Zinc in PDB 7dg7: Dpbb Domain of Vcp-Like Atpase From Methanopyrus Kandleri

The structure of Dpbb Domain of Vcp-Like Atpase From Methanopyrus Kandleri, PDB code: 7dg7 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)	40.44 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	32.078, 29.787, 42.155, 90, 106.42, 90
R / Rfree (%)	20.7 / 22.7

The binding sites of Zinc atom in the Dpbb Domain of Vcp-Like Atpase From Methanopyrus Kandleri (pdb code 7dg7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Dpbb Domain of Vcp-Like Atpase From Methanopyrus Kandleri, PDB code: 7dg7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Dpbb Domain of Vcp-Like Atpase From Methanopyrus Kandleri


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 Methanopyrus Kandleri within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:15.8 occ:1.00 N1 A:IMD102 2.0 14.8 1.0 OE2 A:GLU18 2.1 17.3 1.0 O A:HOH260 2.2 12.5 1.0 C2 A:IMD102 2.8 14.8 1.0 CD A:GLU18 3.0 16.7 1.0 C5 A:IMD102 3.1 16.0 1.0 OE1 A:GLU18 3.3 17.7 1.0 O A:HOH216 3.9 12.5 1.0 N3 A:IMD102 4.0 16.6 1.0 NZ A:LYS59 4.0 17.0 1.0 C4 A:IMD102 4.2 18.9 1.0 CG A:GLU18 4.4 14.9 1.0 CE A:LYS59 4.4 19.0 1.0 CB A:GLU18 4.8 12.7 1.0

Zinc binding site 2 out of 8 in the Dpbb Domain of Vcp-Like Atpase From Methanopyrus Kandleri


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 Methanopyrus Kandleri within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:21.1 occ:0.65 OE2 A:GLU61 1.6 41.5 1.0 N3 A:IMD102 2.0 16.6 1.0 O A:HOH202 2.2 37.4 1.0 O A:HOH225 2.2 21.7 1.0 CD A:GLU61 2.3 31.9 1.0 OE1 A:GLU61 2.5 31.2 1.0 C4 A:IMD102 2.8 18.9 1.0 C2 A:IMD102 3.2 14.8 1.0 CG A:GLU61 3.7 32.0 1.0 O A:HOH241 3.9 30.0 1.0 C5 A:IMD102 4.0 16.0 1.0 CB A:LYS59 4.2 16.4 1.0 N1 A:IMD102 4.2 14.8 1.0 CD A:LYS59 4.5 17.2 1.0 CG A:LYS59 4.6 18.5 1.0 CB A:GLU61 4.7 29.7 1.0 N A:GLU61 4.8 22.5 1.0 N A:LYS60 4.9 21.7 1.0

Zinc binding site 3 out of 8 in the Dpbb Domain of Vcp-Like Atpase From Methanopyrus Kandleri


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 Methanopyrus Kandleri within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn105 b:32.3 occ:0.58 OE2 A:GLU39 2.3 42.5 1.0 O A:HOH261 2.3 30.1 1.0 CD A:GLU39 3.3 36.4 1.0 OE1 A:GLU39 3.9 40.2 1.0 CD A:PRO57 4.1 20.1 1.0 CG A:PRO57 4.3 17.0 1.0 CG A:GLU39 4.5 31.9 1.0 CD2 A:LEU56 4.9 26.6 1.0

Zinc binding site 4 out of 8 in the Dpbb Domain of Vcp-Like Atpase From Methanopyrus Kandleri


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 Methanopyrus Kandleri within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn106 b:12.6 occ:1.00 OE2 A:GLU74 1.9 14.9 1.0 OD1 A:ASP71 2.0 11.9 1.0 O A:LYS22 2.1 15.1 1.0 O A:HOH253 2.2 3.9 1.0 CG A:ASP71 2.7 14.0 1.0 OD2 A:ASP71 2.7 9.4 1.0 CD A:GLU74 2.9 14.2 1.0 C A:LYS22 3.0 12.2 1.0 OE1 A:GLU74 3.2 18.1 1.0 N A:LYS22 3.7 12.7 1.0 O A:HOH206 3.7 18.3 1.0 N A:ARG23 3.8 15.5 1.0 CA A:ARG23 3.9 14.1 1.0 CA A:LYS22 4.0 12.2 1.0 C A:GLY21 4.1 16.6 1.0 CB A:ASP71 4.2 7.9 1.0 CG A:GLU74 4.3 15.1 1.0 N A:GLY21 4.3 14.0 1.0 N A:ALA24 4.3 14.1 1.0 O A:HOH228 4.4 18.2 1.0 CA A:GLY21 4.4 11.7 1.0 CB A:TYR73 4.4 12.1 1.0 N A:GLU74 4.5 12.8 1.0 O A:HOH257 4.5 4.0 1.0 C A:ARG23 4.6 13.3 1.0 CD2 A:TYR73 4.7 15.3 1.0 CB A:GLU74 4.7 12.2 1.0 O A:ALA24 4.8 14.8 1.0 O A:ASP19 4.8 15.1 1.0 CB A:LYS22 4.9 14.0 1.0 O A:GLY21 4.9 15.1 1.0

