Zinc in PDB 4jeb: Crystal Structure of An Engineered RIDC1 Tetramer with Four Interfacial Disulfide Bonds and Four Three-Coordinate Zn(II) Sites

The structure of Crystal Structure of An Engineered RIDC1 Tetramer with Four Interfacial Disulfide Bonds and Four Three-Coordinate Zn(II) Sites, PDB code: 4jeb 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)	48.55 / 2.30
Space group	P 31 1 2
Cell size a, b, c (Å), α, β, γ (°)	54.942, 54.942, 145.658, 90.00, 90.00, 120.00
R / Rfree (%)	24.4 / 30.9

The structure of Crystal Structure of An Engineered RIDC1 Tetramer with Four Interfacial Disulfide Bonds and Four Three-Coordinate Zn(II) Sites also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of An Engineered RIDC1 Tetramer with Four Interfacial Disulfide Bonds and Four Three-Coordinate Zn(II) Sites (pdb code 4jeb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of An Engineered RIDC1 Tetramer with Four Interfacial Disulfide Bonds and Four Three-Coordinate Zn(II) Sites, PDB code: 4jeb:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of An Engineered RIDC1 Tetramer with Four Interfacial Disulfide Bonds and Four Three-Coordinate Zn(II) Sites


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 RIDC1 Tetramer with Four Interfacial Disulfide Bonds and Four Three-Coordinate Zn(II) Sites within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:48.6 occ:1.00 O A:HOH301 2.1 26.2 1.0 NE2 A:HIS73 2.2 48.2 1.0 NE2 A:HIS77 2.3 62.8 1.0 NE2 B:HIS63 2.3 54.8 1.0 CD2 B:HIS63 3.1 53.5 1.0 CD2 A:HIS73 3.1 45.3 1.0 CE1 A:HIS77 3.1 63.1 1.0 CE1 A:HIS73 3.2 45.2 1.0 CD2 A:HIS77 3.4 61.3 1.0 CE1 B:HIS63 3.5 55.7 1.0 CD1 B:TRP66 4.0 46.7 1.0 NE1 B:TRP66 4.1 49.5 1.0 ND1 A:HIS73 4.3 47.0 1.0 CG A:HIS73 4.3 46.0 1.0 CG B:HIS63 4.3 52.6 1.0 ND1 A:HIS77 4.3 62.0 1.0 ND1 B:HIS63 4.5 54.0 1.0 CG A:HIS77 4.5 60.4 1.0 CG B:TRP66 4.8 46.1 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of An Engineered RIDC1 Tetramer with Four Interfacial Disulfide Bonds and Four Three-Coordinate Zn(II) Sites


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 RIDC1 Tetramer with Four Interfacial Disulfide Bonds and Four Three-Coordinate Zn(II) Sites within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:45.0 occ:1.00 O A:HOH304 2.2 60.3 0.5 OD1 A:ASP39 2.2 45.3 1.0 CG A:ASP39 3.1 45.1 1.0 OD2 A:ASP39 3.4 44.6 1.0 O A:ASP39 4.4 42.9 1.0 CB A:ASP39 4.4 43.0 1.0 CA A:ASP39 4.7 42.1 1.0 OG A:SER42 4.7 50.0 1.0 N A:ALA1 4.7 49.8 1.0 O A:ALA1 4.8 49.6 1.0 C A:ASP39 4.9 42.7 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of An Engineered RIDC1 Tetramer with Four Interfacial Disulfide Bonds and Four Three-Coordinate Zn(II) Sites


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 RIDC1 Tetramer with Four Interfacial Disulfide Bonds and Four Three-Coordinate Zn(II) Sites within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:52.5 occ:1.00 NE2 B:HIS77 2.1 63.1 1.0 NE2 A:HIS63 2.1 54.5 1.0 O B:HOH301 2.1 33.1 1.0 NE2 B:HIS73 2.2 47.3 1.0 CE1 A:HIS63 2.7 55.0 1.0 CE1 B:HIS77 2.9 63.6 1.0 CD2 B:HIS73 3.1 44.9 1.0 CD2 B:HIS77 3.2 61.2 1.0 CE1 B:HIS73 3.2 45.2 1.0 CD2 A:HIS63 3.3 54.6 1.0 ND1 A:HIS63 4.0 53.1 1.0 ND1 B:HIS77 4.1 61.4 1.0 CG B:HIS77 4.2 60.7 1.0 CG A:HIS63 4.3 52.8 1.0 ND1 B:HIS73 4.3 46.2 1.0 CG B:HIS73 4.3 46.4 1.0 CD1 A:TRP66 4.5 43.1 0.5 CE3 A:TRP66 4.7 48.5 0.5 CZ3 A:TRP66 4.9 48.2 0.5

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