Zinc in PDB 7b3n: Amip Amidase-3 From Thermus Parvatiensis

The structure of Amip Amidase-3 From Thermus Parvatiensis, PDB code: 7b3n was solved by S.Freitag-Pohl, E.Pohl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.68 / 1.79
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.539, 97.988, 148.723, 90, 90, 90
R / Rfree (%)	18.5 / 22.5

The structure of Amip Amidase-3 From Thermus Parvatiensis also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Zinc atom in the Amip Amidase-3 From Thermus Parvatiensis (pdb code 7b3n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Amip Amidase-3 From Thermus Parvatiensis, PDB code: 7b3n:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Amip Amidase-3 From Thermus Parvatiensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Amip Amidase-3 From Thermus Parvatiensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:37.1 occ:1.00 HD1 A:HIS85 1.2 26.8 0.0 HO2 A:GOL202 1.3 26.3 0.0 HE2 A:HIS17 1.4 33.1 0.0 HO2 A:GOL202 1.9 57.0 0.0 O2 A:GOL202 1.9 56.6 0.5 O2 A:GOL202 2.0 26.4 0.5 ND1 A:HIS85 2.1 26.8 1.0 OE2 A:GLU32 2.1 31.0 1.0 NE2 A:HIS17 2.2 33.2 1.0 O3 A:GOL202 2.3 31.4 0.5 HO3 A:GOL202 2.5 32.2 0.5 O1 A:GOL202 2.8 52.3 0.5 CD A:GLU32 2.8 34.5 1.0 HB3 A:HIS85 2.9 27.6 1.0 OE1 A:GLU32 2.9 31.9 1.0 CD2 A:HIS17 2.9 32.6 1.0 HD2 A:HIS17 2.9 32.8 1.0 C2 A:GOL202 3.0 32.9 0.5 C2 A:GOL202 3.0 54.9 0.5 CE1 A:HIS85 3.0 28.1 1.0 C3 A:GOL202 3.0 33.9 0.5 CG A:HIS85 3.1 29.6 1.0 HE1 A:HIS85 3.1 27.4 1.0 H32 A:GOL202 3.2 50.8 0.5 C1 A:GOL202 3.3 55.6 0.5 H32 A:GOL202 3.3 33.1 0.5 CE1 A:HIS17 3.4 33.5 1.0 H2 A:GOL202 3.4 31.9 0.5 H12 A:GOL202 3.4 54.6 0.5 HO1 A:GOL202 3.4 52.7 0.0 CB A:HIS85 3.5 27.5 1.0 C3 A:GOL202 3.6 49.0 0.5 HE1 A:HIS17 3.7 33.3 1.0 HD21 A:ASN36 3.7 26.5 0.0 H2 A:GOL202 3.8 54.2 0.5 H31 A:GOL202 3.9 33.1 0.5 H A:HIS86 3.9 30.0 1.0 O A:HIS86 4.0 35.4 1.0 HA A:HIS85 4.1 27.0 1.0 CG A:HIS17 4.2 33.0 1.0 HB2 A:HIS85 4.2 27.5 1.0 NE2 A:HIS85 4.2 26.6 1.0 H11 A:GOL202 4.2 54.6 0.5 CD2 A:HIS85 4.2 27.8 1.0 C1 A:GOL202 4.2 34.0 0.5 CG A:GLU32 4.3 31.2 1.0 H12 A:GOL202 4.3 36.2 0.5 HA3 A:GLY16 4.3 27.1 1.0 ND1 A:HIS17 4.3 33.3 1.0 CA A:HIS85 4.4 25.6 1.0 HO3 A:GOL202 4.4 50.6 0.5 H31 A:GOL202 4.4 50.9 0.5 O3 A:GOL202 4.4 51.3 0.5 HG2 A:GLU32 4.5 32.4 1.0 ND2 A:ASN36 4.5 26.6 1.0 HA3 A:GLY23 4.5 39.9 1.0 N A:HIS86 4.6 29.9 1.0 HG3 A:GLU32 4.7 32.4 1.0 H A:ALA24 4.8 42.2 1.0 HD22 A:ASN36 4.8 26.5 0.0 OE2 A:GLU145 4.8 52.1 1.0 HA2 A:GLY23 4.8 39.9 1.0 O1 A:GOL202 4.9 45.9 0.5 HD22 A:LEU143 4.9 28.8 1.0 H11 A:GOL202 5.0 36.2 0.5 OE1 A:GLU145 5.0 48.4 1.0 HE2 A:HIS85 5.0 26.7 0.0

Zinc binding site 2 out of 5 in the Amip Amidase-3 From Thermus Parvatiensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Amip Amidase-3 From Thermus Parvatiensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:36.2 occ:1.00 HD1 B:HIS85 1.3 31.7 0.0 HE2 B:HIS17 1.3 33.1 0.0 O1 B:GOL202 2.0 46.0 1.0 OE2 B:GLU32 2.0 29.0 1.0 ND1 B:HIS85 2.1 31.5 1.0 NE2 B:HIS17 2.2 33.1 1.0 O2 B:GOL202 2.2 38.2 1.0 HO1 B:GOL202 2.7 46.1 0.0 CD B:GLU32 2.8 30.7 1.0 OE1 B:GLU32 2.9 30.0 1.0 HO2 B:GOL202 2.9 38.5 0.0 HB3 B:HIS85 2.9 27.1 1.0 C1 B:GOL202 3.0 48.5 1.0 C2 B:GOL202 3.0 44.0 1.0 CD2 B:HIS17 3.0 31.2 1.0 CE1 B:HIS85 3.1 29.5 1.0 HD2 B:HIS17 3.1 31.9 1.0 CG B:HIS85 3.2 27.8 1.0 HE1 B:HIS85 3.2 30.2 1.0 CE1 B:HIS17 3.3 34.4 1.0 H2 B:GOL202 3.3 43.4 1.0 O B:HOH345 3.3 51.3 1.0 CB B:HIS85 3.5 26.1 1.0 HE1 B:HIS17 3.5 33.7 1.0 H12 B:GOL202 3.6 46.8 1.0 HD21 B:ASN36 3.6 26.0 0.0 H11 B:GOL202 3.6 46.8 1.0 O B:HIS86 4.0 34.8 1.0 H B:HIS86 4.0 28.5 1.0 HA B:HIS85 4.1 27.8 1.0 CG B:GLU32 4.2 28.6 1.0 NE2 B:HIS85 4.2 31.1 1.0 CG B:HIS17 4.2 32.0 1.0 HB2 B:HIS85 4.2 27.1 1.0 CD2 B:HIS85 4.3 28.9 1.0 ND1 B:HIS17 4.3 33.4 1.0 HA3 B:GLY16 4.3 28.3 1.0 HO3 B:GOL202 4.4 51.2 1.0 C3 B:GOL202 4.4 42.8 1.0 CA B:HIS85 4.4 28.4 1.0 ND2 B:ASN36 4.4 26.0 1.0 HG2 B:GLU32 4.4 29.3 1.0 HA3 B:GLY23 4.6 34.6 1.0 HG3 B:GLU32 4.6 29.4 1.0 N B:HIS86 4.6 27.9 1.0 HD22 B:ASN36 4.7 26.0 0.0 H32 B:GOL202 4.7 45.8 1.0 H B:ALA24 4.8 38.0 1.0 OE2 B:GLU145 4.8 48.7 1.0 OE1 B:GLU145 4.9 50.2 1.0 O3 B:GOL202 4.9 55.5 1.0 HA2 B:GLY23 4.9 34.6 1.0

