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

Enzymatic activity of 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;

Protein crystallography data

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

Sodium Binding Sites:

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 7vwd

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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 7vwd

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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 7vwd

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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 7vwd

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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 7vwd

Go back to Sodium Binding Sites List in 7vwd
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

Reference:

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
Page generated: Wed Oct 9 09:22:19 2024

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