Magnesium in PDB 8vhp: Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Cdp and Two Molecules of Atp

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

All present enzymatic activity of Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Cdp and Two Molecules of 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 Cdp and Two Molecules of Atp, PDB code: 8vhp 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) 49.74 / 2.61
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 288.719, 316.613, 158.94, 90, 90, 90
R / Rfree (%) 18.9 / 21

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

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 Cdp and Two Molecules of Atp (pdb code 8vhp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Cdp and Two Molecules of Atp, PDB code: 8vhp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in 8vhp

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Magnesium binding site 1 out of 16 in the Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Cdp and Two Molecules of 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 Cdp and Two Molecules of Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg805

b:55.8
occ:1.00
 O2B A:ATP806 2.1 51.6 1.0
O3G A:ATP804 2.1 54.4 1.0
O1A A:ATP806 2.1 50.6 1.0
O1B A:ATP804 2.1 53.4 1.0
O3G A:ATP806 2.1 51.5 1.0
O1A A:ATP804 2.1 52.6 1.0
PB A:ATP804 2.9 53.9 1.0
O3B A:ATP804 3.0 54.3 1.0
PG A:ATP804 3.1 53.0 1.0
PA A:ATP804 3.2 53.2 1.0
PB A:ATP806 3.2 50.3 1.0
PA A:ATP806 3.3 49.3 1.0
O3A A:ATP804 3.4 54.8 1.0
PG A:ATP806 3.4 55.6 1.0
O3A A:ATP806 3.6 50.4 1.0
O3B A:ATP806 3.7 51.1 1.0
NZ A:LYS91 3.9 58.2 1.0
O2G A:ATP804 4.0 53.8 1.0
O5' A:ATP804 4.1 53.4 1.0
O1G A:ATP806 4.2 55.5 1.0
O1G A:ATP804 4.3 54.3 1.0
O5' A:ATP806 4.3 50.0 1.0
O2B A:ATP804 4.3 55.4 1.0
NZ A:LYS9 4.3 53.8 1.0
CE A:LYS91 4.4 50.0 1.0
O2A A:ATP806 4.4 49.8 1.0
O2A A:ATP804 4.4 54.5 1.0
C5' A:ATP806 4.4 50.3 1.0
O2G A:ATP806 4.5 50.7 1.0
O1B A:ATP806 4.5 51.8 1.0
C8 A:ATP804 4.5 53.8 1.0

Magnesium binding site 2 out of 16 in 8vhp

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Magnesium binding site 2 out of 16 in the Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Cdp and Two Molecules of 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 Cdp and Two Molecules of Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg808

b:51.3
occ:1.00
 O A:HOH978 2.1 64.1 1.0
O A:HOH938 2.1 49.6 1.0
O2A A:ATP807 2.1 46.0 1.0
O2B A:ATP807 2.1 47.9 1.0
O2G A:ATP807 2.1 46.6 1.0
O A:HOH936 2.1 45.0 1.0
PB A:ATP807 3.1 48.4 1.0
PG A:ATP807 3.2 46.5 1.0
O3B A:ATP807 3.3 48.0 1.0
PA A:ATP807 3.4 45.1 1.0
O3A A:ATP807 3.6 48.4 1.0
O3G A:ATP807 3.6 58.5 1.0
C5' A:ATP807 3.9 45.1 1.0
O5' A:ATP807 4.1 45.5 1.0
NH2 A:ARG262 4.1 47.4 1.0
O A:ASP232 4.2 46.3 1.0
O1B A:ATP807 4.4 51.4 1.0
O1A A:ATP807 4.4 45.6 1.0
O1G A:ATP807 4.4 46.8 1.0
CB A:SER233 4.6 46.4 1.0

