Atomistry » Magnesium » PDB 7ku4-7kzu » 7kun
Atomistry »
  Magnesium »
    PDB 7ku4-7kzu »
      7kun »

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

Go back to Magnesium Binding Sites List in 7kun
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

Go back to Magnesium Binding Sites List in 7kun
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

Go back to Magnesium Binding Sites List in 7kun
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

Go back to Magnesium Binding Sites List in 7kun
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

Go back to Magnesium Binding Sites List in 7kun
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

Go back to Magnesium Binding Sites List in 7kun
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

Go back to Magnesium Binding Sites List in 7kun
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

Go back to Magnesium Binding Sites List in 7kun
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: Thu Aug 14 08:40:00 2025

Last articles

Zn in 9Q2D
Zn in 9PZ0
Zn in 9OXS
Zn in 9PYW
Zn in 9PYZ
Zn in 9OXE
Zn in 9PYL
Zn in 9PPR
Zn in 9PEB
Zn in 9O2Z
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy