Zinc in PDB 5ofs: X-Ray Structure of A Zinc Binding GB1 Mutant

The structure of X-Ray Structure of A Zinc Binding GB1 Mutant, PDB code: 5ofs was solved by U.Rothlisberger, E.Bozkurt, R.Hovius, M.A.S.Perez, N.J.Browning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.37 / 1.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	74.452, 75.621, 51.153, 90.00, 90.00, 90.00
R / Rfree (%)	12.5 / 14.5

The structure of X-Ray Structure of A Zinc Binding GB1 Mutant also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the X-Ray Structure of A Zinc Binding GB1 Mutant (pdb code 5ofs). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the X-Ray Structure of A Zinc Binding GB1 Mutant, PDB code: 5ofs:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the X-Ray Structure of A Zinc Binding GB1 Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of A Zinc Binding GB1 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:10.6 occ:1.00 OXT B:GLU61 1.9 13.2 1.0 OE2 A:GLU52 2.0 11.8 1.0 NE2 A:HIS28 2.0 11.0 1.0 NE2 A:HIS55 2.0 10.4 1.0 CD A:GLU52 2.7 10.9 1.0 C B:GLU61 2.8 10.8 1.0 OE1 A:GLU52 2.9 11.7 1.0 CE1 A:HIS55 3.0 11.1 1.0 CE1 A:HIS28 3.0 11.1 1.0 CD2 A:HIS55 3.0 9.4 1.0 CD2 A:HIS28 3.1 10.5 1.0 O B:GLU61 3.1 12.5 1.0 NZ B:LYS15 4.0 26.4 0.5 ND1 A:HIS28 4.1 10.6 1.0 ND1 A:HIS55 4.1 10.7 1.0 O B:HOH201 4.1 34.6 1.0 O B:HOH210 4.1 21.7 1.0 CG A:GLU52 4.2 11.6 1.0 CG A:HIS55 4.2 9.6 1.0 CG A:HIS28 4.2 9.9 1.0 CA B:GLU61 4.2 10.9 1.0 CE B:LYS15 4.3 24.1 0.5 OH A:TYR50 4.4 11.0 1.0 CE B:LYS15 4.4 22.0 0.5 O A:GLU52 4.6 12.3 1.0 SD A:MET6 4.7 13.2 1.0 NZ B:LYS15 4.7 22.0 0.5 CB B:GLU61 4.8 12.2 1.0 CE1 A:PHE8 4.9 11.2 1.0

Zinc binding site 2 out of 6 in the X-Ray Structure of A Zinc Binding GB1 Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of A Zinc Binding GB1 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:11.2 occ:1.00 OE1 C:GLU47 1.9 12.8 1.0 OD1 A:ASP27 2.0 12.8 1.0 OE1 B:GLU47 2.0 13.1 1.0 CD B:GLU47 2.7 13.8 1.0 OE2 B:GLU47 2.7 13.9 1.0 CD C:GLU47 2.8 10.7 1.0 CG A:ASP27 2.9 12.2 1.0 OE2 C:GLU47 3.1 11.1 1.0 OD2 A:ASP27 3.2 13.1 1.0 O A:HOH224 4.0 16.5 1.0 CG B:GLU47 4.1 17.1 1.0 CG C:GLU47 4.2 10.8 1.0 CB A:ASP27 4.2 12.8 1.0 N A:HIS28 4.2 11.0 1.0 O B:HOH231 4.2 16.8 1.0 N A:ALA29 4.6 10.8 1.0 CA A:ASP27 4.6 11.9 1.0 O A:HOH233 4.6 33.3 1.0 CB C:GLU47 4.6 10.8 1.0 CB B:GLU47 4.7 17.9 1.0 C A:ASP27 4.8 11.7 1.0 CB A:ALA29 4.9 14.3 1.0 CB A:HIS28 5.0 10.2 1.0