Magnesium binding site 3 out of 16 in 8vhp

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Magnesium binding site 3 out of 16 in the Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Cdp and Two Molecules of 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 Cdp and Two Molecules of Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg805

b:62.5
occ:1.00
 O1A B:ATP806 2.1 58.0 1.0
O3G B:ATP804 2.1 58.9 1.0
O1A B:ATP804 2.1 64.0 1.0
O1B B:ATP804 2.1 59.3 1.0
O2B B:ATP806 2.1 58.5 1.0
O3G B:ATP806 2.1 59.8 1.0
PB B:ATP804 2.9 59.7 1.0
O3B B:ATP804 2.9 62.1 1.0
PG B:ATP804 3.0 59.1 1.0
PA B:ATP804 3.2 58.5 1.0
PB B:ATP806 3.3 57.8 1.0
PA B:ATP806 3.4 57.3 1.0
O3A B:ATP804 3.4 59.6 1.0
PG B:ATP806 3.5 57.5 1.0
O3A B:ATP806 3.7 58.0 1.0
O2G B:ATP804 3.7 63.2 1.0
O3B B:ATP806 3.7 58.1 1.0
NZ B:LYS91 3.8 58.4 1.0
O5' B:ATP804 4.1 58.0 1.0
CE B:LYS91 4.1 56.4 1.0
O2B B:ATP804 4.3 61.4 1.0
NZ B:LYS9 4.3 66.0 1.0
O1G B:ATP804 4.3 60.5 1.0
O5' B:ATP806 4.3 71.0 1.0
O2G B:ATP806 4.3 60.4 1.0
O2A B:ATP804 4.4 59.7 1.0
O1G B:ATP806 4.4 58.7 1.0
O2A B:ATP806 4.4 57.9 1.0
O1B B:ATP806 4.5 58.2 1.0
C5' B:ATP806 4.6 57.7 1.0
O B:HOH984 4.7 59.2 1.0
C8 B:ATP804 4.9 58.9 1.0

Magnesium binding site 4 out of 16 in 8vhp

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Magnesium binding site 4 out of 16 in the Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Cdp and Two Molecules of 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 Cdp and Two Molecules of Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg808

b:42.3
occ:1.00
 O B:HOH1000 2.1 44.5 1.0
O B:HOH942 2.1 42.4 1.0
O B:HOH921 2.1 43.5 1.0
O2A B:ATP807 2.1 42.3 1.0
O2G B:ATP807 2.1 47.8 1.0
O2B B:ATP807 2.1 42.4 1.0
PB B:ATP807 3.2 45.5 1.0
PG B:ATP807 3.3 43.2 1.0
PA B:ATP807 3.4 42.0 1.0
O3B B:ATP807 3.5 42.7 1.0
O3A B:ATP807 3.7 42.9 1.0
O3G B:ATP807 3.7 51.1 1.0
C5' B:ATP807 3.9 48.3 1.0
O B:ASP232 4.0 47.7 1.0
NH2 B:ARG262 4.0 48.2 1.0
O5' B:ATP807 4.2 42.7 1.0
CB B:SER233 4.5 48.1 1.0
O1A B:ATP807 4.5 43.8 1.0
O1B B:ATP807 4.5 49.6 1.0
O1G B:ATP807 4.5 42.6 1.0
CA B:SER233 5.0 47.6 1.0

Magnesium binding site 5 out of 16 in 8vhp

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Magnesium binding site 5 out of 16 in the Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Cdp and Two Molecules of 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 Cdp and Two Molecules of Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg805

b:58.4
occ:1.00
 O3G C:ATP804 2.1 58.7 1.0
O1A C:ATP806 2.1 57.9 1.0
O1B C:ATP804 2.1 59.3 1.0
O2B C:ATP806 2.1 58.5 1.0
O3G C:ATP806 2.1 58.9 1.0
O1A C:ATP804 2.1 58.7 1.0
PB C:ATP804 3.0 59.3 1.0
O3B C:ATP804 3.2 61.2 1.0
PG C:ATP804 3.2 58.5 1.0
PB C:ATP806 3.2 58.0 1.0
PA C:ATP804 3.2 58.2 1.0
PA C:ATP806 3.3 56.9 1.0
PG C:ATP806 3.3 58.7 1.0
O3A C:ATP804 3.4 59.4 1.0
O3A C:ATP806 3.6 57.7 1.0
O3B C:ATP806 3.6 59.0 1.0
O1G C:ATP806 3.9 60.1 1.0
O2G C:ATP804 3.9 59.7 1.0
O5' C:ATP804 3.9 58.3 1.0
O C:HOH967 4.0 58.7 1.0
NZ C:LYS9 4.1 67.1 1.0
O5' C:ATP806 4.2 56.9 1.0
NZ C:LYS91 4.3 63.4 1.0
O2B C:ATP804 4.4 60.5 1.0
O1G C:ATP804 4.4 59.4 1.0
C5' C:ATP806 4.4 57.0 1.0
O2A C:ATP806 4.4 57.4 1.0
O2A C:ATP804 4.5 58.6 1.0
C8 C:ATP804 4.5 59.6 1.0
O1B C:ATP806 4.5 58.2 1.0
O2G C:ATP806 4.5 69.4 1.0
CE C:LYS91 4.7 58.5 1.0

