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Sodium in PDB 5bmx: Crystal Structure of T75N Mutant of Triosephosphate Isomerase From Plasmodium Falciparum

Enzymatic activity of Crystal Structure of T75N Mutant of Triosephosphate Isomerase From Plasmodium Falciparum

All present enzymatic activity of Crystal Structure of T75N Mutant of Triosephosphate Isomerase From Plasmodium Falciparum:
5.3.1.1;

Protein crystallography data

The structure of Crystal Structure of T75N Mutant of Triosephosphate Isomerase From Plasmodium Falciparum, PDB code: 5bmx was solved by D.Bandyopadhyay, M.R.N.Murthy, H.Balaram, P.Balaram, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 91.75 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.640, 106.720, 179.620, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 21.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of T75N Mutant of Triosephosphate Isomerase From Plasmodium Falciparum (pdb code 5bmx). 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 T75N Mutant of Triosephosphate Isomerase From Plasmodium Falciparum, PDB code: 5bmx:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5bmx

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Sodium binding site 1 out of 4 in the Crystal Structure of T75N Mutant of Triosephosphate Isomerase From Plasmodium Falciparum


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 T75N Mutant of Triosephosphate Isomerase From Plasmodium Falciparum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:10.1
occ:1.00
 O A:GLN223 2.1 9.1 1.0
O A:ILE226 2.3 7.2 1.0
O A:ILE221 2.3 7.7 1.0
O A:HOH474 2.4 18.1 1.0
O A:HOH430 2.4 14.4 1.0
C A:GLN223 3.3 9.9 1.0
C A:ILE221 3.4 8.5 1.0
C A:ILE226 3.4 7.8 1.0
N A:ILE226 3.9 8.2 1.0
CE1 A:TYR5 3.9 13.9 1.0
OH A:TYR5 3.9 17.0 1.0
N A:GLN223 4.0 9.4 1.0
C A:GLN222 4.1 10.6 1.0
C A:GLU224 4.1 10.6 1.0
O A:GLU224 4.1 10.1 1.0
CA A:ILE226 4.1 7.4 1.0
CA A:ILE221 4.2 8.7 1.0
CA A:GLN223 4.2 8.8 1.0
N A:GLU224 4.3 11.0 1.0
CA A:GLU224 4.3 11.9 1.0
CZ A:TYR5 4.3 15.6 1.0
N A:GLN222 4.3 9.3 1.0
N A:ASP227 4.4 7.4 1.0
CA A:GLN222 4.4 11.2 1.0
O A:GLN222 4.4 10.6 1.0
CB A:ILE226 4.4 7.4 1.0
CG1 A:ILE221 4.5 9.3 1.0
O A:HOH513 4.5 24.2 1.0
CA A:ASP227 4.6 7.5 1.0
N A:ASP225 4.6 10.0 1.0
O A:HOH636 4.6 48.8 1.0
OD1 A:ASP227 4.6 8.5 1.0
O A:LEU220 4.8 8.8 1.0
C A:ASP225 4.9 8.8 1.0
CD1 A:TYR5 4.9 13.3 1.0
CB A:ILE221 4.9 9.3 1.0

Sodium binding site 2 out of 4 in 5bmx

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Sodium binding site 2 out of 4 in the Crystal Structure of T75N Mutant of Triosephosphate Isomerase From Plasmodium Falciparum


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 T75N Mutant of Triosephosphate Isomerase From Plasmodium Falciparum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na304

b:12.9
occ:1.00
 O B:GLN223 2.3 12.0 1.0
O B:ILE221 2.3 12.2 1.0
O B:ILE226 2.3 9.7 1.0
O B:HOH555 2.5 24.9 1.0
O B:HOH506 2.5 14.0 1.0
OH B:TYR5 2.9 21.2 1.0
C B:ILE221 3.4 12.0 1.0
C B:GLN223 3.5 12.2 1.0
C B:ILE226 3.5 9.6 1.0
CZ B:TYR5 3.7 17.9 1.0
CE1 B:TYR5 3.8 16.5 1.0
N B:ILE226 4.0 9.5 1.0
C B:GLN222 4.0 15.5 1.0
N B:GLN223 4.0 12.6 1.0
O B:HOH414 4.1 25.1 1.0
C B:GLU224 4.1 14.0 1.0
O B:GLU224 4.2 13.9 1.0
CA B:ILE226 4.2 10.1 1.0
CA B:ILE221 4.3 11.3 1.0
O B:GLN222 4.3 14.7 1.0
CA B:GLU224 4.3 15.2 1.0
N B:GLN222 4.4 11.8 1.0
CA B:GLN223 4.4 12.5 1.0
N B:GLU224 4.4 12.5 1.0
CB B:ILE226 4.5 9.0 1.0
CA B:GLN222 4.5 14.6 1.0
N B:ASP227 4.5 9.8 1.0
CD1 B:ILE221 4.6 13.2 1.0
CG1 B:ILE221 4.6 13.7 1.0
N B:ASP225 4.6 12.4 1.0
OD1 B:ASP227 4.7 13.1 1.0
CA B:ASP227 4.7 9.1 1.0
O B:LEU220 4.7 10.4 1.0
CE2 B:TYR5 4.8 16.2 1.0
O B:HOH618 4.8 41.7 1.0
C B:ASP225 5.0 11.7 1.0

