Sodium in PDB 7vwd: Crystal Structure of the Y53F/N55A Mutant of Leh

All present enzymatic activity of Crystal Structure of the Y53F/N55A Mutant of Leh:
3.3.2.8;

The structure of Crystal Structure of the Y53F/N55A Mutant of Leh, PDB code: 7vwd was solved by G.Qu, X.Li, Z.T.Sun, X.Han, W.D.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.00 / 2.15
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	49.271, 50.391, 64.729, 69.82, 79.87, 63.89
R / Rfree (%)	18.3 / 21.8

The binding sites of Sodium atom in the Crystal Structure of the Y53F/N55A Mutant of Leh (pdb code 7vwd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of the Y53F/N55A Mutant of Leh, PDB code: 7vwd:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of the Y53F/N55A Mutant of Leh


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 the Y53F/N55A Mutant of Leh within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:24.3 occ:1.00 O A:HOH320 2.3 19.0 1.0 OD1 D:ASN92 2.4 21.7 1.0 O A:ALA19 2.5 18.8 1.0 O A:ALA16 2.6 17.6 1.0 O A:ILE88 2.7 18.6 1.0 O A:ALA17 2.8 14.9 1.0 C A:ALA17 3.4 15.9 1.0 CG D:ASN92 3.5 25.4 1.0 C A:ALA19 3.6 19.8 1.0 C A:ALA16 3.7 19.0 1.0 CG2 A:ILE88 3.8 15.2 1.0 CA A:ALA17 3.8 19.2 1.0 C A:ILE88 3.8 19.0 1.0 N A:ALA19 3.8 17.1 1.0 ND2 D:ASN92 3.9 24.6 1.0 N A:ALA17 4.2 18.5 1.0 OE1 A:GLU25 4.3 19.6 1.0 CA A:ALA19 4.3 20.5 1.0 N A:GLY18 4.3 17.0 1.0 CA A:ILE88 4.6 15.8 1.0 C A:GLY18 4.6 19.9 1.0 N A:ILE88 4.6 15.6 1.0 CB D:ASN92 4.7 21.4 1.0 N A:ALA20 4.7 18.4 1.0 O A:HOH302 4.7 19.0 1.0 O D:HOH322 4.8 18.6 1.0 CB A:ILE88 4.8 15.4 1.0 CA A:GLY18 4.8 17.2 1.0 N A:GLY89 4.8 19.2 1.0 CB A:ALA19 4.9 19.7 1.0 OG A:SER21 4.9 23.9 1.0 CA A:ALA16 4.9 17.7 1.0 CA A:ALA20 4.9 21.8 1.0 CA A:GLY89 5.0 16.2 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of the Y53F/N55A Mutant of Leh


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 the Y53F/N55A Mutant of Leh within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:23.9 occ:1.00 O A:SER90 2.4 19.3 1.0 O D:HOH314 2.4 20.8 1.0 O D:SER90 2.4 18.4 1.0 OG A:SER91 2.5 22.2 1.0 O D:HOH331 2.5 28.6 1.0 OG D:SER91 3.5 23.7 1.0 C A:SER90 3.5 19.5 1.0 C D:SER90 3.6 19.8 1.0 CB A:SER91 3.7 21.5 1.0 CA A:SER91 3.9 21.4 1.0 N A:SER91 4.1 17.4 1.0 O D:HOH315 4.1 18.8 1.0 N D:SER90 4.2 18.7 1.0 OG D:SER90 4.3 21.3 1.0 CA D:SER90 4.5 21.1 1.0 N D:SER91 4.6 20.4 1.0 CB D:SER91 4.7 23.3 1.0 CA A:SER90 4.7 18.0 1.0 CA D:SER91 4.8 20.3 1.0 N A:SER90 4.8 18.1 1.0 CB D:SER90 5.0 17.0 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of the Y53F/N55A Mutant of Leh