Magnesium binding site 6 out of 16 in 8vhp

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Magnesium binding site 6 out of 16 in the Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Cdp and Two Molecules of 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 Cdp and Two Molecules of Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg808

b:45.2
occ:1.00
 O C:HOH1013 2.1 44.9 1.0
O C:HOH1000 2.1 44.4 1.0
O2A C:ATP807 2.1 44.7 1.0
O C:HOH924 2.1 48.9 1.0
O2G C:ATP807 2.1 46.7 1.0
O2B C:ATP807 2.1 45.7 1.0
PB C:ATP807 3.2 46.1 1.0
PG C:ATP807 3.2 45.5 1.0
PA C:ATP807 3.4 44.9 1.0
O3B C:ATP807 3.5 46.7 1.0
O3A C:ATP807 3.6 50.0 1.0
O3G C:ATP807 3.6 46.2 1.0
C5' C:ATP807 3.9 46.3 1.0
NH2 C:ARG262 4.0 49.6 1.0
O C:ASP232 4.0 48.5 1.0
O5' C:ATP807 4.1 45.6 1.0
O C:HOH1043 4.2 44.8 1.0
O1A C:ATP807 4.4 45.7 1.0
O1B C:ATP807 4.5 48.3 1.0
CB C:SER233 4.5 48.4 1.0
O1G C:ATP807 4.5 46.8 1.0
CA C:SER233 5.0 48.1 1.0

Magnesium binding site 7 out of 16 in 8vhp

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Magnesium binding site 7 out of 16 in the Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Cdp and Two Molecules of 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 Cdp and Two Molecules of Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg805

b:62.9
occ:1.00
 O3G D:ATP804 2.1 63.5 1.0
O2B D:ATP806 2.1 63.1 1.0
O1B D:ATP804 2.1 64.5 1.0
O1A D:ATP806 2.1 62.0 1.0
O3G D:ATP806 2.1 71.0 1.0
O1A D:ATP804 2.1 62.4 1.0
PB D:ATP804 2.9 64.4 1.0
O3B D:ATP804 2.9 72.8 1.0
PG D:ATP804 3.1 63.5 1.0
PA D:ATP804 3.2 62.5 1.0
PB D:ATP806 3.3 62.7 1.0
O3A D:ATP804 3.3 64.8 1.0
PA D:ATP806 3.3 60.4 1.0
PG D:ATP806 3.4 62.7 1.0
O3A D:ATP806 3.6 62.3 1.0
O3B D:ATP806 3.7 63.8 1.0
O2G D:ATP804 3.9 68.4 1.0
O5' D:ATP806 4.1 65.0 1.0
O5' D:ATP804 4.1 63.0 1.0
O1G D:ATP806 4.1 65.6 1.0
NZ D:LYS91 4.2 61.8 1.0
C5' D:ATP806 4.2 60.5 1.0
O1G D:ATP804 4.2 63.8 1.0
O2B D:ATP804 4.3 65.7 1.0
O2A D:ATP804 4.4 62.7 1.0
NZ D:LYS9 4.4 67.5 1.0
CE D:LYS91 4.4 56.9 1.0
O1B D:ATP806 4.5 64.1 1.0
O2A D:ATP806 4.5 60.8 1.0
O2G D:ATP806 4.5 64.0 1.0
C8 D:ATP804 4.6 65.4 1.0