Zinc binding site 5 out of 8 in the Dpbb Domain of Vcp-Like Atpase From Methanopyrus Kandleri


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 Methanopyrus Kandleri within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn107 b:59.7 occ:1.00 OE2 A:GLU13 2.1 19.3 1.0 N3 A:IMD101 2.2 17.4 1.0 O A:HOH245 2.3 9.4 1.0 OE1 A:GLU13 2.5 13.2 1.0 CD A:GLU13 2.6 17.2 1.0 C2 A:IMD101 2.8 15.9 1.0 C4 A:IMD101 3.4 23.7 1.0 NE A:ARG11 4.0 10.5 1.0 N1 A:IMD101 4.1 21.4 1.0 CG A:GLU13 4.1 12.3 1.0 NH2 A:ARG11 4.3 16.6 1.0 C5 A:IMD101 4.3 17.6 1.0 CZ A:ARG11 4.6 15.8 1.0 O A:HOH215 4.7 18.1 1.0 CG1 A:VAL82 4.9 18.1 1.0 CD A:ARG11 4.9 13.0 1.0 CA A:GLY83 4.9 11.7 1.0

Zinc binding site 6 out of 8 in the Dpbb Domain of Vcp-Like Atpase From Methanopyrus Kandleri


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Dpbb Domain of Vcp-Like Atpase From Methanopyrus Kandleri within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn108 b:61.6 occ:1.00 NZ A:LYS9 2.1 26.1 1.0 O A:HOH240 2.4 13.5 1.0 CE A:LYS9 2.6 20.9 1.0 O A:HOH237 2.9 21.7 1.0 CD A:LYS9 3.5 20.9 1.0 CG A:LYS9 4.6 21.8 1.0 CB A:PRO85 4.7 14.6 1.0 CG A:PRO85 5.0 20.4 1.0

Zinc binding site 7 out of 8 in the Dpbb Domain of Vcp-Like Atpase From Methanopyrus Kandleri


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Dpbb Domain of Vcp-Like Atpase From Methanopyrus Kandleri within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn109 b:50.3 occ:1.00 OE2 A:GLU84 2.2 29.6 1.0 OE1 A:GLU84 2.5 21.8 1.0 O A:HOH250 2.5 45.3 1.0 CD A:GLU84 2.6 23.2 1.0 O A:HOH223 2.6 46.0 1.0 CG A:GLU84 4.1 18.7 1.0 OG A:SER81 4.2 27.5 0.5 OG A:SER81 4.3 27.5 0.5 O A:HOH259 4.4 36.5 1.0 N A:SER81 4.5 13.9 1.0 CB A:SER81 4.6 23.0 0.5 CB A:SER81 4.7 23.0 0.5 O A:GLY79 4.7 15.4 1.0 CA A:ALA80 4.9 13.9 1.0 CB A:GLU84 5.0 18.0 1.0

Zinc binding site 8 out of 8 in the Dpbb Domain of Vcp-Like Atpase From Methanopyrus Kandleri


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Dpbb Domain of Vcp-Like Atpase From Methanopyrus Kandleri within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn110 b:40.4 occ:1.00 OD2 A:ASP41 2.2 31.1 1.0 O A:HOH256 2.4 25.3 1.0 CG A:ASP41 2.9 27.7 1.0 OD1 A:ASP41 2.9 30.1 1.0 OG A:SER38 3.9 34.4 1.0 CB A:SER38 3.9 32.8 1.0 N A:SER38 4.0 28.4 1.0 CB A:ASP41 4.4 27.6 1.0 CA A:SER38 4.5 30.2 1.0 C A:VAL37 4.9 25.7 1.0 CA A:VAL37 5.0 26.2 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