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Sodium in PDB 2pfl: Crystal Structure of Pfl From E.Coli

Enzymatic activity of Crystal Structure of Pfl From E.Coli

All present enzymatic activity of Crystal Structure of Pfl From E.Coli:
2.3.1.54;

Protein crystallography data

The structure of Crystal Structure of Pfl From E.Coli, PDB code: 2pfl was solved by A.Becker, K.Fritz-Wolf, W.Kabsch, J.Knappe, S.Schultz, A.F.V.Wagner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 159.020, 159.020, 160.640, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 24.2

Other elements in 2pfl:

The structure of Crystal Structure of Pfl From E.Coli also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Pfl From E.Coli (pdb code 2pfl). 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 Pfl From E.Coli, PDB code: 2pfl:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2pfl

Go back to Sodium Binding Sites List in 2pfl
Sodium binding site 1 out of 2 in the Crystal Structure of Pfl From E.Coli


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 Pfl From E.Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2001

b:69.9
occ:1.00
OE1 A:GLU700 2.4 83.5 1.0
O A:LEU654 2.4 75.6 1.0
O A:GLY701 2.5 79.3 1.0
O A:ALA652 2.7 74.0 1.0
O A:HOH2279 2.8 56.6 1.0
CD A:GLU700 3.5 84.2 1.0
C A:GLY701 3.5 79.3 1.0
C A:LEU654 3.6 75.1 1.0
C A:ALA652 3.8 74.6 1.0
CG A:GLU700 3.9 84.8 1.0
N A:PHE656 3.9 72.7 1.0
N A:GLY701 4.1 81.6 1.0
CB A:GLU700 4.2 85.4 1.0
O A:HOH2110 4.2 93.2 1.0
N A:GLY702 4.3 78.4 1.0
CA A:GLY701 4.3 80.5 1.0
CA A:ALA652 4.3 74.2 1.0
CB A:PHE656 4.4 70.5 1.0
N A:LEU654 4.4 76.0 1.0
CA A:GLY702 4.4 76.5 1.0
N A:PRO655 4.4 74.5 1.0
CA A:PRO655 4.5 73.9 1.0
CA A:LEU654 4.5 75.3 1.0
OE2 A:GLU700 4.6 84.0 1.0
C A:LYS653 4.6 76.3 1.0
C A:PRO655 4.6 73.5 1.0
C A:GLU700 4.7 83.2 1.0
CA A:PHE656 4.7 72.0 1.0
O A:VAL651 4.8 76.3 1.0
N A:LYS653 4.8 75.3 1.0
C A:GLY702 4.8 75.6 1.0
CD1 A:ILE663 4.9 64.7 1.0
N A:GLN703 4.9 74.1 1.0
O A:LYS653 5.0 76.2 1.0

Sodium binding site 2 out of 2 in 2pfl

Go back to Sodium Binding Sites List in 2pfl
Sodium binding site 2 out of 2 in the Crystal Structure of Pfl From E.Coli


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 Pfl From E.Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2002

b:90.1
occ:1.00
O B:GLY701 2.3 83.3 1.0
OE1 B:GLU700 2.5 88.0 1.0
O B:LEU654 2.6 80.6 1.0
O B:ALA652 2.8 81.7 1.0
C B:GLY701 3.3 83.2 1.0
CD B:GLU700 3.5 88.5 1.0
C B:LEU654 3.8 80.3 1.0
C B:ALA652 3.8 81.4 1.0
CG B:GLU700 3.9 88.5 1.0
N B:PHE656 4.0 78.5 1.0
N B:GLY701 4.1 85.3 1.0
N B:GLY702 4.2 82.0 1.0
CA B:GLY702 4.2 80.5 1.0
CA B:GLY701 4.2 84.1 1.0
CB B:GLU700 4.2 88.4 1.0
CB B:PHE656 4.3 76.6 1.0
CA B:ALA652 4.3 81.1 1.0
N B:LEU654 4.5 81.2 1.0
N B:PRO655 4.6 79.8 1.0
OE2 B:GLU700 4.6 88.2 1.0
C B:GLY702 4.6 79.7 1.0
CA B:PRO655 4.6 79.4 1.0
C B:GLU700 4.7 86.6 1.0
CA B:LEU654 4.7 80.4 1.0
N B:GLN703 4.7 78.1 1.0
O B:VAL651 4.8 81.1 1.0
CA B:PHE656 4.8 77.6 1.0
C B:PRO655 4.8 78.9 1.0
C B:LYS653 4.8 82.1 1.0
CD1 B:ILE663 4.9 72.8 1.0
N B:LYS653 4.9 82.1 1.0

Reference:

A.Becker, K.Fritz-Wolf, W.Kabsch, J.Knappe, S.Schultz, A.F.Volker Wagner. Structure and Mechanism of the Glycyl Radical Enzyme Pyruvate Formate-Lyase. Nat.Struct.Biol. V. 6 969 1999.
ISSN: ISSN 1072-8368
PubMed: 10504733
DOI: 10.1038/13341
Page generated: Tue Dec 15 05:53:55 2020

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