Zinc in PDB 4z7r: The 1.98-Angstrom Crystal Structure of Zn(2+)-Bound Pqqb From Methylobacterium Extorquens

The structure of The 1.98-Angstrom Crystal Structure of Zn(2+)-Bound Pqqb From Methylobacterium Extorquens, PDB code: 4z7r was solved by X.Tu, C.M.Wilmot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.79 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.431, 51.991, 120.536, 90.00, 95.49, 90.00
R / Rfree (%)	17.5 / 22.1

The binding sites of Zinc atom in the The 1.98-Angstrom Crystal Structure of Zn(2+)-Bound Pqqb From Methylobacterium Extorquens (pdb code 4z7r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The 1.98-Angstrom Crystal Structure of Zn(2+)-Bound Pqqb From Methylobacterium Extorquens, PDB code: 4z7r:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the The 1.98-Angstrom Crystal Structure of Zn(2+)-Bound Pqqb From Methylobacterium Extorquens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The 1.98-Angstrom Crystal Structure of Zn(2+)-Bound Pqqb From Methylobacterium Extorquens within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:12.6 occ:0.97 OD1 A:ASN268 2.1 10.6 1.0 SG A:CYS19 2.3 15.2 1.0 SG A:CYS21 2.3 10.1 0.9 SG A:CYS24 2.4 13.0 1.0 CG A:ASN268 3.0 9.7 0.7 CB A:CYS24 3.2 12.2 1.0 CB A:CYS21 3.3 12.2 0.9 CB A:CYS19 3.3 12.1 0.9 CB A:ASN268 3.7 9.8 1.0 N A:CYS21 3.9 12.6 1.0 N A:CYS24 4.0 12.0 1.0 ND2 A:ASN268 4.0 8.8 1.0 O A:HOH512 4.1 28.6 1.0 CA A:CYS21 4.1 12.7 1.0 O A:ASN268 4.2 8.2 1.0 CA A:CYS24 4.2 12.2 1.0 C A:ASN268 4.3 9.0 0.8 C A:CYS19 4.5 12.5 0.9 CA A:CYS19 4.6 12.4 1.0 CG2 A:THR269 4.6 11.6 0.9 CA A:ASN268 4.7 9.5 1.0 C A:CYS21 4.7 12.9 1.0 O A:CYS19 4.8 12.3 1.0 CG1 A:VAL230 4.8 17.9 0.8 N A:ARG20 4.8 13.2 0.8 O A:CYS21 4.8 13.1 1.0 N A:THR269 4.8 9.5 1.0

Zinc binding site 2 out of 4 in the The 1.98-Angstrom Crystal Structure of Zn(2+)-Bound Pqqb From Methylobacterium Extorquens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The 1.98-Angstrom Crystal Structure of Zn(2+)-Bound Pqqb From Methylobacterium Extorquens within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:23.4 occ:0.53 O A:HOH429 2.0 27.2 0.9 OD2 A:ASP92 2.1 13.3 0.5 NE2 A:HIS265 2.1 11.9 0.8 O A:HOH502 2.3 21.8 1.0 CG A:ASP92 2.8 13.5 0.9 OD1 A:ASP92 2.9 14.5 0.6 CE1 A:HIS265 3.0 12.0 0.9 CD2 A:HIS265 3.2 11.3 0.7 O A:HOH490 3.2 42.9 1.0 OD2 A:ASP90 3.8 15.8 0.6 N A:GLY11 3.9 12.0 1.0 ND1 A:HIS265 4.2 11.6 0.9 CG A:HIS265 4.3 11.1 0.6 O A:HOH519 4.3 23.1 0.7 CB A:ASP92 4.3 11.9 0.8 CE1 A:HIS93 4.4 11.6 0.6 NE2 A:HIS93 4.5 11.9 0.7 CA A:GLY11 4.5 11.1 1.0 CB A:ASP90 4.5 14.4 0.9 CG A:ASP90 4.5 15.9 0.6 C A:ALA10 4.7 12.4 0.8 CA A:ALA10 4.8 12.0 0.9 ND1 A:HIS93 4.8 11.0 0.7 CD2 A:HIS93 5.0 11.6 0.8 CB A:ALA10 5.0 11.9 0.9

Zinc binding site 3 out of 4 in the The 1.98-Angstrom Crystal Structure of Zn(2+)-Bound Pqqb From Methylobacterium Extorquens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The 1.98-Angstrom Crystal Structure of Zn(2+)-Bound Pqqb From Methylobacterium Extorquens within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:15.6 occ:0.99 OD1 B:ASN268 2.1 10.8 0.9 SG B:CYS24 2.3 11.5 0.9 SG B:CYS19 2.3 15.1 1.0 SG B:CYS21 2.4 15.2 0.9 CG B:ASN268 3.0 10.0 0.8 CB B:CYS24 3.2 14.1 1.0 CB B:CYS21 3.3 14.2 0.6 CB B:CYS19 3.4 13.0 1.0 CB B:ASN268 3.6 10.4 0.9 N B:CYS21 3.9 14.3 1.0 ND2 B:ASN268 4.0 9.6 1.0 N B:CYS24 4.0 14.7 1.0 CA B:CYS21 4.1 14.4 1.0 O B:HOH498 4.1 18.9 0.9 O B:ASN268 4.2 8.6 0.8 CA B:CYS24 4.2 14.0 0.8 C B:ASN268 4.3 9.9 0.8 C B:CYS19 4.5 12.7 0.7 CA B:CYS19 4.6 13.2 0.9 CG2 B:THR269 4.6 10.4 0.9 CA B:ASN268 4.6 10.1 0.6 C B:CYS21 4.7 14.5 0.7 O B:CYS19 4.7 11.2 1.0 O B:CYS21 4.8 14.4 0.9 N B:THR269 4.8 10.0 1.0 N B:ARG20 4.8 13.8 0.9

Zinc binding site 4 out of 4 in the The 1.98-Angstrom Crystal Structure of Zn(2+)-Bound Pqqb From Methylobacterium Extorquens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The 1.98-Angstrom Crystal Structure of Zn(2+)-Bound Pqqb From Methylobacterium Extorquens within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:49.3 occ:0.41 OD2 B:ASP92 2.5 18.6 0.4 NE2 B:HIS265 2.6 13.3 1.0 O B:HOH492 3.0 31.8 1.0 CG B:ASP92 3.5 18.4 0.7 CD2 B:HIS265 3.6 12.9 0.8 CE1 B:HIS265 3.6 14.1 1.0 OD1 B:ASP92 3.8 18.6 0.6 CE1 B:HIS93 4.1 16.8 0.7 N B:GLY11 4.2 11.8 1.0 NE2 B:HIS93 4.7 17.1 0.7 CA B:GLY11 4.7 12.9 0.9 ND1 B:HIS265 4.7 13.8 0.7 CG B:HIS265 4.8 13.1 0.9 ND1 B:HIS93 4.8 16.6 0.4 CB B:ASP92 4.8 17.1 0.7 OD2 B:ASP90 5.0 22.2 0.5

X.Tu, C.M.Wimot. Crystal Structures Reveal Metal-Binding Plasticity at Active Site of Pqqb To Be Published.