Zinc in PDB 1pb0: Ycdx Protein in Autoinhibited State

The structure of Ycdx Protein in Autoinhibited State, PDB code: 1pb0 was solved by A.Teplyakov, G.Obmolova, P.P.Khil, R.D.Camerini-Otero, G.L.Gilliland, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	134.130, 77.330, 82.280, 90.00, 103.17, 90.00
R / Rfree (%)	16.4 / n/a

The binding sites of Zinc atom in the Ycdx Protein in Autoinhibited State (pdb code 1pb0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Ycdx Protein in Autoinhibited State, PDB code: 1pb0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Ycdx Protein in Autoinhibited State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ycdx Protein in Autoinhibited State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1301 b:15.5 occ:1.00 NE2 A:HIS164 2.0 13.5 1.0 NE2 A:HIS40 2.0 8.5 1.0 NE2 A:HIS15 2.0 10.4 1.0 NE2 A:HIS194 2.1 12.4 1.0 CE1 A:HIS164 2.9 36.9 1.0 CD2 A:HIS15 3.0 19.0 1.0 CE1 A:HIS40 3.0 10.5 1.0 CD2 A:HIS40 3.0 7.9 1.0 CD2 A:HIS164 3.1 22.6 1.0 CD2 A:HIS194 3.1 14.7 1.0 CE1 A:HIS15 3.1 10.1 1.0 CE1 A:HIS194 3.1 6.9 1.0 ND1 A:HIS164 4.1 30.2 1.0 ND1 A:HIS40 4.1 14.4 1.0 CG A:HIS15 4.1 15.0 1.0 ND1 A:HIS15 4.2 14.0 1.0 CG A:HIS164 4.2 31.2 1.0 CG A:HIS40 4.2 13.8 1.0 ND1 A:HIS194 4.2 11.1 1.0 CG A:HIS194 4.2 10.0 1.0 CE1 A:HIS9 4.3 17.5 1.0 ND1 A:HIS9 4.4 11.3 1.0 NE2 A:HIS9 4.4 10.2 1.0 O A:HOH1334 4.5 13.3 1.0 CG A:HIS9 4.5 9.9 1.0 CD2 A:HIS9 4.6 9.3 1.0 CD2 A:LEU163 4.7 37.7 1.0 ZN A:ZN1302 4.9 15.3 1.0 CE A:MET44 4.9 24.6 1.0

Zinc binding site 2 out of 9 in the Ycdx Protein in Autoinhibited State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ycdx Protein in Autoinhibited State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1302 b:15.3 occ:1.00 O A:HOH1334 1.9 13.3 1.0 NE2 A:HIS7 2.0 10.3 1.0 NE2 A:HIS9 2.0 10.2 1.0 OD1 A:ASP192 2.2 15.0 1.0 OE1 A:GLU73 2.3 14.3 1.0 CE1 A:HIS7 2.9 17.0 1.0 CE1 A:HIS9 3.0 17.5 1.0 CD2 A:HIS7 3.0 6.8 1.0 CD A:GLU73 3.0 15.3 1.0 CG A:ASP192 3.1 26.1 1.0 CD2 A:HIS9 3.1 9.3 1.0 ZN A:ZN1303 3.3 17.9 1.0 OE2 A:GLU73 3.4 14.6 1.0 OD2 A:ASP192 3.4 15.5 1.0 CE1 A:HIS40 3.9 10.5 1.0 ND1 A:HIS7 4.0 14.2 1.0 ND1 A:HIS9 4.1 11.3 1.0 CG A:HIS7 4.1 13.6 1.0 CG A:HIS9 4.2 9.9 1.0 CG A:GLU73 4.3 14.4 1.0 CB A:ASP192 4.3 14.2 1.0 CE1 A:HIS194 4.3 6.9 1.0 NE2 A:HIS40 4.4 8.5 1.0 CB A:GLU73 4.5 10.7 1.0 ND1 A:HIS40 4.6 14.4 1.0 CA A:ASP192 4.6 18.0 1.0 NE2 A:HIS101 4.8 18.7 1.0 NE2 A:HIS194 4.8 12.4 1.0 NE2 A:HIS131 4.8 22.6 1.0 ZN A:ZN1301 4.9 15.5 1.0 CD2 A:HIS164 5.0 22.6 1.0

Zinc binding site 3 out of 9 in the Ycdx Protein in Autoinhibited State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ycdx Protein in Autoinhibited State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1303 b:17.9 occ:1.00 NE2 A:HIS101 2.0 18.7 1.0 OE2 A:GLU73 2.1 14.6 1.0 O A:HOH1334 2.1 13.3 1.0 NE2 A:HIS131 2.1 22.6 1.0 CD A:GLU73 2.8 15.3 1.0 CE1 A:HIS101 2.8 22.9 1.0 OE1 A:GLU73 2.9 14.3 1.0 CE1 A:HIS131 3.0 20.3 1.0 CD2 A:HIS101 3.2 18.8 1.0 CD2 A:HIS131 3.2 14.2 1.0 ZN A:ZN1302 3.3 15.3 1.0 ND1 A:HIS101 4.0 19.6 1.0 CE1 A:HIS40 4.1 10.5 1.0 OG A:SER130 4.1 14.9 1.0 CE1 A:HIS7 4.2 17.0 1.0 OD2 A:ASP192 4.2 15.5 1.0 ND1 A:HIS131 4.2 17.5 1.0 CG A:HIS101 4.2 18.4 1.0 CG A:GLU73 4.2 14.4 1.0 NE2 A:HIS7 4.3 10.3 1.0 CG A:HIS131 4.3 25.3 1.0 CD2 A:HIS164 4.4 22.6 1.0 CB A:SER130 4.6 16.3 1.0 CG A:HIS164 4.6 31.2 1.0 ND1 A:HIS40 4.7 14.4 1.0 OD1 A:ASP192 4.7 15.0 1.0 CG A:ASP192 4.8 26.1 1.0 CB A:HIS164 4.9 28.9 1.0 O A:HOH1332 4.9 13.1 1.0

Zinc binding site 4 out of 9 in the Ycdx Protein in Autoinhibited State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ycdx Protein in Autoinhibited State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1311 b:18.9 occ:1.00 NE2 B:HIS15 2.0 15.9 1.0 NE2 B:HIS40 2.0 16.3 1.0 NE2 B:HIS194 2.1 14.1 1.0 NE2 B:HIS164 2.1 22.3 1.0 CE1 B:HIS164 2.9 37.4 1.0 CD2 B:HIS15 2.9 11.4 1.0 CE1 B:HIS40 3.0 11.7 1.0 CE1 B:HIS15 3.0 16.5 1.0 CD2 B:HIS40 3.0 14.8 1.0 CE1 B:HIS194 3.1 16.3 1.0 CD2 B:HIS194 3.2 15.4 1.0 CD2 B:HIS164 3.3 51.8 1.0 ND1 B:HIS40 4.1 19.0 1.0 ND1 B:HIS164 4.1 31.0 1.0 CG B:HIS15 4.1 20.1 1.0 ND1 B:HIS15 4.1 16.0 1.0 CG B:HIS40 4.1 15.5 1.0 ND1 B:HIS194 4.2 19.6 1.0 CG B:HIS194 4.3 13.7 1.0 CG B:HIS164 4.3 43.7 1.0 CE1 B:HIS9 4.4 21.7 1.0 ND1 B:HIS9 4.4 11.4 1.0 NE2 B:HIS9 4.5 11.2 1.0 CG B:HIS9 4.5 10.2 1.0 CD2 B:HIS9 4.5 17.7 1.0 O B:HOH1399 4.5 30.7 1.0 CD2 B:LEU163 4.8 35.9 1.0 ZN B:ZN1312 4.9 19.0 1.0

Zinc binding site 5 out of 9 in the Ycdx Protein in Autoinhibited State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Ycdx Protein in Autoinhibited State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1312 b:19.0 occ:1.00 OE1 B:GLU73 1.9 14.3 1.0 OD1 B:ASP192 2.0 19.9 1.0 NE2 B:HIS9 2.0 11.2 1.0 O B:HOH1399 2.0 30.7 1.0 NE2 B:HIS7 2.1 23.2 1.0 CD B:GLU73 2.9 25.5 1.0 CE1 B:HIS9 3.0 21.7 1.0 CG B:ASP192 3.0 30.7 1.0 CE1 B:HIS7 3.0 20.3 1.0 CD2 B:HIS7 3.0 12.0 1.0 CD2 B:HIS9 3.1 17.7 1.0 OE2 B:GLU73 3.3 19.9 1.0 ZN B:ZN1313 3.3 24.6 1.0 OD2 B:ASP192 3.4 30.6 1.0 CE1 B:HIS40 3.9 11.7 1.0 ND1 B:HIS9 4.1 11.4 1.0 ND1 B:HIS7 4.1 20.3 1.0 CG B:HIS7 4.1 25.6 1.0 CG B:HIS9 4.2 10.2 1.0 CB B:ASP192 4.2 18.8 1.0 CG B:GLU73 4.2 17.1 1.0 CE1 B:HIS194 4.3 16.3 1.0 NE2 B:HIS40 4.4 16.3 1.0 CB B:GLU73 4.5 17.0 1.0 ND1 B:HIS40 4.6 19.0 1.0 CA B:ASP192 4.6 22.6 1.0 NE2 B:HIS101 4.7 19.5 1.0 NE2 B:HIS131 4.7 23.4 1.0 CD2 B:HIS164 4.8 51.8 1.0 NE2 B:HIS194 4.9 14.1 1.0 ZN B:ZN1311 4.9 18.9 1.0 O B:THR38 5.0 12.2 1.0 NE2 B:HIS164 5.0 22.3 1.0

Zinc binding site 6 out of 9 in the Ycdx Protein in Autoinhibited State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Ycdx Protein in Autoinhibited State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1313 b:24.6 occ:1.00 NE2 B:HIS101 1.8 19.5 1.0 OE2 B:GLU73 2.1 19.9 1.0 O B:HOH1399 2.1 30.7 1.0 NE2 B:HIS131 2.2 23.4 1.0 CE1 B:HIS101 2.7 38.8 1.0 CD B:GLU73 2.8 25.5 1.0 CE1 B:HIS131 2.9 19.2 1.0 OE1 B:GLU73 3.0 14.3 1.0 CD2 B:HIS101 3.0 34.3 1.0 ZN B:ZN1312 3.3 19.0 1.0 CD2 B:HIS131 3.4 23.7 1.0 ND1 B:HIS101 3.8 26.6 1.0 CG B:HIS101 4.0 31.7 1.0 CE1 B:HIS40 4.1 11.7 1.0 ND1 B:HIS131 4.1 22.1 1.0 CG B:GLU73 4.1 17.1 1.0 CE1 B:HIS7 4.2 20.3 1.0 NE2 B:HIS7 4.2 23.2 1.0 CD2 B:HIS164 4.2 51.8 1.0 OG B:SER130 4.2 18.4 1.0 OD2 B:ASP192 4.3 30.6 1.0 CG B:HIS131 4.4 20.4 1.0 CG B:HIS164 4.5 43.7 1.0 OD1 B:ASP192 4.6 19.9 1.0 O B:HOH1347 4.6 18.9 1.0 CB B:SER130 4.7 18.4 1.0 ND1 B:HIS40 4.7 19.0 1.0 NE2 B:HIS164 4.8 22.3 1.0 CB B:HIS164 4.8 51.7 1.0 CG B:ASP192 4.8 30.7 1.0 O B:HOH1446 5.0 37.4 1.0

Zinc binding site 7 out of 9 in the Ycdx Protein in Autoinhibited State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Ycdx Protein in Autoinhibited State within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1321 b:14.9 occ:1.00 NE2 C:HIS15 1.9 10.3 1.0 NE2 C:HIS164 2.0 18.5 1.0 NE2 C:HIS194 2.1 16.0 1.0 NE2 C:HIS40 2.1 15.2 1.0 CE1 C:HIS164 2.6 27.6 1.0 CD2 C:HIS15 2.9 12.9 1.0 CE1 C:HIS15 3.0 19.7 1.0 CE1 C:HIS194 3.0 20.5 1.0 CE1 C:HIS40 3.0 13.8 1.0 CD2 C:HIS194 3.1 12.8 1.0 CD2 C:HIS40 3.1 10.4 1.0 CD2 C:HIS164 3.3 29.5 1.0 ND1 C:HIS164 3.9 35.0 1.0 CG C:HIS15 4.0 9.2 1.0 ND1 C:HIS15 4.1 12.7 1.0 ND1 C:HIS194 4.1 13.3 1.0 ND1 C:HIS40 4.2 13.0 1.0 CG C:HIS194 4.2 13.8 1.0 CG C:HIS164 4.2 38.9 1.0 CG C:HIS40 4.2 13.6 1.0 CE1 C:HIS9 4.4 15.5 1.0 NE2 C:HIS9 4.4 12.7 1.0 ND1 C:HIS9 4.4 9.5 1.0 CD2 C:HIS9 4.5 14.1 1.0 CG C:HIS9 4.5 10.2 1.0 O C:HOH1354 4.6 14.6 1.0 CE C:MET44 5.0 20.9 1.0 ZN C:ZN1322 5.0 16.0 1.0

