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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy