Zinc in PDB 8c46: N-Carbamoyl-Beta-Alanine Amidohydrolases From Rhizobium Radiobacter Mdc 8606

The structure of N-Carbamoyl-Beta-Alanine Amidohydrolases From Rhizobium Radiobacter Mdc 8606, PDB code: 8c46 was solved by A.Basle, J.Marles-Wright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	84.92 / 2.00
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.231, 104.622, 145.372, 90, 90, 90
R / Rfree (%)	22.9 / 27

The binding sites of Zinc atom in the N-Carbamoyl-Beta-Alanine Amidohydrolases From Rhizobium Radiobacter Mdc 8606 (pdb code 8c46). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the N-Carbamoyl-Beta-Alanine Amidohydrolases From Rhizobium Radiobacter Mdc 8606, PDB code: 8c46:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the N-Carbamoyl-Beta-Alanine Amidohydrolases From Rhizobium Radiobacter Mdc 8606


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of N-Carbamoyl-Beta-Alanine Amidohydrolases From Rhizobium Radiobacter Mdc 8606 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:30.1 occ:1.00 O A:HOH716 2.0 27.6 1.0 OD1 A:ASP97 2.1 32.6 1.0 NE2 A:HIS86 2.1 22.1 1.0 NE2 A:HIS193 2.2 21.1 1.0 O A:HOH678 2.3 16.5 1.0 CE1 A:HIS86 3.1 21.2 1.0 CD2 A:HIS86 3.2 25.4 1.0 CE1 A:HIS193 3.2 22.0 1.0 HE1 A:HIS86 3.2 22.3 1.0 CD2 A:HIS193 3.2 22.2 1.0 CG A:ASP97 3.3 29.0 1.0 HE1 A:HIS193 3.3 21.3 1.0 HD2 A:HIS86 3.4 23.7 1.0 ZN A:ZN503 3.4 40.4 1.0 HD2 A:HIS193 3.4 22.0 1.0 OE1 A:GLU131 3.5 24.7 1.0 H A:GLY98 3.6 23.6 1.0 OD2 A:ASP97 3.8 35.0 1.0 HA2 A:GLY98 3.8 22.9 1.0 N A:GLY98 3.8 23.6 1.0 CD A:GLU131 4.0 23.7 1.0 HA3 A:GLY98 4.0 24.0 1.0 OE2 A:GLU132 4.1 36.6 1.0 CA A:GLY98 4.1 23.6 1.0 ND1 A:HIS361 4.1 18.0 1.0 ND1 A:HIS86 4.2 24.5 1.0 CG A:HIS86 4.3 24.8 1.0 ND1 A:HIS193 4.3 19.6 1.0 O A:HOH650 4.3 18.0 1.0 C A:ASP97 4.3 27.7 1.0 CG A:HIS193 4.3 21.3 1.0 HE1 A:HIS361 4.4 19.4 1.0 HG3 A:GLU131 4.4 24.3 1.0 NE2 A:GLN196 4.5 31.7 1.0 OE2 A:GLU131 4.5 23.1 1.0 HA A:ASP97 4.5 25.9 1.0 CB A:ASP97 4.5 28.5 1.0 CD A:GLU132 4.6 31.5 1.0 CE1 A:HIS361 4.7 20.5 1.0 CA A:ASP97 4.7 26.0 1.0 CG A:GLU131 4.8 24.7 1.0 HB3 A:GLU131 4.8 26.5 1.0 OE1 A:GLU132 4.8 30.9 1.0 OG A:SER85 5.0 23.0 1.0

Zinc binding site 2 out of 4 in the N-Carbamoyl-Beta-Alanine Amidohydrolases From Rhizobium Radiobacter Mdc 8606


