Zinc in PDB 3tom: Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets

The structure of Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets, PDB code: 3tom was solved by J.B.Brodin, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.80 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	95.690, 37.843, 138.489, 90.00, 112.61, 90.00
R / Rfree (%)	21 / 28.6

The structure of Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets (pdb code 3tom). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets, PDB code: 3tom:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets


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 Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn107 b:27.6 occ:1.00 NE2 A:HIS77 2.0 28.7 1.0 NE2 A:HIS73 2.0 31.9 1.0 NE2 B:HIS63 2.0 28.3 1.0 CE1 A:HIS77 2.7 31.9 1.0 CE1 A:HIS73 2.8 31.0 1.0 CD2 B:HIS63 2.9 25.4 1.0 CE1 B:HIS63 3.0 29.5 1.0 CD2 A:HIS73 3.1 28.4 1.0 CD2 A:HIS77 3.1 30.0 1.0 CD1 B:ILE67 3.2 25.6 1.0 ND1 A:HIS77 3.9 32.4 1.0 ND1 A:HIS73 4.0 29.3 1.0 CG B:HIS63 4.1 25.4 1.0 ND1 B:HIS63 4.1 29.1 1.0 CG A:HIS73 4.1 28.9 1.0 CG A:HIS77 4.2 31.7 1.0 CG1 B:ILE67 4.4 24.0 1.0 O A:HOH120 4.6 29.1 1.0 O B:HOH148 4.7 32.2 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets


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 Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn107 b:18.8 occ:1.00 NE2 A:HIS63 1.9 28.3 1.0 NE2 B:HIS73 2.1 25.4 1.0 NE2 B:HIS77 2.2 21.4 1.0 CE1 B:HIS73 2.7 26.9 1.0 CE1 A:HIS63 2.9 31.9 1.0 CD2 A:HIS63 2.9 27.7 1.0 CD2 B:HIS77 3.2 19.4 1.0 CE1 B:HIS77 3.2 22.8 1.0 CD2 B:HIS73 3.3 22.1 1.0 CG1 A:ILE67 3.8 26.6 1.0 ND1 B:HIS73 3.9 26.4 1.0 ND1 A:HIS63 4.0 30.7 1.0 CG A:HIS63 4.1 28.3 1.0 CD1 A:ILE67 4.1 27.8 1.0 CG B:HIS73 4.2 21.6 1.0 CG B:HIS77 4.3 20.2 1.0 ND1 B:HIS77 4.3 22.5 1.0 O B:HOH147 5.0 33.2 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets


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 Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn108 b:30.0 occ:1.00 OE2 D:GLU49 1.8 24.0 1.0 OD2 B:ASP39 2.0 33.0 1.0 O B:ALA1 2.2 33.8 1.0 O D:HOH152 2.3 37.0 1.0 N B:ALA1 2.5 38.8 1.0 CD D:GLU49 2.7 26.9 1.0 CG B:ASP39 2.8 28.0 1.0 OE1 D:GLU49 2.9 28.5 1.0 C B:ALA1 3.0 35.7 1.0 OD1 B:ASP39 3.0 29.0 1.0 CA B:ALA1 3.2 37.7 1.0 CB B:ALA1 3.7 36.0 1.0 CG D:GLU49 4.1 28.9 1.0 O B:HOH118 4.1 24.5 1.0 CB B:ASP39 4.2 25.4 1.0 N B:ASP2 4.3 36.3 1.0 ND2 B:ASN6 4.4 28.0 1.0 NZ B:LYS42 4.6 35.9 1.0 CA B:ASP2 5.0 34.9 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets


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 Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn107 b:36.2 occ:1.00 NE2 C:HIS77 2.0 37.2 1.0 NE2 D:HIS63 2.1 40.0 1.0 NE2 C:HIS73 2.2 36.3 1.0 CE1 C:HIS77 2.8 38.8 1.0 CD2 C:HIS77 3.0 37.9 1.0 CD2 D:HIS63 3.1 35.5 1.0 CE1 C:HIS73 3.1 36.4 1.0 CE1 D:HIS63 3.1 42.2 1.0 CD2 C:HIS73 3.1 34.3 1.0 CD1 D:ILE67 3.3 34.2 1.0 ND1 C:HIS77 4.0 39.6 1.0 CG C:HIS77 4.1 39.8 1.0 ND1 C:HIS73 4.2 34.2 1.0 ND1 D:HIS63 4.2 40.5 1.0 CG D:HIS63 4.2 35.9 1.0 CG C:HIS73 4.2 34.0 1.0 O D:HOH175 4.4 44.9 1.0 CG1 D:ILE67 4.7 32.3 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn107 b:29.1 occ:1.00 NE2 D:HIS73 1.9 35.0 1.0 NE2 C:HIS63 2.0 37.0 1.0 NE2 D:HIS77 2.1 32.8 1.0 CE1 D:HIS73 2.7 35.1 1.0 CE1 C:HIS63 3.0 39.0 1.0 CE1 D:HIS77 3.0 33.4 1.0 CD2 C:HIS63 3.0 34.0 1.0 CD2 D:HIS73 3.1 32.0 1.0 CD2 D:HIS77 3.1 30.5 1.0 ND1 D:HIS73 3.9 34.0 1.0 CG1 C:ILE67 4.1 34.2 1.0 CG D:HIS73 4.1 30.2 1.0 ND1 C:HIS63 4.1 37.6 1.0 ND1 D:HIS77 4.2 33.1 1.0 CG C:HIS63 4.2 34.9 1.0 CG D:HIS77 4.3 31.1 1.0 CD1 C:ILE67 4.5 35.9 1.0 O C:HOH146 4.8 34.0 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn108 b:32.6 occ:1.00 OE2 B:GLU49 2.0 35.9 1.0 OD2 D:ASP39 2.2 31.4 1.0 O D:HOH151 2.2 32.9 1.0 O D:ALA1 2.2 33.7 1.0 N D:ALA1 2.3 39.3 1.0 CD B:GLU49 2.7 35.8 1.0 OE1 B:GLU49 2.7 37.9 1.0 OD1 D:ASP39 2.8 31.4 1.0 CG D:ASP39 2.8 29.8 1.0 C D:ALA1 3.0 35.3 1.0 CA D:ALA1 3.0 38.0 1.0 CB D:ALA1 3.6 36.8 1.0 CG B:GLU49 4.1 33.9 1.0 N D:ASP2 4.2 35.3 1.0 ND2 D:ASN6 4.3 29.7 1.0 CB D:ASP39 4.3 28.2 1.0 NZ D:LYS42 4.3 36.4 1.0 OD1 D:ASN6 4.8 31.5 1.0 O D:ASP39 4.9 26.2 1.0 CG D:ASN6 5.0 30.4 1.0 CA D:ASP2 5.0 33.4 1.0

J.D.Brodin, X.I.Ambroggio, C.Tang, K.N.Parent, T.S.Baker, F.A.Tezcan. Metal-Directed, Chemically Tunable Assembly of One-, Two- and Three-Dimensional Crystalline Protein Arrays. Nat Chem V. 4 375 2012.
PubMed: 22522257
DOI: 10.1038/NCHEM.1290