Sodium in PDB 7xef: Crystal Structure of the Y53F/N55A Mutant of Leh Complexed with (R)- (1-Benzyl-3-Phenylpyrrolidin-3-Yl)Methanol

Enzymatic activity of Crystal Structure of the Y53F/N55A Mutant of Leh Complexed with (R)- (1-Benzyl-3-Phenylpyrrolidin-3-Yl)Methanol

All present enzymatic activity of Crystal Structure of the Y53F/N55A Mutant of Leh Complexed with (R)- (1-Benzyl-3-Phenylpyrrolidin-3-Yl)Methanol:
3.3.2.8;

Protein crystallography data

The structure of Crystal Structure of the Y53F/N55A Mutant of Leh Complexed with (R)- (1-Benzyl-3-Phenylpyrrolidin-3-Yl)Methanol, PDB code: 7xef was solved by G.Qu, X.Li, Z.T.Sun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.70 / 1.82
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.862, 51.024, 65.077, 69.89, 79.16, 63.81
R / Rfree (%) 14.1 / 19

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Y53F/N55A Mutant of Leh Complexed with (R)- (1-Benzyl-3-Phenylpyrrolidin-3-Yl)Methanol (pdb code 7xef). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of the Y53F/N55A Mutant of Leh Complexed with (R)- (1-Benzyl-3-Phenylpyrrolidin-3-Yl)Methanol, PDB code: 7xef:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 7xef

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Sodium binding site 1 out of 6 in the Crystal Structure of the Y53F/N55A Mutant of Leh Complexed with (R)- (1-Benzyl-3-Phenylpyrrolidin-3-Yl)Methanol


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 Complexed with (R)- (1-Benzyl-3-Phenylpyrrolidin-3-Yl)Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:17.4
occ:1.00
 O B:HOH390 2.2 28.1 1.0
O B:HOH405 2.3 18.9 1.0
O A:HOH452 2.3 21.4 1.0
O A:SER90 2.4 10.6 1.0
O B:SER90 2.4 9.3 1.0
OG A:SER91 2.5 12.3 1.0
C A:SER90 3.5 14.6 1.0
C B:SER90 3.6 11.7 1.0
CB A:SER91 3.6 12.3 1.0
CA A:SER91 3.8 18.5 1.0
OG B:SER91 3.9 17.2 1.0
O B:HOH310 3.9 17.8 1.0
N B:SER90 4.1 9.0 1.0
O A:HOH487 4.1 28.5 1.0
N A:SER91 4.1 9.6 1.0
O A:HOH402 4.1 26.5 1.0
OG B:SER90 4.3 14.0 1.0
CA B:SER90 4.4 7.8 1.0
O B:HOH448 4.5 28.2 1.0
N B:SER91 4.6 12.6 1.0
CA A:SER90 4.7 9.7 1.0
N A:SER90 4.7 7.6 1.0
O A:HOH385 4.8 22.5 1.0
CA B:SER91 4.8 13.0 1.0
CB B:SER91 4.9 9.2 1.0
CB B:SER90 4.9 9.8 1.0

Sodium binding site 2 out of 6 in 7xef

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Sodium binding site 2 out of 6 in the Crystal Structure of the Y53F/N55A Mutant of Leh Complexed with (R)- (1-Benzyl-3-Phenylpyrrolidin-3-Yl)Methanol


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 Complexed with (R)- (1-Benzyl-3-Phenylpyrrolidin-3-Yl)Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:20.6
occ:1.00
 O A:HOH337 2.2 14.2 1.0
O A:ALA19 2.4 9.6 1.0
O A:ILE88 2.5 8.8 1.0
OD1 B:ASN92 2.5 14.8 1.0
O A:ALA16 2.6 11.8 1.0
O A:ALA17 2.8 9.3 1.0
C A:ALA17 3.4 9.3 1.0
CG2 A:ILE88 3.4 9.9 1.0
CG B:ASN92 3.6 32.9 1.0
C A:ILE88 3.6 10.7 1.0
C A:ALA19 3.6 11.7 1.0
C A:ALA16 3.7 18.1 1.0
CA A:ALA17 3.8 11.7 1.0
N A:ALA19 3.9 14.0 1.0
ND2 B:ASN92 4.0 22.7 1.0
OE1 A:GLU25 4.1 12.8 1.0
N A:ILE88 4.2 7.1 1.0
N A:ALA17 4.2 17.0 1.0
N A:GLY18 4.3 8.6 1.0
CA A:ILE88 4.3 6.5 1.0
CA A:ALA19 4.3 14.9 1.0
CB A:ILE88 4.5 6.0 1.0
C A:GLY18 4.5 13.5 1.0
O B:HOH350 4.6 16.8 1.0
N A:GLY89 4.6 7.2 1.0
N A:ALA20 4.7 14.1 1.0
CA A:GLY18 4.7 14.3 1.0
CB B:ASN92 4.8 21.4 1.0
CA A:GLY89 4.8 8.7 1.0
CA A:ALA20 4.9 11.6 1.0
O B:HOH306 4.9 21.7 1.0
CA A:ALA16 4.9 16.0 1.0

