Zinc in PDB 2y4y: Structure of A Domain From the Type IV Pilus Biogenesis Lipoprotein Pilp, From Pseudomonas Aeruginosa

The structure of Structure of A Domain From the Type IV Pilus Biogenesis Lipoprotein Pilp, From Pseudomonas Aeruginosa, PDB code: 2y4y was solved by J.P.Derrick, J.Berry, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.22 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	103.200, 74.510, 74.180, 90.00, 125.80, 90.00
R / Rfree (%)	17.8 / 22.4

The binding sites of Zinc atom in the Structure of A Domain From the Type IV Pilus Biogenesis Lipoprotein Pilp, From Pseudomonas Aeruginosa (pdb code 2y4y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of A Domain From the Type IV Pilus Biogenesis Lipoprotein Pilp, From Pseudomonas Aeruginosa, PDB code: 2y4y:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Structure of A Domain From the Type IV Pilus Biogenesis Lipoprotein Pilp, From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Domain From the Type IV Pilus Biogenesis Lipoprotein Pilp, From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1172 b:16.1 occ:1.00 ND1 A:HIS125 2.0 14.3 1.0 O A:ACT1176 2.0 24.7 1.0 O A:HOH2084 2.0 12.7 1.0 OE1 C:GLU103 2.1 18.9 1.0 CE1 A:HIS125 2.8 15.0 1.0 C A:ACT1176 2.8 22.8 1.0 OXT A:ACT1176 2.9 22.0 1.0 CD C:GLU103 3.0 16.1 1.0 CG A:HIS125 3.1 13.7 1.0 OE2 C:GLU103 3.2 18.9 1.0 O A:HOH2010 3.3 21.5 1.0 CB A:HIS125 3.6 12.4 1.0 NE2 A:HIS125 4.0 13.0 1.0 CD2 A:HIS125 4.2 14.1 1.0 CH3 A:ACT1176 4.3 23.9 1.0 CG C:GLU103 4.3 16.8 1.0 O A:HOH2089 4.4 16.0 1.0 NZ C:LYS171 4.4 17.6 1.0 CA A:HIS125 4.5 11.2 1.0 CB C:GLU103 4.7 14.7 1.0 CD C:LYS119 4.8 19.4 1.0 CD2 A:PHE93 4.8 12.2 1.0 CE C:LYS171 4.9 16.0 1.0 CG1 C:VAL105 4.9 12.6 1.0 CG A:LEU94 5.0 14.7 1.0 CE C:LYS119 5.0 25.8 1.0 CB A:PHE93 5.0 12.1 1.0

Zinc binding site 2 out of 6 in the Structure of A Domain From the Type IV Pilus Biogenesis Lipoprotein Pilp, From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A Domain From the Type IV Pilus Biogenesis Lipoprotein Pilp, From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1175 b:29.8 occ:1.00 OE2 A:GLU163 2.1 23.4 1.0 O A:HOH2087 2.1 30.2 1.0 O A:HOH2086 2.5 39.7 1.0 CD A:GLU163 2.8 20.9 1.0 OE1 A:GLU163 3.0 21.0 1.0 O A:HOH2071 4.1 30.6 1.0 O A:HOH2001 4.1 36.9 1.0 CG A:GLU163 4.3 17.8 1.0 O A:HOH2073 4.5 33.5 1.0 CG1 A:ILE83 4.9 29.1 1.0

Zinc binding site 3 out of 6 in the Structure of A Domain From the Type IV Pilus Biogenesis Lipoprotein Pilp, From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A Domain From the Type IV Pilus Biogenesis Lipoprotein Pilp, From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1172 b:25.1 occ:0.50 O B:HOH2068 2.5 11.1 1.0 ND1 B:HIS125 2.5 23.5 1.0 CE1 B:HIS125 3.5 25.4 1.0 CG B:HIS125 3.5 21.4 1.0 CB B:HIS125 3.8 17.4 1.0 CA B:HIS125 4.2 15.2 1.0 O B:HOH2038 4.2 25.4 1.0 NE2 B:HIS125 4.6 25.8 1.0 CD2 B:HIS125 4.7 24.9 1.0 O B:VAL124 4.8 18.1 1.0 N B:ARG126 5.0 14.8 1.0

