Magnesium 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:

Sodium (Na) 1 atom
Chlorine (Cl) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 3 binding sites of Magnesium where 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:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 8vhu

Go back to Magnesium Binding Sites List in 8vhu
Magnesium binding site 1 out of 3 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 Magnesium with other atoms in the Mg 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:Mg1402

b:49.7
occ:1.00
 O1G A:DTP1401 2.1 56.1 1.0
O A:HOH1979 2.1 49.6 1.0
O1B A:DTP1401 2.1 48.2 1.0
O1A A:DTP1401 2.2 40.6 1.0
O A:HOH1817 2.2 44.6 1.0
O A:HOH1847 2.2 54.7 1.0
PB A:DTP1401 3.1 48.1 1.0
PG A:DTP1401 3.3 59.9 1.0
PA A:DTP1401 3.3 46.8 1.0
O3B A:DTP1401 3.4 157.9 1.0
O3A A:DTP1401 3.5 152.9 1.0
O A:HOH1693 3.6 65.0 1.0
O A:HOH1689 3.8 65.5 1.0
NZ A:LYS9 3.9 48.0 1.0
O A:HOH1947 4.1 63.4 1.0
O2G A:DTP1401 4.1 63.9 1.0
NZ A:LYS91 4.2 50.3 1.0
O2A A:DTP1401 4.3 58.4 1.0
O3G A:DTP1401 4.4 64.0 1.0
O A:HOH1925 4.4 57.1 1.0
O5' A:DTP1401 4.4 50.7 1.0
O2B A:DTP1401 4.5 40.4 1.0
CE A:LYS9 4.7 52.9 1.0
C8 A:DTP1401 4.8 53.5 1.0
O A:HOH2111 4.8 69.7 1.0

Magnesium binding site 2 out of 3 in 8vhu

Go back to Magnesium Binding Sites List in 8vhu
Magnesium binding site 2 out of 3 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 Magnesium with other atoms in the Mg binding site number 2 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:Mg1404

b:39.6
occ:1.00
 O2A A:DTP1403 2.0 32.0 1.0
O1B A:DTP1403 2.0 36.8 1.0
O A:HOH1549 2.0 32.8 1.0
O2G A:DTP1403 2.1 40.4 1.0
O A:HOH1840 2.1 31.6 1.0
O A:HOH1833 2.1 31.6 1.0
PB A:DTP1403 3.1 38.7 1.0
PG A:DTP1403 3.2 37.4 1.0
PA A:DTP1403 3.3 35.4 1.0
O3G A:DTP1403 3.5 40.9 1.0
O3A A:DTP1403 3.6 93.6 1.0
O3B A:DTP1403 3.6 47.0 1.0
O A:HOH1744 3.9 45.3 1.0
O A:ASP232 4.1 37.1 1.0
NH2 A:ARG262 4.2 34.9 1.0
O1A A:DTP1403 4.3 33.9 1.0
O5' A:DTP1403 4.3 38.2 1.0
C5' A:DTP1403 4.4 34.1 1.0
CB A:SER233 4.4 34.8 1.0
O2B A:DTP1403 4.5 34.7 1.0
O1G A:DTP1403 4.5 39.7 1.0
O A:HOH2078 4.6 37.5 1.0
CA A:SER233 4.9 33.9 1.0

Magnesium binding site 3 out of 3 in 8vhu

Go back to Magnesium Binding Sites List in 8vhu
Magnesium binding site 3 out of 3 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 Magnesium with other atoms in the Mg binding site number 3 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
B:Mg1402

b:36.5
occ:1.00
 O1B B:DTP1401 2.1 29.6 1.0
O B:HOH1830 2.1 38.1 1.0
O B:HOH1692 2.1 36.5 1.0
O1G B:DTP1401 2.1 38.8 1.0
O2A B:DTP1401 2.1 29.7 1.0
O B:HOH1804 2.1 37.1 1.0
PB B:DTP1401 3.2 33.8 1.0
PG B:DTP1401 3.2 37.6 1.0
PA B:DTP1401 3.4 33.3 1.0
O3A B:DTP1401 3.6 38.4 1.0
O3G B:DTP1401 3.6 32.4 1.0
O3B B:DTP1401 3.7 37.3 1.0
O B:HOH2078 3.9 65.0 1.0
O B:ASP232 4.1 33.2 1.0
NH2 B:ARG262 4.1 35.6 1.0
O1A B:DTP1401 4.3 37.2 1.0
O B:HOH2051 4.3 36.8 1.0
O5' B:DTP1401 4.3 33.7 1.0
CB B:SER233 4.3 30.8 1.0
C5' B:DTP1401 4.3 32.3 1.0
O B:HOH2038 4.4 70.8 1.0
O B:HOH2086 4.5 63.1 1.0
O2G B:DTP1401 4.5 31.3 1.0
O2B B:DTP1401 4.5 34.8 1.0
CA B:SER233 4.9 37.5 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: Fri Oct 4 22:05:42 2024

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