Zinc in PDB 9dy3: Crystal Structure of C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite Atp-Independent Periplasmic Transporter Family From Pseudomonas Aeruginosa PAO1 in Complex with L-Malate

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 L-Malate, PDB code: 9dy3 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)	29.84 / 1.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	34.505, 44.532, 46.886, 78.95, 84.44, 75.84
R / Rfree (%)	14 / 16.7

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 L-Malate (pdb code 9dy3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 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 L-Malate, PDB code: 9dy3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 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 L-Malate


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 L-Malate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:13.3 occ:0.50 NH2 A:ARG281 1.6 14.2 0.5 O A:HOH503 1.9 16.1 0.5 NH2 A:ARG281 1.9 16.9 0.5 NE2 A:HIS38 2.1 15.3 0.7 O A:HOH730 2.2 7.5 0.3 CZ A:ARG281 2.2 13.8 0.5 NH1 A:ARG281 2.3 10.5 0.5 CZ A:ARG281 2.6 17.1 0.5 NH1 A:ARG281 2.8 18.4 0.5 CE1 A:HIS38 3.1 16.7 0.7 CD2 A:HIS38 3.1 14.2 0.7 NE A:ARG281 3.5 15.5 0.5 NE A:ARG281 3.7 17.3 0.5 OD1 A:ASP278 3.8 15.8 1.0 CD2 A:LEU274 4.2 17.4 1.0 ND1 A:HIS38 4.2 17.3 0.7 O A:HOH592 4.2 30.3 1.0 CG A:HIS38 4.2 13.8 0.7 O A:LEU274 4.3 12.2 1.0 CD A:ARG281 4.5 17.0 0.5 CA A:GLY277 4.5 12.0 1.0 O A:HOH560 4.6 26.2 1.0 CD A:ARG281 4.6 15.1 0.5 C A:GLY277 4.7 12.1 1.0 O A:HOH700 4.7 18.9 1.0 N A:ASP278 4.8 10.9 1.0 CG A:ASP278 4.8 15.1 1.0 CA A:LEU274 4.9 11.6 1.0

Zinc binding site 2 out of 7 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 L-Malate


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 L-Malate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:20.7 occ:0.50 O A:HOH725 1.9 34.4 1.0 O A:HOH764 1.9 25.7 0.5 O A:HOH741 1.9 25.8 1.0 O A:HOH590 2.1 25.3 1.0 O A:HOH517 2.1 29.2 0.5 O A:HOH766 2.3 32.3 0.5 O A:GLY247 3.7 20.6 1.0 O A:HOH766 3.8 43.5 0.5 O A:HOH686 4.0 33.3 1.0 O A:HOH749 4.2 33.4 1.0 O A:HOH736 4.3 26.1 0.5 C A:GLY247 4.3 18.3 1.0 O A:LEU248 4.4 18.0 1.0 CA A:GLY247 4.5 18.8 1.0 O A:ASN246 4.7 19.7 1.0 C A:LEU248 4.9 17.7 1.0

Zinc binding site 3 out of 7 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 L-Malate


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 L-Malate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:10.2 occ:0.30 ZN A:ZN404 0.0 10.2 0.3 ZN A:ZN404 1.0 13.6 0.2 O A:HOH706 1.7 14.8 0.4 OD1 A:ASP235 2.0 15.2 1.0 ND1 A:HIS145 2.0 13.9 0.6 O A:HOH706 2.3 14.4 0.6 CG A:ASP235 2.6 14.3 1.0 OD2 A:ASP235 2.7 20.9 1.0 CE1 A:HIS145 2.8 15.0 0.6 CG A:HIS145 3.2 13.8 0.6 ND1 A:HIS145 3.4 11.6 0.4 CB A:HIS145 3.7 12.7 0.6 CG A:HIS145 4.0 10.8 0.4 NE2 A:HIS145 4.0 15.1 0.6 CA A:HIS145 4.0 11.5 0.6 CB A:ASP235 4.0 11.5 1.0 CB A:HIS145 4.1 9.9 0.4 CG1 A:VAL233 4.1 19.3 1.0 N A:ASN146 4.2 10.4 0.6 CD2 A:HIS145 4.2 14.5 0.6 N A:GLY147 4.2 10.2 0.6 CA A:HIS145 4.2 9.5 0.4 CE1 A:HIS145 4.2 12.0 0.4 O A:LEU234 4.3 11.1 1.0 N A:ASN146 4.3 9.2 0.4 CG1 A:VAL117 4.3 25.8 1.0 CA A:GLY147 4.3 10.9 0.6 C A:HIS145 4.5 10.9 0.6 CG2 A:ILE114 4.6 39.8 1.0 C A:GLY147 4.6 11.0 0.6 O A:GLY147 4.6 12.1 0.6 CD1 A:ILE114 4.6 42.9 1.0 N A:GLY147 4.7 9.3 0.4 C A:ASN146 4.7 9.8 0.6 C A:LEU234 4.7 10.6 1.0 CA A:ASP235 4.7 9.8 1.0 CB A:VAL117 4.7 24.3 1.0 C A:HIS145 4.8 9.0 0.4 N A:ASP235 4.9 9.9 1.0 CG2 A:VAL117 4.9 23.6 1.0 CD2 A:HIS145 4.9 11.5 0.4 CA A:GLY147 5.0 10.0 0.4