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of N-Carbamoyl-Beta-Alanine Amidohydrolases From Rhizobium Radiobacter Mdc 8606 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:40.4 occ:1.00 OD2 A:ASP97 2.0 35.0 1.0 O A:HOH716 2.2 27.6 1.0 OE2 A:GLU132 2.2 36.6 1.0 OE1 A:GLU132 2.2 30.9 1.0 NE2 A:HIS385 2.4 35.6 1.0 CD A:GLU132 2.5 31.5 1.0 CG A:ASP97 2.8 29.0 1.0 OD1 A:ASP97 3.0 32.6 1.0 HD2 A:HIS385 3.1 35.3 1.0 CD2 A:HIS385 3.1 36.2 1.0 NE2 A:GLN196 3.3 31.7 1.0 ZN A:ZN502 3.4 30.1 1.0 CE1 A:HIS385 3.5 36.9 1.0 HE1 A:HIS86 3.8 22.3 1.0 HE1 A:HIS385 3.8 34.5 1.0 OE1 A:GLU131 4.0 24.7 1.0 CG A:GLU132 4.0 31.8 1.0 HG2 A:GLN90 4.0 36.2 1.0 O A:HOH632 4.1 28.2 1.0 CB A:ASP97 4.2 28.5 1.0 HG2 A:GLU132 4.2 31.8 1.0 CE1 A:HIS86 4.3 21.2 1.0 HA A:GLU132 4.4 29.6 1.0 CG A:HIS385 4.4 32.4 1.0 NE2 A:HIS86 4.4 22.1 1.0 HG3 A:GLN90 4.4 35.5 1.0 HB3 A:ASP97 4.5 28.9 1.0 HG3 A:GLU132 4.5 32.5 1.0 HE1 A:HIS193 4.5 21.3 1.0 HB2 A:ASP97 4.5 27.8 1.0 CD A:GLN196 4.5 29.1 1.0 ND1 A:HIS385 4.5 29.8 1.0 CG A:GLN90 4.7 36.2 1.0 NE2 A:HIS193 4.9 21.1 1.0 O A:HOH672 4.9 25.9 1.0 CB A:GLU132 5.0 31.0 1.0 HB3 A:GLU132 5.0 31.3 1.0 NE2 A:GLN90 5.0 36.2 1.0

Zinc binding site 3 out of 4 in the N-Carbamoyl-Beta-Alanine Amidohydrolases From Rhizobium Radiobacter Mdc 8606


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of N-Carbamoyl-Beta-Alanine Amidohydrolases From Rhizobium Radiobacter Mdc 8606 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:38.9 occ:1.00 OD2 B:ASP97 2.0 24.6 1.0 OE1 B:GLU132 2.2 34.8 1.0 OE2 B:GLU132 2.2 34.1 1.0 NE2 B:HIS385 2.3 32.4 1.0 CD B:GLU132 2.5 32.1 1.0 CG B:ASP97 2.8 24.1 1.0 HD2 B:HIS385 3.0 33.3 1.0 CD2 B:HIS385 3.0 31.7 1.0 OD1 B:ASP97 3.1 28.6 1.0 NE2 B:GLN196 3.2 21.5 1.0 CE1 B:HIS385 3.5 34.8 1.0 ZN B:ZN503 3.5 30.4 1.0 HE1 B:HIS385 3.8 34.4 1.0 O B:HOH626 3.8 28.7 1.0 HE1 B:HIS86 3.8 19.8 1.0 HG2 B:GLN90 3.9 32.6 1.0 OE1 B:GLU131 4.0 22.6 1.0 CG B:GLU132 4.0 33.3 1.0 CB B:ASP97 4.2 24.9 1.0 CG B:HIS385 4.3 36.2 1.0 HG3 B:GLN90 4.3 32.0 1.0 HG2 B:GLU132 4.3 32.8 1.0 HA B:GLU132 4.4 30.6 1.0 CD B:GLN196 4.4 21.8 1.0 CE1 B:HIS86 4.4 19.9 1.0 HB3 B:ASP97 4.4 25.5 1.0 ND1 B:HIS385 4.5 36.9 1.0 HB2 B:ASP97 4.5 24.6 1.0 HG3 B:GLU132 4.5 33.2 1.0 NE2 B:HIS86 4.5 18.6 1.0 NE2 B:GLN90 4.5 35.9 1.0 CG B:GLN90 4.6 31.9 1.0 HE1 B:HIS193 4.6 21.7 1.0 O B:HOH671 4.7 39.6 1.0 OE1 B:GLN196 4.8 22.7 1.0 O B:HOH683 4.8 27.7 1.0 HB3 B:GLU132 4.9 31.6 1.0 CB B:GLU132 5.0 31.1 1.0 CD B:GLU131 5.0 24.4 1.0

