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

Protein crystallography data

The structure of 3'-Deoxy Modification at 3' End of Rna Primer Complex with Guanosine Dinucleotide Ligand G(5')Ppp(5')G, PDB code: 7lnf 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) 27.75 / 1.65
Space group P 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 46.822, 46.822, 83.199, 90, 90, 120
R / Rfree (%) 20.8 / 23.9

Other elements in 7lnf:

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

Cobalt (Co) 2 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 8 in 7lnf

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Magnesium binding site 1 out of 8 in the 3'-Deoxy 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 3'-Deoxy 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:Mg107

b:13.4
occ:0.33
 O2D A:GP3106 2.1 12.6 1.0
O3D A:GP3106 2.1 13.3 1.0
C2D A:GP3106 3.0 12.4 1.0
C3D A:GP3106 3.0 12.9 1.0
C4D A:GP3106 3.6 13.9 1.0
C1D A:GP3106 4.3 11.3 1.0
O A:HOH235 4.4 28.7 1.0
O4D A:GP3106 4.5 11.9 1.0
C5D A:GP3106 4.7 15.5 1.0
O A:HOH224 4.7 18.6 1.0

Magnesium binding site 2 out of 8 in 7lnf

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Magnesium binding site 2 out of 8 in the 3'-Deoxy 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 3'-Deoxy 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:Mg108

b:8.0
occ:1.00
 O A:HOH237 2.0 11.7 1.0
O B:HOH223 2.1 10.9 1.0
O B:HOH256 2.1 11.1 1.0
O B:HOH245 2.1 14.2 1.0
O A:HOH209 2.1 12.4 1.0
O B:HOH215 4.1 8.0 1.0
OP2 A:A5 4.2 6.6 1.0
O B:HOH231 4.2 10.7 1.0
O A:HOH218 4.3 22.3 1.0
O A:HOH257 4.3 24.5 1.0
OP2 B:U7 4.4 11.3 1.0
OP1 A:A5 4.4 6.7 1.0
OP1 A:LCG102 4.4 7.6 1.0
OP1 B:C6 4.5 6.4 1.0
P A:A5 4.8 6.7 1.0

Magnesium binding site 3 out of 8 in 7lnf

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Magnesium binding site 3 out of 8 in the 3'-Deoxy 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 3'-Deoxy 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:Mg109

b:41.9
occ:1.00
 O2A A:GP3106 1.9 31.4 1.0
O3B A:GP3106 2.0 36.6 1.0
O2G A:GP3106 2.5 36.2 1.0
PG A:GP3106 2.8 28.3 1.0
O A:HOH202 3.0 31.6 1.0
PA A:GP3106 3.2 22.0 1.0
PB A:GP3106 3.3 36.5 1.0
O2B A:GP3106 3.4 35.6 1.0
O3A A:GP3106 3.6 30.8 1.0
O5E A:GP3106 3.7 24.3 1.0
C5E A:GP3106 3.8 19.3 1.0
O A:HOH235 3.9 28.7 1.0
O1G A:GP3106 4.0 30.8 1.0
O5D A:GP3106 4.2 19.6 1.0
O1A A:GP3106 4.3 27.8 1.0
O1B A:GP3106 4.8 31.9 1.0
C5D A:GP3106 4.9 15.5 1.0

Magnesium binding site 4 out of 8 in 7lnf

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Magnesium binding site 4 out of 8 in the 3'-Deoxy 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 3'-Deoxy 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:Mg110

b:47.2
occ:1.00
 O A:HOH253 2.0 32.4 1.0
O A:HOH216 2.1 33.5 1.0
O A:HOH260 2.2 32.2 1.0
O A:HOH205 2.5 31.7 1.0
O A:HOH232 4.1 23.1 1.0
N7 A:A10 4.2 22.8 1.0
O A:HOH213 4.5 29.6 1.0
N6 A:A10 4.6 24.3 1.0
O B:HOH250 4.6 19.0 1.0
O6 A:G11 4.6 14.5 1.0
N7 A:G11 4.8 19.6 1.0

Magnesium binding site 5 out of 8 in 7lnf

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Magnesium binding site 5 out of 8 in the 3'-Deoxy 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 3'-Deoxy 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:Mg107

b:11.8
occ:0.33
 O2D B:GP3103 2.1 12.1 1.0
O3D B:GP3103 2.1 13.1 1.0
C2D B:GP3103 3.0 12.8 1.0
C3D B:GP3103 3.0 12.8 1.0
C4D B:GP3103 3.6 14.4 1.0
C1D B:GP3103 4.3 11.7 1.0
O4D B:GP3103 4.5 12.3 1.0
C5D B:GP3103 4.7 15.9 1.0
O B:HOH226 4.7 18.0 1.0

Magnesium binding site 6 out of 8 in 7lnf

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Magnesium binding site 6 out of 8 in the 3'-Deoxy 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 3'-Deoxy 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:Mg108

b:38.4
occ:1.00
 O2A B:GP3103 1.9 30.5 1.0
O3B B:GP3103 2.0 36.1 1.0
O2G B:GP3103 2.6 35.9 1.0
PG B:GP3103 2.8 29.2 1.0
PA B:GP3103 3.1 21.1 1.0
O2B B:GP3103 3.2 34.6 1.0
PB B:GP3103 3.3 36.9 1.0
O3A B:GP3103 3.5 30.7 1.0
O5E B:GP3103 3.7 24.7 1.0
C5E B:GP3103 3.9 18.6 1.0
O1G B:GP3103 3.9 30.1 1.0
O5D B:GP3103 4.1 19.4 1.0
O1A B:GP3103 4.2 27.1 1.0
O1B B:GP3103 4.7 31.7 1.0
C5D B:GP3103 4.9 15.9 1.0

Magnesium binding site 7 out of 8 in 7lnf

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Magnesium binding site 7 out of 8 in the 3'-Deoxy 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 3'-Deoxy 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:Mg109

b:8.1
occ:1.00
 O B:HOH236 2.0 10.0 1.0
O A:HOH255 2.1 10.2 1.0
O A:HOH230 2.1 11.0 1.0
O A:HOH245 2.1 14.6 1.0
O B:HOH213 2.1 14.2 1.0
OP2 B:A5 4.2 6.3 1.0
O A:HOH228 4.2 10.5 1.0
O B:HOH217 4.3 22.1 1.0
O B:HOH257 4.4 23.8 1.0
OP2 A:U7 4.4 12.2 1.0
OP1 B:LCG105 4.4 7.6 1.0
OP1 B:A5 4.4 6.8 1.0
OP1 A:C6 4.4 6.4 1.0
P B:A5 4.8 6.6 1.0

Magnesium binding site 8 out of 8 in 7lnf

Go back to Magnesium Binding Sites List in 7lnf
Magnesium binding site 8 out of 8 in the 3'-Deoxy 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 3'-Deoxy 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:Mg110

b:47.3
occ:1.00
 O B:HOH222 2.1 31.8 1.0
O B:HOH263 2.3 27.3 1.0
O B:HOH207 2.3 41.4 1.0
O B:HOH210 2.4 33.1 1.0
O B:HOH229 4.0 22.9 1.0
N7 B:A10 4.1 22.7 1.0
O6 B:G11 4.5 15.1 1.0
N7 B:G11 4.5 18.6 1.0
N6 B:A10 4.6 23.8 1.0
O B:HOH259 4.6 24.7 1.0
O A:HOH250 4.7 18.6 1.0
O B:HOH206 4.8 26.6 1.0
C5 B:A10 4.9 22.8 1.0
C8 B:A10 4.9 22.8 1.0

Reference:

C.Giurgiu, Z.Fang, J.W.Szostak. Sugar Conformation Impacts on Nonezymatic Rna Primer Extension To Be Published.
Page generated: Wed Oct 2 23:29:50 2024

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