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Sodium in PDB 4ccy: Crystal Structure of Carboxylesterase Cesb (Ybfk) From Bacillus Subtilis

Enzymatic activity of Crystal Structure of Carboxylesterase Cesb (Ybfk) From Bacillus Subtilis

All present enzymatic activity of Crystal Structure of Carboxylesterase Cesb (Ybfk) From Bacillus Subtilis:
3.1.1.1;

Protein crystallography data

The structure of Crystal Structure of Carboxylesterase Cesb (Ybfk) From Bacillus Subtilis, PDB code: 4ccy was solved by H.J.Rozeboom, L.F.Godinho, M.Nardini, W.J.Quax, B.W.Dijkstra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 108.60 / 2.04
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 82.110, 44.010, 108.660, 90.00, 91.87, 90.00
R / Rfree (%) 20.362 / 25.013

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Carboxylesterase Cesb (Ybfk) From Bacillus Subtilis (pdb code 4ccy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Carboxylesterase Cesb (Ybfk) From Bacillus Subtilis, PDB code: 4ccy:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4ccy

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Sodium binding site 1 out of 4 in the Crystal Structure of Carboxylesterase Cesb (Ybfk) From Bacillus Subtilis


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 Carboxylesterase Cesb (Ybfk) From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1297

b:13.6
occ:1.00
O A:GLU245 2.3 16.6 1.0
OE1 A:GLN250 2.3 18.1 1.0
O A:HOH2219 2.4 22.4 1.0
O A:HOH2224 2.5 23.6 1.0
O A:TYR248 2.6 16.9 1.0
O A:HOH2144 2.7 18.0 1.0
CD A:GLN250 3.4 18.1 1.0
C A:GLU245 3.5 16.3 1.0
C A:TYR248 3.8 17.4 1.0
NE2 A:GLN250 3.9 18.7 1.0
CB A:GLU245 4.1 14.8 1.0
CA A:GLU245 4.1 15.5 1.0
N A:GLN250 4.1 17.6 1.0
N A:GLU245 4.2 16.0 1.0
CA A:HIS249 4.2 18.5 1.0
O A:HOH2222 4.4 36.3 1.0
N A:HIS249 4.5 17.8 1.0
NE2 A:HIS163 4.5 19.7 1.0
CG A:GLU245 4.5 13.9 1.0
N A:ALA246 4.6 16.4 1.0
O A:HOH2227 4.6 16.5 1.0
C A:HIS244 4.6 16.8 1.0
CG A:GLN250 4.7 17.5 1.0
C A:HIS249 4.7 17.7 1.0
ND1 A:HIS249 4.8 21.5 1.0
O A:GLU243 4.8 17.9 1.0
N A:TYR248 4.8 16.7 1.0
CA A:ALA246 4.9 17.4 1.0
CA A:TYR248 4.9 16.9 1.0
CB A:GLN250 5.0 17.0 1.0
O A:HIS244 5.0 17.1 1.0

Sodium binding site 2 out of 4 in 4ccy

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Sodium binding site 2 out of 4 in the Crystal Structure of Carboxylesterase Cesb (Ybfk) From Bacillus Subtilis


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 Carboxylesterase Cesb (Ybfk) From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1298

b:19.0
occ:1.00
O A:HOH2164 2.2 21.3 1.0
O A:HOH2171 2.3 17.8 1.0
O A:HOH2170 2.3 17.6 1.0
O A:GLY188 2.4 29.4 1.0
O A:TYR191 2.4 22.1 1.0
OG1 A:THR187 2.5 20.6 1.0
CB A:THR187 3.4 21.0 1.0
C A:GLY188 3.6 30.6 1.0
C A:TYR191 3.6 22.3 1.0
OD1 A:ASP192 3.6 21.4 1.0
N A:GLY188 4.0 26.8 1.0
C A:THR187 4.2 25.1 1.0
O A:LYS184 4.2 22.6 1.0
N A:TYR191 4.3 26.9 1.0
N A:ASP192 4.4 21.1 1.0
CG2 A:THR187 4.4 18.9 1.0
CA A:THR187 4.4 22.4 1.0
CA A:GLY188 4.4 29.5 1.0
N A:ASP189 4.5 33.1 1.0
CA A:ASP192 4.5 19.6 1.0
CA A:ASP189 4.5 34.1 1.0
CA A:TYR191 4.5 24.1 1.0
O A:HOH2180 4.6 13.3 1.0
CG A:ASP192 4.7 21.0 1.0
C A:ASP189 4.7 33.2 1.0
O A:HOH2069 4.7 23.6 1.0
O A:THR187 4.8 26.8 1.0
CA A:LYS184 4.8 22.2 1.0
C A:LYS184 4.9 21.8 1.0
O A:ILE183 5.0 19.0 1.0
N A:SER190 5.0 32.6 1.0

