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Magnesium in PDB 5cnt: Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Udp and Datp at 3.25 Angstroms Resolution

Enzymatic activity of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Udp and Datp at 3.25 Angstroms Resolution

All present enzymatic activity of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Udp and Datp at 3.25 Angstroms Resolution:
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Udp and Datp at 3.25 Angstroms Resolution, PDB code: 5cnt was solved by P.Y.-T.Chen, C.M.Zimanyi, M.A.Funk, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.95 / 3.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 274.621, 157.340, 165.200, 90.00, 119.30, 90.00
R / Rfree (%) 19.2 / 22.1

Other elements in 5cnt:

The structure of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Udp and Datp at 3.25 Angstroms Resolution also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Udp and Datp at 3.25 Angstroms Resolution (pdb code 5cnt). 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 the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Udp and Datp at 3.25 Angstroms Resolution, PDB code: 5cnt:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5cnt

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Magnesium binding site 1 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Udp and Datp at 3.25 Angstroms Resolution


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 the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Udp and Datp at 3.25 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:0.7
occ:1.00
 O1A A:DTP804 2.1 0.6 1.0
O2B A:DTP802 2.1 0.6 1.0
O1B A:DTP804 2.1 0.4 1.0
O3G A:DTP802 2.1 0.3 1.0
O2A A:DTP802 2.1 0.5 1.0
O1G A:DTP804 2.1 0.1 1.0
PA A:DTP804 3.2 0.6 1.0
PB A:DTP804 3.2 0.6 1.0
PG A:DTP804 3.3 0.2 1.0
PB A:DTP802 3.3 0.6 1.0
PA A:DTP802 3.5 0.8 1.0
PG A:DTP802 3.5 0.3 1.0
O3A A:DTP804 3.6 0.3 1.0
O3G A:DTP804 3.6 0.8 1.0
O3B A:DTP804 3.7 0.6 1.0
O2A A:DTP804 3.8 0.4 1.0
O3B A:DTP802 3.8 0.6 1.0
O3A A:DTP802 3.8 0.7 1.0
NZ A:LYS9 4.2 0.2 1.0
O2G A:DTP802 4.3 0.4 1.0
O5' A:DTP802 4.4 0.2 1.0
O5' A:DTP804 4.5 0.5 1.0
O1A A:DTP802 4.6 0.7 1.0
O1G A:DTP802 4.6 0.0 1.0
NZ A:LYS91 4.6 99.6 1.0
O2G A:DTP804 4.6 0.6 1.0
O2B A:DTP804 4.6 0.0 1.0
O1B A:DTP802 4.7 0.8 1.0
C8 A:DTP802 4.8 100.0 1.0
CE A:LYS9 4.9 0.6 1.0

Magnesium binding site 2 out of 8 in 5cnt

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Magnesium binding site 2 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Udp and Datp at 3.25 Angstroms Resolution


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 the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Udp and Datp at 3.25 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg806

b:57.2
occ:1.00
 O1A A:DTP805 2.1 58.3 1.0
O2B A:DTP805 2.1 60.5 1.0
O A:HOH909 2.1 61.5 1.0
O A:HOH910 2.1 58.8 1.0
O A:HOH911 2.1 62.2 1.0
O3G A:DTP805 2.1 58.4 1.0
PB A:DTP805 3.1 60.3 1.0
PA A:DTP805 3.2 57.8 1.0
O3A A:DTP805 3.3 61.6 1.0
PG A:DTP805 3.4 58.8 1.0
O3B A:DTP805 3.6 58.5 1.0
O1G A:DTP805 4.1 58.3 1.0
O2A A:DTP805 4.2 57.2 1.0
O A:ASP232 4.2 56.3 1.0
CB A:SER233 4.4 57.3 1.0
O5' A:DTP805 4.4 56.1 1.0
C5' A:DTP805 4.5 57.5 1.0
O1B A:DTP805 4.5 57.5 1.0
O2G A:DTP805 4.5 58.5 1.0
NH2 A:ARG262 4.5 59.4 1.0
CA A:SER233 4.9 55.5 1.0

Magnesium binding site 3 out of 8 in 5cnt

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Magnesium binding site 3 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Udp and Datp at 3.25 Angstroms Resolution


