Arsenic in PDB 7ea4: Crystal Structure of L182E D-Succinylase (Dsa) From Cupriavidus Sp. P4-10-C

The structure of Crystal Structure of L182E D-Succinylase (Dsa) From Cupriavidus Sp. P4-10-C, PDB code: 7ea4 was solved by M.Yamasaki, Y.Sumida, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.93 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.057, 129.806, 200.68, 90, 90, 90
R / Rfree (%)	16.4 / 20.8

The structure of Crystal Structure of L182E D-Succinylase (Dsa) From Cupriavidus Sp. P4-10-C also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Calcium	(Ca)	2 atoms

The binding sites of Arsenic atom in the Crystal Structure of L182E D-Succinylase (Dsa) From Cupriavidus Sp. P4-10-C (pdb code 7ea4). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 2 binding sites of Arsenic where determined in the Crystal Structure of L182E D-Succinylase (Dsa) From Cupriavidus Sp. P4-10-C, PDB code: 7ea4:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in the Crystal Structure of L182E D-Succinylase (Dsa) From Cupriavidus Sp. P4-10-C


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Crystal Structure of L182E D-Succinylase (Dsa) From Cupriavidus Sp. P4-10-C within 5.0Å range: probe atom residue distance (Å) B Occ A:As901 b:111.1 occ:1.00 AS A:CAD901 0.0 111.1 1.0 O2 A:CAD901 1.7 37.3 1.0 O1 A:CAD901 1.9 82.7 1.0 C2 A:CAD901 2.0 42.2 1.0 C1 A:CAD901 2.0 31.6 1.0 H23 A:CAD901 2.5 50.6 1.0 H21 A:CAD901 2.5 50.6 1.0 H22 A:CAD901 2.5 50.6 1.0 H13 A:CAD901 2.5 37.9 1.0 H12 A:CAD901 2.5 37.9 1.0 H11 A:CAD901 2.5 37.9 1.0 HO1 A:CAD901 2.6 99.2 1.0 O A:HOH1010 3.3 15.9 1.0 O A:HOH1158 3.5 23.2 1.0 O A:ARG713 4.5 11.9 1.0 CA A:PRO715 4.7 17.0 1.0 NH2 A:ARG713 4.9 21.6 1.0 N A:PRO715 5.0 15.4 1.0

Arsenic binding site 2 out of 2 in the Crystal Structure of L182E D-Succinylase (Dsa) From Cupriavidus Sp. P4-10-C


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Crystal Structure of L182E D-Succinylase (Dsa) From Cupriavidus Sp. P4-10-C within 5.0Å range: probe atom residue distance (Å) B Occ A:As904 b:122.5 occ:1.00 AS A:CAD904 0.0 122.5 1.0 O2 A:CAD904 1.7 30.4 1.0 O1 A:CAD904 1.9 42.1 1.0 C2 A:CAD904 2.0 44.7 1.0 C1 A:CAD904 2.0 49.4 1.0 H21 A:CAD904 2.5 53.6 1.0 H22 A:CAD904 2.5 53.6 1.0 H23 A:CAD904 2.5 53.6 1.0 H11 A:CAD904 2.5 59.2 1.0 H13 A:CAD904 2.5 59.2 1.0 H12 A:CAD904 2.5 59.2 1.0 HO1 A:CAD904 2.6 50.5 1.0 OE2 A:GLU223 3.5 37.9 1.0 O A:ASN484 3.9 13.0 1.0 CD A:GLU223 4.0 43.5 1.0 O A:HOH1420 4.3 35.4 1.0 N A:GLU223 4.4 20.7 1.0 O A:HOH1315 4.4 32.3 1.0 OE1 A:GLU223 4.5 48.3 1.0 O A:HOH1211 4.7 26.2 1.0 CG A:GLU223 4.7 29.8 1.0 OH A:TYR497 4.7 22.0 1.0 CA A:PRO222 4.7 17.7 1.0 O A:LEU221 4.8 25.5 1.0 CB A:GLU223 5.0 23.7 1.0 OG1 A:THR220 5.0 36.6 1.0

Y.Sumida, M.Yamasaki, Y.Nishiya, S.Kumagai, T.Yamada, M.Azuma. Protein Engineering of D-Succinylase From Cupriavidus Sp. For D-Amino Acid Synthesis and the Structural Implications. Adv.Synth.Catal. V. 363 4770 2021.
ISSN: ESSN 1615-4169
DOI: 10.1002/ADSC.202100587