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Magnesium in PDB 5cnu: Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Adp and Dgtp at 3.40 Angstroms Resolution

Enzymatic activity of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Adp and Dgtp at 3.40 Angstroms Resolution

All present enzymatic activity of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Adp and Dgtp at 3.40 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 Adp and Dgtp at 3.40 Angstroms Resolution, PDB code: 5cnu 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) 49.65 / 3.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 274.340, 157.009, 166.039, 90.00, 119.72, 90.00
R / Rfree (%) 18.5 / 22.1

Other elements in 5cnu:

The structure of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Adp and Dgtp at 3.40 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 Adp and Dgtp at 3.40 Angstroms Resolution (pdb code 5cnu). 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 Adp and Dgtp at 3.40 Angstroms Resolution, PDB code: 5cnu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5cnu

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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 Adp and Dgtp at 3.40 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 Adp and Dgtp at 3.40 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:51.0
occ:1.00
 O1B A:DGT801 2.1 53.5 1.0
O2A A:DGT801 2.1 51.5 1.0
O1G A:DGT801 2.1 50.9 1.0
O A:HOH911 2.1 49.7 1.0
O A:HOH910 2.1 55.9 1.0
O A:HOH908 2.1 51.5 1.0
PB A:DGT801 3.1 54.1 1.0
PA A:DGT801 3.3 53.4 1.0
PG A:DGT801 3.3 52.6 1.0
O3A A:DGT801 3.5 54.3 1.0
O3B A:DGT801 3.6 53.4 1.0
O3G A:DGT801 4.2 51.7 1.0
O1A A:DGT801 4.3 50.3 1.0
C5' A:DGT801 4.4 51.0 1.0
O5' A:DGT801 4.4 50.5 1.0
O A:ASP232 4.4 50.6 1.0
O2G A:DGT801 4.4 52.4 1.0
CB A:SER233 4.5 48.8 1.0
O2B A:DGT801 4.5 52.9 1.0
NH2 A:ARG262 4.6 51.1 1.0

Magnesium binding site 2 out of 8 in 5cnu

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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 Adp and Dgtp at 3.40 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 Adp and Dgtp at 3.40 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg805

b:89.8
occ:1.00
 O2B A:DAT804 2.1 95.0 1.0
O A:HOH909 2.1 84.9 1.0
O A:HOH914 2.1 86.0 1.0
O2A A:DAT804 2.1 89.3 1.0
O A:HOH912 2.1 86.4 1.0
O A:HOH913 2.1 84.1 1.0
PB A:DAT804 3.3 96.6 1.0
PA A:DAT804 3.3 92.1 1.0
O3A A:DAT804 3.6 92.3 1.0
O3B A:DAT804 3.8 91.8 1.0
O5' A:DAT804 4.3 88.7 1.0
NZ A:LYS9 4.4 92.8 1.0
O1A A:DAT804 4.5 86.5 1.0
O1B A:DAT804 4.5 92.5 1.0
C8 A:DAT804 4.6 89.9 1.0
NZ A:LYS91 4.8 82.0 1.0

Magnesium binding site 3 out of 8 in 5cnu

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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 Adp and Dgtp at 3.40 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 Adp and Dgtp at 3.40 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:76.4
occ:1.00
 O1B B:DAT802 2.1 76.7 1.0
O B:HOH920 2.1 70.6 1.0
O B:HOH918 2.1 71.4 1.0
O B:HOH919 2.1 70.6 1.0
O1A B:DAT802 2.1 74.9 1.0
O B:HOH921 2.1 66.0 1.0
PB B:DAT802 3.3 76.8 1.0
PA B:DAT802 3.3 74.6 1.0
O3A B:DAT802 3.6 73.3 1.0
O3B B:DAT802 3.9 71.7 1.0
O5' B:DAT802 4.0 70.5 1.0
NZ B:LYS9 4.4 74.9 1.0
O2B B:DAT802 4.5 73.5 1.0
O2A B:DAT802 4.6 66.4 1.0
NZ B:LYS91 4.7 69.8 1.0
C8 B:DAT802 4.8 70.8 1.0

Magnesium binding site 4 out of 8 in 5cnu

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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 Adp and Dgtp at 3.40 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 Adp and Dgtp at 3.40 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg805

b:57.6
occ:1.00
 O1B B:DGT804 2.1 59.0 1.0
O1A B:DGT804 2.1 55.3 1.0
O3G B:DGT804 2.1 58.9 1.0
O B:HOH916 2.1 63.6 1.0
O B:HOH917 2.1 55.3 1.0
O B:HOH915 2.1 59.9 1.0
PB B:DGT804 3.1 60.9 1.0
PG B:DGT804 3.2 62.5 1.0
PA B:DGT804 3.3 56.0 1.0
O3B B:DGT804 3.5 61.1 1.0
O3A B:DGT804 3.6 58.8 1.0
O2G B:DGT804 3.6 63.0 1.0
O B:ASP232 4.2 54.5 1.0
O2A B:DGT804 4.3 57.4 1.0
C5' B:DGT804 4.3 56.2 1.0
O5' B:DGT804 4.4 55.4 1.0
NH2 B:ARG262 4.5 57.2 1.0
CB B:SER233 4.5 54.7 1.0
O2B B:DGT804 4.5 61.7 1.0
O1G B:DGT804 4.5 60.3 1.0
CA B:SER233 4.9 54.3 1.0