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 the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Udp and Datp at 3.25 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:88.1
occ:1.00
 O1B B:DTP802 2.1 86.3 1.0
O2A B:DTP804 2.1 91.7 1.0
O2B B:DTP804 2.1 89.7 1.0
O1A B:DTP802 2.1 85.6 1.0
O1G B:DTP802 2.1 85.7 1.0
O3G B:DTP804 2.1 91.7 1.0
PB B:DTP804 3.1 96.1 1.0
PB B:DTP802 3.2 82.9 1.0
PA B:DTP804 3.2 96.9 1.0
PG B:DTP804 3.3 95.6 1.0
PA B:DTP802 3.4 84.0 1.0
PG B:DTP802 3.4 84.6 1.0
O3A B:DTP804 3.5 95.7 1.0
O3B B:DTP804 3.5 93.8 1.0
O3A B:DTP802 3.7 83.6 1.0
O3B B:DTP802 3.7 83.6 1.0
O5' B:DTP804 4.0 90.8 1.0
O2G B:DTP804 4.1 93.5 1.0
O5' B:DTP802 4.2 81.5 1.0
O2G B:DTP802 4.3 82.2 1.0
NZ B:LYS9 4.3 85.1 1.0
NZ B:LYS91 4.3 81.2 1.0
O1G B:DTP804 4.5 91.0 1.0
O1B B:DTP804 4.5 91.0 1.0
O3G B:DTP802 4.5 84.4 1.0
O1A B:DTP804 4.5 94.6 1.0
O2A B:DTP802 4.6 80.3 1.0
O2B B:DTP802 4.6 82.7 1.0
C8 B:DTP802 4.9 79.7 1.0

Magnesium binding site 4 out of 8 in 5cnt

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Magnesium binding site 4 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Udp and Datp at 3.25 Angstroms Resolution


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 the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Udp and Datp at 3.25 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg806

b:67.7
occ:1.00
 O2B B:DTP805 2.1 67.6 1.0
O2A B:DTP805 2.1 65.6 1.0
O1G B:DTP805 2.1 68.5 1.0
O B:HOH909 2.1 67.8 1.0
O B:HOH906 2.1 72.8 1.0
O B:HOH910 2.1 65.8 1.0
PB B:DTP805 3.1 70.6 1.0
PG B:DTP805 3.2 71.1 1.0
PA B:DTP805 3.2 65.3 1.0
O3A B:DTP805 3.3 70.3 1.0
O3G B:DTP805 3.5 74.4 1.0
O3B B:DTP805 3.5 69.8 1.0
O1A B:DTP805 4.3 66.2 1.0
O5' B:DTP805 4.3 65.6 1.0
C5' B:DTP805 4.3 66.0 1.0
O B:ASP232 4.5 65.2 1.0
O1B B:DTP805 4.5 70.1 1.0
CB B:SER233 4.5 65.3 1.0
O2G B:DTP805 4.5 71.1 1.0
NH2 B:ARG262 4.6 67.9 1.0

Magnesium binding site 5 out of 8 in 5cnt

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Magnesium binding site 5 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Udp and Datp at 3.25 Angstroms Resolution


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 the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Udp and Datp at 3.25 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg803

b:0.2
occ:1.00
 O2A C:DTP804 2.1 0.9 1.0
O1G C:DTP802 2.1 0.6 1.0
O1B C:DTP802 2.1 0.9 1.0
O2B C:DTP804 2.1 0.9 1.0
O1A C:DTP802 2.1 0.4 1.0
O3G C:DTP804 2.1 0.6 1.0
PB C:DTP802 3.2 0.3 1.0
PA C:DTP804 3.3 0.7 1.0
PB C:DTP804 3.3 0.8 1.0
PA C:DTP802 3.4 0.5 1.0
PG C:DTP802 3.4 0.5 1.0
PG C:DTP804 3.5 0.8 1.0
O3A C:DTP804 3.6 0.7 1.0
O3A C:DTP802 3.6 0.7 1.0
O3B C:DTP802 3.7 0.8 1.0
NZ C:LYS91 3.7 0.1 1.0
O3B C:DTP804 3.8 0.9 1.0
O5' C:DTP804 3.8 0.4 1.0
O2G C:DTP802 4.0 0.6 1.0
O2A C:DTP802 4.3 0.6 1.0
O2G C:DTP804 4.3 0.1 1.0
O5' C:DTP802 4.5 0.9 1.0
O3G C:DTP802 4.6 0.3 1.0
O1G C:DTP804 4.6 0.1 1.0
O2B C:DTP802 4.6 0.5 1.0
O1A C:DTP804 4.6 0.3 1.0
O1B C:DTP804 4.6 0.3 1.0
CE C:LYS91 4.9 0.5 1.0
NZ C:LYS9 5.0 0.3 1.0

Magnesium binding site 6 out of 8 in 5cnt

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Magnesium binding site 6 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Udp and Datp at 3.25 Angstroms Resolution


