Zinc in PDB 5l32: Crystal Structure of the Zn-RIDC1 Complex Bearing Six Interfacial Disulfide Bonds

The structure of Crystal Structure of the Zn-RIDC1 Complex Bearing Six Interfacial Disulfide Bonds, PDB code: 5l32 was solved by L.A.Churchfield, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.81 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.060, 62.533, 72.437, 90.00, 99.01, 90.00
R / Rfree (%)	21.4 / 25

The structure of Crystal Structure of the Zn-RIDC1 Complex Bearing Six Interfacial Disulfide Bonds 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 Bearing Six Interfacial Disulfide Bonds (pdb code 5l32). 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 Bearing Six Interfacial Disulfide Bonds, PDB code: 5l32:
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 Bearing Six 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 the Zn-RIDC1 Complex Bearing Six Interfacial Disulfide Bonds within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:31.9 occ:1.00 OD1 D:ASP74 1.8 34.5 1.0 NE2 C:HIS63 2.1 34.9 1.0 NE2 A:HIS77 2.2 28.6 1.0 NE2 A:HIS73 2.2 34.2 1.0 CG D:ASP74 2.8 41.2 1.0 CD2 C:HIS63 2.9 39.8 1.0 CE1 A:HIS73 3.0 35.6 1.0 CE1 A:HIS77 3.1 42.1 1.0 OD2 D:ASP74 3.1 41.1 1.0 CD2 A:HIS77 3.2 34.0 1.0 CE1 C:HIS63 3.3 46.1 1.0 CD2 A:HIS73 3.4 38.3 1.0 O D:HOH304 4.0 33.8 1.0 CG C:HIS63 4.1 38.5 1.0 CD1 C:ILE67 4.2 30.7 1.0 ND1 A:HIS73 4.2 33.3 1.0 CB D:ASP74 4.2 30.2 1.0 ND1 A:HIS77 4.3 34.1 1.0 ND1 C:HIS63 4.3 39.6 1.0 CG A:HIS77 4.3 37.5 1.0 CG A:HIS73 4.4 35.0 1.0 CA D:ASP74 4.8 35.1 1.0 O D:ASP74 4.9 34.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Zn-RIDC1 Complex Bearing Six 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 the Zn-RIDC1 Complex Bearing Six Interfacial Disulfide Bonds within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:31.4 occ:1.00 NE2 A:HIS63 1.8 28.1 1.0 OD1 B:ASP74 1.8 39.9 1.0 NE2 C:HIS77 2.2 28.9 1.0 NE2 C:HIS73 2.2 30.3 1.0 CE1 A:HIS63 2.7 29.5 1.0 CG B:ASP74 2.8 42.0 1.0 CD2 A:HIS63 2.9 29.8 1.0 CE1 C:HIS73 3.1 36.9 1.0 CD2 C:HIS77 3.1 33.6 1.0 OD2 B:ASP74 3.1 39.4 1.0 CE1 C:HIS77 3.2 36.5 1.0 CD2 C:HIS73 3.3 37.0 1.0 ND1 A:HIS63 3.9 35.4 1.0 CG A:HIS63 4.0 34.2 1.0 CB B:ASP74 4.2 36.9 1.0 CD1 A:ILE67 4.2 32.1 1.0 ND1 C:HIS73 4.3 31.3 1.0 CG C:HIS77 4.3 34.3 1.0 ND1 C:HIS77 4.3 34.3 1.0 CG C:HIS73 4.4 34.7 1.0 O C:HOH318 4.8 35.0 1.0 CA B:ASP74 4.8 31.7 1.0 O B:ASP74 4.8 34.7 1.0 CG1 A:ILE67 4.9 32.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Zn-RIDC1 Complex Bearing Six 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 the Zn-RIDC1 Complex Bearing Six Interfacial Disulfide Bonds within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:30.4 occ:1.00 OD1 A:ASP74 1.9 32.9 1.0 NE2 D:HIS73 2.1 35.5 1.0 NE2 B:HIS63 2.1 34.2 1.0 NE2 D:HIS77 2.1 39.7 1.0 CE1 D:HIS73 2.8 34.6 1.0 CG A:ASP74 2.9 37.4 1.0 CD2 B:HIS63 3.0 36.5 1.0 CE1 D:HIS77 3.1 43.1 1.0 OD2 A:ASP74 3.1 34.2 1.0 CD2 D:HIS77 3.1 41.3 1.0 CE1 B:HIS63 3.1 42.8 1.0 CD2 D:HIS73 3.3 38.2 1.0 ND1 D:HIS73 4.0 33.9 1.0 CD1 B:ILE67 4.1 24.6 1.0 CG B:HIS63 4.2 35.2 1.0 ND1 D:HIS77 4.2 36.1 1.0 ND1 B:HIS63 4.2 35.2 1.0 CG D:HIS77 4.3 41.2 1.0 CG D:HIS73 4.3 33.3 1.0 CB A:ASP74 4.3 34.1 1.0 O D:HOH311 4.7 36.2 1.0 CG1 B:ILE67 4.7 31.7 1.0 O D:HOH304 4.8 33.8 1.0 CA A:ASP74 4.9 29.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Zn-RIDC1 Complex Bearing Six 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 the Zn-RIDC1 Complex Bearing Six Interfacial Disulfide Bonds within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:32.5 occ:1.00 OD1 C:ASP74 2.0 34.8 1.0 NE2 B:HIS77 2.0 36.2 1.0 NE2 D:HIS63 2.1 37.9 1.0 NE2 B:HIS73 2.2 38.0 1.0 CD2 D:HIS63 2.9 39.7 1.0 CE1 B:HIS77 3.0 42.0 1.0 CE1 B:HIS73 3.0 33.6 1.0 CG C:ASP74 3.1 38.5 1.0 CD2 B:HIS77 3.1 39.2 1.0 CE1 D:HIS63 3.3 44.1 1.0 CD2 B:HIS73 3.3 39.7 1.0 OD2 C:ASP74 3.4 41.2 1.0 CG D:HIS63 4.1 40.0 1.0 ND1 B:HIS77 4.1 39.9 1.0 CD1 D:ILE67 4.2 33.8 1.0 CG B:HIS77 4.2 38.7 1.0 ND1 B:HIS73 4.2 35.3 1.0 ND1 D:HIS63 4.3 41.2 1.0 CG B:HIS73 4.4 38.5 1.0 CB C:ASP74 4.4 34.8 1.0 O B:HOH315 4.6 43.9 1.0 CA C:ASP74 4.9 35.7 1.0 O C:ASP74 4.9 37.7 1.0

L.A.Churchfield, A.Medina-Morales, J.D.Brodin, A.Perez, F.A.Tezcan. De Novo Design of An Allosteric Metalloprotein Assembly with Strained Disulfide Bonds. J.Am.Chem.Soc. V. 138 13163 2016.
ISSN: ESSN 1520-5126
PubMed: 27649076
DOI: 10.1021/JACS.6B08458