Zinc in PDB 3htr: Crystal Structure of Prc-Barrel Domain Protein From Rhodopseudomonas Palustris

The structure of Crystal Structure of Prc-Barrel Domain Protein From Rhodopseudomonas Palustris, PDB code: 3htr was solved by Y.Kim, C.Tesar, R.Jedrzejczak, J.Kinney, G.Babnigg, C.Harwood, C.Kerfeld, A.Joachimiak, Midwest Center For Structuralgenomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.01 / 2.06
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	25.644, 63.061, 61.866, 90.00, 99.39, 90.00
R / Rfree (%)	19.3 / 23.1

The binding sites of Zinc atom in the Crystal Structure of Prc-Barrel Domain Protein From Rhodopseudomonas Palustris (pdb code 3htr). 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 Prc-Barrel Domain Protein From Rhodopseudomonas Palustris, PDB code: 3htr:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Prc-Barrel Domain Protein From Rhodopseudomonas Palustris


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 Prc-Barrel Domain Protein From Rhodopseudomonas Palustris within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn118 b:40.0 occ:1.00 O A:ACY120 2.0 37.5 1.0 O A:HOH122 2.1 66.6 1.0 OE2 A:GLU7 2.1 39.7 1.0 O A:HOH133 2.4 48.3 1.0 OE1 A:GLU7 2.6 34.9 1.0 CD A:GLU7 2.7 38.5 1.0 C A:ACY120 2.7 43.0 1.0 OXT A:ACY120 2.8 42.4 1.0 O A:HOH138 2.8 85.7 1.0 NZ A:LYS16 4.2 53.4 1.0 CH3 A:ACY120 4.2 44.9 1.0 CE2 A:TYR72 4.2 44.3 1.0 CG A:GLU7 4.2 32.1 1.0 CD2 A:TYR72 4.4 42.5 1.0 CZ A:TYR72 4.4 42.8 1.0 NZ B:LYS40 4.6 43.6 1.0 CD1 A:ILE12 4.7 42.1 1.0 CG A:TYR72 4.7 40.9 1.0 CE1 A:TYR72 4.7 38.2 1.0 CE B:LYS40 4.8 43.6 1.0 CE A:LYS16 4.8 52.6 1.0 OH A:TYR72 4.8 42.3 1.0 CD1 A:TYR72 4.9 38.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Prc-Barrel Domain Protein From Rhodopseudomonas Palustris


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 Prc-Barrel Domain Protein From Rhodopseudomonas Palustris within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn119 b:35.0 occ:1.00 NE2 A:HIS62 2.0 46.3 1.0 OD2 A:ASP60 2.1 40.9 1.0 OE1 A:GLU34 2.2 32.0 1.0 OE2 B:GLU4 2.4 38.9 1.0 OE1 B:GLU4 2.7 43.7 1.0 CD A:GLU34 2.8 38.1 1.0 OE2 A:GLU34 2.8 40.8 1.0 CD B:GLU4 2.9 43.6 1.0 CE1 A:HIS62 2.9 54.1 1.0 CG A:ASP60 2.9 42.2 1.0 OD1 A:ASP60 3.0 46.8 1.0 CD2 A:HIS62 3.0 42.3 1.0 N A:GLY57 3.8 55.8 1.0 ND1 A:HIS62 4.0 54.7 1.0 CG A:HIS62 4.1 43.8 1.0 OG A:SER51 4.2 31.5 1.0 CG A:GLU34 4.3 39.0 1.0 CA A:GLY57 4.3 57.3 1.0 CB A:ASP60 4.3 39.6 1.0 CG B:GLU4 4.4 48.3 1.0 CB A:SER51 4.4 33.5 1.0 O B:HOH136 4.7 50.3 1.0 CB A:GLU34 4.8 34.6 1.0 NH1 A:ARG35 4.8 33.1 1.0 C A:LEU56 4.9 54.0 1.0 O A:HOH141 4.9 58.6 1.0 CA A:LEU56 5.0 55.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Prc-Barrel Domain Protein From Rhodopseudomonas Palustris


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 Prc-Barrel Domain Protein From Rhodopseudomonas Palustris within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn118 b:39.9 occ:1.00 NE2 B:HIS62 2.0 51.6 1.0 OE2 A:GLU4 2.1 46.3 1.0 OE1 B:GLU34 2.1 43.5 1.0 OD2 B:ASP60 2.2 43.2 1.0 OE1 A:GLU4 2.6 42.1 1.0 CD A:GLU4 2.7 46.3 1.0 OE2 B:GLU34 2.8 44.5 1.0 CD B:GLU34 2.8 41.4 1.0 CE1 B:HIS62 2.8 58.9 1.0 CG B:ASP60 2.9 44.8 1.0 OD1 B:ASP60 2.9 47.6 1.0 CD2 B:HIS62 3.1 50.2 1.0 CA B:GLY57 3.4 71.3 1.0 N B:GLY57 3.6 71.8 1.0 ND1 B:HIS62 4.0 56.7 1.0 CG B:HIS62 4.2 49.2 1.0 CG A:GLU4 4.2 50.8 1.0 OG B:SER51 4.3 35.6 1.0 C B:GLY57 4.3 75.2 1.0 CG B:GLU34 4.3 39.8 1.0 CB B:SER51 4.3 35.6 1.0 CB B:ASP60 4.3 45.2 1.0 O B:HOH135 4.3 56.4 1.0 O B:GLY57 4.5 78.4 1.0 C B:LEU56 4.8 71.4 1.0 CB B:GLU34 4.8 37.9 1.0 NH1 B:ARG35 4.9 39.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Prc-Barrel Domain Protein From Rhodopseudomonas Palustris


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 Prc-Barrel Domain Protein From Rhodopseudomonas Palustris within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn119 b:39.7 occ:1.00 OE2 B:GLU7 2.0 31.3 1.0 OXT B:ACY120 2.1 44.7 1.0 OXT A:ACY121 2.5 68.6 1.0 CD B:GLU7 2.7 31.9 1.0 OE1 B:GLU7 2.8 31.4 1.0 C B:ACY120 2.8 40.7 1.0 O B:ACY120 2.9 37.2 1.0 C A:ACY121 3.6 71.5 1.0 O A:ACY121 4.0 73.1 1.0 NZ A:LYS40 4.1 40.1 1.0 CE B:LYS16 4.1 50.3 1.0 CG B:GLU7 4.2 32.1 1.0 CE2 B:TYR72 4.2 37.4 1.0 CD2 B:TYR72 4.3 37.0 1.0 CH3 B:ACY120 4.3 34.0 1.0 CZ B:TYR72 4.4 37.4 1.0 CE A:LYS40 4.5 40.9 1.0 CG B:TYR72 4.6 37.9 1.0 CD1 B:ILE12 4.7 46.0 1.0 CE1 B:TYR72 4.7 38.5 1.0 CH3 A:ACY121 4.8 71.4 1.0 CD1 B:TYR72 4.9 38.2 1.0 OH B:TYR72 4.9 40.6 1.0 NZ B:LYS16 4.9 48.9 1.0

Y.Kim, C.Tesar, R.Jedrzejczak, J.Kinney, G.Babnigg, C.Harwood, C.Kerfeld, A.Joachimiak. Crystal Structure of Prc-Barrel Domain Protein From Rhodopseudomonas Palustris To Be Published.