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Sodium in PDB 2wsj: Crystal Structure of Single Point Mutant GLU71SER P-Coumaric Acid Decarboxylase

Protein crystallography data

The structure of Crystal Structure of Single Point Mutant GLU71SER P-Coumaric Acid Decarboxylase, PDB code: 2wsj was solved by H.Rodriguez, I.Angulo, B.De Las Rivas, N.Campillo, J.A.Paez, R.Munoz, J.M.Mancheno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.96 / 2.24
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 108.811, 52.756, 82.095, 90.00, 122.44, 90.00
R / Rfree (%) 17.8 / 25.9

Other elements in 2wsj:

The structure of Crystal Structure of Single Point Mutant GLU71SER P-Coumaric Acid Decarboxylase also contains other interesting chemical elements:

Barium (Ba) 1 atom
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Single Point Mutant GLU71SER P-Coumaric Acid Decarboxylase (pdb code 2wsj). 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 Single Point Mutant GLU71SER P-Coumaric Acid Decarboxylase, PDB code: 2wsj:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 2wsj

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Sodium binding site 1 out of 4 in the Crystal Structure of Single Point Mutant GLU71SER P-Coumaric Acid Decarboxylase


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 Single Point Mutant GLU71SER P-Coumaric Acid Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1181

b:17.4
occ:1.00
OD2 A:ASP37 2.7 15.8 1.0
N A:ILE151 3.0 19.2 1.0
O A:ASN147 3.0 17.8 1.0
O A:GLU148 3.6 18.8 1.0
CB A:VAL150 3.6 18.8 1.0
N A:VAL150 3.6 18.9 1.0
O A:ILE151 3.7 19.4 1.0
C A:GLU148 3.8 18.8 1.0
CG A:ASP37 3.8 16.7 1.0
CA A:ILE151 3.8 19.1 1.0
CA A:VAL150 3.9 18.8 1.0
CE2 A:TYR29 3.9 15.7 1.0
CD2 A:TYR29 3.9 16.3 1.0
C A:VAL150 3.9 18.9 1.0
C A:ILE151 4.0 19.3 1.0
CA A:GLU148 4.0 18.9 1.0
CB A:ILE151 4.0 19.5 1.0
C A:ASN147 4.1 18.1 1.0
CG1 A:ILE151 4.3 18.9 1.0
CB A:ASP37 4.3 16.5 1.0
NZ A:LYS31 4.5 21.9 1.0
CG1 A:VAL150 4.5 19.1 1.0
CD A:LYS31 4.5 19.0 1.0
N A:ASP149 4.5 18.5 1.0
N A:GLU148 4.5 18.6 1.0
C A:ASP149 4.6 18.9 1.0
CG2 A:VAL150 4.6 17.4 1.0
OD1 A:ASP37 4.8 17.1 1.0
O A:HOH2072 4.9 20.2 1.0
N A:SER152 4.9 19.2 1.0
OE1 A:GLU148 5.0 24.6 1.0

Sodium binding site 2 out of 4 in 2wsj

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Sodium binding site 2 out of 4 in the Crystal Structure of Single Point Mutant GLU71SER P-Coumaric Acid Decarboxylase


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 Single Point Mutant GLU71SER P-Coumaric Acid Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1182

b:35.8
occ:1.00
OE1 A:GLN53 2.7 19.4 1.0
NE2 A:GLN109 2.8 19.1 1.0
OH A:TYR38 2.9 19.8 1.0
OG A:SER71 2.9 16.9 1.0
CB A:SER71 3.5 16.7 1.0
CD A:PRO72 3.5 15.9 1.0
NH2 A:ARG48 3.5 16.4 1.0
CD A:GLN109 3.7 19.5 1.0
CG1 A:VAL50 3.7 16.4 1.0
CD A:GLN53 3.7 18.4 1.0
OE1 A:GLN109 3.8 18.7 1.0
CG2 A:VAL50 3.8 16.8 1.0
CA A:SER71 3.9 16.2 1.0
CZ A:TYR38 4.0 18.6 1.0
O2 A:IPA1180 4.0 24.5 1.0
O A:HOH2026 4.1 13.1 1.0
CG A:GLN53 4.3 17.4 1.0
CB A:VAL50 4.4 17.1 1.0
NE1 A:TRP69 4.4 14.6 1.0
CE1 A:TYR38 4.4 18.1 1.0
N A:PRO72 4.5 16.1 1.0
CG A:PRO72 4.5 15.4 1.0
CD1 A:TRP69 4.6 14.2 1.0
CB A:GLN53 4.7 18.4 1.0
CZ A:ARG48 4.7 17.3 1.0
NE2 A:GLN53 4.8 16.4 1.0
C A:SER71 4.8 16.1 1.0
O A:HOH2048 5.0 16.0 1.0