Zinc binding site 3 out of 5 in the Amip Amidase-3 From Thermus Parvatiensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Amip Amidase-3 From Thermus Parvatiensis within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:46.3 occ:1.00 HD1 C:HIS85 1.3 33.2 0.0 HE2 C:HIS17 1.3 45.6 0.0 HO2 C:GOL202 1.5 33.3 0.0 O2 C:GOL202 2.1 33.2 0.5 ND1 C:HIS85 2.2 33.0 1.0 OE2 C:GLU32 2.2 39.0 1.0 O3 C:GOL202 2.2 42.4 0.5 NE2 C:HIS17 2.2 45.4 1.0 HO2 C:GOL202 2.2 51.6 0.0 O2 C:GOL202 2.4 52.0 0.5 HO3 C:GOL202 2.5 42.3 0.5 HO3 C:GOL202 2.8 42.2 0.5 CD C:GLU32 2.8 41.5 1.0 OE1 C:GLU32 2.8 40.6 1.0 C3 C:GOL202 2.9 42.1 0.5 C2 C:GOL202 2.9 43.9 0.5 HB3 C:HIS85 3.0 36.1 1.0 CD2 C:HIS17 3.0 42.4 1.0 CE1 C:HIS85 3.1 33.0 1.0 HD2 C:HIS17 3.1 42.8 1.0 CG C:HIS85 3.2 35.2 1.0 HE1 C:HIS85 3.2 33.5 1.0 O1 C:GOL202 3.2 63.0 0.5 H2 C:GOL202 3.2 40.8 0.5 CE1 C:HIS17 3.3 45.6 1.0 H32 C:GOL202 3.3 42.6 0.5 O3 C:GOL202 3.5 41.1 0.5 CB C:HIS85 3.5 36.2 1.0 C2 C:GOL202 3.5 51.4 0.5 HE1 C:HIS17 3.6 45.2 1.0 HD21 C:ASN36 3.7 35.2 0.0 HO1 C:GOL202 3.8 62.5 0.0 H31 C:GOL202 3.8 42.6 0.5 C1 C:GOL202 3.9 56.9 0.5 H C:HIS86 3.9 36.6 1.0 HA C:HIS85 4.0 35.2 1.0 C3 C:GOL202 4.0 44.8 0.5 O C:HIS86 4.0 46.7 1.0 H11 C:GOL202 4.2 56.9 0.5 CG C:HIS17 4.2 41.1 1.0 HA3 C:GLY16 4.2 35.3 1.0 NE2 C:HIS85 4.2 35.2 1.0 H31 C:GOL202 4.3 45.4 0.5 CD2 C:HIS85 4.3 29.9 1.0 CG C:GLU32 4.3 41.3 1.0 C1 C:GOL202 4.3 41.2 0.5 ND1 C:HIS17 4.3 44.9 1.0 HB2 C:HIS85 4.3 36.1 1.0 H2 C:GOL202 4.3 51.2 0.5 CA C:HIS85 4.3 36.7 1.0 H12 C:GOL202 4.4 44.1 0.5 HA3 C:GLY23 4.5 48.4 1.0 ND2 C:ASN36 4.5 34.9 1.0 HG2 C:GLU32 4.6 42.1 1.0 N C:HIS86 4.6 37.2 1.0 OE2 C:GLU145 4.7 53.9 1.0 HG3 C:GLU32 4.7 42.1 1.0 H C:ALA24 4.7 49.8 1.0 H12 C:GOL202 4.7 56.9 0.5 HD22 C:ASN36 4.8 35.2 0.0 H11 C:GOL202 4.9 44.1 0.5 HA2 C:GLY23 4.9 48.4 1.0 H32 C:GOL202 4.9 45.4 0.5 HD22 C:LEU143 5.0 33.5 1.0 OE1 C:GLU145 5.0 55.5 1.0

Zinc binding site 4 out of 5 in the Amip Amidase-3 From Thermus Parvatiensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Amip Amidase-3 From Thermus Parvatiensis within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:43.2 occ:1.00 HD1 D:HIS85 1.2 33.9 0.0 HE2 D:HIS17 1.4 35.6 0.0 OE2 D:GLU32 2.0 31.6 1.0 ND1 D:HIS85 2.1 34.0 1.0 NE2 D:HIS17 2.3 35.6 1.0 O2 D:GOL202 2.3 43.5 1.0 O1 D:GOL202 2.4 41.3 1.0 HB3 D:HIS85 2.7 32.2 1.0 CD D:GLU32 2.7 30.0 1.0 HO2 D:GOL202 2.8 43.4 0.0 OE1 D:GLU32 2.8 34.1 1.0 HO1 D:GOL202 3.0 41.3 0.0 O D:HOH315 3.0 58.0 1.0 CD2 D:HIS17 3.0 33.4 1.0 HD2 D:HIS17 3.0 34.4 1.0 CE1 D:HIS85 3.0 32.9 1.0 CG D:HIS85 3.0 32.3 1.0 HE1 D:HIS85 3.2 32.9 1.0 C1 D:GOL202 3.3 54.4 1.0 CB D:HIS85 3.3 32.9 1.0 C2 D:GOL202 3.3 51.9 1.0 CE1 D:HIS17 3.4 35.9 1.0 HD21 D:ASN36 3.6 29.9 0.0 HE1 D:HIS17 3.7 36.0 1.0 H11 D:GOL202 3.7 50.4 1.0 H D:HIS86 3.7 35.6 1.0 H2 D:GOL202 3.9 52.6 1.0 O D:HIS86 3.9 41.0 1.0 HA D:HIS85 3.9 32.1 1.0 HB2 D:HIS85 4.1 32.2 1.0 H12 D:GOL202 4.1 50.4 1.0 CG D:GLU32 4.2 35.0 1.0 CD2 D:HIS85 4.2 32.6 1.0 NE2 D:HIS85 4.2 31.8 1.0 CA D:HIS85 4.2 30.8 1.0 CG D:HIS17 4.3 35.6 1.0 HA3 D:GLY16 4.3 30.4 1.0 ND2 D:ASN36 4.4 29.8 1.0 ND1 D:HIS17 4.4 36.9 1.0 HG2 D:GLU32 4.4 33.2 1.0 N D:HIS86 4.4 35.4 1.0 H32 D:GOL202 4.5 59.6 1.0 C3 D:GOL202 4.5 63.3 1.0 HA3 D:GLY23 4.5 39.0 1.0 HG3 D:GLU32 4.5 33.2 1.0 H D:ALA24 4.7 42.5 1.0 HD22 D:ASN36 4.7 29.9 0.0 OE2 D:GLU145 4.7 49.4 1.0 HO3 D:GOL202 4.8 60.8 1.0 C D:HIS85 4.9 34.0 1.0 C D:HIS86 4.9 38.4 1.0 OE1 D:GLU145 4.9 49.3 1.0 HB3 D:GLU32 5.0 34.4 1.0 HE2 D:HIS85 5.0 31.8 0.0

