Magnesium in PDB 8vho: Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit Bound to Datp

Enzymatic activity of Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit Bound to Datp

All present enzymatic activity of Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit Bound to Datp:
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit Bound to Datp, PDB code: 8vho 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) 49.79 / 2.55
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 118.513, 118.513, 290.295, 90, 90, 90
R / Rfree (%) 16.5 / 20.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit Bound to Datp (pdb code 8vho). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit Bound to Datp, PDB code: 8vho:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8vho

Go back to Magnesium Binding Sites List in 8vho
Magnesium binding site 1 out of 4 in the Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit Bound to Datp


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 E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit Bound to Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:80.4
occ:1.00
 O2G A:DTP801 2.1 69.0 1.0
O2B A:DTP801 2.1 87.0 1.0
O A:HOH1085 2.1 77.8 1.0
O A:HOH925 2.1 73.3 1.0
O A:HOH1103 2.1 60.8 1.0
O1A A:DTP801 2.1 78.9 1.0
PB A:DTP801 3.2 84.0 1.0
PG A:DTP801 3.3 76.5 1.0
PA A:DTP801 3.4 74.3 1.0
O3A A:DTP801 3.6 100.0 1.0
O3B A:DTP801 3.6 112.5 1.0
O1G A:DTP801 4.0 79.7 1.0
O2A A:DTP801 4.3 72.3 1.0
NZ A:LYS91 4.3 66.2 1.0
O1B A:DTP801 4.5 85.8 1.0
O5' A:DTP801 4.5 57.9 1.0
O3G A:DTP801 4.5 77.2 1.0
CE A:LYS9 5.0 79.5 1.0

Magnesium binding site 2 out of 4 in 8vho

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Magnesium binding site 2 out of 4 in the Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit Bound to Datp


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 E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit Bound to Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg804

b:44.7
occ:1.00
 O A:HOH976 2.1 45.0 1.0
O A:HOH1044 2.1 37.7 1.0
O1G A:DTP803 2.1 51.6 1.0
O A:HOH919 2.1 50.6 1.0
O1A A:DTP803 2.1 50.7 1.0
O1B A:DTP803 2.1 38.9 1.0
PA A:DTP803 2.9 41.4 1.0
PB A:DTP803 2.9 45.7 1.0
O3A A:DTP803 3.1 39.7 1.0
PG A:DTP803 3.2 50.0 1.0
O5' A:DTP803 3.2 46.3 1.0
O3B A:DTP803 3.3 48.1 1.0
O3G A:DTP803 3.8 48.3 1.0
O A:ASP232 4.1 43.6 1.0
NH2 A:ARG262 4.2 43.0 1.0
C5' A:DTP803 4.2 46.9 1.0
O2A A:DTP803 4.3 43.5 1.0
O A:HOH1147 4.3 41.7 1.0
O2B A:DTP803 4.3 46.9 1.0
CB A:SER233 4.4 36.3 1.0
O2G A:DTP803 4.5 43.9 1.0
CA A:SER233 4.8 39.2 1.0

Magnesium binding site 3 out of 4 in 8vho

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Magnesium binding site 3 out of 4 in the Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit Bound to Datp


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 E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit Bound to Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:76.9
occ:1.00
 O1A B:DTP801 2.1 72.7 1.0
O3G B:DTP801 2.1 62.2 1.0
O2B B:DTP801 2.1 81.8 1.0
O B:HOH1168 2.1 69.9 1.0
O B:HOH1173 2.1 84.3 1.0
O B:HOH1248 2.1 62.8 1.0
PB B:DTP801 3.3 78.5 1.0
PA B:DTP801 3.4 67.0 1.0
PG B:DTP801 3.5 63.9 1.0
O3A B:DTP801 3.6 59.3 1.0
O3B B:DTP801 3.7 104.8 1.0
O5' B:DTP801 4.3 50.8 1.0
O2G B:DTP801 4.4 61.3 1.0
O2A B:DTP801 4.4 65.7 1.0
O1G B:DTP801 4.4 67.8 1.0
O1B B:DTP801 4.5 78.8 1.0
NZ B:LYS91 4.6 61.5 1.0
C8 B:DTP801 4.7 62.0 1.0
CE B:LYS9 4.8 73.5 1.0
NZ B:LYS9 4.9 74.5 1.0

Magnesium binding site 4 out of 4 in 8vho

Go back to Magnesium Binding Sites List in 8vho
Magnesium binding site 4 out of 4 in the Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit Bound to Datp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit Bound to Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg804

b:48.5
occ:1.00
 O B:HOH1069 2.1 45.7 1.0
O B:HOH1009 2.1 56.4 1.0
O B:HOH1199 2.1 59.0 1.0
O1G B:DTP803 2.1 54.3 1.0
O1A B:DTP803 2.1 49.2 1.0
O1B B:DTP803 2.1 42.7 1.0
PB B:DTP803 3.1 47.9 1.0
PG B:DTP803 3.1 49.8 1.0
PA B:DTP803 3.3 44.8 1.0
O3B B:DTP803 3.4 46.5 1.0
O3A B:DTP803 3.5 54.6 1.0
O3G B:DTP803 3.7 52.8 1.0
O2A B:DTP803 4.3 42.9 1.0
O5' B:DTP803 4.4 37.9 1.0
O B:ASP232 4.4 41.0 1.0
NH2 B:ARG262 4.4 41.9 1.0
O2B B:DTP803 4.4 45.7 1.0
CB B:SER233 4.4 38.2 1.0
O2G B:DTP803 4.5 40.8 1.0
C5' B:DTP803 4.5 37.7 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: Fri Oct 4 22:05:02 2024

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