Magnesium in PDB 8vhq: Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Datp and Atp

Enzymatic activity of Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Datp and Atp

All present enzymatic activity of Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Datp and Atp:
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Datp and Atp, PDB code: 8vhq 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) 49.62 / 3.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 112.695, 139.929, 300.766, 90, 90, 90
R / Rfree (%) 20.4 / 23.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Datp and Atp (pdb code 8vhq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Datp and Atp, PDB code: 8vhq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8vhq

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Magnesium binding site 1 out of 8 in the Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Datp and Atp


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 W28A Variant Bound to Datp and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:69.6
occ:1.00
 O1G A:DTP801 2.1 113.2 1.0
O2G A:ATP803 2.1 114.3 1.0
O1B A:ATP803 2.1 98.2 1.0
O2A A:DTP801 2.1 94.0 1.0
O1A A:ATP803 2.1 82.6 1.0
O2B A:DTP801 2.1 88.9 1.0
PB A:ATP803 3.1 101.3 1.0
PB A:DTP801 3.2 95.9 1.0
PA A:ATP803 3.3 98.9 1.0
PG A:DTP801 3.3 114.8 1.0
PG A:ATP803 3.3 120.6 1.0
PA A:DTP801 3.3 86.2 1.0
O3A A:ATP803 3.4 85.9 1.0
O3B A:ATP803 3.5 93.5 1.0
O3A A:DTP801 3.5 70.2 1.0
O3B A:DTP801 3.5 66.9 1.0
O5' A:DTP801 4.0 83.7 1.0
O1G A:ATP803 4.0 123.5 1.0
O2G A:DTP801 4.1 121.7 1.0
O5' A:ATP803 4.2 112.7 1.0
C5' A:ATP803 4.3 102.8 1.0
O2A A:ATP803 4.4 108.1 1.0
O2B A:ATP803 4.4 101.3 1.0
O1A A:DTP801 4.5 87.7 1.0
O3G A:ATP803 4.5 121.1 1.0
O1B A:DTP801 4.5 93.4 1.0
O3G A:DTP801 4.5 114.3 1.0
NZ A:LYS91 4.6 108.5 1.0
C8 A:DTP801 4.6 115.8 1.0
NZ A:LYS9 4.7 119.7 1.0
CE A:LYS91 4.9 126.0 1.0

Magnesium binding site 2 out of 8 in 8vhq

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Magnesium binding site 2 out of 8 in the Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Datp and Atp


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 W28A Variant Bound to Datp and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg805

b:55.0
occ:1.00
 O1A A:DTP804 2.1 79.7 1.0
O1G A:DTP804 2.1 83.6 1.0
O1B A:DTP804 2.1 79.0 1.0
PB A:DTP804 3.0 74.4 1.0
PA A:DTP804 3.1 78.7 1.0
PG A:DTP804 3.1 79.7 1.0
O3A A:DTP804 3.4 55.0 1.0
O3B A:DTP804 3.4 55.0 1.0
O3G A:DTP804 3.6 73.5 1.0
O5' A:DTP804 3.7 68.2 1.0
O A:ASP232 4.2 98.1 1.0
NH2 A:ARG262 4.3 91.4 1.0
O2B A:DTP804 4.4 66.9 1.0
O2A A:DTP804 4.4 70.8 1.0
O2G A:DTP804 4.5 76.3 1.0
CB A:SER233 4.6 97.2 1.0
C5' A:DTP804 4.9 63.2 1.0

Magnesium binding site 3 out of 8 in 8vhq

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Magnesium binding site 3 out of 8 in the Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Datp and Atp