Sodium binding site 3 out of 4 in 2wsj

Go back to Sodium Binding Sites List in 2wsj
Sodium binding site 3 out of 4 in the Crystal Structure of Single Point Mutant GLU71SER P-Coumaric Acid Decarboxylase


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 Single Point Mutant GLU71SER P-Coumaric Acid Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1180

b:19.1
occ:1.00
O B:GLY42 2.7 18.8 1.0
OH B:TYR26 3.0 15.4 1.0
N B:VAL45 3.2 18.1 1.0
N B:MET44 3.3 18.4 1.0
C B:GLY43 3.5 18.7 1.0
CG2 B:VAL45 3.6 18.6 1.0
CG2 B:ILE40 3.6 17.1 1.0
CA B:GLY43 3.6 18.7 1.0
CZ B:TYR26 3.7 17.1 1.0
C B:GLY42 3.7 18.9 1.0
CE1 B:TYR26 3.8 17.6 1.0
CA B:VAL45 3.9 18.2 1.0
C B:VAL45 4.0 18.2 1.0
N B:ALA46 4.1 18.2 1.0
N B:GLY43 4.1 18.6 1.0
CA B:MET44 4.1 18.3 1.0
C B:MET44 4.1 18.1 1.0
CD1 B:TRP24 4.1 24.4 1.0
O B:GLY43 4.2 19.1 1.0
CB B:VAL45 4.4 18.3 1.0
O B:HOH2016 4.4 35.7 1.0
O B:VAL45 4.5 18.0 1.0
CB B:MET44 4.5 18.7 1.0
CG B:TRP24 4.6 22.6 1.0
NE1 B:TRP24 4.6 25.5 1.0
CE2 B:TYR26 4.8 16.9 1.0
CA B:ALA46 4.8 18.1 1.0
CB B:TRP24 4.9 21.0 1.0
CB B:ILE40 5.0 16.9 1.0

Sodium binding site 4 out of 4 in 2wsj

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Sodium binding site 4 out of 4 in the Crystal Structure of Single Point Mutant GLU71SER P-Coumaric Acid Decarboxylase


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 Single Point Mutant GLU71SER P-Coumaric Acid Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1181

b:20.2
occ:1.00
OE2 B:GLU25 2.6 23.2 1.0
OG1 B:THR138 2.7 16.3 1.0
OG1 B:THR19 2.8 15.2 1.0
C B:TYR18 3.5 14.8 1.0
N B:THR19 3.5 15.4 1.0
NH1 B:ARG164 3.6 16.8 1.0
CD B:GLU25 3.6 22.9 1.0
CG2 B:THR138 3.6 16.1 1.0
CA B:TYR18 3.7 14.6 1.0
CG2 B:ILE17 3.7 14.1 1.0
CB B:THR138 3.7 17.0 1.0
N B:TYR18 3.8 14.5 1.0
CG B:GLU25 3.9 20.5 1.0
O B:TYR18 3.9 14.6 1.0
CB B:THR19 3.9 15.7 1.0
C B:ILE17 4.1 14.9 1.0
CA B:THR19 4.2 15.6 1.0
O B:ILE17 4.3 15.5 1.0
CB B:ILE17 4.6 14.7 1.0
O B:ASN136 4.6 16.8 1.0
OE1 B:GLU25 4.7 25.8 1.0
CB B:GLU25 4.7 19.4 1.0
CZ B:ARG164 4.7 17.5 1.0
N B:THR138 4.7 17.0 1.0
CA B:THR138 4.8 16.8 1.0
CA B:ILE17 4.9 14.8 1.0

Reference:

H.Rodriguez, I.Angulo, B.De Las Rivas, N.Campillo, J.A.Paez, R.Munoz, J.M.Mancheno. P-Coumaric Acid Decarboxylase From Lactobacillus Plantarum: Structural Insights Into the Active Site and Decarboxylation Catalytic Mechanism. Proteins V. 78 1662 2010.
ISSN: ISSN 0887-3585
PubMed: 20112419
DOI: 10.1002/PROT.22684
Page generated: Tue Dec 15 05:58:16 2020

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