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Sodium in PDB 4afy: Crystal Structure of the Fimx Eal Domain in Complex with Reaction Product Pgpg

Enzymatic activity of Crystal Structure of the Fimx Eal Domain in Complex with Reaction Product Pgpg

All present enzymatic activity of Crystal Structure of the Fimx Eal Domain in Complex with Reaction Product Pgpg:
3.1.4.52;

Protein crystallography data

The structure of Crystal Structure of the Fimx Eal Domain in Complex with Reaction Product Pgpg, PDB code: 4afy was solved by J.Robert-Paganin, S.Nonin-Lecomte, S.Rety, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.209 / 2.01
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 104.330, 104.330, 154.240, 90.00, 90.00, 90.00
R / Rfree (%) 20.85 / 23.9

Other elements in 4afy:

The structure of Crystal Structure of the Fimx Eal Domain in Complex with Reaction Product Pgpg also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Fimx Eal Domain in Complex with Reaction Product Pgpg (pdb code 4afy). 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 the Fimx Eal Domain in Complex with Reaction Product Pgpg, PDB code: 4afy:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4afy

Go back to Sodium Binding Sites List in 4afy
Sodium binding site 1 out of 2 in the Crystal Structure of the Fimx Eal Domain in Complex with Reaction Product Pgpg


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 the Fimx Eal Domain in Complex with Reaction Product Pgpg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na803

b:50.9
occ:1.00
O A:HOH2072 2.2 42.1 1.0
O A:THR611 2.7 36.6 1.0
O A:THR582 2.8 42.5 1.0
CB A:ALA592 3.5 35.1 1.0
C A:THR582 3.6 39.0 1.0
CB A:THR582 3.7 37.4 1.0
CA A:THR582 3.7 38.3 1.0
C A:THR611 3.8 45.4 1.0
CB A:LEU585 3.8 42.6 1.0
CG2 A:THR611 3.8 41.1 1.0
CB A:THR611 3.9 42.3 1.0
N A:ALA592 3.9 35.4 1.0
N A:ALA586 4.1 37.1 1.0
CG2 A:THR582 4.2 33.6 1.0
C A:GLN591 4.3 40.0 1.0
CD1 A:LEU585 4.3 40.9 1.0
CA A:ALA592 4.3 29.4 1.0
OE1 A:GLN613 4.4 34.5 1.0
O A:CYS590 4.4 38.1 1.0
CA A:THR611 4.5 37.9 1.0
NE2 A:GLN613 4.5 43.5 1.0
CA A:GLN591 4.5 40.7 1.0
CB A:ALA586 4.6 46.6 1.0
CG A:LEU585 4.7 39.9 1.0
C A:LEU585 4.7 36.7 1.0
CA A:ALA586 4.7 44.2 1.0
CA A:LEU585 4.7 35.5 1.0
N A:GLN583 4.8 41.4 1.0
N A:VAL612 4.8 35.4 1.0
O A:GLN591 4.8 33.1 1.0
CD A:GLN613 4.9 46.6 1.0
OG1 A:THR582 4.9 38.2 1.0
N A:LEU585 5.0 44.5 1.0

Sodium binding site 2 out of 2 in 4afy

Go back to Sodium Binding Sites List in 4afy
Sodium binding site 2 out of 2 in the Crystal Structure of the Fimx Eal Domain in Complex with Reaction Product Pgpg


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 the Fimx Eal Domain in Complex with Reaction Product Pgpg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na804

b:39.4
occ:1.00
O A:THR661 2.8 25.7 1.0
CG A:GLN664 3.0 32.8 1.0
N A:ALA665 3.5 31.7 1.0
CB A:GLN664 3.6 31.2 1.0
CG2 A:THR661 3.6 28.4 1.0
CE A:LYS635 3.7 49.7 1.0
CB A:ALA665 3.8 28.3 1.0
C A:THR661 3.8 29.9 1.0
NZ A:LYS635 3.8 48.4 1.0
CA A:ALA665 3.9 27.4 1.0
C A:GLN664 4.0 29.7 1.0
CA A:THR661 4.1 25.5 1.0
CD A:GLN664 4.3 39.0 1.0
CA A:GLN664 4.4 30.8 1.0
CB A:THR661 4.4 27.8 1.0
CD A:LYS635 4.5 45.5 1.0
O A:GLN664 4.7 27.5 1.0
CG A:LYS635 4.7 39.9 1.0
NE2 A:GLN664 4.8 31.8 1.0
N A:GLN664 4.9 30.3 1.0
O A:HOH2098 5.0 50.4 1.0
N A:LEU662 5.0 28.4 1.0

Reference:

J.Robert-Paganin, S.Nonin-Lecomte, S.Rety. Crystal Structure of An Eal Domain in Complex with Reaction Product 5'-Pgpg Plos One V. 7 52424 2012.
ISSN: ISSN 1932-6203
PubMed: 23285035
DOI: 10.1371/JOURNAL.PONE.0052424
Page generated: Tue Dec 15 06:32:54 2020

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