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Sodium in PDB 3m9y: Crystal Structure of Triosephosphate Isomerase From Methicillin Resistant Staphylococcus Aureus at 1.9 Angstrom Resolution

Enzymatic activity of Crystal Structure of Triosephosphate Isomerase From Methicillin Resistant Staphylococcus Aureus at 1.9 Angstrom Resolution

All present enzymatic activity of Crystal Structure of Triosephosphate Isomerase From Methicillin Resistant Staphylococcus Aureus at 1.9 Angstrom Resolution:
5.3.1.1;

Protein crystallography data

The structure of Crystal Structure of Triosephosphate Isomerase From Methicillin Resistant Staphylococcus Aureus at 1.9 Angstrom Resolution, PDB code: 3m9y was solved by S.Mukherjee, D.Dutta, B.Saha, A.K.Das, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.478, 79.478, 175.006, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 20.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Triosephosphate Isomerase From Methicillin Resistant Staphylococcus Aureus at 1.9 Angstrom Resolution (pdb code 3m9y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Triosephosphate Isomerase From Methicillin Resistant Staphylococcus Aureus at 1.9 Angstrom Resolution, PDB code: 3m9y:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3m9y

Go back to Sodium Binding Sites List in 3m9y
Sodium binding site 1 out of 2 in the Crystal Structure of Triosephosphate Isomerase From Methicillin Resistant Staphylococcus Aureus at 1.9 Angstrom Resolution


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 Triosephosphate Isomerase From Methicillin Resistant Staphylococcus Aureus at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na254

b:28.2
occ:1.00
O B:MET225 2.3 25.3 1.0
O B:HOH305 2.4 19.2 1.0
O B:ILE230 2.4 24.6 1.0
O B:HOH327 2.4 17.3 1.0
O B:GLN227 2.5 23.0 1.0
O B:HOH359 2.6 19.9 1.0
C B:MET225 3.4 25.0 1.0
O B:HOH438 3.5 40.0 1.0
C B:ILE230 3.5 23.6 1.0
C B:GLN227 3.7 24.9 1.0
N B:GLN227 4.1 24.7 1.0
C B:ALA226 4.1 25.5 1.0
CA B:MET225 4.2 23.9 1.0
N B:ILE230 4.2 23.4 1.0
CA B:ILE230 4.3 23.4 1.0
N B:ALA226 4.3 24.4 1.0
O B:HOH378 4.4 25.5 1.0
O B:THR228 4.4 26.4 1.0
CA B:GLN227 4.5 25.5 1.0
CA B:ALA226 4.5 26.1 1.0
O B:HOH435 4.5 25.1 1.0
C B:THR228 4.5 25.6 1.0
O B:ALA226 4.5 25.8 1.0
N B:ASP231 4.5 23.3 1.0
CB B:ILE230 4.6 23.9 1.0
N B:THR228 4.6 25.5 1.0
CA B:ASP231 4.6 22.1 1.0
CA B:THR228 4.7 26.1 1.0
O B:HOH426 4.8 23.0 1.0
CE B:MET225 4.8 21.6 1.0
OD1 B:ASP231 4.8 27.8 1.0
O B:TYR224 4.8 22.6 1.0
N B:ASP229 4.9 24.5 1.0
O B:HOH394 5.0 39.3 1.0

Sodium binding site 2 out of 2 in 3m9y

Go back to Sodium Binding Sites List in 3m9y
Sodium binding site 2 out of 2 in the Crystal Structure of Triosephosphate Isomerase From Methicillin Resistant Staphylococcus Aureus at 1.9 Angstrom Resolution


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 Triosephosphate Isomerase From Methicillin Resistant Staphylococcus Aureus at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na255

b:25.6
occ:1.00
OG1 A:THR80 2.8 22.5 1.0
N B:ILE44 3.2 15.9 1.0
O B:HOH308 3.3 23.0 1.0
N B:ALA43 3.4 16.3 1.0
CB B:PRO42 3.5 18.6 1.0
O A:HOH293 3.6 23.3 1.0
CB A:THR80 3.6 18.5 1.0
CB B:ILE44 3.6 18.7 1.0
CG2 B:ILE44 3.6 17.8 1.0
CA A:THR80 3.6 18.1 1.0
CG2 A:THR80 3.7 19.9 1.0
C B:PRO42 3.8 17.7 1.0
CB B:ALA43 4.0 19.0 1.0
CA B:ALA43 4.0 16.9 1.0
CA B:ILE44 4.0 17.8 1.0
C B:ALA43 4.0 15.6 1.0
CB A:ALA43 4.0 19.7 1.0
CA B:PRO42 4.1 17.3 1.0
O A:GLU79 4.1 18.5 1.0
O A:HOH313 4.2 25.7 1.0
N A:THR80 4.3 19.4 1.0
C A:GLU79 4.4 19.1 1.0
O A:HOH261 4.5 17.1 1.0
O B:PRO42 4.6 17.0 1.0
C A:THR80 4.9 20.2 1.0
CG1 B:ILE44 4.9 19.2 1.0
CG B:PRO42 5.0 16.3 1.0

Reference:

S.Mukherjee, A.Roychowdhury, D.Dutta, A.K.Das. Crystal Structures of Triosephosphate Isomerase From Methicillin Resistant Staphylococcus Aureus MRSA252 Provide Structural Insights Into Novel Modes of Ligand Binding and Unique Conformations of Catalytic Loop Biochimie V. 94 2532 2012.
ISSN: ISSN 0300-9084
PubMed: 22813930
DOI: 10.1016/J.BIOCHI.2012.07.001
Page generated: Tue Dec 15 06:17:17 2020

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