Zinc binding site 4 out of 7 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 L-Malate


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 L-Malate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:13.6 occ:0.20 ZN A:ZN404 0.0 13.6 0.2 ZN A:ZN404 1.0 10.2 0.3 ND1 A:HIS145 2.1 13.9 0.6 OD2 A:ASP235 2.1 20.9 1.0 OD1 A:ASP235 2.1 15.2 1.0 O A:HOH706 2.3 14.8 0.4 CG A:ASP235 2.3 14.3 1.0 ND1 A:HIS145 2.6 11.6 0.4 CG A:HIS145 2.9 13.8 0.6 CE1 A:HIS145 3.1 15.0 0.6 CB A:HIS145 3.2 12.7 0.6 O A:HOH706 3.2 14.4 0.6 CE1 A:HIS145 3.3 12.0 0.4 CG A:HIS145 3.3 10.8 0.4 CA A:HIS145 3.6 11.5 0.6 CB A:HIS145 3.7 9.9 0.4 CB A:ASP235 3.9 11.5 1.0 CA A:HIS145 3.9 9.5 0.4 CG1 A:VAL117 3.9 25.8 1.0 CD2 A:HIS145 4.1 14.5 0.6 NE2 A:HIS145 4.2 15.1 0.6 NE2 A:HIS145 4.3 12.3 0.4 CD2 A:HIS145 4.3 11.5 0.4 N A:ASN146 4.3 10.4 0.6 CB A:VAL117 4.4 24.3 1.0 C A:HIS145 4.4 10.9 0.6 CG2 A:ILE114 4.5 39.8 1.0 CG1 A:VAL233 4.5 19.3 1.0 N A:ASN146 4.6 9.2 0.4 NE2 A:GLN121 4.6 20.5 1.0 N A:HIS145 4.7 10.5 0.6 CA A:ASP235 4.8 9.8 1.0 OE1 A:GLN121 4.8 21.4 1.0 C A:HIS145 4.8 9.0 0.4 O A:LEU234 4.9 11.1 1.0 N A:HIS145 4.9 9.6 0.4 CG2 A:VAL117 4.9 23.6 1.0 N A:GLY147 4.9 10.2 0.6

Zinc binding site 5 out of 7 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 L-Malate


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 L-Malate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:34.4 occ:0.30 OD1 A:ASP112 2.1 39.1 1.0 NH2 A:ARG302 2.4 54.5 1.0 O A:HOH616 2.6 45.5 1.0 NH1 A:ARG302 2.7 53.5 1.0 CZ A:ARG302 2.9 50.7 1.0 CG A:ASP112 3.1 37.1 1.0 OD2 A:ASP112 3.6 40.1 1.0 O A:PHE109 4.0 27.6 1.0 NE A:ARG302 4.2 47.4 1.0 CB A:ASP112 4.4 35.0 1.0 O A:LEU110 4.4 25.7 1.0 ND2 A:ASN328 4.6 30.4 1.0 CA A:ASP112 4.6 31.9 1.0 OE1 A:GLN306 4.7 48.3 1.0 N A:ASP112 4.7 28.7 1.0 CG A:ASN328 4.9 30.6 1.0