Zinc binding site 4 out of 4 in the N-Carbamoyl-Beta-Alanine Amidohydrolases From Rhizobium Radiobacter Mdc 8606


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of N-Carbamoyl-Beta-Alanine Amidohydrolases From Rhizobium Radiobacter Mdc 8606 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:30.4 occ:1.00 OD1 B:ASP97 2.1 28.6 1.0 O B:HOH685 2.2 22.5 1.0 NE2 B:HIS86 2.2 18.6 1.0 NE2 B:HIS193 2.2 20.2 1.0 CE1 B:HIS86 3.1 19.9 1.0 CE1 B:HIS193 3.1 22.7 1.0 CD2 B:HIS193 3.2 20.9 1.0 HE1 B:HIS86 3.2 19.8 1.0 CG B:ASP97 3.2 24.1 1.0 CD2 B:HIS86 3.2 20.2 1.0 HE1 B:HIS193 3.3 21.7 1.0 HD2 B:HIS193 3.4 20.8 1.0 HD2 B:HIS86 3.4 19.8 1.0 ZN B:ZN502 3.5 38.9 1.0 OE1 B:GLU131 3.5 22.6 1.0 H B:GLY98 3.6 24.0 1.0 OD2 B:ASP97 3.7 24.6 1.0 N B:GLY98 3.8 24.5 1.0 HA2 B:GLY98 3.8 24.8 1.0 CD B:GLU131 4.0 24.4 1.0 HA3 B:GLY98 4.1 25.6 1.0 ND1 B:HIS361 4.1 18.1 1.0 OE2 B:GLU132 4.1 34.1 1.0 CA B:GLY98 4.1 25.4 1.0 ND1 B:HIS86 4.2 20.8 1.0 ND1 B:HIS193 4.3 21.6 1.0 HE1 B:HIS361 4.3 19.8 1.0 CG B:HIS193 4.3 19.6 1.0 C B:ASP97 4.3 24.8 1.0 CG B:HIS86 4.3 21.8 1.0 OE2 B:GLU131 4.4 24.0 1.0 NE2 B:GLN196 4.4 21.5 1.0 HG3 B:GLU131 4.4 24.4 1.0 HA B:ASP97 4.5 24.4 1.0 CB B:ASP97 4.5 24.9 1.0 O B:HOH639 4.5 21.8 1.0 CE1 B:HIS361 4.6 21.3 1.0 CD B:GLU132 4.6 32.1 1.0 CA B:ASP97 4.7 25.6 1.0 OE1 B:GLU132 4.7 34.8 1.0 CG B:GLU131 4.8 24.3 1.0 HB3 B:GLU131 4.9 26.3 1.0 CD B:GLN196 5.0 21.8 1.0

A.Paloyan, A.Sargsyan, M.D.Karapetyan, A.Hambardzumyan, S.Kocharov, H.Panosyan, K.Dyukova, M.Kinosyan, A.Kreuger, C.Piergentili, W.A.Stanley, K.Y.Djoko, A.Basle, J.Marles-Wright, G.Antranikian. Structural and Biochemical Characterisation of the N-Carbamoyl-Beta-Alanine Amidohydrolase From Rhizobium Radiobacter Mdc 8606. Febs J. 2023.
ISSN: ISSN 1742-464X
PubMed: 37634202
DOI: 10.1111/FEBS.16943