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Sodium in PDB 4fhz: Crystal Structure of A Carboxyl Esterase at 2.0 Angstrom Resolution

Enzymatic activity of Crystal Structure of A Carboxyl Esterase at 2.0 Angstrom Resolution

All present enzymatic activity of Crystal Structure of A Carboxyl Esterase at 2.0 Angstrom Resolution:
3.1.1.1;

Protein crystallography data

The structure of Crystal Structure of A Carboxyl Esterase at 2.0 Angstrom Resolution, PDB code: 4fhz was solved by L.Wu, J.Ma, J.Zhou, H.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.34 / 2.01
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 72.042, 72.042, 113.583, 90.00, 90.00, 120.00
R / Rfree (%) 15.9 / 21.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Carboxyl Esterase at 2.0 Angstrom Resolution (pdb code 4fhz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure of A Carboxyl Esterase at 2.0 Angstrom Resolution, PDB code: 4fhz:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 4fhz

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Sodium binding site 1 out of 7 in the Crystal Structure of A Carboxyl Esterase at 2.0 Angstrom Resolution


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 A Carboxyl Esterase at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:48.0
occ:1.00
 O A:ASP102 2.9 36.1 1.0
O A:HOH431 3.1 65.4 1.0
N A:THR54 3.1 42.0 1.0
O A:HOH412 3.2 53.6 1.0
CA A:LEU53 3.3 43.8 1.0
OG1 A:THR54 3.6 43.7 1.0
C A:LEU53 3.7 44.2 1.0
C A:ASP102 3.7 35.2 1.0
CD2 A:LEU53 3.8 48.6 1.0
O A:ALA103 3.8 37.2 1.0
CB A:LEU53 3.8 38.9 1.0
CB A:ASP102 3.9 36.5 1.0
O A:LYS52 3.9 47.4 1.0
CA A:THR54 4.2 42.1 1.0
O A:THR54 4.2 37.9 1.0
C A:ALA103 4.2 35.2 1.0
CA A:ASP102 4.2 34.2 1.0
CB A:THR54 4.3 42.4 1.0
CA A:PRO104 4.3 41.0 1.0
N A:ASP102 4.4 38.1 1.0
CG A:LEU53 4.4 42.9 1.0
CG2 A:THR54 4.4 45.5 1.0
N A:LEU53 4.4 45.9 1.0
N A:PRO104 4.5 36.8 1.0
C A:LYS52 4.6 48.0 1.0
C A:THR54 4.7 43.6 1.0
N A:ALA103 4.7 33.2 1.0
O A:LEU53 4.9 45.5 1.0
CG A:ASP102 5.0 45.0 1.0
CA A:ALA103 5.0 31.4 1.0

Sodium binding site 2 out of 7 in 4fhz

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Sodium binding site 2 out of 7 in the Crystal Structure of A Carboxyl Esterase at 2.0 Angstrom Resolution


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 A Carboxyl Esterase at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:52.7
occ:1.00
 OD1 A:ASP102 2.8 45.6 1.0
N A:ALA80 3.1 41.2 1.0
N A:GLY79 3.4 35.2 1.0
CB A:ALA80 3.5 45.5 1.0
OD2 A:ASP102 3.6 49.9 1.0
CG A:ASP102 3.6 45.0 1.0
CG A:ASP78 3.7 47.6 1.0
CA A:GLY79 3.8 39.0 1.0
CA A:ALA80 3.8 44.9 1.0
CB A:ASP78 3.8 39.4 1.0
C A:GLY79 3.9 41.6 1.0
OD1 A:ASP78 3.9 50.4 1.0
OD2 A:ASP78 4.1 52.6 1.0
C A:ASP78 4.2 34.3 1.0
CA A:ASP78 4.7 37.7 1.0

Sodium binding site 3 out of 7 in 4fhz

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Sodium binding site 3 out of 7 in the Crystal Structure of A Carboxyl Esterase at 2.0 Angstrom Resolution


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 A Carboxyl Esterase at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:48.6
occ:1.00
 O A:HOH436 2.9 45.6 1.0
O A:GLY187 2.9 39.1 1.0
N A:GLY190 3.1 36.5 1.0
C A:GLY187 3.3 36.1 1.0
N A:SER189 3.4 33.2 1.0
C A:PHE188 3.5 34.0 1.0
CG2 A:THR168 3.6 36.8 1.0
CA A:GLY190 3.7 36.5 1.0
CD2 A:LEU210 3.8 40.7 1.0
O A:GLY190 3.8 39.1 1.0
N A:PHE188 3.8 32.7 1.0
C A:GLY190 3.8 40.4 1.0
O A:PHE188 3.9 35.1 1.0
CA A:PHE188 4.0 34.2 1.0
O A:VAL211 4.0 35.4 1.0
CA A:GLY187 4.0 36.4 1.0
C A:SER189 4.1 37.9 1.0
CA A:SER189 4.1 36.8 1.0
ND1 A:HIS212 4.3 38.9 1.0
OG1 A:THR168 4.4 33.9 1.0
CB A:LEU210 4.4 37.8 1.0
N A:VAL211 4.4 34.3 1.0
CB A:THR168 4.4 36.0 1.0
CA A:LEU210 4.6 37.5 1.0
CG A:LEU210 4.6 42.4 1.0
N A:ARG191 4.7 41.5 1.0
C A:VAL211 4.8 35.6 1.0
C A:LEU210 5.0 38.2 1.0