Sodium binding site 3 out of 4 in 4ccy

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Sodium binding site 3 out of 4 in the Crystal Structure of Carboxylesterase Cesb (Ybfk) From Bacillus Subtilis


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 Carboxylesterase Cesb (Ybfk) From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1297

b:14.1
occ:1.00
O B:GLU245 2.3 18.7 1.0
OE1 B:GLN250 2.3 19.5 1.0
O B:HOH2112 2.4 23.5 1.0
O B:HOH2167 2.5 15.0 1.0
O B:HOH2171 2.5 25.0 1.0
O B:TYR248 2.7 18.7 1.0
CD B:GLN250 3.4 19.3 1.0
C B:GLU245 3.5 18.6 1.0
NE2 B:GLN250 3.9 19.9 1.0
C B:TYR248 3.9 19.0 1.0
N B:GLN250 4.1 19.1 1.0
CA B:GLU245 4.2 17.6 1.0
CB B:GLU245 4.2 16.9 1.0
N B:GLU245 4.3 18.1 1.0
CA B:HIS249 4.3 20.2 1.0
NE2 B:HIS163 4.5 22.5 1.0
O B:HOH2172 4.5 16.3 1.0
N B:HIS249 4.5 19.3 1.0
N B:ALA246 4.6 18.9 1.0
CG B:GLU245 4.6 16.2 1.0
C B:HIS244 4.7 18.9 1.0
ND1 B:HIS249 4.7 23.4 1.0
CG B:GLN250 4.7 18.8 1.0
C B:HIS249 4.8 19.5 1.0
CA B:ALA246 4.8 19.9 1.0
N B:TYR248 4.9 18.8 1.0
O B:GLU243 4.9 19.4 1.0
CA B:TYR248 5.0 18.7 1.0
CB B:GLN250 5.0 18.6 1.0

Sodium binding site 4 out of 4 in 4ccy

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Sodium binding site 4 out of 4 in the Crystal Structure of Carboxylesterase Cesb (Ybfk) From Bacillus Subtilis


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 Carboxylesterase Cesb (Ybfk) From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1298

b:24.6
occ:1.00
O B:HOH2129 2.1 24.0 1.0
O B:GLY188 2.3 33.1 1.0
O B:HOH2134 2.3 22.9 1.0
O B:TYR191 2.4 24.7 1.0
OG1 B:THR187 2.5 22.5 1.0
O B:HOH2133 2.6 19.4 1.0
C B:GLY188 3.5 34.3 1.0
CB B:THR187 3.5 23.0 1.0
C B:TYR191 3.6 25.2 1.0
OD1 B:ASP192 3.6 24.3 1.0
N B:GLY188 4.0 28.9 1.0
C B:THR187 4.2 27.4 1.0
O B:HOH2137 4.2 38.4 1.0
O B:LYS184 4.3 25.7 1.0
N B:TYR191 4.3 31.1 1.0
CA B:GLY188 4.3 32.6 1.0
N B:ASP189 4.4 37.8 1.0
CA B:ASP189 4.4 39.9 1.0
N B:ASP192 4.5 23.7 1.0
CA B:THR187 4.5 24.7 1.0
CA B:TYR191 4.5 27.8 1.0
C B:ASP189 4.6 39.5 1.0
CA B:ASP192 4.6 21.6 1.0
CG2 B:THR187 4.6 21.4 1.0
CG B:ASP192 4.7 24.4 1.0
O B:HOH2141 4.7 13.6 1.0
O B:THR187 4.8 29.4 1.0
CA B:LYS184 4.8 23.5 1.0
O B:ASP189 4.9 39.9 1.0
O B:ILE183 4.9 21.3 1.0
N B:SER190 5.0 38.7 1.0
C B:LYS184 5.0 24.4 1.0
O B:HOH2051 5.0 19.8 1.0

Reference:

H.J.Rozeboom, L.F.Godinho, M.Nardini, W.J.Quax, B.W.Dijkstra. Crystal Structures of Two Bacillus Carboxylesterases with Different Enantioselectivities. Biochim.Biophys.Acta V.1844 567 2014.
ISSN: ISSN 0006-3002
PubMed: 24418394
DOI: 10.1016/J.BBAPAP.2014.01.003
Page generated: Tue Dec 15 06:35:34 2020

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