Zinc binding site 8 out of 9 in the Ycdx Protein in Autoinhibited State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Ycdx Protein in Autoinhibited State within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1322 b:16.0 occ:1.00 O C:HOH1354 2.0 14.6 1.0 NE2 C:HIS7 2.0 16.0 1.0 NE2 C:HIS9 2.1 12.7 1.0 OD1 C:ASP192 2.2 11.9 1.0 OE1 C:GLU73 2.2 12.6 1.0 CE1 C:HIS7 2.9 17.0 1.0 CE1 C:HIS9 3.0 15.5 1.0 CG C:ASP192 3.0 24.6 1.0 CD2 C:HIS9 3.1 14.1 1.0 CD C:GLU73 3.1 14.6 1.0 CD2 C:HIS7 3.1 7.7 1.0 OD2 C:ASP192 3.3 24.4 1.0 ZN C:ZN1323 3.4 17.6 1.0 OE2 C:GLU73 3.4 16.6 1.0 CE1 C:HIS40 3.9 13.8 1.0 ND1 C:HIS7 4.1 20.3 1.0 ND1 C:HIS9 4.1 9.5 1.0 CG C:HIS9 4.2 10.2 1.0 CG C:HIS7 4.2 13.9 1.0 CE1 C:HIS194 4.2 20.5 1.0 CB C:ASP192 4.3 15.4 1.0 CG C:GLU73 4.3 9.2 1.0 NE2 C:HIS40 4.4 15.2 1.0 CA C:ASP192 4.6 14.3 1.0 CB C:GLU73 4.6 10.4 1.0 ND1 C:HIS40 4.6 13.0 1.0 CD2 C:HIS164 4.7 29.5 1.0 NE2 C:HIS101 4.8 10.6 1.0 NE2 C:HIS131 4.8 9.8 1.0 NE2 C:HIS194 4.8 16.0 1.0 NE2 C:HIS164 4.9 18.5 1.0 ZN C:ZN1321 5.0 14.9 1.0

Zinc binding site 9 out of 9 in the Ycdx Protein in Autoinhibited State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Ycdx Protein in Autoinhibited State within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1323 b:17.6 occ:1.00 NE2 C:HIS101 2.0 10.6 1.0 OE2 C:GLU73 2.0 16.6 1.0 O C:HOH1354 2.1 14.6 1.0 NE2 C:HIS131 2.1 9.8 1.0 CD C:GLU73 2.8 14.6 1.0 CE1 C:HIS101 2.9 22.0 1.0 OE1 C:GLU73 3.0 12.6 1.0 CE1 C:HIS131 3.0 18.1 1.0 CD2 C:HIS101 3.1 15.6 1.0 CD2 C:HIS131 3.2 15.9 1.0 ZN C:ZN1322 3.4 16.0 1.0 OG C:SER130 4.0 14.3 1.0 ND1 C:HIS101 4.0 16.6 1.0 CG C:HIS101 4.1 23.4 1.0 OD2 C:ASP192 4.1 24.4 1.0 ND1 C:HIS131 4.2 16.4 1.0 CE1 C:HIS40 4.2 13.8 1.0 CG C:GLU73 4.2 9.2 1.0 CE1 C:HIS7 4.2 17.0 1.0 CD2 C:HIS164 4.3 29.5 1.0 CG C:HIS131 4.3 14.1 1.0 NE2 C:HIS7 4.3 16.0 1.0 CG C:HIS164 4.5 38.9 1.0 CB C:SER130 4.6 13.8 1.0 CB C:HIS164 4.7 51.2 1.0 ND1 C:HIS40 4.7 13.0 1.0 OD1 C:ASP192 4.7 11.9 1.0 O C:HOH1347 4.8 12.1 1.0 CG C:ASP192 4.8 24.6 1.0 NE2 C:HIS164 4.9 18.5 1.0

A.Teplyakov, G.Obmolova, P.P.Khil, R.D.Camerini-Otero, G.L.Gilliland. Autoregulation of Ycdx Protein To Be Published.