Zinc in PDB 3qw0: Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmb Crosslinks

The structure of Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmb Crosslinks, PDB code: 3qw0 was solved by E.N.Salgado, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.50 / 1.84
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.626, 76.399, 93.265, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 24.3

The structure of Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmb Crosslinks also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmb Crosslinks (pdb code 3qw0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmb Crosslinks, PDB code: 3qw0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmb Crosslinks


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmb Crosslinks within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn500 b:12.5 occ:1.00 NE2 A:HIS73 1.9 15.6 1.0 NE2 D:HIS63 2.0 5.8 1.0 OD2 C:ASP74 2.1 15.2 1.0 NE2 A:HIS77 2.1 13.1 1.0 OD1 C:ASP74 2.4 18.6 1.0 CG C:ASP74 2.6 14.0 1.0 CE1 A:HIS73 2.8 20.0 1.0 CD2 D:HIS63 3.0 11.1 1.0 CD2 A:HIS73 3.0 14.7 1.0 CE1 D:HIS63 3.0 14.2 1.0 CD2 A:HIS77 3.0 12.2 1.0 CE1 A:HIS77 3.2 13.9 1.0 ND1 A:HIS73 4.0 16.7 1.0 CG A:HIS73 4.1 13.9 1.0 ND1 D:HIS63 4.1 14.6 1.0 CB C:ASP74 4.1 14.6 1.0 CG D:HIS63 4.1 13.8 1.0 CG A:HIS77 4.2 8.2 1.0 ND1 A:HIS77 4.2 11.2 1.0 O C:HOH409 4.2 25.2 1.0 O C:HOH378 4.3 24.6 1.0 O A:HOH143 4.6 22.9 1.0 CD1 D:ILE67 4.7 17.4 1.0 CA C:ASP74 4.8 12.8 1.0 O C:ASP74 4.9 11.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmb Crosslinks


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmb Crosslinks within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn500 b:15.1 occ:1.00 NE2 C:HIS63 2.0 12.1 1.0 NE2 B:HIS73 2.1 12.7 1.0 NE2 B:HIS77 2.1 11.2 1.0 OD2 D:ASP74 2.2 15.1 1.0 OD1 D:ASP74 2.5 17.9 1.0 CG D:ASP74 2.6 13.6 1.0 CD2 C:HIS63 2.9 10.2 1.0 CD2 B:HIS77 3.0 7.4 1.0 CE1 B:HIS73 3.0 15.3 1.0 CD2 B:HIS73 3.0 12.2 1.0 CE1 C:HIS63 3.1 10.5 1.0 CE1 B:HIS77 3.1 12.0 1.0 CG C:HIS63 4.1 13.2 1.0 ND1 C:HIS63 4.1 11.4 1.0 ND1 B:HIS73 4.1 14.9 1.0 ND1 B:HIS77 4.2 10.4 1.0 CB D:ASP74 4.2 13.5 1.0 CG B:HIS77 4.2 11.9 1.0 O D:HOH324 4.2 31.1 1.0 CG B:HIS73 4.2 14.2 1.0 O B:HOH359 4.4 29.7 1.0 CD1 C:ILE67 4.6 15.2 1.0 O D:ASP74 4.7 13.6 1.0 O D:HOH148 4.8 19.0 1.0 CA D:ASP74 4.8 14.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmb Crosslinks


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmb Crosslinks within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn500 b:12.6 occ:1.00 NE2 B:HIS63 1.9 9.1 1.0 OD2 A:ASP74 2.0 12.8 1.0 NE2 C:HIS77 2.0 12.9 1.0 NE2 C:HIS73 2.0 9.9 1.0 CG A:ASP74 2.7 14.7 1.0 OD1 A:ASP74 2.8 16.6 1.0 CD2 B:HIS63 2.9 9.4 1.0 CE1 B:HIS63 2.9 10.9 1.0 CE1 C:HIS73 3.0 12.8 1.0 CD2 C:HIS77 3.0 11.0 1.0 CE1 C:HIS77 3.0 9.7 1.0 CD2 C:HIS73 3.1 5.0 1.0 ND1 B:HIS63 4.0 13.1 1.0 CG B:HIS63 4.0 10.7 1.0 ND1 C:HIS73 4.1 12.3 1.0 O A:HOH143 4.1 22.9 1.0 ND1 C:HIS77 4.1 10.3 1.0 CG C:HIS77 4.2 8.3 1.0 CB A:ASP74 4.2 12.5 1.0 CD1 B:ILE67 4.2 12.7 1.0 CG C:HIS73 4.2 8.9 1.0 O C:HOH242 4.4 30.2 1.0 O C:HOH378 4.5 24.6 1.0 O A:HOH174 4.7 20.7 1.0 CA A:ASP74 4.8 10.9 1.0 O A:ASP74 4.8 11.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmb Crosslinks


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmb Crosslinks within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn500 b:13.4 occ:1.00 NE2 D:HIS73 1.9 12.2 1.0 NE2 D:HIS77 2.0 8.9 1.0 NE2 A:HIS63 2.0 12.8 1.0 OD2 B:ASP74 2.2 13.8 1.0 OD1 B:ASP74 2.3 18.1 1.0 CG B:ASP74 2.6 12.3 1.0 CE1 D:HIS73 2.8 24.2 1.0 CD2 A:HIS63 2.9 11.0 1.0 CE1 D:HIS77 3.0 13.1 1.0 CD2 D:HIS73 3.0 17.6 1.0 CD2 D:HIS77 3.0 6.9 1.0 CE1 A:HIS63 3.1 11.3 1.0 ND1 D:HIS73 4.0 23.6 1.0 CB B:ASP74 4.1 12.3 1.0 CG A:HIS63 4.1 11.3 1.0 CG D:HIS73 4.1 17.1 1.0 ND1 D:HIS77 4.1 9.7 1.0 ND1 A:HIS63 4.1 10.7 1.0 CG D:HIS77 4.2 13.2 1.0 O D:HOH165 4.3 23.8 1.0 O B:HOH359 4.5 29.7 1.0 O D:HOH324 4.7 31.1 1.0 O B:ASP74 4.7 12.0 1.0 CA B:ASP74 4.8 12.4 1.0 O B:HOH221 4.8 22.1 1.0 CD1 A:ILE67 4.9 14.9 1.0 O B:HOH266 4.9 25.1 1.0

E.N.Salgado, J.D.Brodin, M.M.To, F.A.Tezcan. Templated Construction of A Zn-Selective Protein Dimerization Motif. Inorg.Chem. V. 50 6323 2011.
ISSN: ISSN 0020-1669
PubMed: 21648390
DOI: 10.1021/IC200746M