Atomistry » Sodium » PDB 7wlw-7xef » 7xef
Atomistry »
  Sodium »
    PDB 7wlw-7xef »
      7xef »

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

Go back to Sodium Binding Sites List in 7xef
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

Go back to Sodium Binding Sites List in 7xef
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

Go back to Sodium Binding Sites List in 7xef
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

Go back to Sodium Binding Sites List in 7xef
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

Go back to Sodium Binding Sites List in 7xef
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

Go back to Sodium Binding Sites List in 7xef
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: Wed Oct 9 09:41:16 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy