Magnesium in PDB 7kun: 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G

Protein crystallography data

The structure of 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G, PDB code: 7kun was solved by Z.Fang, C.Giurgiu, J.W.Szostak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.58
Space group P 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 48.783, 48.783, 82.434, 90, 90, 120
R / Rfree (%) 19.4 / 23

Other elements in 7kun:

The structure of 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G (pdb code 7kun). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G, PDB code: 7kun:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7kun

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Magnesium binding site 1 out of 8 in the 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:6.6
occ:0.33
 O2D B:GP3101 2.1 6.8 1.0
O3D B:GP3101 2.1 8.1 1.0
C2D B:GP3101 3.0 7.2 1.0
C3D B:GP3101 3.0 7.4 1.0
C4D B:GP3101 3.6 8.3 1.0
C1D B:GP3101 4.2 7.3 1.0
O4D B:GP3101 4.4 7.1 1.0
O B:HOH226 4.4 25.0 1.0
O B:HOH217 4.5 17.5 1.0
C5D B:GP3101 4.8 9.3 1.0

Magnesium binding site 2 out of 8 in 7kun

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Magnesium binding site 2 out of 8 in the 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:18.0
occ:1.00
 O B:HOH248 2.0 18.8 1.0
O A:HOH232 2.1 16.7 1.0
O B:HOH258 2.1 16.6 1.0
O B:HOH240 2.2 15.2 1.0
O A:HOH222 2.2 9.9 1.0
O A:HOH211 2.2 17.3 1.0
O B:HOH230 4.0 14.1 1.0
OP2 A:A5 4.1 7.8 1.0
OP1 A:A5 4.2 6.7 1.0
O B:HOH233 4.2 19.4 1.0
O A:HOH228 4.3 27.5 1.0
O B:HOH256 4.4 30.6 1.0
OP1 A:LCG4 4.5 8.0 1.0
OP1 B:C6 4.5 7.0 1.0
OP2 B:U7 4.6 14.1 1.0
P A:A5 4.7 6.8 1.0

Magnesium binding site 3 out of 8 in 7kun

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Magnesium binding site 3 out of 8 in the 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg104

b:34.1
occ:1.00
 O2G B:GP3101 2.0 40.4 1.0
O2A B:GP3101 2.0 16.1 1.0
O B:HOH202 2.2 39.0 1.0
O B:HOH226 2.8 25.0 1.0
PA B:GP3101 3.2 14.0 1.0
PG B:GP3101 3.3 32.8 1.0
O3B B:GP3101 3.5 36.7 1.0
O2B B:GP3101 3.7 37.7 1.0
O5D B:GP3101 3.7 11.5 1.0
O3A B:GP3101 4.0 19.4 1.0
PB B:GP3101 4.0 33.1 1.0
C5D B:GP3101 4.2 9.3 1.0
O5E B:GP3101 4.3 23.4 1.0
O1G B:GP3101 4.3 25.6 1.0
C5E B:GP3101 4.4 20.2 1.0
O1A B:GP3101 4.5 18.5 1.0
O3D B:GP3101 4.9 8.1 1.0
C3D B:GP3101 5.0 7.4 1.0

Magnesium binding site 4 out of 8 in 7kun

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Magnesium binding site 4 out of 8 in the 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg105

b:69.2
occ:1.00
 O A:HOH264 2.2 21.7 0.3
O A:HOH218 2.3 21.8 1.0
O B:HOH223 2.3 22.2 1.0
O A:HOH241 2.4 24.6 1.0
O B:HOH245 2.5 21.2 1.0
O A:HOH214 3.8 23.9 1.0
O B:HOH215 3.9 23.9 1.0
OP1 A:C6 4.5 7.3 1.0
OP1 A:A5 4.5 6.7 1.0
OP1 B:C6 4.6 7.0 1.0
OP1 B:A5 4.7 6.8 1.0

