site 2 out of 5 in the Complex of Zinc Finger Antiviral Protein Rbd and Khnyn Ctd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complex of Zinc Finger Antiviral Protein Rbd and Khnyn Ctd within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:48.0 occ:1.00 NE2 A:HIS110 2.1 56.8 1.0 SG A:CYS96 2.3 66.7 1.0 SG A:CYS88 2.3 44.2 1.0 SG A:CYS106 2.4 52.5 1.0 CE1 A:HIS110 3.1 57.0 1.0 CD2 A:HIS110 3.1 55.8 1.0 CB A:CYS88 3.3 40.2 1.0 CB A:CYS106 3.4 52.7 1.0 CB A:CYS96 3.5 65.8 1.0 CG A:HIS110 4.2 54.9 1.0 ND1 A:HIS110 4.2 56.6 1.0 CB A:ASN91 4.4 49.0 1.0 O A:TYR108 4.4 51.0 1.0 CD2 A:TYR98 4.6 67.6 1.0 CA A:CYS88 4.7 39.6 1.0 CB A:TYR98 4.8 66.9 1.0 CA A:CYS106 4.8 53.6 1.0 CA A:CYS96 4.9 65.6 1.0 N A:ASN91 4.9 47.7 1.0

Zinc binding site 3 out of 5 in the Complex of Zinc Finger Antiviral Protein Rbd and Khnyn Ctd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Complex of Zinc Finger Antiviral Protein Rbd and Khnyn Ctd within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:35.7 occ:1.00 NE2 A:HIS172 2.2 32.1 1.0 SG A:CYS150 2.2 33.8 1.0 SG A:CYS168 2.3 40.6 1.0 SG A:CYS162 2.5 69.5 1.0 CD2 A:HIS172 3.1 30.3 1.0 CB A:CYS150 3.1 31.8 1.0 CE1 A:HIS172 3.2 32.9 1.0 CB A:CYS168 3.3 44.9 1.0 CB A:CYS162 3.3 71.0 1.0 CG A:HIS172 4.2 29.3 1.0 ND1 A:HIS172 4.3 32.2 1.0 OG A:SER152 4.5 45.3 1.0 O A:ARG170 4.5 31.9 1.0 CA A:CYS150 4.6 32.0 1.0 CA A:CYS168 4.7 46.2 1.0 CA A:CYS162 4.7 72.0 1.0 O A:HOH711 4.8 60.7 1.0

Zinc binding site 4 out of 5 in the Complex of Zinc Finger Antiviral Protein Rbd and Khnyn Ctd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Complex of Zinc Finger Antiviral Protein Rbd and Khnyn Ctd within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:32.4 occ:1.00 NE2 A:HIS191 2.1 23.1 1.0 SG A:CYS182 2.3 49.8 1.0 SG A:CYS174 2.3 30.8 1.0 SG A:CYS187 2.4 43.9 1.0 CE1 A:HIS191 3.0 24.1 1.0 CD2 A:HIS191 3.2 23.1 1.0 CB A:CYS174 3.2 28.7 1.0 CB A:CYS182 3.5 48.7 1.0 CB A:CYS187 3.5 45.7 1.0 ND1 A:HIS191 4.2 23.4 1.0 CG A:HIS191 4.2 22.8 1.0 O A:ARG189 4.3 35.1 1.0 O A:HOH605 4.5 33.7 1.0 CB A:PHE177 4.5 27.3 1.0 CA A:CYS174 4.7 28.1 1.0 N A:PHE177 4.7 29.2 1.0 CA A:CYS182 4.8 48.9 1.0 CB A:ARG189 4.9 39.2 1.0 CA A:CYS187 4.9 47.1 1.0

Zinc binding site 5 out of 5 in the Complex of Zinc Finger Antiviral Protein Rbd and Khnyn Ctd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Complex of Zinc Finger Antiviral Protein Rbd and Khnyn Ctd within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:24.6 occ:1.00 NE2 A:HIS17 2.1 25.4 1.0 NE2 B:HIS692 2.1 21.8 1.0 OE2 A:GLU29 2.1 40.9 1.0 O A:HOH706 2.4 24.9 1.0 CD A:GLU29 2.8 37.2 1.0 OE1 A:GLU29 2.9 37.0 1.0 CE1 A:HIS17 2.9 26.4 1.0 CD2 B:HIS692 3.0 21.2 1.0 CE1 B:HIS692 3.2 21.6 1.0 CD2 A:HIS17 3.2 24.5 1.0 ND1 A:HIS17 4.1 26.3 1.0 CG B:HIS692 4.2 20.7 1.0 CG A:HIS17 4.2 24.1 1.0 ND1 B:HIS692 4.2 22.3 1.0 CG A:GLU29 4.3 30.6 1.0 CG2 A:ILE13 4.4 18.6 1.0 O A:HOH700 4.4 42.4 1.0 CB A:GLU29 4.9 27.7 1.0 O B:HOH916 4.9 30.3 1.0

J.A.Bohn, J.L.Meagher, M.A.Takata, D.Goncalves-Carneiro, Z.C.Yeoh, M.D.Ohi, J.L.Smith, P.D.Bieniasz. Functional Anatomy of Zinc Finger Antiviral Protein Complexes. Nat Commun V. 15 10834 2024.
ISSN: ESSN 2041-1723
PubMed: 39738020
DOI: 10.1038/S41467-024-55192-Z