Zinc in PDB 9dsy: Crystal Structure of C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite Atp-Independent Periplasmic Transporter Family From Pseudomonas Aeruginosa PAO1 in Complex with Succinic Acid

The structure of Crystal Structure of C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite Atp-Independent Periplasmic Transporter Family From Pseudomonas Aeruginosa PAO1 in Complex with Succinic Acid, PDB code: 9dsy was solved by G.Minasov, S.Shukla, L.Shuvalova, K.J.F.Satchell, Center For Structuralbiology Of Infectious Diseases (Csbid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.85 / 1.35
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	34.585, 44.495, 47.239, 78.78, 84.22, 75.83
R / Rfree (%)	17.3 / 18.9

The binding sites of Zinc atom in the Crystal Structure of C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite Atp-Independent Periplasmic Transporter Family From Pseudomonas Aeruginosa PAO1 in Complex with Succinic Acid (pdb code 9dsy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite Atp-Independent Periplasmic Transporter Family From Pseudomonas Aeruginosa PAO1 in Complex with Succinic Acid, PDB code: 9dsy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite Atp-Independent Periplasmic Transporter Family From Pseudomonas Aeruginosa PAO1 in Complex with Succinic Acid


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 C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite Atp-Independent Periplasmic Transporter Family From Pseudomonas Aeruginosa PAO1 in Complex with Succinic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:22.2 occ:0.50 O A:HOH627 1.9 28.0 0.5 OE2 A:GLU177 2.0 32.3 1.0 O A:HOH657 2.0 22.1 1.0 CD A:GLU177 3.1 31.2 1.0 OE1 A:GLU177 3.5 40.3 1.0 O A:PRO187 3.8 18.9 1.0 CG A:GLU177 4.3 24.7 1.0 N A:LYS189 4.4 15.5 1.0 CG A:LYS189 4.4 20.0 1.0 CA A:ARG188 4.6 18.0 1.0 C A:PRO187 4.6 18.1 1.0 CD A:LYS189 4.7 24.7 1.0 CE A:LYS189 4.8 30.4 1.0 CB A:LYS189 4.9 17.4 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite Atp-Independent Periplasmic Transporter Family From Pseudomonas Aeruginosa PAO1 in Complex with Succinic Acid


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 C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite Atp-Independent Periplasmic Transporter Family From Pseudomonas Aeruginosa PAO1 in Complex with Succinic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:18.7 occ:0.50 NH2 A:ARG281 1.8 21.5 0.5 NH1 A:ARG281 1.9 18.1 0.5 NE2 A:HIS38 2.2 25.8 1.0 CZ A:ARG281 2.6 21.6 0.5 CZ A:ARG281 2.7 20.1 0.5 NH2 A:ARG281 2.9 22.9 0.5 NH1 A:ARG281 2.9 23.3 0.5 CE1 A:HIS38 3.2 26.5 1.0 CD2 A:HIS38 3.2 22.6 1.0 NE A:ARG281 3.6 19.2 0.5 OD1 A:ASP278 3.8 18.2 1.0 NE A:ARG281 3.8 19.1 0.5 O A:HOH607 3.9 22.4 0.5 CD2 A:LEU274 4.2 12.9 0.5 ND1 A:HIS38 4.3 28.1 1.0 O A:LEU274 4.4 10.9 0.5 CG A:HIS38 4.4 21.0 1.0 O A:HOH677 4.4 23.7 0.5 CG A:LEU274 4.4 11.5 0.5 O A:LEU274 4.4 9.9 0.5 CD A:ARG281 4.5 16.5 0.5 ZN A:ZN404 4.7 32.9 0.5 CG A:ASP278 4.7 15.7 1.0 CA A:GLY277 4.7 11.6 1.0 C A:GLY277 4.8 11.7 1.0 CD A:ARG281 4.9 17.8 0.5 N A:ASP278 4.9 11.3 1.0 CA A:LEU274 4.9 10.7 0.5 CA A:LEU274 4.9 10.7 0.5 CD2 A:LEU274 4.9 11.7 0.5

Zinc binding site 3 out of 5 in the Crystal Structure of C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite Atp-Independent Periplasmic Transporter Family From Pseudomonas Aeruginosa PAO1 in Complex with Succinic Acid


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 C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite Atp-Independent Periplasmic Transporter Family From Pseudomonas Aeruginosa PAO1 in Complex with Succinic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:32.9 occ:0.50 O A:HOH719 1.9 31.8 1.0 O A:HOH725 1.9 43.6 1.0 CE1 A:HIS38 2.6 26.5 1.0 ND1 A:HIS38 3.2 28.1 1.0 NE2 A:HIS38 3.6 25.8 1.0 O A:HOH509 3.6 35.1 0.5 O A:HOH516 3.7 45.1 1.0 CG A:HIS38 4.4 21.0 1.0 NH2 A:ARG281 4.5 22.9 0.5 CD2 A:HIS38 4.6 22.6 1.0 ZN A:ZN403 4.7 18.7 0.5

Zinc binding site 4 out of 5 in the Crystal Structure of C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite Atp-Independent Periplasmic Transporter Family From Pseudomonas Aeruginosa PAO1 in Complex with Succinic Acid


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 C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite Atp-Independent Periplasmic Transporter Family From Pseudomonas Aeruginosa PAO1 in Complex with Succinic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:27.6 occ:0.50 O A:HOH696 1.9 35.2 1.0 NE2 A:HIS145 2.1 19.5 1.0 OD2 A:ASP118 2.4 49.0 1.0 CG A:ASP118 2.6 45.4 1.0 OD1 A:ASP118 2.9 47.6 1.0 O A:HOH693 3.0 44.4 1.0 CD2 A:HIS145 3.0 19.0 1.0 CE1 A:HIS145 3.1 19.6 1.0 CB A:ASP118 3.4 41.8 1.0 O A:HOH716 3.5 24.1 0.5 CB A:ASN268 3.9 12.1 1.0 CG A:HIS145 4.2 17.6 1.0 ND1 A:HIS145 4.2 19.5 1.0 ND2 A:ASN268 4.2 14.5 1.0 CG A:ASN268 4.4 13.2 1.0 O A:HOH556 4.4 22.1 1.0 CA A:ASP118 4.5 36.7 1.0 O A:ASN268 4.8 14.1 1.0 CG2 A:ILE114 4.9 52.6 1.0 CA A:ASN268 5.0 10.9 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite Atp-Independent Periplasmic Transporter Family From Pseudomonas Aeruginosa PAO1 in Complex with Succinic Acid


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 C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite Atp-Independent Periplasmic Transporter Family From Pseudomonas Aeruginosa PAO1 in Complex with Succinic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:27.4 occ:0.50 OE1 A:GLU266 1.9 25.5 1.0 O A:HOH718 2.1 38.8 1.0 CD A:GLU266 2.9 22.8 1.0 CG A:GLU266 3.5 18.4 1.0 CB A:GLU266 3.9 15.0 1.0 O A:HOH503 3.9 27.1 0.5 OE2 A:GLU266 4.0 25.2 1.0 CE A:LYS269 4.1 19.8 1.0 NZ A:LYS269 4.1 20.4 1.0 NE2 A:GLN270 4.5 19.6 0.5 CA A:GLU266 4.8 13.5 1.0

G.Minasov, S.Shukla, L.Shuvalova, K.J.F.Satchell, Center For Structural Biology Of Infectious Diseases (Csbid). Crystal Structure of C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite Atp-Independent Periplasmic Transporter Family From Pseudomonas Aeruginosa PAO1 in Complex with Succinic Acid To Be Published.