Zinc binding site 5 out of 5 in the Amip Amidase-3 From Thermus Parvatiensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Amip Amidase-3 From Thermus Parvatiensis within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn201 b:48.6 occ:1.00 HE2 E:HIS17 1.3 39.2 0.0 HD1 E:HIS85 1.3 39.2 0.0 HO3 E:GOL202 1.7 57.6 1.0 O1 E:GOL202 2.1 58.5 1.0 OE2 E:GLU32 2.2 40.4 1.0 NE2 E:HIS17 2.2 39.1 1.0 ND1 E:HIS85 2.2 39.0 1.0 O3 E:GOL202 2.5 54.5 1.0 HO1 E:GOL202 2.6 58.6 0.0 HO2 E:GOL202 2.7 65.0 0.0 OE1 E:GLU32 2.7 39.5 1.0 CD E:GLU32 2.8 38.4 1.0 HB3 E:HIS85 2.8 38.7 1.0 O2 E:GOL202 2.9 64.8 1.0 CD2 E:HIS17 3.0 41.2 1.0 HD2 E:HIS17 3.1 40.4 1.0 CE1 E:HIS85 3.1 40.1 1.0 CG E:HIS85 3.2 41.1 1.0 C1 E:GOL202 3.2 70.7 1.0 CE1 E:HIS17 3.3 39.7 1.0 HE1 E:HIS85 3.3 40.3 1.0 C2 E:GOL202 3.3 72.0 1.0 C3 E:GOL202 3.4 65.5 1.0 CB E:HIS85 3.5 37.2 1.0 HE1 E:HIS17 3.5 40.1 1.0 HD21 E:ASN36 3.6 35.5 0.0 H11 E:GOL202 3.8 67.9 1.0 H12 E:GOL202 3.9 67.9 1.0 H E:HIS86 3.9 40.8 1.0 O E:HIS86 3.9 39.8 1.0 HA E:HIS85 4.0 38.9 1.0 H31 E:GOL202 4.0 64.1 1.0 H32 E:GOL202 4.1 64.1 1.0 HB2 E:HIS85 4.2 38.7 1.0 CG E:GLU32 4.2 41.6 1.0 CG E:HIS17 4.2 40.4 1.0 HA3 E:GLY16 4.3 42.4 1.0 NE2 E:HIS85 4.3 42.2 1.0 H2 E:GOL202 4.3 69.1 1.0 CA E:HIS85 4.3 39.8 1.0 CD2 E:HIS85 4.3 41.8 1.0 ND1 E:HIS17 4.3 42.3 1.0 ND2 E:ASN36 4.4 35.3 1.0 HA3 E:GLY23 4.5 46.2 1.0 HG2 E:GLU32 4.5 40.2 1.0 N E:HIS86 4.6 41.3 1.0 HG3 E:GLU32 4.6 40.2 1.0 HD22 E:ASN36 4.7 35.5 0.0 H E:ALA24 4.7 45.6 1.0 OE2 E:GLU145 4.7 60.8 1.0 OE1 E:GLU145 4.9 60.5 1.0 C E:HIS85 5.0 38.3 1.0 HB3 E:GLU32 5.0 40.4 1.0

S.Freitag-Pohl, E.Pohl. Amip Amidase-3 From Thermus Parvatiensis To Be Published.