Zinc binding site 4 out of 6 in the Structure of A Domain From the Type IV Pilus Biogenesis Lipoprotein Pilp, From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of A Domain From the Type IV Pilus Biogenesis Lipoprotein Pilp, From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1173 b:27.3 occ:1.00 OE1 B:GLU163 2.1 29.3 1.0 O B:HOH2069 2.2 29.5 1.0 CD B:GLU163 2.9 25.4 1.0 OE2 B:GLU163 3.0 30.1 1.0 CG B:GLU163 4.3 20.0 1.0 CD1 B:ILE151 4.9 20.1 1.0

Zinc binding site 5 out of 6 in the Structure of A Domain From the Type IV Pilus Biogenesis Lipoprotein Pilp, From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of A Domain From the Type IV Pilus Biogenesis Lipoprotein Pilp, From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1172 b:15.3 occ:1.00 O C:HOH2076 2.0 14.6 1.0 OE1 B:GLU103 2.0 11.0 1.0 ND1 C:HIS125 2.1 12.3 1.0 O C:HOH2077 2.1 21.6 1.0 CD B:GLU103 2.8 11.5 1.0 OE2 B:GLU103 2.9 13.2 1.0 CE1 C:HIS125 2.9 13.1 1.0 O C:HOH2010 3.2 16.5 1.0 CG C:HIS125 3.2 11.4 1.0 O C:HOH2039 3.2 22.1 1.0 CB C:HIS125 3.6 9.4 1.0 NE2 C:HIS125 4.1 12.9 1.0 NZ B:LYS171 4.2 18.9 1.0 CG B:GLU103 4.2 11.0 1.0 CD2 C:HIS125 4.2 12.7 1.0 O B:HOH2015 4.5 17.2 1.0 CA C:HIS125 4.5 10.8 1.0 O C:HOH2008 4.6 31.8 1.0 CD B:LYS119 4.6 15.3 1.0 CE B:LYS171 4.7 18.5 1.0 CB B:GLU103 4.7 12.2 1.0 CD2 C:PHE93 4.8 15.1 1.0 CB C:PHE93 4.8 10.3 1.0 CG1 B:VAL105 4.8 10.9 1.0 CE B:LYS119 4.9 16.6 1.0 CG C:LEU94 4.9 13.8 1.0 CD B:LYS171 5.0 16.9 1.0

Zinc binding site 6 out of 6 in the Structure of A Domain From the Type IV Pilus Biogenesis Lipoprotein Pilp, From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of A Domain From the Type IV Pilus Biogenesis Lipoprotein Pilp, From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1172 b:18.6 occ:1.00 O D:HOH2061 2.0 14.7 1.0 OE1 A:GLU103 2.0 13.5 1.0 O D:HOH2062 2.0 20.6 1.0 ND1 D:HIS125 2.0 14.5 1.0 CD A:GLU103 2.8 14.1 1.0 OE2 A:GLU103 2.9 17.3 1.0 CE1 D:HIS125 2.9 18.1 1.0 O D:HOH2063 2.9 27.8 1.0 O D:HOH2064 3.1 19.3 1.0 CG D:HIS125 3.2 16.5 1.0 CB D:HIS125 3.6 13.4 1.0 NE2 D:HIS125 4.1 16.4 1.0 CD2 D:HIS125 4.2 15.8 1.0 CG A:GLU103 4.3 13.7 1.0 NZ A:LYS171 4.3 18.7 1.0 CA D:HIS125 4.5 13.4 1.0 O A:HOH2018 4.5 16.6 1.0 O D:HOH2005 4.6 29.9 1.0 CE A:LYS171 4.8 16.6 1.0 CB A:GLU103 4.8 13.1 1.0 CD A:LYS119 4.8 21.9 1.0 CD2 D:PHE93 4.8 15.0 1.0 CG1 A:VAL105 4.9 16.1 1.0 CB D:PHE93 4.9 15.8 1.0 CD A:LYS171 5.0 16.2 1.0

J.Berry, J.P.Derrick. Structure of A Domain From the Type IV Pilus Biogenesis Lipoprotein Pilp, From Pseudomonas Aeruginosa To Be Published.