Zinc in PDB 6l1w: Zinc-Finger Antiviral Protein (Zap) Bound to Rna

The structure of Zinc-Finger Antiviral Protein (Zap) Bound to Rna, PDB code: 6l1w was solved by X.Luo, X.Wang, Y.Gao, J.Zhu, S.Liu, G.Gao, P.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.27 / 2.19
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	34.450, 80.548, 84.172, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 24.5

The binding sites of Zinc atom in the Zinc-Finger Antiviral Protein (Zap) Bound to Rna (pdb code 6l1w). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Zinc-Finger Antiviral Protein (Zap) Bound to Rna, PDB code: 6l1w:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Zinc-Finger Antiviral Protein (Zap) Bound to Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zinc-Finger Antiviral Protein (Zap) Bound to Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:34.3 occ:1.00 NE2 A:HIS110 1.9 47.1 1.0 SG A:CYS106 2.2 36.0 1.0 SG A:CYS96 2.4 41.6 1.0 SG A:CYS88 2.4 30.4 1.0 CE1 A:HIS110 2.8 51.4 1.0 CD2 A:HIS110 3.0 49.9 1.0 CB A:CYS96 3.3 39.8 1.0 CB A:CYS88 3.3 26.6 1.0 CB A:CYS106 3.3 60.1 1.0 ND1 A:HIS110 3.9 50.0 1.0 N2 C:G2 4.0 35.2 1.0 CG A:HIS110 4.0 51.5 1.0 CB A:ASN91 4.2 32.4 1.0 N A:ASN91 4.6 30.4 1.0 O A:TYR108 4.6 38.4 1.0 CA A:CYS96 4.7 40.8 1.0 CA A:CYS88 4.7 22.3 1.0 N1 C:G2 4.7 39.7 1.0 CA A:CYS106 4.8 60.5 1.0 C2 C:G2 4.9 37.0 1.0 CB A:LEU90 5.0 30.8 1.0 CA A:ASN91 5.0 32.1 1.0

Zinc binding site 2 out of 4 in the Zinc-Finger Antiviral Protein (Zap) Bound to Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zinc-Finger Antiviral Protein (Zap) Bound to Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:20.2 occ:1.00 NE2 A:HIS86 2.0 16.1 1.0 SG A:CYS82 2.3 21.5 1.0 SG A:CYS73 2.4 19.3 1.0 SG A:CYS78 2.4 20.7 1.0 CE1 A:HIS86 2.8 24.5 1.0 CB A:CYS78 3.1 22.1 1.0 CD2 A:HIS86 3.1 21.1 1.0 CB A:CYS82 3.1 18.8 1.0 CB A:CYS73 3.2 16.5 1.0 ND1 A:HIS86 3.9 20.8 1.0 O A:HOH487 4.1 38.3 1.0 CG A:HIS86 4.1 20.1 1.0 O A:HOH477 4.2 40.9 1.0 O A:HOH452 4.5 21.4 1.0 CA A:CYS78 4.5 27.4 1.0 CA A:CYS73 4.5 18.1 1.0 CA A:CYS82 4.6 21.2 1.0 CD A:ARG75 4.8 51.2 1.0 CB A:SER84 4.9 19.3 1.0 NE A:ARG75 4.9 57.8 1.0 CG A:ARG75 4.9 41.7 1.0

Zinc binding site 3 out of 4 in the Zinc-Finger Antiviral Protein (Zap) Bound to Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Zinc-Finger Antiviral Protein (Zap) Bound to Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:51.5 occ:1.00 NE2 A:HIS172 2.0 51.3 1.0 SG A:CYS168 2.1 37.9 1.0 SG A:CYS150 2.3 49.8 1.0 SG A:CYS162 2.8 63.2 1.0 CE1 A:HIS172 2.8 50.1 1.0 CB A:CYS162 2.9 83.4 1.0 CB A:CYS150 3.0 39.6 1.0 CD2 A:HIS172 3.0 48.6 1.0 CB A:CYS168 3.2 69.1 1.0 ND1 A:HIS172 3.9 48.7 1.0 CG A:HIS172 4.0 44.8 1.0 OG A:SER152 4.1 52.4 1.0 CA A:CYS162 4.2 91.2 1.0 CA A:CYS150 4.4 37.5 1.0 CA A:CYS168 4.5 69.6 1.0 CB A:TYR153 4.7 51.7 1.0 N A:TYR153 4.8 53.5 1.0 O A:ARG170 4.9 45.6 1.0 CB A:ARG170 4.9 40.5 1.0 O A:CYS162 4.9 94.8 1.0

Zinc binding site 4 out of 4 in the Zinc-Finger Antiviral Protein (Zap) Bound to Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Zinc-Finger Antiviral Protein (Zap) Bound to Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:30.8 occ:1.00 NE2 A:HIS191 2.0 29.1 1.0 SG A:CYS174 2.3 27.2 1.0 SG A:CYS182 2.3 31.2 1.0 SG A:CYS187 2.5 36.4 1.0 CB A:CYS174 3.0 21.6 1.0 CD2 A:HIS191 3.0 28.6 1.0 CE1 A:HIS191 3.0 28.6 1.0 CB A:CYS187 3.2 51.4 1.0 CB A:CYS182 3.4 30.9 1.0 ND1 A:HIS191 4.1 27.7 1.0 CG A:HIS191 4.1 34.1 1.0 O A:ARG189 4.2 40.1 1.0 CB A:PHE177 4.4 19.0 1.0 CA A:CYS174 4.4 24.7 1.0 CA A:CYS182 4.7 32.8 1.0 N A:PHE177 4.7 24.4 1.0 CA A:CYS187 4.7 54.8 1.0 CB A:ARG189 4.9 43.6 1.0

X.Luo, X.Wang, Y.Gao, J.Zhu, S.Liu, G.Gao, P.Gao. Molecular Mechanism of Rna Recognition By Zinc-Finger Antiviral Protein (Zap) Cell Rep 2020.
ISSN: ESSN 2211-1247