Sodium binding site 3 out of 4 in 5bmx

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Sodium binding site 3 out of 4 in the Crystal Structure of T75N Mutant of Triosephosphate Isomerase From Plasmodium Falciparum


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 T75N Mutant of Triosephosphate Isomerase From Plasmodium Falciparum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na302

b:14.4
occ:1.00
 O C:ILE221 2.2 14.3 1.0
O C:ILE226 2.3 12.5 1.0
O C:GLN223 2.3 14.1 1.0
O C:HOH524 2.4 18.0 1.0
O C:HOH491 2.4 26.6 1.0
OH C:TYR5 3.0 29.8 1.0
C C:ILE221 3.4 12.8 1.0
C C:ILE226 3.5 11.5 1.0
C C:GLN223 3.5 15.4 1.0
CZ C:TYR5 3.7 22.5 1.0
CE1 C:TYR5 3.8 21.8 1.0
N C:GLN223 4.0 15.2 1.0
N C:ILE226 4.0 10.0 1.0
C C:GLN222 4.0 17.9 1.0
C C:GLU224 4.2 13.5 1.0
CA C:ILE226 4.2 10.3 1.0
O C:GLU224 4.2 13.2 1.0
CA C:ILE221 4.3 14.8 1.0
CA C:GLN223 4.3 14.9 1.0
N C:GLN222 4.3 14.1 1.0
O C:GLN222 4.4 18.3 1.0
CA C:GLU224 4.4 16.2 1.0
CD1 C:ILE221 4.4 16.2 1.0
N C:GLU224 4.4 14.5 1.0
N C:ASP227 4.5 9.6 1.0
CB C:ILE226 4.5 10.0 1.0
CG1 C:ILE221 4.5 18.0 1.0
CA C:GLN222 4.6 16.9 1.0
CA C:ASP227 4.7 9.2 1.0
N C:ASP225 4.7 12.9 1.0
O C:LEU220 4.7 14.1 1.0
OD1 C:ASP227 4.8 13.4 1.0
CE2 C:TYR5 4.8 21.6 1.0
CD1 C:TYR5 5.0 19.2 1.0
C C:ASP225 5.0 11.0 1.0

Sodium binding site 4 out of 4 in 5bmx

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Sodium binding site 4 out of 4 in the Crystal Structure of T75N Mutant of Triosephosphate Isomerase From Plasmodium Falciparum


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 T75N Mutant of Triosephosphate Isomerase From Plasmodium Falciparum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na303

b:17.5
occ:1.00
 O D:ILE221 2.2 13.7 1.0
O D:GLN223 2.3 21.6 1.0
O D:HOH500 2.3 22.7 1.0
O D:HOH535 2.4 29.0 1.0
O D:ILE226 2.4 16.6 1.0
OH D:TYR5 2.9 36.2 1.0
C D:ILE221 3.5 17.0 1.0
C D:GLN223 3.5 22.9 1.0
C D:ILE226 3.6 15.3 1.0
CZ D:TYR5 3.7 27.4 1.0
CE1 D:TYR5 3.8 27.4 1.0
N D:GLN223 4.0 19.4 1.0
C D:GLN222 4.1 22.8 1.0
O D:GLU224 4.1 19.4 1.0
N D:ILE226 4.2 15.5 1.0
C D:GLU224 4.2 20.0 1.0
CD1 D:ILE221 4.3 18.9 1.0
CA D:GLN223 4.4 21.0 1.0
N D:GLU224 4.4 21.5 1.0
CA D:ILE221 4.4 18.3 1.0
CA D:GLU224 4.4 22.9 1.0
CA D:ILE226 4.4 15.7 1.0
N D:GLN222 4.4 17.7 1.0
O D:GLN222 4.5 22.4 1.0
CA D:GLN222 4.5 20.1 1.0
N D:ASP227 4.6 14.4 1.0
OD1 D:ASP227 4.6 21.0 1.0
CB D:ILE226 4.7 14.5 1.0
CA D:ASP227 4.7 12.6 1.0
N D:ASP225 4.7 20.3 1.0
CE2 D:TYR5 4.8 28.5 1.0
CG1 D:ILE221 4.9 20.9 1.0
O D:LEU220 4.9 15.4 1.0

Reference:

D.Bandyopadhyay, M.R.Murthy, H.Balaram, P.Balaram. Probing the Role of Highly Conserved Residues in Triosephosphate Isomerase - Analysis of Site Specific Mutants at Positions 64 and 75 in the Plasmodial Enzyme Febs J. V. 282 3863 2015.
ISSN: ISSN 1742-464X
PubMed: 26206206
DOI: 10.1111/FEBS.13384
Page generated: Mon Oct 7 20:06:03 2024

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