Zinc in PDB 8tfm: Porx with Zn (Primitive Orthorhombic Crystal Form)

The structure of Porx with Zn (Primitive Orthorhombic Crystal Form), PDB code: 8tfm was solved by A.Saran, N.Zeytuni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.58 / 2.72
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.868, 97.058, 132.037, 90, 90, 90
R / Rfree (%)	20.4 / 26.1

The binding sites of Zinc atom in the Porx with Zn (Primitive Orthorhombic Crystal Form) (pdb code 8tfm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Porx with Zn (Primitive Orthorhombic Crystal Form), PDB code: 8tfm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Porx with Zn (Primitive Orthorhombic Crystal Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Porx with Zn (Primitive Orthorhombic Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:71.0 occ:1.00 OD1 A:ASP11 2.2 71.3 1.0 OD2 A:ASP54 2.3 64.9 1.0 O A:ASN56 2.5 63.0 1.0 O A:HOH705 2.8 46.9 1.0 CG A:ASP11 3.1 73.7 1.0 OD2 A:ASP11 3.2 76.0 1.0 CG A:ASP54 3.4 58.4 1.0 C A:ASN56 3.7 65.5 1.0 OD1 A:ASP54 3.9 56.8 1.0 OE1 A:GLU12 4.0 75.9 1.0 OD1 A:ASP10 4.1 67.4 1.0 CB A:ASP11 4.5 73.5 1.0 CG A:GLU12 4.6 83.5 1.0 CB A:ASN56 4.6 68.0 1.0 CD A:GLU12 4.6 80.7 1.0 CA A:ASN56 4.7 65.1 1.0 CB A:ASP54 4.7 57.1 1.0 N A:MET57 4.7 66.6 1.0 CA A:MET57 4.8 68.5 1.0 CG A:ASP10 4.8 65.7 1.0 NZ A:LYS104 4.9 64.2 1.0 N A:ASP11 4.9 68.2 1.0 N A:ASN56 4.9 64.4 1.0 OD2 A:ASP10 5.0 68.4 1.0

Zinc binding site 2 out of 6 in the Porx with Zn (Primitive Orthorhombic Crystal Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Porx with Zn (Primitive Orthorhombic Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:87.9 occ:1.00 OD2 A:ASP414 1.8 99.1 1.0 NE2 A:HIS415 2.0 92.9 1.0 OG1 A:THR271 2.4 77.7 1.0 OD2 A:ASP237 2.4 69.5 1.0 CG A:ASP414 2.5 92.4 1.0 OD1 A:ASP237 2.7 69.5 1.0 OD1 A:ASP414 2.8 95.9 1.0 CG A:ASP237 2.8 70.0 1.0 CD2 A:HIS415 2.9 85.5 1.0 CE1 A:HIS415 2.9 90.8 1.0 CB A:THR271 3.5 78.7 1.0 CA A:THR271 3.6 84.3 1.0 N A:THR271 3.6 83.2 1.0 ND1 A:HIS415 3.9 86.6 1.0 CG A:HIS415 3.9 82.0 1.0 CB A:ASP414 4.0 90.6 1.0 CG2 A:THR271 4.0 74.2 1.0 N A:ASN238 4.1 74.7 1.0 CB A:ASP237 4.2 72.6 1.0 CB A:ASN238 4.5 73.2 1.0 C A:ALA270 4.5 84.9 1.0 CA A:ASP237 4.6 73.6 1.0 CA A:ASN238 4.6 70.2 1.0 O A:HOH708 4.6 64.1 1.0 C A:ASP237 4.7 73.9 1.0 CE1 A:HIS499 4.8 86.1 1.0 NE2 A:HIS499 4.9 85.4 1.0

Zinc binding site 3 out of 6 in the Porx with Zn (Primitive Orthorhombic Crystal Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Porx with Zn (Primitive Orthorhombic Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:107.1 occ:1.00 OD1 A:ASP360 2.2 73.4 1.0 NE2 A:HIS499 2.4 85.4 1.0 CE1 A:HIS364 2.8 91.5 1.0 CG A:ASP360 3.0 77.8 1.0 O A:HOH708 3.0 64.1 1.0 CE1 A:HIS499 3.1 86.1 1.0 OD2 A:ASP360 3.1 80.3 1.0 ND1 A:HIS364 3.4 91.2 1.0 CD2 A:HIS499 3.5 81.0 1.0 NE2 A:HIS364 3.9 89.7 1.0 ND1 A:HIS499 4.3 83.1 1.0 CB A:ASP360 4.4 79.2 1.0 CG A:HIS499 4.5 78.8 1.0 OG1 A:THR271 4.6 77.7 1.0 CG A:HIS364 4.7 85.7 1.0 CD2 A:HIS364 4.9 89.4 1.0 OD2 A:ASP237 4.9 69.5 1.0