Sodium binding site 3 out of 6 in 7xef

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Sodium binding site 3 out of 6 in the Crystal Structure of the Y53F/N55A Mutant of Leh Complexed with (R)- (1-Benzyl-3-Phenylpyrrolidin-3-Yl)Methanol


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 Complexed with (R)- (1-Benzyl-3-Phenylpyrrolidin-3-Yl)Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:33.5
occ:1.00
 O B:ALA19 2.3 22.3 1.0
O B:ALA16 2.4 20.1 1.0
O B:HOH431 2.4 28.6 1.0
O A:HOH410 2.5 21.1 1.0
OG B:SER21 3.0 26.0 1.0
C B:ALA19 3.3 20.9 1.0
C B:ALA16 3.6 29.2 1.0
ND2 A:ASN92 3.6 22.4 1.0
N B:ALA19 3.9 16.1 1.0
CA B:ALA19 4.0 15.3 1.0
CB B:SER21 4.1 19.9 1.0
CB B:ALA19 4.2 23.8 1.0
N B:SER21 4.2 14.8 1.0
O B:ALA17 4.3 12.7 1.0
CB B:ALA16 4.3 21.0 1.0
CA B:ALA16 4.3 34.8 1.0
N B:ALA20 4.4 22.6 1.0
O A:HOH376 4.4 32.3 1.0
C B:ALA20 4.4 29.5 1.0
C B:ALA17 4.5 14.0 1.0
CG A:ASN92 4.5 17.9 1.0
OE1 B:GLU25 4.5 13.3 1.0
CG2 B:ILE88 4.6 8.2 1.0
N B:ALA17 4.6 37.0 1.0
OD1 A:ASN92 4.6 23.3 1.0
CA B:ALA20 4.6 20.7 1.0
CA B:ALA17 4.7 28.4 1.0
CA B:SER21 4.7 22.9 1.0
O B:ILE88 4.8 10.3 1.0
O B:ALA20 4.9 22.1 1.0
C B:GLY18 5.0 18.2 1.0

Sodium binding site 4 out of 6 in 7xef

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Sodium binding site 4 out of 6 in the Crystal Structure of the Y53F/N55A Mutant of Leh Complexed with (R)- (1-Benzyl-3-Phenylpyrrolidin-3-Yl)Methanol


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 Complexed with (R)- (1-Benzyl-3-Phenylpyrrolidin-3-Yl)Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na207

b:37.3
occ:1.00
 O C:HOH308 2.3 15.6 1.0
O C:ALA16 2.3 14.0 1.0
O C:HOH342 2.5 17.1 1.0
O C:ALA19 2.5 18.0 1.0
OG C:SER21 2.6 22.2 1.0
OD1 D:ASN92 2.8 26.0 1.0
CG D:ASN92 3.4 19.5 1.0
ND2 D:ASN92 3.4 23.7 1.0
C C:ALA16 3.4 26.3 1.0
C C:ALA19 3.5 16.1 1.0
CB C:SER21 3.9 20.9 1.0
N C:ALA19 4.0 15.2 1.0
CB C:ALA19 4.0 16.9 1.0
CB C:ALA16 4.1 17.5 1.0
CA C:ALA19 4.1 21.2 1.0
CA C:ALA16 4.2 21.4 1.0
N C:ALA17 4.3 16.2 1.0
N C:SER21 4.4 16.1 1.0
CA C:ALA17 4.4 13.2 1.0
O C:ALA17 4.4 15.2 1.0
C C:ALA17 4.4 12.2 1.0
C C:ALA20 4.5 30.0 1.0
O C:ILE88 4.5 8.7 1.0
OE1 C:GLU25 4.6 12.5 1.0
N C:ALA20 4.6 10.4 1.0
CA C:SER21 4.7 19.8 1.0
CB D:ASN92 4.7 19.2 1.0
CA C:ALA20 4.8 12.8 1.0
O C:ALA20 4.8 21.6 1.0
CG2 C:ILE88 4.9 9.2 1.0

