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Magnesium in PDB 6aui: Human Ribonucleotide Reductase Large Subunit (Alpha) with Datp and Cdp

Enzymatic activity of Human Ribonucleotide Reductase Large Subunit (Alpha) with Datp and Cdp

All present enzymatic activity of Human Ribonucleotide Reductase Large Subunit (Alpha) with Datp and Cdp:
1.17.4.1;

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Human Ribonucleotide Reductase Large Subunit (Alpha) with Datp and Cdp (pdb code 6aui). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Human Ribonucleotide Reductase Large Subunit (Alpha) with Datp and Cdp, PDB code: 6aui:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 6aui

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Magnesium binding site 1 out of 12 in the Human Ribonucleotide Reductase Large Subunit (Alpha) with Datp and Cdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Ribonucleotide Reductase Large Subunit (Alpha) with Datp and Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:95.5
occ:1.00
 O2A A:DTP801 2.1 91.5 1.0
O3G A:DTP801 2.1 91.5 1.0
O A:HOH902 2.1 93.9 1.0
O A:HOH906 2.1 89.8 1.0
O A:HOH905 2.1 90.2 1.0
O1B A:DTP801 2.1 91.5 1.0
PG A:DTP801 3.1 91.5 1.0
PB A:DTP801 3.2 91.5 1.0
O3B A:DTP801 3.3 91.5 1.0
PA A:DTP801 3.5 91.5 1.0
O2G A:DTP801 3.7 91.5 1.0
O3A A:DTP801 3.8 91.5 1.0
NZ A:LYS17 4.3 0.5 1.0
O1A A:DTP801 4.3 91.5 1.0
O1G A:DTP801 4.5 91.5 1.0
O2B A:DTP801 4.5 91.5 1.0
O5' A:DTP801 4.5 91.5 1.0
NZ A:LYS5 4.6 0.9 1.0
CE A:LYS5 4.8 0.9 1.0
CE A:LYS17 4.9 0.5 1.0

Magnesium binding site 2 out of 12 in 6aui

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Magnesium binding site 2 out of 12 in the Human Ribonucleotide Reductase Large Subunit (Alpha) with Datp and Cdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Ribonucleotide Reductase Large Subunit (Alpha) with Datp and Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg804

b:70.9
occ:1.00
 O1B A:DTP803 2.0 73.5 1.0
O1A A:DTP803 2.1 73.5 1.0
O A:HOH901 2.1 72.6 1.0
O A:HOH904 2.1 75.3 1.0
O2G A:DTP803 2.1 73.5 1.0
O A:HOH903 2.1 71.4 1.0
PG A:DTP803 3.0 73.5 1.0
O3G A:DTP803 3.0 73.5 1.0
PB A:DTP803 3.0 73.5 1.0
PA A:DTP803 3.1 73.5 1.0
O3A A:DTP803 3.3 73.5 1.0
O3B A:DTP803 3.5 73.5 1.0
O2A A:DTP803 3.8 73.5 1.0
O1G A:DTP803 4.3 73.5 1.0
O2B A:DTP803 4.3 73.5 1.0
O5' A:DTP803 4.4 73.5 1.0
NH2 A:ARG256 4.5 90.3 1.0
CB A:SER227 4.5 94.0 1.0
C5' A:DTP803 4.6 73.5 1.0
O A:ASP226 4.6 97.5 1.0

Magnesium binding site 3 out of 12 in 6aui

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Magnesium binding site 3 out of 12 in the Human Ribonucleotide Reductase Large Subunit (Alpha) with Datp and Cdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Ribonucleotide Reductase Large Subunit (Alpha) with Datp and Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:0.7
occ:1.00
 O1A B:DTP801 2.1 95.9 1.0
O2G B:DTP801 2.1 95.9 1.0
O2B B:DTP801 2.1 95.9 1.0
O B:HOH905 2.1 93.9 1.0
O B:HOH902 2.1 0.1 1.0
O B:HOH904 2.1 94.5 1.0
PG B:DTP801 3.1 95.9 1.0
PB B:DTP801 3.2 95.9 1.0
O3B B:DTP801 3.3 95.9 1.0
PA B:DTP801 3.5 95.9 1.0
O1G B:DTP801 3.6 95.9 1.0
O3A B:DTP801 3.8 95.9 1.0
NZ B:LYS17 4.0 0.9 1.0
O2A B:DTP801 4.3 95.9 1.0
NZ B:LYS5 4.4 0.1 1.0
O1B B:DTP801 4.4 95.9 1.0
O5' B:DTP801 4.5 95.9 1.0
CE B:LYS5 4.5 0.1 1.0
O3G B:DTP801 4.5 95.9 1.0
CE B:LYS17 4.7 0.9 1.0
CD B:LYS5 4.8 0.1 1.0
C8 B:DTP801 4.9 95.9 1.0