Zinc binding site 4 out of 6 in the Porx with Zn (Primitive Orthorhombic Crystal Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Porx with Zn (Primitive Orthorhombic Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:58.5 occ:1.00 OD2 B:ASP414 1.6 47.9 1.0 OG1 B:THR271 2.1 57.8 1.0 OD2 B:ASP237 2.3 58.0 1.0 NE2 B:HIS415 2.3 47.9 1.0 OD1 B:ASP237 2.5 54.1 1.0 CG B:ASP414 2.5 47.9 1.0 CG B:ASP237 2.7 54.8 1.0 OD1 B:ASP414 2.9 44.5 1.0 CB B:THR271 3.0 60.3 1.0 CD2 B:HIS415 3.1 46.6 1.0 CE1 B:HIS415 3.3 47.1 1.0 CA B:THR271 3.3 59.4 1.0 CG2 B:THR271 3.5 60.7 1.0 N B:THR271 3.6 55.3 1.0 CB B:ASP414 3.9 47.4 1.0 CB B:ASP237 4.1 53.9 1.0 CG B:HIS415 4.2 46.8 1.0 ND1 B:HIS415 4.2 47.5 1.0 N B:ASN238 4.3 53.4 1.0 O B:HOH711 4.5 52.4 1.0 C B:ALA270 4.5 52.8 1.0 CA B:ASP237 4.5 52.5 1.0 CB B:ASN238 4.8 56.4 1.0 CD B:ARG275 4.8 56.3 1.0 C B:THR271 4.8 57.3 1.0 CE1 B:HIS499 4.8 50.0 1.0 C B:ASP237 4.8 51.7 1.0 CA B:ASN238 4.9 54.1 1.0 NH1 B:ARG275 5.0 59.1 1.0

Zinc binding site 5 out of 6 in the Porx with Zn (Primitive Orthorhombic Crystal Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Porx with Zn (Primitive Orthorhombic Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:67.4 occ:1.00 OD1 B:ASP360 2.0 51.9 1.0 NE2 B:HIS364 2.2 53.9 1.0 NE2 B:HIS499 2.3 51.3 1.0 O B:HOH711 2.6 52.4 1.0 CG B:ASP360 2.8 53.8 1.0 OD2 B:ASP360 3.1 53.9 1.0 CE1 B:HIS499 3.1 50.0 1.0 CD2 B:HIS364 3.1 53.4 1.0 CE1 B:HIS364 3.2 58.7 1.0 CD2 B:HIS499 3.4 49.2 1.0 CB B:ASP360 4.2 51.1 1.0 ND1 B:HIS364 4.3 58.3 1.0 CG B:HIS364 4.3 55.4 1.0 ND1 B:HIS499 4.3 47.0 1.0 CG B:HIS499 4.5 48.0 1.0 OG1 B:THR271 4.5 57.8 1.0 ND2 B:ASN238 4.6 53.1 1.0 OD2 B:ASP237 4.8 58.0 1.0 CE1 B:HIS415 5.0 47.1 1.0

Zinc binding site 6 out of 6 in the Porx with Zn (Primitive Orthorhombic Crystal Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Porx with Zn (Primitive Orthorhombic Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:64.2 occ:1.00 OD2 B:ASP54 2.5 58.7 1.0 O B:ASN56 2.6 59.8 1.0 OD1 B:ASP11 2.6 65.0 1.0 O B:HOH704 2.8 44.8 1.0 CG B:ASP11 3.4 63.6 1.0 OD2 B:ASP11 3.5 63.6 1.0 CG B:ASP54 3.6 50.7 1.0 NZ B:LYS83 3.6 88.4 1.0 C B:ASN56 3.8 63.3 1.0 OD1 B:ASP54 3.9 46.9 1.0 O B:HOH710 4.1 38.2 1.0 OE1 B:GLU12 4.2 74.2 1.0 CE B:LYS83 4.4 94.5 1.0 CB B:ASN56 4.4 69.1 1.0 OD1 B:ASP10 4.5 60.1 1.0 CA B:ASN56 4.5 62.0 1.0 CD B:LYS83 4.6 99.3 1.0 N B:ASN56 4.8 56.3 1.0 N B:MET57 4.8 64.9 1.0 CB B:ASP54 4.9 50.1 1.0 CB B:ASP11 4.9 57.9 1.0

A.Saran, N.Zeytuni. Porx with Zn (Primitive Orthorhombic Crystal Form) To Be Published.