Zinc binding site 3 out of 6 in the X-Ray Structure of A Zinc Binding GB1 Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Structure of A Zinc Binding GB1 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:10.7 occ:1.00 OE2 B:GLU52 2.0 12.4 1.0 NE2 B:HIS28 2.0 10.3 1.0 NE2 B:HIS55 2.0 10.9 1.0 CD B:GLU52 2.8 12.0 1.0 OE1 B:GLU52 2.9 12.9 1.0 CE1 B:HIS28 2.9 10.6 1.0 CE1 B:HIS55 3.0 12.4 1.0 CD2 B:HIS55 3.0 10.2 1.0 CD2 B:HIS28 3.1 10.2 1.0 ND1 B:HIS28 4.1 10.1 1.0 ND1 B:HIS55 4.1 12.3 1.0 CG B:HIS28 4.2 9.3 1.0 CG B:HIS55 4.2 10.7 1.0 CG B:GLU52 4.2 14.0 1.0 OH B:TYR50 4.4 12.5 1.0 CE C:LYS33 4.6 21.9 1.0 NZ C:LYS33 4.6 25.2 1.0 O B:GLU52 4.6 13.8 1.0 SD B:MET6 4.6 14.7 1.0 CE2 B:PHE8 4.9 11.2 1.0

Zinc binding site 4 out of 6 in the X-Ray Structure of A Zinc Binding GB1 Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Structure of A Zinc Binding GB1 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:10.8 occ:1.00 OE2 C:GLU52 2.0 11.2 1.0 NE2 C:HIS28 2.0 10.8 1.0 NE2 C:HIS55 2.0 10.5 1.0 CD C:GLU52 2.7 11.9 1.0 OE1 C:GLU52 2.8 12.4 1.0 CE1 C:HIS28 2.9 11.5 1.0 CE1 C:HIS55 3.0 11.6 1.0 CD2 C:HIS55 3.1 10.1 1.0 CD2 C:HIS28 3.1 10.1 1.0 ND1 C:HIS28 4.1 11.5 1.0 O B:HOH225 4.1 27.4 1.0 ND1 C:HIS55 4.1 10.6 1.0 CG C:GLU52 4.2 12.7 1.0 CG C:HIS55 4.2 10.0 1.0 CG C:HIS28 4.2 10.2 1.0 OH C:TYR50 4.2 11.8 1.0 O C:HOH220 4.3 18.9 1.0 O C:HOH224 4.4 44.9 1.0 SD C:MET6 4.5 12.4 1.0 O C:GLU52 4.6 13.7 1.0 CE2 C:PHE8 4.9 10.1 1.0 CZ C:PHE8 5.0 10.0 1.0

Zinc binding site 5 out of 6 in the X-Ray Structure of A Zinc Binding GB1 Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of X-Ray Structure of A Zinc Binding GB1 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn101 b:11.5 occ:1.00 OE2 D:GLU52 2.0 12.8 1.0 NE2 D:HIS28 2.0 10.2 1.0 NE2 D:HIS55 2.0 11.7 1.0 CD D:GLU52 2.7 12.6 1.0 OE1 D:GLU52 2.9 12.8 1.0 CE1 D:HIS28 2.9 12.2 1.0 CE1 D:HIS55 3.0 12.2 1.0 CD2 D:HIS55 3.0 10.9 1.0 CD2 D:HIS28 3.1 10.5 1.0 ND1 D:HIS28 4.1 12.9 1.0 O D:HOH250 4.1 24.6 1.0 ND1 D:HIS55 4.2 11.5 1.0 CG D:GLU52 4.2 13.4 1.0 CG D:HIS28 4.2 10.3 1.0 CG D:HIS55 4.2 10.9 1.0 OH D:TYR50 4.3 11.6 1.0 O D:HOH235 4.4 25.6 1.0 SD D:MET6 4.7 13.5 1.0 O D:GLU52 4.7 14.3 1.0 CE1 D:PHE8 4.9 11.5 1.0

Zinc binding site 6 out of 6 in the X-Ray Structure of A Zinc Binding GB1 Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of X-Ray Structure of A Zinc Binding GB1 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn102 b:10.6 occ:1.00 OE1 D:GLU47 2.0 10.6 1.0 CL D:CL104 2.2 10.5 1.0 CD D:GLU47 2.8 10.6 1.0 OE2 D:GLU47 2.9 11.1 1.0 O D:HOH223 3.8 41.7 1.0 O D:HOH247 4.0 25.8 1.0 CG D:GLU47 4.2 11.2 1.0 O D:HOH254 4.3 21.8 1.0 CB D:GLU47 4.9 10.9 1.0

E.Bozkurt, M.A.S.Perez, R.Hovius, N.J.Browning, U.Rothlisberger. Genetic Algorithm Based Design and Experimental Characterization of A Highly Thermostable Metalloprotein. J. Am. Chem. Soc. V. 140 4517 2018.
ISSN: ESSN 1520-5126
PubMed: 29336153
DOI: 10.1021/JACS.7B10660