Magnesium binding site 8 out of 16 in 8vhp

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Magnesium binding site 8 out of 16 in the Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Cdp and Two Molecules of 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 Cdp and Two Molecules of Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg808

b:47.0
occ:1.00
 O D:HOH918 2.1 45.3 1.0
O D:HOH927 2.1 45.6 1.0
O D:HOH981 2.1 51.0 1.0
O2A D:ATP807 2.1 45.7 1.0
O2G D:ATP807 2.1 45.4 1.0
O2B D:ATP807 2.1 46.4 1.0
PB D:ATP807 3.2 47.2 1.0
PG D:ATP807 3.3 45.5 1.0
PA D:ATP807 3.4 45.1 1.0
O3B D:ATP807 3.5 47.1 1.0
O3A D:ATP807 3.6 47.5 1.0
C5' D:ATP807 3.9 45.6 1.0
O3G D:ATP807 3.9 48.2 1.0
O D:ASP232 4.0 45.3 1.0
NH2 D:ARG262 4.0 46.1 1.0
O5' D:ATP807 4.1 45.9 1.0
O1A D:ATP807 4.4 45.6 1.0
O1B D:ATP807 4.5 49.9 1.0
O1G D:ATP807 4.5 46.2 1.0
CB D:SER233 4.6 45.8 1.0

Magnesium binding site 9 out of 16 in 8vhp

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Magnesium binding site 9 out of 16 in the Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Cdp and Two Molecules of Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Cdp and Two Molecules of Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg805

b:58.1
occ:1.00
 O3G E:ATP804 2.1 58.6 1.0
O1B E:ATP804 2.1 59.0 1.0
O2B E:ATP806 2.1 57.8 1.0
O3G E:ATP806 2.1 57.8 1.0
O1A E:ATP806 2.1 57.7 1.0
O1A E:ATP804 2.1 58.2 1.0
PB E:ATP804 2.8 59.4 1.0
O3B E:ATP804 2.9 60.5 1.0
PG E:ATP804 3.0 58.2 1.0
PA E:ATP804 3.2 58.0 1.0
O3A E:ATP804 3.2 59.1 1.0
PB E:ATP806 3.3 57.0 1.0
PA E:ATP806 3.4 56.9 1.0
PG E:ATP806 3.5 57.2 1.0
O3A E:ATP806 3.7 57.2 1.0
O3B E:ATP806 3.7 57.8 1.0
O2G E:ATP804 3.7 60.6 1.0
O5' E:ATP804 4.1 57.8 1.0
O E:HOH996 4.2 58.9 1.0
O2B E:ATP804 4.2 61.1 1.0
CE E:LYS91 4.3 64.0 1.0
NZ E:LYS91 4.3 64.0 1.0
O1G E:ATP804 4.3 59.5 1.0
NZ E:LYS9 4.3 65.5 1.0
O2A E:ATP804 4.3 59.5 1.0
O5' E:ATP806 4.3 58.6 1.0
O2G E:ATP806 4.4 57.0 1.0
O1G E:ATP806 4.4 58.8 1.0
O2A E:ATP806 4.5 57.4 1.0
C5' E:ATP806 4.5 57.4 1.0
O1B E:ATP806 4.5 57.9 1.0
C8 E:ATP804 4.7 59.3 1.0
CE E:LYS9 5.0 65.7 1.0

Magnesium binding site 10 out of 16 in 8vhp

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Magnesium binding site 10 out of 16 in the Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Cdp and Two Molecules of Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of E. Coli Class Ia Ribonucleotide Reductase Alpha Subunit W28A Variant Bound to Cdp and Two Molecules of Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg808

b:55.5
occ:1.00
 O E:HOH977 2.1 51.1 1.0
O2A E:ATP807 2.1 51.6 1.0
O E:HOH926 2.1 51.5 1.0
O2G E:ATP807 2.1 56.5 1.0
O E:HOH988 2.1 56.6 1.0
O2B E:ATP807 2.1 60.7 1.0
PB E:ATP807 3.1 52.1 1.0
PG E:ATP807 3.2 54.0 1.0
O3B E:ATP807 3.3 52.2 1.0
PA E:ATP807 3.3 52.9 1.0
O3A E:ATP807 3.5 62.3 1.0
O3G E:ATP807 3.6 55.3 1.0
C5' E:ATP807 3.9 57.4 1.0
O5' E:ATP807 4.1 52.3 1.0
NH2 E:ARG262 4.2 59.8 1.0
O E:ASP232 4.3 56.8 1.0
O1B E:ATP807 4.4 53.9 1.0
O1A E:ATP807 4.4 52.0 1.0
O1G E:ATP807 4.5 52.3 1.0
CB E:SER233 4.7 55.6 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 22:05:11 2024

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