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Sodium in PDB 8vhu: Crystal Structure of Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit

Enzymatic activity of Crystal Structure of Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit

All present enzymatic activity of Crystal Structure of Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit:
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit, PDB code: 8vhu was solved by M.A.Funk, C.M.Zimanyi, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.15 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.214, 111.207, 209.701, 90, 90, 90
R / Rfree (%) 15.9 / 19.2

Other elements in 8vhu:

The structure of Crystal Structure of Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Chlorine (Cl) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit (pdb code 8vhu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit, PDB code: 8vhu:

Sodium binding site 1 out of 1 in 8vhu

Go back to Sodium Binding Sites List in 8vhu
Sodium binding site 1 out of 1 in the Crystal Structure of Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit


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 Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1405

b:44.4
occ:1.00
 O A:HOH1700 2.6 26.9 1.0
O A:HOH1651 2.7 27.8 1.0
OG A:SER242 2.8 32.4 1.0
OG B:SER242 2.9 33.0 1.0
O B:ASN238 3.0 29.6 1.0
O A:ASN238 3.3 34.0 1.0
OG B:SER241 3.7 35.5 1.0
N B:SER242 3.7 32.7 1.0
CB B:SER241 3.7 29.0 1.0
OG A:SER241 3.8 37.3 1.0
C B:ASN238 3.8 30.1 1.0
N A:SER242 3.9 29.7 1.0
CA B:ASN238 4.0 25.8 1.0
CB A:SER242 4.0 25.1 1.0
CB A:SER241 4.0 32.4 1.0
CB B:SER242 4.1 28.4 1.0
C A:ASN238 4.1 33.3 1.0
CA B:SER242 4.2 28.8 1.0
CA A:SER242 4.2 28.6 1.0
CA A:ASN238 4.3 30.7 1.0
C B:SER241 4.3 33.5 1.0
CB B:ASN238 4.3 26.7 1.0
OD1 B:ASN238 4.4 33.1 1.0
O A:HOH1976 4.4 28.0 1.0
OD1 A:ASN238 4.4 36.8 1.0
CB A:ASN238 4.5 30.2 1.0
C A:SER241 4.5 34.3 1.0
CA B:SER241 4.6 30.7 1.0
CG B:ASN238 4.6 31.4 1.0
CG A:ASN238 4.7 34.4 1.0
NE2 B:HIS284 4.8 30.6 1.0
CA A:SER241 4.9 34.4 1.0
NE2 A:HIS284 4.9 35.0 1.0
O B:HOH2018 4.9 31.7 1.0

Reference:

M.A.Funk, C.M.Zimanyi, G.A.Andree, A.E.Hamilos, C.L.Drennan. How Atp and Datp Act As Molecular Switches to Regulate Enzymatic Activity in the Prototypical Bacterial Class Ia Ribonucleotide Reductase. Biochemistry 2024.
ISSN: ISSN 0006-2960
PubMed: 39164005
DOI: 10.1021/ACS.BIOCHEM.4C00329
Page generated: Wed Oct 9 14:02:02 2024

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