Sodium binding site 4 out of 7 in 4fhz

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Sodium binding site 4 out of 7 in the Crystal Structure of A Carboxyl Esterase at 2.0 Angstrom Resolution


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 A Carboxyl Esterase at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:48.1
occ:1.00
 O A:ARG108 2.8 37.5 1.0
O A:HOH458 2.9 53.6 1.0
O A:HOH457 2.9 44.8 1.0
C A:ARG108 3.5 41.3 1.0
CA A:ARG108 3.6 40.2 1.0
CB A:ARG108 4.2 40.5 1.0
CG A:ARG108 4.4 45.0 1.0
O A:CYS107 4.6 37.4 1.0
N A:ALA109 4.8 38.5 1.0
N A:ARG108 4.8 36.5 1.0
O A:HOH484 4.8 69.9 1.0

Sodium binding site 5 out of 7 in 4fhz

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Sodium binding site 5 out of 7 in the Crystal Structure of A Carboxyl Esterase at 2.0 Angstrom Resolution


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 A Carboxyl Esterase at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na306

b:30.8
occ:1.00
 N A:GLY74 3.2 30.8 1.0
CA A:HIS73 3.5 30.7 1.0
CB A:HIS73 3.5 31.4 1.0
CG A:LEU82 3.7 47.1 1.0
CD2 A:PHE164 3.8 31.3 1.0
C A:HIS73 3.9 31.1 1.0
CB A:PHE164 4.0 29.4 1.0
CB A:ALA77 4.1 28.8 1.0
CD1 A:LEU82 4.2 41.4 1.0
CG A:PHE164 4.2 32.1 1.0
CA A:GLY74 4.3 32.8 1.0
CB A:LEU82 4.5 45.6 1.0
CD2 A:LEU82 4.6 49.8 1.0
CE2 A:PHE164 4.6 32.5 1.0
N A:HIS73 4.8 31.3 1.0
CG A:HIS73 4.8 33.0 1.0
N A:LEU82 4.8 49.2 1.0
CB A:ASP81 4.8 63.9 1.0

Sodium binding site 6 out of 7 in 4fhz

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Sodium binding site 6 out of 7 in the Crystal Structure of A Carboxyl Esterase at 2.0 Angstrom Resolution


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 A Carboxyl Esterase at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na307

b:70.4
occ:1.00
 N A:LEU192 3.2 42.7 1.0
O A:ASP223 3.3 48.0 1.0
CB A:ARG191 3.3 48.7 1.0
N A:ALA227 3.6 43.9 1.0
CB A:ALA227 3.8 39.5 1.0
O A:LEU192 3.8 52.3 1.0
CA A:ARG191 3.8 41.4 1.0
CB A:ASP223 3.8 47.8 1.0
CB A:LEU226 3.9 57.2 1.0
CA A:ALA227 4.0 43.8 1.0
CA A:ASP223 4.0 48.6 1.0
C A:ASP223 4.0 47.9 1.0
C A:ARG191 4.0 42.1 1.0
CA A:LEU192 4.1 49.4 1.0
CB A:LEU192 4.1 52.0 1.0
CG A:ASP223 4.2 53.0 1.0
C A:LEU226 4.3 48.2 1.0
CG A:ARG191 4.3 52.7 1.0
C A:LEU192 4.4 53.2 1.0
OD1 A:ASP223 4.4 53.8 1.0
CD A:ARG191 4.6 58.7 1.0
CA A:LEU226 4.7 52.3 1.0
OD2 A:ASP223 4.9 54.4 1.0
CD1 A:LEU226 4.9 66.1 1.0

Sodium binding site 7 out of 7 in 4fhz

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Sodium binding site 7 out of 7 in the Crystal Structure of A Carboxyl Esterase at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of A Carboxyl Esterase at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na308

b:30.0
occ:1.00
 OG A:SER165 2.9 33.7 1.0
N A:TYR75 3.1 34.1 1.0
O A:HOH401 3.2 33.6 1.0
N A:GLN166 3.2 31.7 1.0
CB A:TYR75 3.4 33.0 1.0
CB A:SER165 3.4 32.8 1.0
C1 A:PEG305 3.4 64.8 1.0
CB A:GLN166 3.5 30.1 1.0
CA A:TYR75 3.8 33.2 1.0
CA A:GLN166 3.9 30.9 1.0
C A:GLY74 4.1 34.2 1.0
CA A:GLY74 4.1 32.8 1.0
O2 A:PEG305 4.2 61.6 1.0
C A:SER165 4.2 34.6 1.0
O1 A:PEG305 4.4 68.2 1.0
CA A:SER165 4.4 33.2 1.0
C2 A:PEG305 4.5 61.4 1.0
CG A:TYR75 4.6 36.0 1.0
O A:TYR75 4.6 33.1 1.0
C A:TYR75 4.8 34.8 1.0
CD1 A:ILE119 4.8 39.5 1.0
CG A:GLN166 4.8 32.4 1.0
NE2 A:HIS248 4.8 32.5 1.0

Reference:

J.Ma, L.Wu, F.Guo, J.Gu, X.Tang, L.Jiang, J.Liu, J.Zhou, H.Yu. Enhanced Enantioselectivity of A Carboxyl Esterase From Rhodobacter Sphaeroides By Directed Evolution. Appl.Microbiol.Biotechnol. V. 97 4897 2013.
ISSN: ISSN 0175-7598
PubMed: 22987200
DOI: 10.1007/S00253-012-4396-2
Page generated: Mon Oct 7 15:22:36 2024

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