Magnesium binding site 5 out of 8 in 5cnu

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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 Adp and Dgtp at 3.40 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 Adp and Dgtp at 3.40 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg803

b:94.8
occ:1.00
 O C:HOH905 2.1 90.4 1.0
O1B C:DAT802 2.1 94.3 1.0
O C:HOH908 2.1 81.5 1.0
O1A C:DAT802 2.1 94.1 1.0
O C:HOH907 2.1 93.9 1.0
O C:HOH909 2.1 85.6 1.0
PB C:DAT802 3.3 93.7 1.0
PA C:DAT802 3.3 95.4 1.0
O3A C:DAT802 3.6 91.8 1.0
O3B C:DAT802 3.8 93.1 1.0
O5' C:DAT802 4.2 91.8 1.0
NZ C:LYS9 4.5 89.7 1.0
O2A C:DAT802 4.5 88.8 1.0
O2B C:DAT802 4.5 93.3 1.0
NZ C:LYS91 4.6 87.7 1.0
C8 C:DAT802 5.0 91.4 1.0

Magnesium binding site 6 out of 8 in 5cnu

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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 Adp and Dgtp at 3.40 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 Adp and Dgtp at 3.40 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg805

b:72.6
occ:1.00
 O2B C:DGT804 2.1 75.3 1.0
O2A C:DGT804 2.1 72.8 1.0
O3G C:DGT804 2.1 71.5 1.0
O C:HOH903 2.1 73.7 1.0
O C:HOH906 2.1 72.8 1.0
O C:HOH904 2.1 72.0 1.0
PB C:DGT804 3.1 74.0 1.0
PA C:DGT804 3.2 73.7 1.0
PG C:DGT804 3.3 73.6 1.0
O3A C:DGT804 3.4 73.7 1.0
O3B C:DGT804 3.6 74.8 1.0
O2G C:DGT804 4.0 72.9 1.0
O C:ASP232 4.1 72.5 1.0
O1A C:DGT804 4.3 72.1 1.0
O5' C:DGT804 4.3 72.2 1.0
C5' C:DGT804 4.4 72.5 1.0
NH2 C:ARG262 4.4 73.9 1.0
CB C:SER233 4.5 74.3 1.0
O1B C:DGT804 4.5 72.0 1.0
O1G C:DGT804 4.5 73.0 1.0
CA C:SER233 4.9 72.5 1.0

Magnesium binding site 7 out of 8 in 5cnu

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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 Adp and Dgtp at 3.40 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 Adp and Dgtp at 3.40 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg803

b:88.0
occ:1.00
 O D:HOH903 2.1 81.1 1.0
O2B D:DAT802 2.1 85.6 1.0
O D:HOH912 2.1 78.3 1.0
O D:HOH911 2.1 80.2 1.0
O2A D:DAT802 2.1 81.5 1.0
O D:HOH913 2.1 77.0 1.0
PB D:DAT802 3.1 85.3 1.0
PA D:DAT802 3.3 80.5 1.0
O3B D:DAT802 3.4 81.8 1.0
O3A D:DAT802 3.6 80.9 1.0
O5' D:DAT802 4.1 77.9 1.0
NZ D:LYS9 4.3 84.9 1.0
NZ D:LYS91 4.5 77.6 1.0
O1B D:DAT802 4.5 82.7 1.0
O1A D:DAT802 4.6 76.3 1.0
C8 D:DAT802 4.6 75.8 1.0

Magnesium binding site 8 out of 8 in 5cnu

Go back to Magnesium Binding Sites List in 5cnu
Magnesium binding site 8 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Adp and Dgtp at 3.40 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 Adp and Dgtp at 3.40 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg805

b:72.5
occ:1.00
 O1B D:DGT804 2.1 73.4 1.0
O1A D:DGT804 2.1 72.8 1.0
O1G D:DGT804 2.1 72.8 1.0
O D:HOH909 2.1 72.1 1.0
O D:HOH910 2.1 74.1 1.0
O D:HOH908 2.1 73.3 1.0
PB D:DGT804 3.1 72.1 1.0
PG D:DGT804 3.3 75.2 1.0
PA D:DGT804 3.3 74.5 1.0
O3B D:DGT804 3.5 74.3 1.0
O3A D:DGT804 3.6 73.0 1.0
O3G D:DGT804 3.8 76.6 1.0
O D:ASP232 4.2 69.7 1.0
NH2 D:ARG262 4.3 69.6 1.0
C5' D:DGT804 4.3 71.4 1.0
O5' D:DGT804 4.3 71.9 1.0
O2A D:DGT804 4.4 71.9 1.0
O2B D:DGT804 4.5 70.2 1.0
O2G D:DGT804 4.5 71.6 1.0
CB D:SER233 4.7 71.1 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 02:15:04 2024

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