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Sodium in PDB 2xcd: Structure of Yncf,the Genomic Dutpase From Bacillus Subtilis

Enzymatic activity of Structure of Yncf,the Genomic Dutpase From Bacillus Subtilis

All present enzymatic activity of Structure of Yncf,the Genomic Dutpase From Bacillus Subtilis:
3.6.1.23;

Protein crystallography data

The structure of Structure of Yncf,the Genomic Dutpase From Bacillus Subtilis, PDB code: 2xcd was solved by J.Garcia, L.Burchell, M.Takezawa, N.J.Rzechorzek, M.Fogg, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.810, 98.840, 99.110, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 18.4

Other elements in 2xcd:

The structure of Structure of Yncf,the Genomic Dutpase From Bacillus Subtilis also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Yncf,the Genomic Dutpase From Bacillus Subtilis (pdb code 2xcd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Structure of Yncf,the Genomic Dutpase From Bacillus Subtilis, PDB code: 2xcd:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 2xcd

Go back to Sodium Binding Sites List in 2xcd
Sodium binding site 1 out of 6 in the Structure of Yncf,the Genomic Dutpase 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 Structure of Yncf,the Genomic Dutpase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1131

b:30.0
occ:1.00
 OG A:SER65 3.0 19.8 1.0
N A:SER65 3.2 20.0 1.0
CB A:SER65 3.4 20.0 1.0
N A:SER64 3.7 20.9 1.0
CB A:ARG63 3.8 21.2 1.0
CA A:SER65 3.9 20.0 1.0
CZ A:ARG63 3.9 30.2 1.0
NH1 A:ARG63 3.9 31.5 1.0
NH2 A:ARG63 4.1 29.9 1.0
CB A:SER64 4.1 22.6 1.0
CA A:SER64 4.2 22.1 1.0
C A:SER64 4.2 22.0 1.0
C A:ARG63 4.3 21.1 1.0
NE A:ARG63 4.4 32.7 1.0
CA A:ARG63 4.6 20.8 1.0
CG A:ARG63 4.7 24.5 1.0
O A:HOH2068 4.8 31.6 1.0
C A:SER65 4.9 18.9 1.0
OG A:SER64 4.9 23.4 1.0
CD A:ARG63 4.9 26.9 1.0

Sodium binding site 2 out of 6 in 2xcd

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Sodium binding site 2 out of 6 in the Structure of Yncf,the Genomic Dutpase 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 Structure of Yncf,the Genomic Dutpase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1131

b:26.1
occ:1.00
 OG1 B:THR15 3.0 27.9 1.0
O F:HOH2117 3.2 23.8 1.0
NE F:ARG109 3.4 20.5 1.0
NH2 F:ARG109 3.4 20.6 1.0
O B:HOH2018 3.4 34.7 1.0
O B:HOH2015 3.4 31.5 1.0
CA B:GLY107 3.6 24.0 1.0
CZ F:ARG109 3.8 20.0 1.0
CB B:THR15 3.8 28.8 1.0
N B:GLY107 3.9 23.0 1.0
NH1 F:ARG29 4.0 28.5 1.0
N B:THR15 4.2 28.7 1.0
O B:THR13 4.2 30.8 1.0
CG B:LYS106 4.2 27.4 1.0
O B:LYS106 4.2 22.2 1.0
C B:LYS106 4.3 22.7 1.0
CE B:LYS106 4.3 32.0 1.0
CD F:ARG109 4.5 23.6 1.0
NH2 F:ARG29 4.5 24.5 1.0
CA B:THR15 4.6 28.7 1.0
CZ F:ARG29 4.6 23.4 1.0
NZ B:LYS106 4.7 31.6 1.0
CG F:ARG109 4.8 23.4 1.0
CD B:LYS106 4.8 30.8 1.0
C B:GLY107 5.0 24.9 1.0

Sodium binding site 3 out of 6 in 2xcd

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Sodium binding site 3 out of 6 in the Structure of Yncf,the Genomic Dutpase 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 Structure of Yncf,the Genomic Dutpase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1132

b:24.8
occ:1.00
 OG C:SER65 2.9 22.4 1.0
O C:HOH2068 3.3 31.2 1.0
N C:SER65 3.4 22.2 1.0
CB C:SER65 3.7 22.8 1.0
N C:SER64 3.8 22.7 1.0
NH1 C:ARG63 3.9 30.3 1.0
CB C:ARG63 3.9 20.4 1.0
CZ C:ARG63 3.9 30.4 1.0
NH2 C:ARG63 4.0 30.9 1.0
CB C:SER64 4.0 22.4 1.0
CA C:SER65 4.2 22.6 1.0
CA C:SER64 4.2 22.1 1.0
C C:SER64 4.3 22.3 1.0
C C:ARG63 4.5 22.1 1.0
NE C:ARG63 4.5 30.2 1.0
CA C:ARG63 4.7 22.0 1.0
CG C:ARG63 4.9 23.7 1.0
O C:HOH2069 5.0 27.6 1.0