Magnesium binding site 4 out of 12 in 6aui

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Magnesium binding site 4 out of 12 in the Human Ribonucleotide Reductase Large Subunit (Alpha) with Datp and Cdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Ribonucleotide Reductase Large Subunit (Alpha) with Datp and Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg804

b:79.0
occ:1.00
 O2B B:DTP803 2.0 80.2 1.0
O B:HOH901 2.1 82.0 1.0
O B:HOH903 2.1 82.2 1.0
O2A B:DTP803 2.1 80.2 1.0
O2G B:DTP803 2.1 80.2 1.0
O B:HOH906 2.1 79.0 1.0
PB B:DTP803 3.0 80.2 1.0
PG B:DTP803 3.0 80.2 1.0
O1G B:DTP803 3.1 80.2 1.0
PA B:DTP803 3.2 80.2 1.0
O3A B:DTP803 3.3 80.2 1.0
O3B B:DTP803 3.5 80.2 1.0
O1A B:DTP803 3.9 80.2 1.0
O1B B:DTP803 4.3 80.2 1.0
NH2 B:ARG256 4.3 84.2 1.0
O3G B:DTP803 4.4 80.2 1.0
O5' B:DTP803 4.5 80.2 1.0
C5' B:DTP803 4.6 80.2 1.0
O B:ASP226 4.6 93.4 1.0
CB B:SER227 4.7 90.5 1.0

Magnesium binding site 5 out of 12 in 6aui

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Magnesium binding site 5 out of 12 in the Human Ribonucleotide Reductase Large Subunit (Alpha) with Datp and Cdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human Ribonucleotide Reductase Large Subunit (Alpha) with Datp and Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:96.8
occ:1.00
 O3G C:DTP801 2.1 91.9 1.0
O2A C:DTP801 2.1 91.9 1.0
O C:HOH902 2.1 97.5 1.0
O C:HOH905 2.1 88.3 1.0
O C:HOH906 2.1 87.1 1.0
O1B C:DTP801 2.1 91.9 1.0
PG C:DTP801 3.1 91.9 1.0
PB C:DTP801 3.2 91.9 1.0
O3B C:DTP801 3.4 91.9 1.0
PA C:DTP801 3.5 91.9 1.0
O2G C:DTP801 3.6 91.9 1.0
O3A C:DTP801 3.8 91.9 1.0
NZ C:LYS17 4.0 0.3 1.0
O1A C:DTP801 4.3 91.9 1.0
O1G C:DTP801 4.4 91.9 1.0
O5' C:DTP801 4.5 91.9 1.0
NZ C:LYS5 4.5 0.6 1.0
O2B C:DTP801 4.5 91.9 1.0
CE C:LYS17 4.6 0.3 1.0
CE C:LYS5 4.6 0.6 1.0
C8 C:DTP801 5.0 91.9 1.0
CD C:LYS5 5.0 0.6 1.0

Magnesium binding site 6 out of 12 in 6aui

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Magnesium binding site 6 out of 12 in the Human Ribonucleotide Reductase Large Subunit (Alpha) with Datp and Cdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human Ribonucleotide Reductase Large Subunit (Alpha) with Datp and Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg804

b:68.0
occ:1.00
 O1B C:DTP803 2.0 69.1 1.0
O1A C:DTP803 2.1 69.1 1.0
O2G C:DTP803 2.1 69.1 1.0
O C:HOH901 2.1 68.9 1.0
O C:HOH903 2.1 71.1 1.0
O C:HOH904 2.1 66.4 1.0
PG C:DTP803 3.0 69.1 1.0
O3G C:DTP803 3.0 69.1 1.0
PB C:DTP803 3.0 69.1 1.0
PA C:DTP803 3.2 69.1 1.0
O3A C:DTP803 3.3 69.1 1.0
O3B C:DTP803 3.5 69.1 1.0
O2A C:DTP803 3.9 69.1 1.0
O1G C:DTP803 4.3 69.1 1.0
O2B C:DTP803 4.4 69.1 1.0
O5' C:DTP803 4.4 69.1 1.0
NH2 C:ARG256 4.5 93.2 1.0
CB C:SER227 4.5 94.8 1.0
C5' C:DTP803 4.6 69.1 1.0
O C:ASP226 4.6 99.8 1.0

Magnesium binding site 7 out of 12 in 6aui

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Magnesium binding site 7 out of 12 in the Human Ribonucleotide Reductase Large Subunit (Alpha) with Datp and Cdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Human Ribonucleotide Reductase Large Subunit (Alpha) with Datp and Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:86.3
occ:1.00
 O1A D:DTP801 2.1 81.0 1.0
O2G D:DTP801 2.1 81.0 1.0
O2B D:DTP801 2.1 81.0 1.0
O D:HOH902 2.1 85.0 1.0
O D:HOH906 2.1 77.2 1.0
O D:HOH905 2.1 77.8 1.0
PG D:DTP801 3.1 81.0 1.0
PB D:DTP801 3.2 81.0 1.0
O3B D:DTP801 3.3 81.0 1.0
PA D:DTP801 3.5 81.0 1.0
O1G D:DTP801 3.6 81.0 1.0
O3A D:DTP801 3.8 81.0 1.0
NZ D:LYS17 3.9 0.2 1.0
O2A D:DTP801 4.2 81.0 1.0
NZ D:LYS5 4.3 0.8 1.0
O1B D:DTP801 4.4 81.0 1.0
CE D:LYS5 4.4 0.8 1.0
O5' D:DTP801 4.4 81.0 1.0
O3G D:DTP801 4.5 81.0 1.0
CE D:LYS17 4.6 0.2 1.0
CD D:LYS5 4.8 0.8 1.0
C8 D:DTP801 4.9 81.0 1.0

