Zinc in PDB 7dg9: Dpbb Domain of Vcp-Like Atpase From Aeropyrum Pernix

The structure of Dpbb Domain of Vcp-Like Atpase From Aeropyrum Pernix, PDB code: 7dg9 was solved by S.Yagi, S.Tagami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.08 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	26.04, 31.066, 94.156, 90, 90, 90
R / Rfree (%)	16.9 / 20.7

The binding sites of Zinc atom in the Dpbb Domain of Vcp-Like Atpase From Aeropyrum Pernix (pdb code 7dg9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Dpbb Domain of Vcp-Like Atpase From Aeropyrum Pernix, PDB code: 7dg9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Dpbb Domain of Vcp-Like Atpase From Aeropyrum Pernix


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dpbb Domain of Vcp-Like Atpase From Aeropyrum Pernix within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:20.3 occ:0.31 ZN A:ZN102 2.2 39.5 0.3 OE1 A:GLU9 4.0 26.7 1.0 CD A:GLU9 4.8 33.5 1.0 OE2 A:GLU9 4.8 31.6 1.0

Zinc binding site 2 out of 5 in the Dpbb Domain of Vcp-Like Atpase From Aeropyrum Pernix


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dpbb Domain of Vcp-Like Atpase From Aeropyrum Pernix within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:39.5 occ:0.31 ZN A:ZN101 2.2 20.3 0.3 OE1 A:GLU9 2.5 26.7 1.0 OE2 A:GLU9 2.8 31.6 1.0 CD A:GLU9 2.9 33.5 1.0 CG A:GLU9 4.4 14.1 1.0

Zinc binding site 3 out of 5 in the Dpbb Domain of Vcp-Like Atpase From Aeropyrum Pernix


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Dpbb Domain of Vcp-Like Atpase From Aeropyrum Pernix within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:24.4 occ:0.21 O A:HOH316 2.4 40.7 1.0 O A:HOH219 3.5 31.4 1.0 O A:HOH282 4.0 28.1 1.0 O A:HOH268 4.0 33.4 1.0 NZ A:LYS91 4.1 46.8 1.0 O A:HOH209 4.2 39.2 1.0 O A:HOH241 4.3 22.2 1.0 O A:HOH204 4.4 26.1 1.0 CE A:LYS91 4.4 30.6 1.0 OD2 A:ASP41 4.8 18.0 1.0 CG A:ASP41 4.9 19.0 1.0

Zinc binding site 4 out of 5 in the Dpbb Domain of Vcp-Like Atpase From Aeropyrum Pernix


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Dpbb Domain of Vcp-Like Atpase From Aeropyrum Pernix within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:18.3 occ:0.51 O A:HOH296 2.0 29.4 1.0 O A:HOH310 2.2 31.8 1.0 OD1 A:ASP85 2.2 18.3 1.0 O A:HOH235 2.2 25.9 1.0 ZN A:ZN105 2.4 27.2 0.2 CG A:ASP85 3.2 15.2 1.0 OD2 A:ASP85 3.5 16.2 1.0 OG1 A:THR82 4.3 17.3 1.0 CB A:ASP85 4.6 12.3 1.0 O A:HOH279 4.7 21.1 1.0 CA A:ASP85 4.9 10.0 1.0

Zinc binding site 5 out of 5 in the Dpbb Domain of Vcp-Like Atpase From Aeropyrum Pernix


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Dpbb Domain of Vcp-Like Atpase From Aeropyrum Pernix within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn105 b:27.2 occ:0.19 OD2 A:ASP85 2.3 16.2 1.0 ZN A:ZN104 2.4 18.3 0.5 OD1 A:ASP85 2.9 18.3 1.0 CG A:ASP85 2.9 15.2 1.0 O A:HOH296 3.2 29.4 1.0 O A:HOH234 3.5 34.1 1.0 O A:HOH235 3.5 25.9 1.0 OG1 A:THR82 4.1 17.3 1.0 N A:THR82 4.4 8.2 1.0 CB A:ASP85 4.4 12.3 1.0 CG2 A:THR82 4.4 13.7 1.0 O A:HOH310 4.6 31.8 1.0 O A:GLY80 4.7 18.1 1.0 CA A:VAL81 4.8 7.6 1.0 CB A:THR82 4.8 14.3 1.0 C A:VAL81 5.0 8.6 1.0

S.Yagi, A.K.Padhi, J.Vucinic, S.Barbe, T.Schiex, R.Nakagawa, D.Simoncini, K.Y.J.Zhang, S.Tagami. Seven Amino Acid Types Suffice to Reconstruct the Core Fold of Rna Polymerase Biorxiv 2021.
DOI: 10.1101/2021.02.22.432383