Zinc in PDB 4jea: Crystal Structure of An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds

The structure of Crystal Structure of An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds, PDB code: 4jea was solved by F.A.Tezcan, A.M.Medina-Morales, A.Perez, J.D.Brodin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.94 / 1.22
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.850, 64.788, 74.177, 90.00, 98.18, 90.00
R / Rfree (%)	13.1 / 17.9

The structure of Crystal Structure of An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds (pdb code 4jea). 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 An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds, PDB code: 4jea:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds


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 An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:12.2 occ:1.00 OD2 D:ASP74 2.0 13.6 1.0 NE2 B:HIS63 2.1 12.7 1.0 NE2 A:HIS77 2.1 13.2 1.0 NE2 A:HIS73 2.1 11.4 1.0 CG D:ASP74 2.8 13.1 1.0 OD1 D:ASP74 2.9 15.5 1.0 CE1 A:HIS77 3.0 21.6 1.0 CD2 B:HIS63 3.1 13.4 1.0 CE1 B:HIS63 3.1 15.8 1.0 CD2 A:HIS73 3.1 12.2 1.0 CE1 A:HIS73 3.1 13.5 1.0 CD2 A:HIS77 3.2 12.3 1.0 ND1 A:HIS77 4.2 21.7 1.0 ND1 B:HIS63 4.2 15.4 1.0 CD1 B:ILE67 4.2 21.5 1.0 ND1 A:HIS73 4.2 13.1 1.0 CG B:HIS63 4.2 13.4 1.0 CB D:ASP74 4.3 13.3 1.0 CG A:HIS73 4.3 12.2 1.0 CG A:HIS77 4.3 14.4 1.0 O2 D:SO4203 4.5 40.0 1.0 O1 D:SO4203 4.8 43.8 1.0 CG1 B:ILE67 5.0 16.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds


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 An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:11.0 occ:1.00 OD2 C:ASP74 2.0 12.3 1.0 NE2 A:HIS63 2.1 11.2 1.0 NE2 B:HIS73 2.1 11.1 1.0 NE2 B:HIS77 2.1 11.8 1.0 CG C:ASP74 2.8 11.9 1.0 OD1 C:ASP74 2.9 13.8 1.0 CE1 B:HIS77 3.0 16.1 1.0 CD2 A:HIS63 3.0 12.0 1.0 CE1 B:HIS73 3.0 12.8 1.0 CE1 A:HIS63 3.0 14.5 1.0 CD2 B:HIS73 3.1 11.2 1.0 CD2 B:HIS77 3.2 11.6 1.0 CD1 A:ILE67 4.1 15.2 0.5 ND1 A:HIS63 4.2 14.1 1.0 ND1 B:HIS73 4.2 13.0 1.0 ND1 B:HIS77 4.2 17.2 1.0 CG A:HIS63 4.2 11.6 1.0 CB C:ASP74 4.3 12.6 1.0 CG B:HIS73 4.3 11.2 1.0 CG B:HIS77 4.3 12.5 1.0 O C:HOH401 4.4 43.3 1.0 O1 C:SO4203 4.5 36.6 1.0 O4 C:SO4203 4.6 37.3 1.0 CG1 A:ILE67 4.7 13.3 0.5

Zinc binding site 3 out of 4 in the Crystal Structure of An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds


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 An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:11.2 occ:1.00 OD2 B:ASP74 2.0 12.4 1.0 NE2 C:HIS73 2.0 10.9 1.0 NE2 D:HIS63 2.0 11.3 1.0 NE2 C:HIS77 2.1 13.7 1.0 CG B:ASP74 2.8 12.1 1.0 OD1 B:ASP74 2.9 14.9 1.0 CE1 C:HIS77 3.0 22.7 1.0 CD2 D:HIS63 3.0 12.3 1.0 CD2 C:HIS73 3.1 12.3 1.0 CE1 D:HIS63 3.1 14.2 1.0 CE1 C:HIS73 3.1 12.9 1.0 CD2 C:HIS77 3.1 11.7 1.0 CD1 D:ILE67 4.1 20.0 1.0 ND1 C:HIS77 4.1 24.1 1.0 ND1 D:HIS63 4.2 13.6 1.0 ND1 C:HIS73 4.2 12.8 1.0 CG D:HIS63 4.2 11.6 1.0 CG C:HIS73 4.2 11.3 1.0 CG C:HIS77 4.3 13.4 1.0 CB B:ASP74 4.3 12.2 1.0 O3 C:SO4203 4.5 37.5 1.0 CG1 D:ILE67 4.8 16.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds


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 An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:11.5 occ:1.00 NE2 C:HIS63 2.0 11.4 1.0 OD2 A:ASP74 2.0 12.3 1.0 NE2 D:HIS77 2.1 13.7 1.0 NE2 D:HIS73 2.1 12.2 1.0 CG A:ASP74 2.8 12.9 1.0 OD1 A:ASP74 2.9 15.1 1.0 CE1 D:HIS77 3.0 21.6 1.0 CE1 C:HIS63 3.0 14.5 1.0 CD2 C:HIS63 3.0 12.8 1.0 CD2 D:HIS73 3.1 11.8 1.0 CE1 D:HIS73 3.1 13.6 1.0 CD2 D:HIS77 3.1 12.7 1.0 CD1 C:ILE67 4.1 20.1 1.0 ND1 D:HIS77 4.2 24.2 1.0 ND1 D:HIS73 4.2 13.4 1.0 ND1 C:HIS63 4.2 14.7 1.0 CG C:HIS63 4.2 11.6 1.0 CG D:HIS73 4.2 11.8 1.0 CB A:ASP74 4.3 12.9 1.0 CG D:HIS77 4.3 14.7 1.0 O D:HOH326 4.6 47.5 1.0 O3 D:SO4203 4.6 32.8 1.0 CG1 C:ILE67 4.9 16.3 1.0

A.Medina-Morales, A.Perez, J.D.Brodin, F.A.Tezcan. In Vitro and Cellular Self-Assembly of A Zn-Binding Protein Cryptand Via Templated Disulfide Bonds. J.Am.Chem.Soc. V. 135 12013 2013.
ISSN: ISSN 0002-7863
PubMed: 23905754
DOI: 10.1021/JA405318D