Zinc binding site 6 out of 7 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 L-Malate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite Atp-Independent Periplasmic Transporter Family From Pseudomonas Aeruginosa PAO1 in Complex with L-Malate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:35.1 occ:0.30 ZN A:ZN406 0.0 35.1 0.3 ZN A:ZN406 1.8 32.6 0.3 NE2 A:HIS145 1.9 15.1 0.6 CE1 A:HIS145 2.6 15.0 0.6 O A:ASN146 2.7 9.8 0.6 O A:ASN146 2.9 9.5 0.4 CD2 A:HIS145 3.0 14.5 0.6 CA A:GLY147 3.4 10.9 0.6 CA A:GLY147 3.6 10.0 0.4 O A:HOH576 3.6 24.5 1.0 C A:ASN146 3.6 9.8 0.6 OE1 A:GLU272 3.6 35.2 1.0 CD A:GLU272 3.7 28.9 1.0 ND1 A:HIS145 3.7 13.9 0.6 N A:GLU272 3.7 12.2 1.0 OE2 A:GLU272 3.7 37.5 1.0 C A:ASN146 3.7 9.2 0.4 CA A:GLU272 3.8 13.9 1.0 CG A:HIS145 3.9 13.8 0.6 N A:GLY147 4.0 10.2 0.6 CB A:ALA271 4.0 10.9 1.0 CB A:GLU272 4.0 17.3 1.0 N A:GLY147 4.0 9.3 0.4 C A:ALA271 4.1 10.6 1.0 CD1 A:ILE114 4.4 42.9 1.0 O A:HOH605 4.4 19.8 1.0 CG A:GLU272 4.4 23.6 1.0 O A:ALA271 4.4 10.6 1.0 CG1 A:ILE114 4.5 41.9 1.0 ND2 A:ASN275 4.5 12.2 1.0 CG2 A:ILE114 4.6 39.8 1.0 CA A:ALA271 4.7 10.7 1.0 CB A:HIS145 4.7 9.9 0.4 C A:GLY147 4.7 11.0 0.6 C A:GLY147 4.8 9.9 0.4 CA A:ASN146 4.9 9.9 0.6 CA A:ASN146 4.9 8.9 0.4 N A:ASN146 5.0 9.2 0.4 N A:MSE148 5.0 10.7 0.4 N A:MSE148 5.0 11.4 0.6

Zinc binding site 7 out of 7 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 L-Malate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite Atp-Independent Periplasmic Transporter Family From Pseudomonas Aeruginosa PAO1 in Complex with L-Malate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:32.6 occ:0.30 ZN A:ZN406 0.0 32.6 0.3 ZN A:ZN406 1.8 35.1 0.3 O A:ASN146 2.7 9.5 0.4 O A:ASN146 2.7 9.8 0.6 O A:HOH576 3.0 24.5 1.0 OE2 A:GLU272 3.2 37.5 1.0 CA A:GLY147 3.2 10.0 0.4 ND2 A:ASN275 3.2 12.2 1.0 CA A:GLU272 3.2 13.9 1.0 CA A:GLY147 3.3 10.9 0.6 N A:GLU272 3.5 12.2 1.0 CD A:GLU272 3.6 28.9 1.0 O A:ALA271 3.6 10.6 1.0 C A:ASN146 3.6 9.2 0.4 NE2 A:HIS145 3.7 15.1 0.6 C A:ALA271 3.7 10.6 1.0 C A:ASN146 3.7 9.8 0.6 O A:HOH504 3.8 24.1 1.0 N A:GLY147 3.9 9.3 0.4 CB A:GLU272 3.9 17.3 1.0 O A:HOH713 3.9 24.7 1.0 CG A:ASN275 4.0 10.6 1.0 CB A:ASN275 4.0 10.4 1.0 N A:GLY147 4.0 10.2 0.6 OE1 A:GLU272 4.1 35.2 1.0 CE1 A:HIS145 4.1 15.0 0.6 CG A:GLU272 4.1 23.6 1.0 C A:GLU272 4.4 13.5 1.0 CB A:ALA271 4.4 10.9 1.0 C A:GLY147 4.4 9.9 0.4 O A:GLU272 4.5 13.7 1.0 CD2 A:HIS145 4.6 14.5 0.6 N A:MSE148 4.6 10.7 0.4 C A:GLY147 4.6 11.0 0.6 CA A:ALA271 4.7 10.7 1.0 N A:MSE148 4.7 11.4 0.6

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 L-Malate. To Be Published.