Atomistry » Sodium » PDB 6e8t-6eqe » 6eep
Atomistry »
  Sodium »
    PDB 6e8t-6eqe »
      6eep »

Sodium in PDB 6eep: Crystal Structure of Ribose-5-Phosphate Isomerase From Legionella Pneumophila

Enzymatic activity of Crystal Structure of Ribose-5-Phosphate Isomerase From Legionella Pneumophila

All present enzymatic activity of Crystal Structure of Ribose-5-Phosphate Isomerase From Legionella Pneumophila:
5.3.1.6;

Protein crystallography data

The structure of Crystal Structure of Ribose-5-Phosphate Isomerase From Legionella Pneumophila, PDB code: 6eep 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) 32.19 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 104.630, 67.930, 74.000, 90.00, 119.54, 90.00
R / Rfree (%) 15.8 / 21.6

Sodium Binding Sites:

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

Sodium binding site 1 out of 2 in 6eep

Go back to Sodium Binding Sites List in 6eep
Sodium binding site 1 out of 2 in the Crystal Structure of Ribose-5-Phosphate Isomerase From Legionella Pneumophila


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:35.6
occ:1.00
O B:HOH421 2.4 31.0 1.0
O A:ILE187 2.4 18.3 1.0
O A:ASN185 2.5 28.8 1.0
O B:HOH515 2.7 30.5 1.0
O A:VAL190 2.8 18.9 1.0
C A:ILE187 3.3 21.5 1.0
C A:ASN185 3.7 21.8 1.0
N A:VAL190 3.7 21.5 1.0
C A:VAL190 3.8 16.3 1.0
O B:VAL191 3.8 20.5 1.0
N A:ILE187 3.9 21.6 1.0
C A:VAL186 3.9 23.7 1.0
OE1 B:GLU192 4.0 22.2 1.0
O A:HOH467 4.0 26.3 1.0
CA A:PRO188 4.0 21.3 1.0
N A:PRO188 4.0 20.8 1.0
O B:HOH430 4.1 33.5 1.0
N A:GLY189 4.1 19.8 1.0
CA A:VAL190 4.1 17.0 1.0
CB A:VAL190 4.1 19.0 1.0
CA A:ILE187 4.2 24.8 1.0
CA A:VAL186 4.3 19.8 1.0
O A:VAL186 4.3 23.7 1.0
C A:PRO188 4.4 19.1 1.0
N A:VAL186 4.5 22.4 1.0
CA A:ASN185 4.6 18.1 1.0
C A:GLY189 4.7 25.1 1.0
CG B:ASN185 4.7 19.4 1.0
OD1 B:ASN185 4.9 26.8 1.0
ND2 B:ASN185 4.9 20.1 1.0
CB B:ASN185 4.9 23.1 1.0
CG1 A:VAL190 4.9 18.1 1.0
CD B:GLU192 4.9 26.6 1.0
C B:VAL191 4.9 24.1 1.0
CA A:GLY189 4.9 18.0 1.0
N A:VAL191 5.0 20.2 1.0

Sodium binding site 2 out of 2 in 6eep

Go back to Sodium Binding Sites List in 6eep
Sodium binding site 2 out of 2 in the Crystal Structure of Ribose-5-Phosphate Isomerase From Legionella Pneumophila


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:34.5
occ:1.00
O A:HOH459 2.3 49.2 1.0
O B:ASN185 2.5 21.7 1.0
O A:HOH431 2.5 40.0 1.0
O B:ILE187 2.5 19.3 1.0
O B:VAL190 2.7 20.1 1.0
O A:HOH467 2.8 26.3 1.0
C B:ILE187 3.4 22.2 1.0
C B:ASN185 3.6 20.4 1.0
C B:VAL190 3.7 20.1 1.0
N B:VAL190 3.7 16.0 1.0
O A:VAL191 3.9 21.2 1.0
C B:VAL186 3.9 30.3 1.0
N B:ILE187 3.9 24.7 1.0
O B:HOH515 3.9 30.5 1.0
CB B:VAL190 4.0 17.6 1.0
CA B:VAL190 4.0 15.7 1.0
OE1 A:GLU192 4.0 24.5 1.0
O A:HOH409 4.2 35.6 1.0
N B:PRO188 4.2 23.1 1.0
O B:VAL186 4.2 24.2 1.0
CA B:PRO188 4.2 20.0 1.0
N B:GLY189 4.2 17.6 1.0
CA B:VAL186 4.3 22.6 1.0
CA B:ILE187 4.3 23.4 1.0
N B:VAL186 4.4 20.0 1.0
C B:PRO188 4.5 19.9 1.0
CA B:ASN185 4.5 24.4 1.0
CG A:ASN185 4.6 22.8 1.0
C B:GLY189 4.7 18.9 1.0
CG1 B:VAL190 4.7 15.5 1.0
ND2 A:ASN185 4.8 19.2 1.0
CB A:ASN185 4.8 16.3 1.0
OD1 A:ASN185 4.9 22.1 1.0
O B:LEU184 4.9 23.6 1.0
N B:VAL191 4.9 15.8 1.0

Reference:

K.N.Braverman, D.M.Dranow, S.J.Mayclin, D.D.Lorimer, P.S.Horanyi, T.E.Edwards. Crystal Structure of Ribose-5-Phosphate Isomerase From Legionella Pneumophila To Be Published.
Page generated: Tue Dec 15 12:10:30 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