Calcium 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
Arsenic	(As)	2 atoms

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

Calcium 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 Calcium with other atoms in the Ca 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:Ca908 b:11.8 occ:1.00 OD1 A:ASP357 2.2 14.8 1.0 OD1 A:ASN185 2.3 11.1 1.0 O A:GLU356 2.3 14.0 1.0 OE2 A:GLU189 2.4 16.9 1.0 OD2 A:ASP354 2.4 12.4 1.0 OD1 A:ASP354 2.5 10.9 1.0 O A:GLY487 2.6 13.6 1.0 CG A:ASP354 2.8 12.8 1.0 CG A:ASN185 3.4 12.2 1.0 C A:GLU356 3.4 12.0 1.0 CG A:ASP357 3.5 14.1 1.0 CD A:GLU189 3.5 21.1 1.0 C A:GLY487 3.6 16.6 1.0 CA A:GLY487 3.8 13.6 1.0 ND2 A:ASN185 3.9 11.3 1.0 CA A:ASP357 3.9 11.8 1.0 O A:HOH1072 4.0 17.3 1.0 CG A:GLU189 4.0 15.2 1.0 N A:ASP357 4.1 11.8 1.0 NH2 A:ARG482 4.1 10.3 1.0 CB A:ASP357 4.3 8.7 1.0 CB A:ASP354 4.3 13.1 1.0 N A:ASN185 4.4 10.8 1.0 OD2 A:ASP357 4.4 13.8 1.0 CZ A:ARG482 4.5 10.5 1.0 OE1 A:GLU189 4.5 17.3 1.0 NE A:ARG482 4.5 12.7 1.0 N A:GLU356 4.5 10.4 1.0 CA A:GLU356 4.6 9.6 1.0 CB A:ASN185 4.7 12.5 1.0 O A:HOH1013 4.7 16.7 1.0 N A:LEU488 4.8 12.5 1.0 C A:ASN185 4.9 14.3 1.0 O A:ASN185 4.9 13.0 1.0 CA A:ASN185 4.9 13.6 1.0

Calcium 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 Calcium with other atoms in the Ca 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 B:Ca904 b:13.0 occ:1.00 OE2 B:GLU189 2.3 13.4 1.0 OD1 B:ASP357 2.3 14.1 1.0 OD2 B:ASP354 2.3 12.2 1.0 OD1 B:ASN185 2.4 12.4 1.0 O B:GLU356 2.4 13.4 1.0 O B:GLY487 2.5 14.4 1.0 OD1 B:ASP354 2.6 12.3 1.0 CG B:ASP354 2.8 16.4 1.0 CD B:GLU189 3.4 19.7 1.0 C B:GLY487 3.5 17.1 1.0 C B:GLU356 3.5 13.0 1.0 CG B:ASN185 3.5 13.3 1.0 CG B:ASP357 3.5 12.0 1.0 CA B:GLY487 3.7 17.7 1.0 CA B:ASP357 3.9 15.6 1.0 ND2 B:ASN185 3.9 14.9 1.0 CG B:GLU189 4.0 17.0 1.0 O B:HOH1124 4.0 18.6 1.0 NH2 B:ARG482 4.1 13.6 1.0 N B:ASP357 4.1 10.3 1.0 CB B:ASP357 4.3 13.8 1.0 CB B:ASP354 4.3 11.2 1.0 OD2 B:ASP357 4.4 17.6 1.0 OE1 B:GLU189 4.4 17.7 1.0 N B:ASN185 4.5 12.5 1.0 CZ B:ARG482 4.5 16.9 1.0 NE B:ARG482 4.5 14.6 1.0 N B:GLU356 4.6 11.8 1.0 O B:HOH1011 4.6 22.2 1.0 CA B:GLU356 4.6 15.4 1.0 N B:LEU488 4.7 13.3 1.0 CB B:ASN185 4.8 10.4 1.0 C B:ASN185 5.0 13.0 1.0 CA B:ASN185 5.0 13.0 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