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 the Y53F/N55A Mutant of Leh within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:26.2 occ:1.00 O B:ALA16 2.3 15.7 1.0 O B:HOH314 2.4 19.5 1.0 OD1 C:ASN92 2.4 21.9 1.0 O B:ALA19 2.4 18.1 1.0 CG C:ASN92 3.4 26.4 1.0 C B:ALA16 3.5 18.5 1.0 O B:ILE88 3.6 20.0 1.0 C B:ALA19 3.6 19.6 1.0 O B:ALA17 3.6 17.4 1.0 ND2 C:ASN92 3.7 26.3 1.0 C B:ALA17 3.9 19.8 1.0 N B:ALA19 4.0 17.3 1.0 CA B:ALA17 4.2 19.8 1.0 CA B:ALA19 4.3 19.6 1.0 CG2 B:ILE88 4.3 15.8 1.0 N B:ALA17 4.3 17.9 1.0 OE1 B:GLU25 4.4 16.5 1.0 CB B:ALA16 4.5 14.3 1.0 CA B:ALA16 4.6 16.5 1.0 N B:ALA20 4.7 18.3 1.0 CB B:ALA19 4.7 18.5 1.0 N B:GLY18 4.7 16.4 1.0 CB C:ASN92 4.7 23.6 1.0 CB B:SER21 4.7 22.4 1.0 C B:ILE88 4.7 17.2 1.0 OG B:SER21 4.8 24.8 1.0 C B:GLY18 4.8 17.2 1.0 CA B:ALA20 4.9 18.4 1.0 C B:ALA20 4.9 20.1 1.0 N B:SER21 4.9 20.1 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of the Y53F/N55A Mutant of Leh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Y53F/N55A Mutant of Leh within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:36.9 occ:1.00 O C:SER90 2.4 22.2 1.0 O B:SER90 2.7 14.7 1.0 OG C:SER91 3.0 27.7 1.0 OG B:SER91 3.2 19.1 1.0 C C:SER90 3.6 20.3 1.0 C B:SER90 3.9 17.6 1.0 CB C:SER91 4.2 23.6 1.0 CA C:SER91 4.4 23.7 1.0 N C:SER91 4.4 20.4 1.0 CB B:SER91 4.4 16.8 1.0 OG C:SER90 4.5 19.2 1.0 N C:SER90 4.6 19.1 1.0 CA B:SER91 4.7 17.1 1.0 CA C:SER90 4.7 20.7 1.0 N B:SER91 4.7 17.1 1.0 N B:SER90 4.7 16.0 1.0 CA B:SER90 4.9 15.7 1.0 OG B:SER90 5.0 13.9 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of the Y53F/N55A Mutant of Leh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Y53F/N55A Mutant of Leh within 5.0Å range: probe atom residue distance (Å) B Occ C:Na202 b:29.9 occ:1.00 OD1 B:ASN92 2.4 26.1 1.0 O C:HOH325 2.5 19.8 1.0 O C:ALA16 2.5 24.8 1.0 O C:ALA19 2.5 23.8 1.0 OG C:SER21 2.7 30.6 1.0 CG B:ASN92 3.5 24.8 1.0 C C:ALA16 3.6 27.4 1.0 C C:ALA19 3.7 23.1 1.0 CB C:SER21 3.8 24.8 1.0 ND2 B:ASN92 3.9 27.1 1.0 CB C:ALA16 4.1 25.3 1.0 N C:SER21 4.3 21.7 1.0 CA C:ALA16 4.3 25.7 1.0 CA C:ALA19 4.4 26.3 1.0 N C:ALA19 4.4 19.4 1.0 OE1 C:GLU25 4.5 18.7 1.0 CB C:ALA19 4.5 21.8 1.0 C C:ALA20 4.5 21.9 1.0 N C:ALA17 4.5 29.2 1.0 O C:ILE88 4.6 18.6 1.0 CA C:SER21 4.6 23.6 1.0 CA C:ALA17 4.6 25.0 1.0 N C:ALA20 4.7 19.6 1.0 CB B:ASN92 4.7 20.5 1.0 CA C:ALA20 4.8 21.8 1.0 C C:ALA17 4.8 22.6 1.0 O C:ALA17 4.9 22.4 1.0

J.K.Li, G.Qu, X.Li, Y.Tian, C.Cui, F.G.Zhang, W.Zhang, J.A.Ma, M.T.Reetz, Z.Sun. Rational Enzyme Design For Enabling Biocatalytic Baldwin Cyclization and Asymmetric Synthesis of Chiral Heterocycles. Nat Commun V. 13 7813 2022.
ISSN: ESSN 2041-1723
PubMed: 36535947
DOI: 10.1038/S41467-022-35468-Y