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 W28A Variant Bound to Datp and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:94.3
occ:1.00
 O1G B:DTP801 2.1 95.0 1.0
O1A B:ATP803 2.1 93.9 1.0
O2G B:ATP803 2.1 110.5 1.0
O2A B:DTP801 2.1 99.7 1.0
O2B B:DTP801 2.1 85.6 1.0
O1B B:ATP803 2.1 87.3 1.0
PB B:ATP803 3.1 87.9 1.0
PB B:DTP801 3.2 89.4 1.0
PA B:ATP803 3.2 97.5 1.0
PG B:DTP801 3.3 103.1 1.0
PA B:DTP801 3.3 109.4 1.0
PG B:ATP803 3.4 110.4 1.0
O3A B:ATP803 3.4 76.0 1.0
O3B B:DTP801 3.5 83.4 1.0
O3B B:ATP803 3.5 74.2 1.0
O3A B:DTP801 3.5 72.7 1.0
O5' B:DTP801 3.9 80.9 1.0
O5' B:ATP803 4.1 108.6 1.0
O2G B:DTP801 4.2 100.5 1.0
O1G B:ATP803 4.2 106.7 1.0
C5' B:ATP803 4.2 107.8 1.0
NZ B:LYS9 4.2 116.8 1.0
O3G B:DTP801 4.4 111.6 1.0
O2A B:ATP803 4.4 97.0 1.0
O3G B:ATP803 4.4 107.7 1.0
O2B B:ATP803 4.5 83.5 1.0
O1B B:DTP801 4.5 89.3 1.0
O1A B:DTP801 4.5 113.6 1.0
C8 B:DTP801 4.5 85.8 1.0
CE B:LYS91 4.8 122.1 1.0
NZ B:LYS91 4.8 109.8 1.0

Magnesium binding site 4 out of 8 in 8vhq

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Magnesium binding site 4 out of 8 in the Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Datp and Atp


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 W28A Variant Bound to Datp and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg805

b:55.0
occ:1.00
 O1A B:DTP804 2.1 85.6 1.0
O1G B:DTP804 2.1 69.2 1.0
O1B B:DTP804 2.1 81.3 1.0
PB B:DTP804 3.1 68.5 1.0
PA B:DTP804 3.2 71.4 1.0
PG B:DTP804 3.2 73.4 1.0
O3A B:DTP804 3.4 55.0 1.0
O3B B:DTP804 3.4 55.0 1.0
O3G B:DTP804 3.8 66.7 1.0
O5' B:DTP804 3.8 68.8 1.0
O B:ASP232 4.3 99.1 1.0
NH2 B:ARG262 4.4 81.3 1.0
O2B B:DTP804 4.5 67.8 1.0
O2A B:DTP804 4.5 71.4 1.0
O2G B:DTP804 4.5 79.7 1.0
CB B:SER233 4.6 77.6 1.0
C5' B:DTP804 5.0 63.6 1.0

Magnesium binding site 5 out of 8 in 8vhq

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Magnesium binding site 5 out of 8 in the Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Datp and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Datp and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:88.2
occ:1.00
 O1A C:ATP803 2.1 122.8 1.0
O1G C:DTP801 2.1 149.6 1.0
O2B C:DTP801 2.1 132.9 1.0
O2A C:DTP801 2.1 160.9 1.0
O2G C:ATP803 2.1 122.0 1.0
O1B C:ATP803 2.1 126.4 1.0
PB C:ATP803 3.1 122.5 1.0
PB C:DTP801 3.2 131.2 1.0
PA C:ATP803 3.3 133.2 1.0
PA C:DTP801 3.3 154.2 1.0
PG C:DTP801 3.3 147.9 1.0
PG C:ATP803 3.3 126.2 1.0
O3A C:ATP803 3.4 116.0 1.0
O3B C:ATP803 3.5 155.2 1.0
O3A C:DTP801 3.5 98.1 1.0
O3B C:DTP801 3.5 93.5 1.0
O5' C:DTP801 3.9 86.7 1.0
O1G C:ATP803 4.2 126.9 1.0
O5' C:ATP803 4.3 179.7 1.0
O3G C:DTP801 4.3 147.4 1.0
O2A C:ATP803 4.4 145.4 1.0
O2G C:DTP801 4.4 147.7 1.0
C8 C:DTP801 4.4 110.2 1.0
NZ C:LYS9 4.4 150.9 1.0
O3G C:ATP803 4.4 129.1 1.0
C5' C:ATP803 4.4 180.2 1.0
O1B C:DTP801 4.5 130.2 1.0
O2B C:ATP803 4.5 117.3 1.0
O1A C:DTP801 4.5 149.4 1.0
NZ C:LYS91 4.8 145.9 1.0
N7 C:DTP801 4.9 113.3 1.0

