Zinc in PDB 5bu7: Crystal Structure of An Engineered Protein That Forms Nanotubes with Tunable Diameters

The structure of Crystal Structure of An Engineered Protein That Forms Nanotubes with Tunable Diameters, PDB code: 5bu7 was solved by J.D.Brodin, S.J.Smith, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.80 / 2.46
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	52.890, 52.890, 257.080, 90.00, 90.00, 120.00
R / Rfree (%)	22.5 / 29.2

The structure of Crystal Structure of An Engineered Protein That Forms Nanotubes with Tunable Diameters also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of An Engineered Protein That Forms Nanotubes with Tunable Diameters (pdb code 5bu7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of An Engineered Protein That Forms Nanotubes with Tunable Diameters, PDB code: 5bu7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Crystal Structure of An Engineered Protein That Forms Nanotubes with Tunable Diameters


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 Protein That Forms Nanotubes with Tunable Diameters within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:55.5 occ:1.00 OD2 A:ASP39 2.1 64.0 1.0 N A:ALA1 2.1 52.4 1.0 O A:ALA1 2.3 42.0 1.0 OD1 A:ASP39 2.7 61.0 1.0 CG A:ASP39 2.7 57.1 1.0 C A:ALA1 3.0 46.1 1.0 CA A:ALA1 3.1 48.7 1.0 NZ A:LYS42 3.8 74.8 1.0 CB A:ALA1 4.1 46.9 1.0 CB A:ASP39 4.2 52.6 1.0 N A:ASP2 4.3 50.8 1.0 CE A:LYS42 4.3 74.2 1.0 ND2 A:ASN6 4.5 41.1 1.0 O A:ASP39 4.9 36.1 1.0

Zinc binding site 2 out of 7 in the Crystal Structure of An Engineered Protein That Forms Nanotubes with Tunable Diameters


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 Protein That Forms Nanotubes with Tunable Diameters within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:44.8 occ:0.50 OE2 A:GLU8 1.8 46.2 1.0 OD2 A:ASP12 2.0 46.8 1.0 CG A:ASP12 2.7 50.6 1.0 OD1 A:ASP12 2.8 50.7 1.0 CD A:GLU8 3.0 49.6 1.0 OE1 A:GLU8 3.8 57.5 1.0 CG A:GLU8 4.1 51.8 1.0 CB A:ASP12 4.2 47.5 1.0 O A:GLU8 4.6 36.6 1.0 CB A:GLU8 4.6 47.7 1.0

Zinc binding site 3 out of 7 in the Crystal Structure of An Engineered Protein That Forms Nanotubes with Tunable Diameters


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 Protein That Forms Nanotubes with Tunable Diameters within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:36.2 occ:1.00 NE2 A:HIS73 2.0 32.8 1.0 NE2 A:HIS77 2.1 32.9 1.0 NE2 B:HIS63 2.3 43.6 1.0 CE1 A:HIS73 2.8 33.2 1.0 CD2 A:HIS77 3.1 30.7 1.0 CE1 A:HIS77 3.1 30.7 1.0 CD2 A:HIS73 3.1 32.9 1.0 CD2 B:HIS63 3.2 42.7 1.0 CE1 B:HIS63 3.2 46.0 1.0 ND1 A:HIS73 3.9 33.4 1.0 CD1 B:ILE67 4.0 34.6 1.0 CG A:HIS73 4.1 34.0 1.0 ND1 A:HIS77 4.2 31.7 1.0 CG A:HIS77 4.2 31.9 1.0 ND1 B:HIS63 4.2 51.8 1.0 CG B:HIS63 4.3 45.0 1.0 CG1 B:ILE67 4.9 33.6 1.0

Zinc binding site 4 out of 7 in the Crystal Structure of An Engineered Protein That Forms Nanotubes with Tunable Diameters


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 Protein That Forms Nanotubes with Tunable Diameters within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:48.9 occ:0.50 OE1 A:GLU27 1.8 72.8 1.0 O B:HOH319 2.1 50.1 1.0 NE2 B:HIS59 2.3 70.1 1.0 OE1 A:GLU31 2.3 70.6 1.0 OE2 A:GLU31 2.5 59.1 1.0 CD A:GLU31 2.6 62.8 1.0 CD A:GLU27 2.9 69.0 1.0 CE1 B:HIS59 2.9 69.7 1.0 OE2 A:GLU27 3.4 67.7 1.0 CD2 B:HIS59 3.5 74.0 1.0 CG A:GLU31 3.8 53.2 1.0 OD1 B:ASP54 3.9 96.2 1.0 CD A:LYS28 4.0 62.7 1.0 ND1 B:HIS59 4.1 73.1 1.0 CG A:GLU27 4.2 59.3 1.0 O B:HOH311 4.3 52.4 1.0 NH2 B:ARG62 4.4 74.1 1.0 O B:HOH323 4.4 53.8 1.0 CG B:HIS59 4.4 71.9 1.0 CA A:LYS28 4.4 46.9 1.0 CG A:LYS28 4.4 55.8 1.0 O A:GLU27 4.5 43.3 1.0 CB A:GLU27 4.5 52.9 1.0 C A:GLU27 4.5 44.6 1.0 N A:LYS28 4.5 46.9 1.0 CB A:GLU31 4.7 47.7 1.0