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 the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Udp and Datp at 3.25 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg806

b:94.3
occ:1.00
 O1B C:DTP805 2.1 94.6 1.0
O1G C:DTP805 2.1 91.8 1.0
O1A C:DTP805 2.1 93.8 1.0
O C:HOH902 2.1 97.1 1.0
O C:HOH903 2.1 93.9 1.0
O C:HOH904 2.1 95.0 1.0
PB C:DTP805 3.1 92.8 1.0
PG C:DTP805 3.3 94.0 1.0
PA C:DTP805 3.3 94.8 1.0
O3B C:DTP805 3.5 95.7 1.0
O3A C:DTP805 3.6 91.8 1.0
O3G C:DTP805 3.9 96.3 1.0
O C:ASP232 4.1 94.9 1.0
O2A C:DTP805 4.3 94.9 1.0
O5' C:DTP805 4.4 94.7 1.0
C5' C:DTP805 4.5 95.4 1.0
NH2 C:ARG262 4.5 94.9 1.0
O2B C:DTP805 4.5 92.2 1.0
O2G C:DTP805 4.5 92.8 1.0
CB C:SER233 4.6 95.9 1.0
CA C:SER233 5.0 94.7 1.0

Magnesium binding site 7 out of 8 in 5cnt

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Magnesium binding site 7 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Udp and Datp at 3.25 Angstroms Resolution


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 the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Udp and Datp at 3.25 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg803

b:0.8
occ:1.00
 O2B D:DTP802 2.1 0.1 1.0
O1A D:DTP804 2.1 0.7 1.0
O3G D:DTP802 2.1 0.2 1.0
O1B D:DTP804 2.1 0.0 1.0
O2A D:DTP802 2.1 99.5 1.0
O1G D:DTP804 2.1 0.7 1.0
PG D:DTP802 3.2 0.1 1.0
PB D:DTP802 3.2 99.4 1.0
PB D:DTP804 3.3 0.7 1.0
PA D:DTP804 3.4 0.1 1.0
PG D:DTP804 3.4 0.9 1.0
PA D:DTP802 3.4 97.5 1.0
O2G D:DTP802 3.6 99.8 1.0
O3A D:DTP802 3.7 99.6 1.0
O3B D:DTP802 3.7 0.8 1.0
O3A D:DTP804 3.7 0.4 1.0
O3B D:DTP804 3.8 0.0 1.0
O2G D:DTP804 3.9 0.1 1.0
NZ D:LYS91 4.0 96.9 1.0
O5' D:DTP804 4.0 0.5 1.0
NZ D:LYS9 4.2 0.7 1.0
O5' D:DTP802 4.4 97.2 1.0
O1A D:DTP802 4.4 95.2 1.0
O1G D:DTP802 4.6 0.7 1.0
O1B D:DTP802 4.6 98.6 1.0
O3G D:DTP804 4.6 0.0 1.0
O2B D:DTP804 4.7 0.9 1.0
O2A D:DTP804 4.7 0.6 1.0
CE D:LYS9 5.0 1.0 1.0

Magnesium binding site 8 out of 8 in 5cnt

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Magnesium binding site 8 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Udp and Datp at 3.25 Angstroms Resolution


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 the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Udp and Datp at 3.25 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg806

b:87.9
occ:1.00
 O2B D:DTP805 2.1 88.4 1.0
O2A D:DTP805 2.1 88.1 1.0
O3G D:DTP805 2.1 86.9 1.0
O D:HOH904 2.1 90.8 1.0
O D:HOH905 2.1 86.3 1.0
O D:HOH903 2.1 86.2 1.0
PB D:DTP805 3.1 88.5 1.0
PA D:DTP805 3.3 88.0 1.0
PG D:DTP805 3.3 90.7 1.0
O3A D:DTP805 3.4 89.2 1.0
O3B D:DTP805 3.6 91.1 1.0
O1G D:DTP805 4.0 94.8 1.0
O1A D:DTP805 4.2 85.1 1.0
O5' D:DTP805 4.4 87.5 1.0
C5' D:DTP805 4.4 87.1 1.0
O1B D:DTP805 4.5 85.6 1.0
O2G D:DTP805 4.6 89.9 1.0
O D:ASP232 4.6 83.8 1.0
CB D:SER233 4.6 85.5 1.0
NH2 D:ARG262 4.7 87.3 1.0

Reference:

C.M.Zimanyi, P.Y.Chen, G.Kang, M.A.Funk, C.L.Drennan. Molecular Basis For Allosteric Specificity Regulation in Class Ia Ribonucleotide Reductase From Escherichia Coli. Elife V. 5 07141 2016.
ISSN: ESSN 2050-084X
PubMed: 26754917
DOI: 10.7554/ELIFE.07141
Page generated: Sun Sep 29 02:15:03 2024

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