Sodium in PDB 8hp6: Crystal Structure of (S)-2-Haloacid Dehalogenase D12A Mutant

The structure of Crystal Structure of (S)-2-Haloacid Dehalogenase D12A Mutant, PDB code: 8hp6 was solved by Q.Yang, L.Wang, X.Xu, X.Xing, J.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.80 / 2.20
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	151.726, 151.726, 151.726, 90, 90, 90
R / Rfree (%)	16.6 / 20.1

The binding sites of Sodium atom in the Crystal Structure of (S)-2-Haloacid Dehalogenase D12A Mutant (pdb code 8hp6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of (S)-2-Haloacid Dehalogenase D12A Mutant, PDB code: 8hp6:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of (S)-2-Haloacid Dehalogenase D12A Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of (S)-2-Haloacid Dehalogenase D12A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:28.8 occ:1.00 OG A:SER121 2.9 46.1 1.0 O A:HOH578 3.0 37.2 1.0 N A:CYS13 3.1 28.6 1.0 N A:TYR14 3.1 31.2 1.0 N A:ASN122 3.3 27.4 1.0 O A:HOH548 3.5 35.1 1.0 CA A:SER121 3.5 29.6 1.0 CD2 A:TYR14 3.7 33.1 1.0 CA A:CYS13 3.7 29.5 1.0 CB A:SER121 3.7 30.1 1.0 CB A:CYS13 3.8 30.7 1.0 NZ A:LYS152 3.8 29.3 1.0 C A:CYS13 3.9 31.0 1.0 C A:SER121 3.9 26.2 1.0 CB A:TYR14 4.1 31.6 1.0 CA A:TYR14 4.1 28.4 1.0 C A:ALA12 4.2 31.9 1.0 CA A:ASN122 4.3 26.9 1.0 CG A:TYR14 4.3 29.2 1.0 O A:LEU120 4.3 27.6 1.0 CA A:ALA12 4.4 26.1 1.0 CB A:ASN122 4.4 28.0 1.0 CE A:LYS152 4.5 27.7 1.0 CB A:ALA12 4.5 24.5 1.0 O A:HOH512 4.5 28.5 1.0 O A:TYR14 4.6 34.0 1.0 CE2 A:TYR14 4.6 33.6 1.0 O A:ASN122 4.6 31.8 1.0 C A:ASN122 4.7 28.4 1.0 N A:SER121 4.7 24.8 1.0 C A:TYR14 4.8 30.6 1.0 C A:LEU120 4.9 27.9 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of (S)-2-Haloacid Dehalogenase D12A Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of (S)-2-Haloacid Dehalogenase D12A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:30.3 occ:1.00 OG B:SER121 2.5 42.0 1.0 O B:HOH517 3.1 44.1 1.0 N B:CYS13 3.2 39.1 1.0 N B:TYR14 3.2 35.2 1.0 N B:ASN122 3.2 29.4 1.0 O B:HOH501 3.3 42.9 1.0 CA B:SER121 3.4 33.6 1.0 CB B:SER121 3.4 35.4 1.0 CD2 B:TYR14 3.7 35.0 1.0 NZ B:LYS152 3.8 29.4 1.0 CA B:CYS13 3.9 34.4 1.0 C B:SER121 3.9 30.5 1.0 CB B:CYS13 3.9 33.7 1.0 C B:CYS13 4.0 35.8 1.0 O B:HOH488 4.1 43.4 1.0 CB B:TYR14 4.1 30.7 1.0 CA B:TYR14 4.2 30.6 1.0 C B:ALA12 4.2 34.6 1.0 O B:LEU120 4.2 30.7 1.0 CA B:ASN122 4.3 27.9 1.0 CA B:ALA12 4.4 31.7 1.0 CB B:ASN122 4.4 30.7 1.0 CG B:TYR14 4.4 32.9 1.0 CE B:LYS152 4.4 33.5 1.0 CB B:ALA12 4.4 31.8 1.0 O B:HOH493 4.5 35.8 1.0 O B:TYR14 4.5 34.1 1.0 O B:ASN122 4.6 33.4 1.0 N B:SER121 4.6 31.4 1.0 CE2 B:TYR14 4.7 37.2 1.0 C B:ASN122 4.7 33.6 1.0 C B:TYR14 4.8 34.8 1.0 C B:LEU120 4.9 29.8 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of (S)-2-Haloacid Dehalogenase D12A Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of (S)-2-Haloacid Dehalogenase D12A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:30.4 occ:1.00 OG C:SER121 2.7 46.4 1.0 O C:HOH523 3.0 46.2 1.0 N C:ASN122 3.1 25.3 1.0 CA C:SER121 3.3 31.0 1.0 N C:TYR14 3.3 29.6 1.0 N C:CYS13 3.4 30.2 1.0 CB C:SER121 3.5 37.4 1.0 O C:HOH503 3.5 38.3 1.0 CD2 C:TYR14 3.7 30.0 1.0 C C:SER121 3.7 29.2 1.0 NZ C:LYS152 3.8 27.4 1.0 CA C:CYS13 4.0 33.5 1.0 CB C:CYS13 4.0 30.1 1.0 CB C:TYR14 4.1 28.1 1.0 C C:CYS13 4.1 32.4 1.0 CA C:ASN122 4.2 29.0 1.0 O C:HOH458 4.2 40.5 1.0 CA C:TYR14 4.2 30.7 1.0 O C:LEU120 4.3 34.3 1.0 CB C:ASN122 4.3 30.3 1.0 O C:HOH506 4.4 32.9 1.0 CG C:TYR14 4.4 32.5 1.0 C C:ALA12 4.4 34.1 1.0 CE C:LYS152 4.5 33.1 1.0 CB C:ALA12 4.5 32.1 1.0 O C:ASN122 4.5 33.5 1.0 CA C:ALA12 4.5 34.8 1.0 N C:SER121 4.5 35.6 1.0 O C:TYR14 4.6 28.1 1.0 C C:ASN122 4.6 32.9 1.0 CE2 C:TYR14 4.6 32.4 1.0 C C:LEU120 4.8 34.2 1.0 C C:TYR14 4.8 30.6 1.0 O C:SER121 5.0 34.1 1.0 CG C:ASN122 5.0 34.9 1.0

X.Xu, Q.Yang, L.Wang, J.Zheng, Y.Gu, X.W.Xing, J.Zhou. Enzymatic Hydrolysis on L-Azetidine-2-Carboxylate Ring Opening Catalysis Science and 2023TECHNOLOGY.
ISSN: ESSN 2044-4761
DOI: 10.1039/D3CY00366C