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Sodium in PDB 7e5q: Crystal Structure of Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH

Protein crystallography data

The structure of Crystal Structure of Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH, PDB code: 7e5q was solved by P.Dhankhar, V.Dalal, P.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.34 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.855, 117.342, 135.441, 90, 90, 90
R / Rfree (%) 18 / 23.3

Other elements in 7e5q:

The structure of Crystal Structure of Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH also contains other interesting chemical elements:

Chlorine (Cl) 9 atoms
Iron (Fe) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH (pdb code 7e5q). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH, PDB code: 7e5q:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 7e5q

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Sodium binding site 1 out of 8 in the Crystal Structure of Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH


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 Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na416

b:48.6
occ:1.00
 O A:HOH504 2.6 42.6 1.0
C3 A:PEG413 2.6 45.6 1.0
NZ A:LYS278 2.8 50.0 1.0
N A:VAL263 3.2 33.8 1.0
O4 A:PEG413 3.3 60.2 1.0
C2 A:PEG413 3.5 52.7 1.0
C4 A:PEG413 3.6 54.3 1.0
O2 A:PEG413 3.6 59.2 1.0
CA A:PRO262 3.7 38.5 1.0
CE A:LYS278 3.7 45.6 1.0
CG2 A:VAL263 3.7 32.5 1.0
C A:PRO262 4.0 40.2 1.0
CB A:VAL263 4.0 34.8 1.0
O A:HOH522 4.0 32.5 1.0
CA A:VAL263 4.2 31.6 1.0
CB A:PRO262 4.3 45.6 1.0
O A:HOH754 4.5 57.6 1.0
O A:ASP261 4.5 37.9 1.0
CD A:LYS278 4.7 44.8 1.0
O A:HOH719 4.7 46.6 1.0
O A:HOH616 4.7 44.7 1.0
NH2 A:ARG246 4.8 34.0 1.0
N A:PRO262 4.8 44.1 1.0
O2D A:HEM401 4.9 35.9 1.0
C1 A:PEG413 5.0 48.8 1.0

Sodium binding site 2 out of 8 in 7e5q

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Sodium binding site 2 out of 8 in the Crystal Structure of Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH


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 Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na414

b:27.3
occ:1.00
 N A:LEU295 3.2 32.1 1.0
N B:VAL165 3.4 28.6 1.0
O B:HOH611 3.4 57.9 1.0
O2 A:PEG415 3.4 51.5 1.0
O B:VAL165 3.4 30.7 1.0
CB A:LEU295 3.8 41.0 1.0
CA B:PHE164 3.8 34.6 1.0
CB B:PHE164 3.9 38.5 1.0
CG A:LEU295 3.9 35.0 1.0
CA A:GLY294 4.0 27.1 1.0
C3 A:PEG415 4.0 58.8 1.0
CA A:LEU295 4.0 34.4 1.0
C A:GLY294 4.1 34.8 1.0
C B:PHE164 4.1 32.8 1.0
C4 A:PEG415 4.1 52.2 1.0
C B:VAL165 4.2 31.7 1.0
O A:LEU295 4.2 50.1 1.0
CA B:VAL165 4.3 27.0 1.0
O4 A:PEG415 4.3 51.1 1.0
CD1 A:LEU295 4.4 40.3 1.0
C2 A:PEG415 4.5 56.8 1.0
C A:LEU295 4.6 45.2 1.0
O B:HOH560 4.7 41.8 1.0
CB B:VAL165 4.7 34.9 1.0

Sodium binding site 3 out of 8 in 7e5q

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Sodium binding site 3 out of 8 in the Crystal Structure of Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH


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 Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na415

b:34.1
occ:1.00
 OG1 B:THR292 3.0 32.9 1.0
N B:GLY294 3.1 31.2 1.0
O B:HOH673 3.4 43.4 1.0
NZ A:LYS167 3.5 35.2 1.0
CE B:MET302 3.5 30.7 0.6
C B:THR292 3.6 32.0 1.0
CD A:LYS167 3.6 29.0 1.0
O B:THR292 3.6 33.2 1.0
CB B:THR292 3.6 27.4 1.0
N B:GLU293 3.8 29.9 1.0
CA B:GLU293 3.8 30.9 1.0
CE1 A:TYR25 3.8 26.4 1.0
CG A:LYS167 3.8 21.3 1.0
C B:GLU293 3.9 34.0 1.0
CA B:GLY294 3.9 32.8 1.0
CE A:LYS167 4.0 28.6 1.0
CA B:THR292 4.3 29.9 1.0
CB A:LYS167 4.3 24.1 1.0
CD1 A:TYR25 4.5 26.3 1.0
CG1 A:VAL165 4.6 28.5 1.0
CZ A:TYR25 4.7 25.4 1.0
OH A:TYR25 4.7 26.8 1.0
O A:VAL165 4.8 29.2 1.0
N A:LYS167 5.0 25.6 1.0
C B:GLY294 5.0 33.6 1.0
CG2 B:THR292 5.0 26.9 1.0
O B:GLY294 5.0 34.1 1.0
O A:HOH525 5.0 32.6 1.0

Sodium binding site 4 out of 8 in 7e5q

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Sodium binding site 4 out of 8 in the Crystal Structure of Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH


