Sodium in PDB 6mc0: Crystal Structure of Ribose-5-Phosphate Isomerase From Legionella Pneumophila with Bound Substrate Ribose-5-Phosphate and Product Ribulose-5-Phosphate

Enzymatic activity of Crystal Structure of Ribose-5-Phosphate Isomerase From Legionella Pneumophila with Bound Substrate Ribose-5-Phosphate and Product Ribulose-5-Phosphate

All present enzymatic activity of Crystal Structure of Ribose-5-Phosphate Isomerase From Legionella Pneumophila with Bound Substrate Ribose-5-Phosphate and Product Ribulose-5-Phosphate:
5.3.1.6;

Protein crystallography data

The structure of Crystal Structure of Ribose-5-Phosphate Isomerase From Legionella Pneumophila with Bound Substrate Ribose-5-Phosphate and Product Ribulose-5-Phosphate, PDB code: 6mc0 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.25 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 103.290, 67.560, 73.320, 90.00, 118.82, 90.00
R / Rfree (%) 15.4 / 20.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Ribose-5-Phosphate Isomerase From Legionella Pneumophila with Bound Substrate Ribose-5-Phosphate and Product Ribulose-5-Phosphate (pdb code 6mc0). 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 Ribose-5-Phosphate Isomerase From Legionella Pneumophila with Bound Substrate Ribose-5-Phosphate and Product Ribulose-5-Phosphate, PDB code: 6mc0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6mc0

Go back to Sodium Binding Sites List in 6mc0
Sodium binding site 1 out of 2 in the Crystal Structure of Ribose-5-Phosphate Isomerase From Legionella Pneumophila with Bound Substrate Ribose-5-Phosphate and Product Ribulose-5-Phosphate


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 Ribose-5-Phosphate Isomerase From Legionella Pneumophila with Bound Substrate Ribose-5-Phosphate and Product Ribulose-5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:44.6
occ:1.00
 O B:HOH442 2.5 24.2 1.0
O A:ILE187 2.6 21.9 1.0
O B:HOH474 2.7 28.5 1.0
O A:ASN185 2.7 27.8 1.0
O A:VAL190 2.8 21.0 1.0
C A:ILE187 3.4 21.5 1.0
O B:VAL191 3.7 24.1 1.0
N A:VAL190 3.8 19.9 1.0
C A:ASN185 3.8 30.6 1.0
OE1 B:GLU192 3.8 23.6 1.0
C A:VAL190 3.8 18.6 1.0
N A:ILE187 3.9 20.9 1.0
C A:VAL186 4.0 21.3 1.0
O B:HOH433 4.0 26.0 1.0
O A:HOH451 4.0 29.7 1.0
CA A:PRO188 4.0 26.5 1.0
N A:PRO188 4.1 25.5 1.0
N A:GLY189 4.1 22.1 1.0
CA A:VAL190 4.2 17.9 1.0
CB A:VAL190 4.2 21.8 1.0
O A:VAL186 4.3 23.6 1.0
CA A:ILE187 4.3 25.8 1.0
CA A:VAL186 4.4 21.4 1.0
C A:PRO188 4.4 26.7 1.0
CG B:ASN185 4.5 23.1 1.0
N A:VAL186 4.6 22.6 1.0
C A:GLY189 4.7 21.2 1.0
ND2 B:ASN185 4.7 20.6 1.0
CB B:ASN185 4.7 24.8 1.0
OD1 B:ASN185 4.8 21.4 1.0
CA A:ASN185 4.8 22.5 1.0
CD B:GLU192 4.8 23.6 1.0
C B:VAL191 4.8 21.7 1.0
CA A:GLY189 5.0 20.0 1.0

Sodium binding site 2 out of 2 in 6mc0

Go back to Sodium Binding Sites List in 6mc0
Sodium binding site 2 out of 2 in the Crystal Structure of Ribose-5-Phosphate Isomerase From Legionella Pneumophila with Bound Substrate Ribose-5-Phosphate and Product Ribulose-5-Phosphate


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 Ribose-5-Phosphate Isomerase From Legionella Pneumophila with Bound Substrate Ribose-5-Phosphate and Product Ribulose-5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:36.9
occ:1.00
 O A:HOH451 2.5 29.7 1.0
O A:HOH442 2.6 33.8 1.0
O B:ASN185 2.7 24.5 1.0
O B:VAL190 2.7 23.4 1.0
O B:ILE187 2.7 21.4 1.0
O A:VAL191 3.6 24.2 1.0
C B:ILE187 3.7 20.2 1.0
C B:VAL190 3.7 16.1 1.0
C B:ASN185 3.8 24.8 1.0
N B:VAL190 3.8 16.2 1.0
O B:HOH474 3.8 28.5 1.0
OE1 A:GLU192 3.9 21.5 1.0
O A:HOH422 3.9 33.0 1.0
C B:VAL186 4.1 21.6 1.0
CA B:VAL190 4.1 21.0 1.0
CB B:VAL190 4.1 20.1 1.0
N B:ILE187 4.1 26.8 1.0
N B:GLY189 4.3 18.2 1.0
CA B:PRO188 4.3 18.2 1.0
O B:VAL186 4.3 22.0 1.0
N B:PRO188 4.3 21.4 1.0
CA B:VAL186 4.4 22.4 1.0
CG A:ASN185 4.5 24.5 1.0
N B:VAL186 4.5 27.3 1.0
CA B:ILE187 4.6 21.1 1.0
ND2 A:ASN185 4.6 23.8 1.0
C B:PRO188 4.6 21.9 1.0
CA B:ASN185 4.7 24.2 1.0
OD1 A:ASN185 4.7 21.0 1.0
CB A:ASN185 4.7 19.1 1.0
C B:GLY189 4.7 25.1 1.0
C A:VAL191 4.8 18.5 1.0
N B:VAL191 4.9 19.3 1.0
CG1 B:VAL190 4.9 18.5 1.0
CD A:GLU192 4.9 21.9 1.0

Reference:

K.N.Braverman, D.M.Dranow, J.Abendroth, D.D.Lorimer, P.S.Horanyi, T.E.Edwards. Crystal Structure of Ribose-5-Phosphate Isomerase From Legionella Pneumophila with Bound Substrate Ribose-5-Phosphate and Product Ribulose-5-Phosphate To Be Published.
Page generated: Tue Dec 15 12:35:07 2020

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