Magnesium binding site 6 out of 8 in 8vhq

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Magnesium binding site 6 out of 8 in the Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Datp and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Datp and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg805

b:55.0
occ:1.00
 O1A C:DTP804 2.1 105.2 1.0
O1G C:DTP804 2.1 107.3 1.0
O1B C:DTP804 2.1 106.8 1.0
PB C:DTP804 3.1 94.2 1.0
PA C:DTP804 3.1 103.4 1.0
PG C:DTP804 3.3 115.8 1.0
O3A C:DTP804 3.4 62.0 1.0
O3B C:DTP804 3.5 63.0 1.0
O5' C:DTP804 3.7 103.7 1.0
O C:ASP232 4.0 110.7 1.0
NH2 C:ARG262 4.3 119.9 1.0
O2G C:DTP804 4.3 114.5 1.0
O3G C:DTP804 4.3 118.8 1.0
CB C:SER233 4.4 112.3 1.0
O2A C:DTP804 4.4 96.0 1.0
O2B C:DTP804 4.5 91.7 1.0
C5' C:DTP804 4.9 96.6 1.0
CA C:SER233 5.0 109.9 1.0

Magnesium binding site 7 out of 8 in 8vhq

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Magnesium binding site 7 out of 8 in the Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Datp and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Datp and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:189.4
occ:1.00
 O2G D:ATP803 2.1 168.4 1.0
O1G D:DTP801 2.1 146.7 1.0
O1A D:ATP803 2.1 125.1 1.0
O2A D:DTP801 2.1 163.2 1.0
O2B D:DTP801 2.1 166.3 1.0
O1B D:ATP803 2.1 156.5 1.0
PB D:ATP803 3.1 154.2 1.0
PB D:DTP801 3.2 156.0 1.0
PA D:ATP803 3.2 132.8 1.0
PA D:DTP801 3.3 159.2 1.0
PG D:ATP803 3.3 170.4 1.0
PG D:DTP801 3.3 145.3 1.0
O3A D:ATP803 3.4 157.9 1.0
O3B D:ATP803 3.5 104.7 1.0
O3A D:DTP801 3.5 85.7 1.0
O3B D:DTP801 3.5 120.7 1.0
O5' D:DTP801 3.9 114.6 1.0
O1G D:ATP803 4.1 169.6 1.0
O5' D:ATP803 4.1 140.6 1.0
C5' D:ATP803 4.2 138.5 1.0
NZ D:LYS9 4.3 153.8 1.0
O3G D:DTP801 4.3 153.5 1.0
O2G D:DTP801 4.4 144.4 1.0
O2A D:ATP803 4.4 139.3 1.0
O3G D:ATP803 4.5 171.9 1.0
O2B D:ATP803 4.5 152.3 1.0
O1B D:DTP801 4.5 152.1 1.0
O1A D:DTP801 4.5 155.3 1.0
NZ D:LYS91 4.6 156.9 1.0
CE D:LYS91 4.8 154.4 1.0
C8 D:DTP801 4.8 156.2 1.0

Magnesium binding site 8 out of 8 in 8vhq

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Magnesium binding site 8 out of 8 in the Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Datp and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Datp and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg805

b:80.9
occ:1.00
 O1G D:DTP804 2.1 89.7 1.0
O1A D:DTP804 2.1 132.5 1.0
O1B D:DTP804 2.1 103.6 1.0
PB D:DTP804 3.1 102.5 1.0
PA D:DTP804 3.2 127.0 1.0
PG D:DTP804 3.2 101.4 1.0
O3A D:DTP804 3.4 56.8 1.0
O3B D:DTP804 3.4 119.5 1.0
O3G D:DTP804 3.8 102.3 1.0
O5' D:DTP804 3.8 83.7 1.0
NH2 D:ARG262 4.4 123.4 1.0
O D:ASP232 4.4 121.1 1.0
O2B D:DTP804 4.4 101.0 1.0
O2A D:DTP804 4.5 123.7 1.0
CB D:SER233 4.5 119.9 1.0
O2G D:DTP804 4.5 100.6 1.0
C5' D:DTP804 5.0 86.9 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 22:05:21 2024

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