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 Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na416

b:49.3
occ:1.00
 N B:LYS352 3.5 39.4 1.0
CG B:LYS351 3.7 52.5 1.0
CB B:TYR9 3.8 35.4 1.0
CA B:LYS351 3.9 40.2 1.0
C B:LYS351 4.2 38.4 1.0
CB B:LYS351 4.3 51.9 1.0
CB B:LYS352 4.3 46.4 1.0
N B:GLY10 4.3 36.4 1.0
C B:TYR9 4.5 35.9 1.0
CA B:LYS352 4.5 42.2 1.0
O B:CYS350 4.5 35.4 1.0
CA B:GLY10 4.6 36.8 1.0
CG B:TYR9 4.7 31.7 1.0
CA B:TYR9 4.8 37.2 1.0
O B:TYR9 4.9 34.0 1.0

Sodium binding site 5 out of 8 in 7e5q

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Sodium binding site 5 out of 8 in the Crystal Structure of Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH


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 Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na417

b:47.0
occ:1.00
 O B:HOH507 2.4 45.2 1.0
O B:HOH582 2.9 51.3 1.0
O B:GLY349 3.0 34.6 1.0
O B:HOH512 3.4 43.1 1.0
C B:GLY348 3.6 33.7 1.0
O B:THR215 3.7 35.4 1.0
CA B:GLY348 3.7 32.8 1.0
N B:GLY349 3.9 35.8 1.0
O B:HOH645 4.0 44.4 1.0
O B:GLY348 4.0 32.6 1.0
C B:GLY349 4.0 38.9 1.0
O B:HOH662 4.2 41.3 1.0
N B:GLY348 4.3 33.0 1.0
O B:TRP213 4.3 39.9 1.0
CA B:GLY349 4.6 31.5 1.0
O B:HOH612 4.6 34.3 1.0
O B:HOH535 4.7 35.6 1.0
O B:HOH576 4.7 49.5 1.0
O B:HOH709 4.8 36.3 1.0
O B:LYS11 4.8 32.3 1.0
C B:THR215 4.9 33.9 1.0

Sodium binding site 6 out of 8 in 7e5q

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Sodium binding site 6 out of 8 in the Crystal Structure of Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH


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 Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na418

b:65.8
occ:1.00
 N B:GLY99 2.8 73.2 1.0
N B:ASP98 3.3 72.9 1.0
CA B:GLY99 3.5 71.0 1.0
C B:ASP98 3.8 70.1 1.0
CA B:ASP98 3.8 72.9 1.0
C B:LYS97 3.8 66.3 1.0
O B:GLU96 4.0 57.1 1.0
CA B:LYS97 4.1 63.9 1.0
C B:GLU96 4.1 51.0 1.0
N B:LYS97 4.2 57.6 1.0
CB B:GLU96 4.2 51.1 1.0
C B:GLY99 4.4 72.8 1.0
O B:LYS97 4.6 69.1 1.0
CA B:GLU96 4.8 51.0 1.0
N B:LYS100 4.9 74.6 1.0
O B:ASP98 4.9 68.2 1.0

Sodium binding site 7 out of 8 in 7e5q

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Sodium binding site 7 out of 8 in the Crystal Structure of Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH


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 Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na419

b:63.3
occ:1.00
 NH2 B:ARG180 3.6 42.2 1.0
O A:HOH715 3.8 58.0 1.0
OD1 A:ASP78 4.1 50.1 1.0
CB A:ALA77 4.2 47.1 1.0
O B:SER249 4.2 43.3 1.0
CB B:SER249 4.4 42.6 1.0
OG B:SER249 4.5 44.8 1.0
CZ B:ARG180 4.6 39.9 1.0
CA B:SER249 4.6 41.1 1.0
C B:SER249 4.7 45.7 1.0

Sodium binding site 8 out of 8 in 7e5q

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Sodium binding site 8 out of 8 in the Crystal Structure of Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na420

b:56.5
occ:1.00
 C2 B:GOL413 2.8 62.0 1.0
C3 B:GOL413 2.9 54.8 1.0
OG1 B:THR336 3.1 34.0 1.0
OG1 B:THR338 3.3 32.4 1.0
O2 B:GOL413 3.6 53.2 1.0
OD1 B:ASN333 3.6 44.0 1.0
O3 B:GOL413 3.9 48.5 1.0
CB B:THR336 3.9 35.8 1.0
O B:HOH650 3.9 42.6 1.0
CG2 B:ILE225 3.9 29.4 1.0
C1 B:GOL413 4.0 52.4 1.0
O B:HOH600 4.2 52.4 1.0
N B:THR338 4.3 35.8 1.0
O1 B:GOL413 4.4 60.0 1.0
C B:THR336 4.5 35.8 1.0
N B:GLN337 4.5 31.1 1.0
CB B:THR338 4.6 32.0 1.0
C B:GLN337 4.7 34.2 1.0
O B:THR336 4.7 36.7 1.0
CA B:GLN337 4.7 34.3 1.0
CG B:ASN333 4.7 41.3 1.0
CD1 B:ILE225 4.8 30.7 1.0
CA B:THR336 4.9 34.9 1.0
CA B:THR338 4.9 34.0 1.0
CG2 B:THR336 4.9 34.4 1.0
CG1 B:ILE225 4.9 32.8 1.0
CA B:ASN333 4.9 35.7 1.0
O B:HOH628 5.0 46.9 1.0

Reference:

P.Dhankhar, V.Dalal, A.K.Sharma, P.Kumar. Structural Insights at Acidic pH of Dye-Decolorizing Peroxidase From Bacillus Subtilis. Proteins 2022.
ISSN: ESSN 1097-0134
PubMed: 36345957
DOI: 10.1002/PROT.26444
Page generated: Tue Oct 8 16:39:30 2024

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