Sodium binding site 5 out of 6 in 7xef

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Sodium binding site 5 out of 6 in the Crystal Structure of the Y53F/N55A Mutant of Leh Complexed with (R)- (1-Benzyl-3-Phenylpyrrolidin-3-Yl)Methanol


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 Complexed with (R)- (1-Benzyl-3-Phenylpyrrolidin-3-Yl)Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na203

b:29.8
occ:1.00
 O D:HOH329 2.3 18.9 1.0
O D:HOH309 2.4 27.4 1.0
O D:ILE88 2.4 13.9 1.0
OD1 C:ASN92 2.6 19.6 1.0
O D:ALA17 2.7 9.7 1.0
O D:ALA19 2.7 11.2 1.0
O D:ALA16 2.8 11.8 1.0
C D:ALA17 3.3 10.1 1.0
CG2 D:ILE88 3.3 9.1 1.0
C D:ILE88 3.5 11.5 1.0
CG C:ASN92 3.6 21.9 1.0
CA D:ALA17 3.7 11.1 1.0
C D:ALA19 3.8 9.3 1.0
N D:ALA19 3.8 11.5 1.0
C D:ALA16 3.9 14.8 1.0
N D:ILE88 4.0 6.6 1.0
ND2 C:ASN92 4.1 20.0 1.0
CA D:ILE88 4.2 5.1 1.0
N D:GLY18 4.2 7.5 1.0
OE2 D:GLU25 4.2 13.6 1.0
N D:ALA17 4.3 14.9 1.0
CB D:ILE88 4.3 6.0 1.0
CA D:ALA19 4.4 10.9 1.0
OG C:SER91 4.4 8.1 0.4
C D:GLY18 4.4 11.3 1.0
O C:HOH377 4.5 10.1 1.0
CA D:GLY18 4.6 14.1 1.0
N D:GLY89 4.6 7.1 1.0
CB C:ASN92 4.8 11.9 1.0
O C:HOH313 4.8 20.9 1.0
CA D:GLY89 4.9 8.4 1.0
N D:ALA20 4.9 9.0 1.0
CB C:SER91 5.0 9.3 0.6

Sodium binding site 6 out of 6 in 7xef

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Sodium binding site 6 out of 6 in the Crystal Structure of the Y53F/N55A Mutant of Leh Complexed with (R)- (1-Benzyl-3-Phenylpyrrolidin-3-Yl)Methanol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of the Y53F/N55A Mutant of Leh Complexed with (R)- (1-Benzyl-3-Phenylpyrrolidin-3-Yl)Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na204

b:20.5
occ:1.00
 O C:HOH339 2.2 26.1 1.0
O D:HOH427 2.2 24.1 1.0
O C:HOH384 2.3 23.9 1.0
O D:SER90 2.3 11.1 1.0
O C:SER90 2.4 10.8 1.0
OG D:SER91 2.6 16.4 1.0
C D:SER90 3.5 11.8 1.0
C C:SER90 3.6 13.6 1.0
OG C:SER91 3.7 5.3 0.6
CB D:SER91 3.8 10.6 1.0
O D:HOH393 3.8 25.2 1.0
O C:HOH309 3.9 16.0 1.0
CA D:SER91 4.0 9.2 1.0
C2 C:EDO205 4.0 29.8 1.0
O C:HOH472 4.1 28.2 1.0
N C:SER90 4.1 5.7 1.0
N D:SER91 4.2 9.8 1.0
O C:HOH440 4.3 32.9 1.0
OG C:SER90 4.3 11.1 1.0
O2 C:EDO205 4.4 22.7 1.0
CA C:SER90 4.4 8.0 1.0
N D:SER90 4.5 9.6 1.0
N C:SER91 4.6 7.3 1.0
CA D:SER90 4.6 10.1 1.0
CB C:SER91 4.7 9.4 0.4
CA C:SER91 4.7 9.4 0.4
CA C:SER91 4.7 9.4 0.6
CB C:SER91 4.8 9.3 0.6
OG D:SER90 4.9 10.2 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: Fri Apr 7 17:09:06 2023

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