Sodium binding site 4 out of 6 in 2xcd

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Sodium binding site 4 out of 6 in the Structure of Yncf,the Genomic Dutpase 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 Structure of Yncf,the Genomic Dutpase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1131

b:24.7
occ:1.00
 O D:HOH2014 3.0 26.3 1.0
OG1 D:THR15 3.1 27.4 1.0
CA D:GLY107 3.5 23.4 1.0
N D:GLY107 3.9 23.5 1.0
CB D:THR15 4.0 30.2 1.0
O D:LYS106 4.1 24.3 1.0
CG D:LYS106 4.1 23.7 1.0
O D:THR13 4.2 34.2 1.0
C D:LYS106 4.2 23.8 1.0
N D:THR15 4.2 30.7 1.0
CE D:LYS106 4.7 29.0 1.0
CA D:THR15 4.7 30.4 1.0
C D:GLY107 4.8 22.3 1.0

Sodium binding site 5 out of 6 in 2xcd

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Sodium binding site 5 out of 6 in the Structure of Yncf,the Genomic Dutpase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Yncf,the Genomic Dutpase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1132

b:25.5
occ:1.00
 OG1 E:THR15 3.2 25.4 1.0
O E:HOH2012 3.4 31.3 1.0
O E:HOH2015 3.4 30.1 1.0
CA E:GLY107 3.6 22.4 1.0
N E:GLY107 3.9 22.5 1.0
CB E:THR15 4.0 26.4 1.0
CG E:LYS106 4.1 25.1 1.0
O E:THR13 4.2 30.9 1.0
N E:THR15 4.2 26.9 1.0
C E:LYS106 4.3 22.5 1.0
O E:LYS106 4.3 23.6 1.0
CE E:LYS106 4.5 29.0 1.0
CD E:LYS106 4.7 27.2 1.0
CA E:THR15 4.7 27.3 1.0
C E:GLY107 5.0 22.0 1.0

Sodium binding site 6 out of 6 in 2xcd

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Sodium binding site 6 out of 6 in the Structure of Yncf,the Genomic Dutpase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Yncf,the Genomic Dutpase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na1132

b:22.3
occ:1.00
 O F:HOH2075 2.9 45.5 1.0
OG F:SER65 3.0 24.0 1.0
N F:SER65 3.3 23.1 1.0
CB F:SER65 3.5 22.5 1.0
NH2 F:ARG63 3.8 30.1 1.0
N F:SER64 3.8 21.8 1.0
CZ F:ARG63 3.9 30.2 1.0
CG B:LYS105 3.9 21.8 1.0
CB F:ARG63 3.9 19.8 1.0
CB F:SER64 4.0 23.5 0.5
CA F:SER65 4.0 22.4 1.0
CE B:LYS105 4.0 27.3 1.0
NH1 F:ARG63 4.1 32.2 1.0
CB F:SER64 4.1 22.3 0.5
CD B:LYS105 4.1 25.0 1.0
CA F:SER64 4.2 23.3 0.5
C F:SER64 4.2 22.7 1.0
CA F:SER64 4.2 22.2 0.5
NE F:ARG63 4.3 30.1 1.0
C F:ARG63 4.5 21.0 1.0
O F:HOH2072 4.6 41.9 1.0
OG F:SER64 4.7 27.7 0.5
CA F:ARG63 4.7 20.8 1.0
CG F:ARG63 4.8 22.1 1.0
NZ B:LYS105 4.9 30.9 1.0
OG F:SER64 4.9 19.6 0.5
O B:HOH2104 5.0 22.6 1.0
C F:SER65 5.0 21.7 1.0
CB B:LYS105 5.0 22.9 1.0

Reference:

J.Garcia-Nafria, L.Burchell, M.Takezawa, N.J.Rzechorzek, M.Fogg, K.S.Wilson. The Structure of the Genomic Bacillus Subtilis Dutpase: Novel Features in the Phe-Lid. Acta Crystallogr.,Sect.D V. 66 953 2010.
ISSN: ISSN 0907-4449
PubMed: 20823546
DOI: 10.1107/S0907444910026272
Page generated: Mon Oct 7 05:09:15 2024

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