Magnesium binding site 8 out of 12 in 6aui

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Magnesium binding site 8 out of 12 in the Human Ribonucleotide Reductase Large Subunit (Alpha) with Datp and Cdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Human Ribonucleotide Reductase Large Subunit (Alpha) with Datp and Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg804

b:61.4
occ:1.00
 O2B D:DTP803 2.0 63.1 1.0
O D:HOH901 2.1 63.1 1.0
O D:HOH903 2.1 65.9 1.0
O2A D:DTP803 2.1 63.1 1.0
O2G D:DTP803 2.1 63.1 1.0
O D:HOH904 2.1 60.9 1.0
PB D:DTP803 2.9 63.1 1.0
PG D:DTP803 3.0 63.1 1.0
PA D:DTP803 3.1 63.1 1.0
O3A D:DTP803 3.2 63.1 1.0
O1G D:DTP803 3.2 63.1 1.0
O3B D:DTP803 3.5 63.1 1.0
O1A D:DTP803 3.8 63.1 1.0
O1B D:DTP803 4.3 63.1 1.0
NH2 D:ARG256 4.3 0.9 1.0
O3G D:DTP803 4.4 63.1 1.0
O5' D:DTP803 4.4 63.1 1.0
C5' D:DTP803 4.6 63.1 1.0
O D:ASP226 4.6 0.5 1.0
CB D:SER227 4.7 0.4 1.0

Magnesium binding site 9 out of 12 in 6aui

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Magnesium binding site 9 out of 12 in the Human Ribonucleotide Reductase Large Subunit (Alpha) with Datp and Cdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Human Ribonucleotide Reductase Large Subunit (Alpha) with Datp and Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg802

b:93.7
occ:1.00
 O2A E:DTP801 2.1 90.2 1.0
O3G E:DTP801 2.1 90.2 1.0
O E:HOH902 2.1 92.6 1.0
O E:HOH903 2.1 89.6 1.0
O1B E:DTP801 2.1 90.2 1.0
O E:HOH906 2.1 89.2 1.0
PG E:DTP801 3.1 90.2 1.0
PB E:DTP801 3.2 90.2 1.0
O3B E:DTP801 3.3 90.2 1.0
PA E:DTP801 3.5 90.2 1.0
O2G E:DTP801 3.7 90.2 1.0
O3A E:DTP801 3.8 90.2 1.0
NZ E:LYS17 4.3 0.0 1.0
O1A E:DTP801 4.3 90.2 1.0
O1G E:DTP801 4.5 90.2 1.0
O2B E:DTP801 4.5 90.2 1.0
O5' E:DTP801 4.5 90.2 1.0
NZ E:LYS5 4.6 0.8 1.0
CE E:LYS5 4.8 0.8 1.0
CD E:LYS5 5.0 0.8 1.0
CE E:LYS17 5.0 0.0 1.0

Magnesium binding site 10 out of 12 in 6aui

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Magnesium binding site 10 out of 12 in the Human Ribonucleotide Reductase Large Subunit (Alpha) with Datp and Cdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Human Ribonucleotide Reductase Large Subunit (Alpha) with Datp and Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg804

b:69.7
occ:1.00
 O1B E:DTP803 2.0 71.5 1.0
O1A E:DTP803 2.1 71.5 1.0
O E:HOH901 2.1 70.3 1.0
O2G E:DTP803 2.1 71.5 1.0
O E:HOH904 2.1 72.2 1.0
O E:HOH905 2.1 69.2 1.0
PG E:DTP803 3.0 71.5 1.0
O3G E:DTP803 3.0 71.5 1.0
PB E:DTP803 3.0 71.5 1.0
PA E:DTP803 3.1 71.5 1.0
O3A E:DTP803 3.3 71.5 1.0
O3B E:DTP803 3.5 71.5 1.0
O2A E:DTP803 3.8 71.5 1.0
O1G E:DTP803 4.3 71.5 1.0
O2B E:DTP803 4.3 71.5 1.0
O5' E:DTP803 4.4 71.5 1.0
NH2 E:ARG256 4.5 78.1 1.0
CB E:SER227 4.5 83.6 1.0
O E:ASP226 4.6 87.2 1.0
C5' E:DTP803 4.6 71.5 1.0

Reference:

E.J.Brignole, K.L.Tsai, J.Chittuluru, H.Li, Y.Aye, P.A.Penczek, J.Stubbe, C.L.Drennan, F.Asturias. 3.3- Angstrom Resolution Cryo-Em Structure of Human Ribonucleotide Reductase with Substrate and Allosteric Regulators Bound. Elife V. 7 2018.
ISSN: ESSN 2050-084X
PubMed: 29460780
DOI: 10.7554/ELIFE.31502
Page generated: Mon Sep 30 19:22:07 2024

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