Magnesium binding site 5 out of 8 in 7kun

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Magnesium binding site 5 out of 8 in the 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg102

b:6.4
occ:0.33
 O2D A:GP3101 2.1 6.8 1.0
O3D A:GP3101 2.1 8.3 1.0
C2D A:GP3101 3.0 7.1 1.0
C3D A:GP3101 3.0 7.3 1.0
C4D A:GP3101 3.6 8.2 1.0
C1D A:GP3101 4.2 7.0 1.0
O A:HOH225 4.4 25.5 1.0
O4D A:GP3101 4.4 7.0 1.0
O A:HOH216 4.5 18.1 1.0
C5D A:GP3101 4.8 9.4 1.0

Magnesium binding site 6 out of 8 in 7kun

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Magnesium binding site 6 out of 8 in the 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg103

b:17.1
occ:1.00
 O A:HOH248 2.0 18.3 1.0
O B:HOH237 2.1 15.9 1.0
O A:HOH259 2.1 17.1 1.0
O A:HOH237 2.1 15.3 1.0
O B:HOH212 2.2 17.1 1.0
O B:HOH222 2.2 9.8 1.0
OP2 B:A5 4.1 8.0 1.0
OP1 B:A5 4.2 6.8 1.0
O A:HOH220 4.2 19.2 1.0
O B:HOH232 4.3 27.4 1.0
OP1 A:C6 4.5 7.3 1.0
OP1 B:LCG4 4.5 8.4 1.0
P B:A5 4.6 6.6 1.0
OP2 A:U7 4.7 13.5 1.0

Magnesium binding site 7 out of 8 in 7kun

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Magnesium binding site 7 out of 8 in the 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg104

b:35.3
occ:1.00
 O2G A:GP3101 2.0 40.8 1.0
O2A A:GP3101 2.0 16.4 1.0
O A:HOH202 2.2 42.0 1.0
O A:HOH225 2.8 25.5 1.0
PA A:GP3101 3.2 14.2 1.0
PG A:GP3101 3.3 33.3 1.0
O3B A:GP3101 3.5 35.4 1.0
O2B A:GP3101 3.6 35.9 1.0
O5D A:GP3101 3.7 11.5 1.0
O3A A:GP3101 3.9 18.6 1.0
PB A:GP3101 3.9 33.4 1.0
C5D A:GP3101 4.2 9.4 1.0
O1G A:GP3101 4.2 27.0 1.0
O5E A:GP3101 4.3 22.8 1.0
C5E A:GP3101 4.4 20.0 1.0
O1A A:GP3101 4.4 18.2 1.0
O3D A:GP3101 4.9 8.3 1.0
C3D A:GP3101 4.9 7.3 1.0

Magnesium binding site 8 out of 8 in 7kun

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Magnesium binding site 8 out of 8 in the 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of 2'-F Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg105

b:42.4
occ:1.00
 O A:HOH210 1.8 33.9 1.0
O B:HOH225 2.5 24.7 1.0
O6 B:GF214 2.7 7.0 1.0
O A:HOH263 2.9 38.4 1.0
O B:HOH251 3.4 27.8 1.0
N4 B:C13 3.5 11.7 1.0
O A:HOH212 3.8 13.7 1.0
C6 B:GF214 3.8 6.6 1.0
O A:HOH249 3.9 22.6 1.0
O6A A:GP3101 4.0 6.8 1.0
O A:HOH243 4.0 33.3 1.0
N7 B:GF214 4.1 7.0 1.0
N4 A:LCC3 4.2 6.0 1.0
C5 B:GF214 4.3 6.5 1.0
C4 B:C13 4.5 13.2 1.0
N7A A:GP3101 4.6 6.5 1.0
O6 A:LCG4 4.6 8.4 1.0
O A:HOH235 4.7 19.4 1.0
O A:HOH227 4.8 27.3 1.0
C6A A:GP3101 4.8 5.9 1.0
C5A A:GP3101 5.0 5.8 1.0
N1 B:GF214 5.0 6.2 1.0

Reference:

C.Giurgiu, Z.Fang, H.R.M.Aitken, S.C.Kim, L.Pazienza, S.Mittal, J.W.Szostak. Structure-Activity Relationships in Nonenzymatic Template-Directed Rna Synthesis. Angew.Chem.Int.Ed.Engl. 2021.
ISSN: ESSN 1521-3773
PubMed: 34428345
DOI: 10.1002/ANIE.202109714
Page generated: Fri Sep 24 15:18:52 2021

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