Zinc binding site 5 out of 7 in the Crystal Structure of An Engineered Protein That Forms Nanotubes with Tunable Diameters


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 Protein That Forms Nanotubes with Tunable Diameters within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:40.0 occ:1.00 NE2 B:HIS77 2.0 36.3 1.0 NE2 B:HIS73 2.1 33.4 1.0 NE2 A:HIS63 2.1 40.1 1.0 CD2 A:HIS63 2.9 40.8 1.0 CE1 B:HIS73 2.9 35.0 1.0 CE1 B:HIS77 3.0 39.4 1.0 CD2 B:HIS77 3.1 38.2 1.0 CE1 A:HIS63 3.1 47.4 1.0 CD2 B:HIS73 3.1 33.6 1.0 CG A:HIS63 4.1 44.9 1.0 ND1 B:HIS73 4.1 32.7 1.0 ND1 B:HIS77 4.1 40.9 1.0 CD1 A:ILE67 4.1 38.2 1.0 ND1 A:HIS63 4.1 45.6 1.0 CG B:HIS77 4.2 41.4 1.0 CG B:HIS73 4.2 32.4 1.0 O B:HOH307 4.7 38.8 1.0 CG1 A:ILE67 5.0 37.0 1.0

Zinc binding site 6 out of 7 in the Crystal Structure of An Engineered Protein That Forms Nanotubes with Tunable Diameters


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 Protein That Forms Nanotubes with Tunable Diameters within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:46.5 occ:0.30 O B:ALA1 2.1 58.8 1.0 O B:HOH316 2.1 42.0 1.0 N B:ALA1 2.2 55.0 1.0 OD2 B:ASP39 2.4 65.4 1.0 C B:ALA1 2.8 58.5 1.0 CA B:ALA1 3.0 60.6 1.0 OD1 B:ASP39 3.1 60.2 1.0 CG B:ASP39 3.1 56.2 1.0 CB B:ALA1 4.1 63.0 1.0 N B:ASP2 4.1 51.5 1.0 NZ B:LYS42 4.2 87.3 1.0 CE B:LYS42 4.5 82.5 1.0 CB B:ASP39 4.6 51.5 1.0 ND2 B:ASN6 4.7 55.2 1.0 CA B:ASP2 4.8 52.5 1.0

Zinc binding site 7 out of 7 in the Crystal Structure of An Engineered Protein That Forms Nanotubes with Tunable Diameters


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of An Engineered Protein That Forms Nanotubes with Tunable Diameters within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn204 b:51.8 occ:0.50 OE1 B:GLU27 1.9 75.2 1.0 OE1 B:GLU31 2.3 67.5 1.0 O A:HOH311 2.3 45.9 1.0 NE2 A:HIS59 2.4 58.3 1.0 OE2 B:GLU31 2.5 69.9 1.0 CD B:GLU31 2.6 71.8 1.0 CE1 A:HIS59 2.9 58.2 1.0 CD B:GLU27 3.1 76.5 1.0 OE2 B:GLU27 3.5 79.4 1.0 OD1 A:ASP54 3.6 0.6 1.0 CD2 A:HIS59 3.6 59.5 1.0 CG B:GLU31 3.9 63.9 1.0 ND1 A:HIS59 4.1 59.6 1.0 O A:HOH302 4.2 56.3 1.0 CD B:LYS28 4.2 79.3 1.0 NH2 A:ARG62 4.3 54.7 1.0 CG B:GLU27 4.4 75.1 1.0 CG A:HIS59 4.5 58.6 1.0 CG B:LYS28 4.6 75.1 1.0 CA B:LYS28 4.6 62.2 1.0 CG A:ASP54 4.7 94.3 1.0 O B:GLU27 4.7 62.5 1.0 N B:LYS28 4.7 65.7 1.0 CB B:GLU27 4.7 69.4 1.0 O B:HOH309 4.7 42.9 1.0 C B:GLU27 4.7 62.9 1.0 CB B:GLU31 4.8 59.7 1.0

J.D.Brodin, S.J.Smith, F.A.Tezcan. Designed, Helical Protein Nanotubes with Tunable Diameters From A Single Building Block. To Be Published.