Cadmium in PDB 4j0d: Tannin Acyl Hydrolase From Lactobacillus Plantarum (Cadmium)

The structure of Tannin Acyl Hydrolase From Lactobacillus Plantarum (Cadmium), PDB code: 4j0d was solved by B.Ren, M.Wu, Q.Wang, X.Peng, H.Wen, Q.Chen, W.J.Mckinstry, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.02 / 1.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.940, 62.918, 84.070, 70.58, 85.70, 78.96
R / Rfree (%)	14.3 / 17.5

The binding sites of Cadmium atom in the Tannin Acyl Hydrolase From Lactobacillus Plantarum (Cadmium) (pdb code 4j0d). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Tannin Acyl Hydrolase From Lactobacillus Plantarum (Cadmium), PDB code: 4j0d:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Tannin Acyl Hydrolase From Lactobacillus Plantarum (Cadmium)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Tannin Acyl Hydrolase From Lactobacillus Plantarum (Cadmium) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd501 b:35.4 occ:0.42 ND1 A:HIS281 2.3 17.7 1.0 O B:HOH970 2.3 52.3 1.0 O B:HOH969 2.5 58.3 1.0 O A:HOH940 2.7 55.9 1.0 CE1 A:HIS281 3.2 24.1 1.0 CG A:HIS281 3.2 25.4 1.0 CB A:HIS281 3.5 25.9 1.0 NZ A:LYS273 3.7 59.8 1.0 NZ B:LYS273 4.0 45.2 1.0 CE B:LYS273 4.2 41.1 1.0 NE2 A:HIS281 4.3 21.0 1.0 CD2 A:HIS281 4.4 21.0 1.0 OE1 B:GLN271 4.5 43.7 1.0 CG2 A:THR283 4.7 23.1 1.0 O A:HOH758 4.8 40.3 1.0 CE A:LYS273 4.9 53.4 1.0

Cadmium binding site 2 out of 4 in the Tannin Acyl Hydrolase From Lactobacillus Plantarum (Cadmium)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Tannin Acyl Hydrolase From Lactobacillus Plantarum (Cadmium) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd502 b:27.1 occ:0.16 ND1 A:HIS451 1.7 16.9 1.0 CE1 A:HIS451 2.1 22.9 1.0 OD1 A:ASP419 2.3 17.9 1.0 OD2 A:ASP419 2.4 17.2 1.0 CG A:ASP419 2.7 19.5 1.0 CG A:HIS451 2.8 17.3 1.0 CB A:ASP421 2.8 13.3 1.0 NE2 A:HIS451 3.2 20.9 1.0 CD2 A:HIS451 3.6 22.7 1.0 CG A:ASP421 3.6 24.1 1.0 CB A:HIS451 3.6 15.1 1.0 CB A:CYS204 3.7 13.9 1.0 CA A:ASP421 3.8 11.1 1.0 CE1 A:HIS415 3.9 16.0 1.0 OD1 A:ASP421 3.9 28.0 1.0 N A:ASP421 3.9 12.0 1.0 CD1 A:ILE206 4.0 17.2 1.0 SG A:CYS204 4.1 16.9 1.0 CB A:ASP419 4.2 12.2 1.0 CA A:HIS451 4.2 15.6 1.0 N A:THR422 4.3 12.5 1.0 C A:ASP421 4.3 14.8 1.0 OD2 A:ASP421 4.3 30.2 1.0 O A:CYS204 4.5 12.5 1.0 ND1 A:HIS415 4.5 15.9 1.0 NE2 A:HIS415 4.6 17.9 1.0 O A:HOH627 4.9 14.3 1.0 CG1 A:ILE206 4.9 12.9 1.0 CG2 A:THR422 4.9 12.2 1.0 CA A:CYS204 4.9 9.5 1.0

Cadmium binding site 3 out of 4 in the Tannin Acyl Hydrolase From Lactobacillus Plantarum (Cadmium)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Tannin Acyl Hydrolase From Lactobacillus Plantarum (Cadmium) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd501 b:31.1 occ:0.41 O B:HOH972 2.0 52.7 1.0 ND1 B:HIS281 2.2 16.6 1.0 O B:HOH984 2.3 56.6 1.0 O B:HOH973 3.1 69.6 1.0 CG B:HIS281 3.2 19.3 1.0 CE1 B:HIS281 3.2 21.8 1.0 CB B:HIS281 3.4 20.0 1.0 NE2 B:HIS281 4.3 16.0 1.0 CD2 B:HIS281 4.3 15.6 1.0 O B:HOH859 4.4 39.3 1.0 CG2 B:THR283 4.7 16.0 1.0 NZ B:LYS273 4.9 45.2 1.0 CA B:HIS281 5.0 19.0 1.0

Cadmium binding site 4 out of 4 in the Tannin Acyl Hydrolase From Lactobacillus Plantarum (Cadmium)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Tannin Acyl Hydrolase From Lactobacillus Plantarum (Cadmium) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd502 b:76.7 occ:0.13 ND1 B:HIS451 2.1 13.2 1.0 CE1 B:HIS451 2.3 18.6 1.0 OD1 B:ASP419 2.4 14.4 1.0 OD2 B:ASP419 2.5 13.1 1.0 CG B:ASP419 2.8 14.6 1.0 CB B:ASP421 3.1 10.7 1.0 CG B:HIS451 3.3 13.1 1.0 CE1 B:HIS415 3.4 13.3 1.0 NE2 B:HIS451 3.5 18.9 1.0 CB B:CYS204 3.6 10.2 1.0 CD1 B:ILE206 3.8 14.5 1.0 CA B:ASP421 3.8 8.1 1.0 N B:ASP421 3.8 7.9 1.0 N B:THR422 3.9 9.4 1.0 CG B:ASP421 4.0 22.8 1.0 CD2 B:HIS451 4.0 18.4 1.0 ND1 B:HIS415 4.1 12.6 1.0 C B:ASP421 4.1 10.5 1.0 CB B:HIS451 4.2 15.9 1.0 SG B:CYS204 4.2 12.6 1.0 NE2 B:HIS415 4.3 12.4 1.0 CB B:ASP419 4.3 7.3 1.0 OD1 B:ASP421 4.3 24.7 1.0 O B:CYS204 4.3 9.6 1.0 CG2 B:THR422 4.4 9.4 1.0 CA B:CYS204 4.7 7.6 1.0 CG1 B:ILE206 4.7 9.7 1.0 CA B:HIS451 4.7 11.9 1.0 OD2 B:ASP421 4.8 25.0 1.0 C B:CYS204 4.9 8.2 1.0 CB B:THR422 4.9 10.5 1.0 C B:ASP419 5.0 10.6 1.0 O B:ASP421 5.0 11.3 1.0

B.Ren, M.Wu, Q.Wang, X.Peng, H.Wen, W.J.Mckinstry, Q.Chen. Crystal Structure of Tannase From Lactobacillus Plantarum J.Mol.Biol. 2013.
ISSN: ESSN 1089-8638
PubMed: 23648840
DOI: 10.1016/J.JMB.2013.04.032