Magnesium in PDB 6c8d: Rna-Dgmp Complex with Mg Ion

Protein crystallography data

The structure of Rna-Dgmp Complex with Mg Ion, PDB code: 6c8d was solved by W.Zhang, J.W.Szostak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.92
Space group P 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 49.547, 49.547, 81.337, 90.00, 90.00, 120.00
R / Rfree (%) 21.9 / 28.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Rna-Dgmp Complex with Mg Ion (pdb code 6c8d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Rna-Dgmp Complex with Mg Ion, PDB code: 6c8d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 6c8d

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Magnesium binding site 1 out of 9 in the Rna-Dgmp Complex with Mg Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rna-Dgmp Complex with Mg Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:34.3
occ:1.00
 O B:HOH228 2.0 42.2 1.0
O A:HOH206 2.1 36.9 1.0
O A:HOH201 2.1 35.4 1.0
O B:HOH229 2.1 26.1 1.0
O B:HOH215 2.1 31.8 1.0
O B:HOH204 4.0 32.5 1.0
OP1 A:LCG4 4.1 27.2 1.0
O B:HOH213 4.1 23.0 1.0
OP2 A:A5 4.3 30.5 1.0
OP2 B:U7 4.3 30.4 1.0
OP1 A:A5 4.4 29.9 1.0
OP1 B:C6 4.6 30.7 1.0
OP2 A:LCG4 4.8 27.8 1.0
P A:LCG4 4.8 30.0 1.0
P A:A5 4.8 32.4 1.0
O A:HOH215 4.8 40.1 1.0
OP1 B:U7 4.9 39.9 1.0

Magnesium binding site 2 out of 9 in 6c8d

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Magnesium binding site 2 out of 9 in the Rna-Dgmp Complex with Mg Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rna-Dgmp Complex with Mg Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg104

b:32.3
occ:1.00
 O A:HOH208 2.0 32.3 1.0
O A:HOH221 2.0 34.4 1.0
O B:HOH214 2.0 34.2 1.0
O B:HOH208 2.0 33.4 1.0
O B:HOH232 2.1 28.7 1.0
O A:HOH232 2.2 26.8 1.0
O4 A:U7 4.1 29.4 1.0
O4 B:U7 4.1 30.2 1.0
O A:HOH223 4.3 30.9 1.0
O B:HOH224 4.3 30.6 1.0
O4 B:U8 4.4 31.5 1.0
O4 A:U8 4.5 33.5 1.0
C4 A:U7 4.9 34.7 1.0
C4 B:U7 4.9 33.9 1.0

Magnesium binding site 3 out of 9 in 6c8d

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Magnesium binding site 3 out of 9 in the Rna-Dgmp Complex with Mg Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Rna-Dgmp Complex with Mg Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg105

b:46.8
occ:1.00
 O A:HOH225 2.0 35.8 1.0
O A:HOH230 2.0 42.1 1.0
O A:HOH234 2.0 44.2 1.0
O A:HOH235 2.1 35.7 1.0
O A:HOH203 2.2 40.6 1.0
O A:HOH212 2.2 39.5 1.0
N7 A:A10 4.2 36.4 1.0
O A:HOH231 4.3 40.5 1.0
N6 A:A10 4.4 34.5 1.0
O6 A:G11 4.4 32.7 1.0
O B:HOH227 4.4 35.9 1.0
O A:HOH213 4.5 39.4 1.0
N7 A:G11 4.6 35.2 1.0
C5 A:A10 4.9 36.0 1.0

Magnesium binding site 4 out of 9 in 6c8d

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Magnesium binding site 4 out of 9 in the Rna-Dgmp Complex with Mg Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Rna-Dgmp Complex with Mg Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg106

b:58.7
occ:0.33
 O B:HOH202 2.2 27.7 0.5
O3' B:DG101 4.2 48.1 1.0
C2' B:DG101 4.5 41.8 1.0
C3' B:DG101 4.9 43.8 1.0

Magnesium binding site 5 out of 9 in 6c8d

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Magnesium binding site 5 out of 9 in the Rna-Dgmp Complex with Mg Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Rna-Dgmp Complex with Mg Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg107

b:63.6
occ:1.00
 O B:HOH222 1.9 60.7 1.0
O A:HOH209 2.0 45.6 1.0
O A:HOH220 2.1 47.1 1.0
O A:HOH233 2.2 54.5 1.0
O B:HOH223 2.3 59.7 1.0
N7 B:DG101 2.4 32.4 1.0
C8 B:DG101 3.1 30.6 1.0
C5 B:DG101 3.6 33.2 1.0
O B:HOH225 3.7 44.4 1.0
O6 B:DG101 3.8 36.0 1.0
O6 A:G14 3.9 32.1 1.0
C6 B:DG101 4.2 34.1 1.0
N7 A:G14 4.3 31.7 1.0
N9 B:DG101 4.4 32.7 1.0
OP2 B:DG101 4.5 56.2 1.0
C6 A:G14 4.6 28.2 1.0
OP1 B:DG101 4.6 76.6 1.0
C4 B:DG101 4.7 32.7 1.0
C5 A:G14 4.7 30.4 1.0
N7 B:DG102 4.9 33.0 1.0

Magnesium binding site 6 out of 9 in 6c8d

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Magnesium binding site 6 out of 9 in the Rna-Dgmp Complex with Mg Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Rna-Dgmp Complex with Mg Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg103

b:35.0
occ:1.00
 O A:HOH228 2.0 38.4 1.0
O B:HOH211 2.1 36.8 1.0
O A:HOH211 2.1 32.9 1.0
O B:HOH220 2.1 28.5 1.0
O A:HOH229 2.1 28.4 1.0
O B:HOH201 2.1 33.9 1.0
OP1 B:LCG4 4.0 28.1 1.0
O A:HOH205 4.2 35.4 1.0
OP2 B:A5 4.2 30.9 1.0
OP2 A:U7 4.3 32.8 1.0
OP1 B:A5 4.4 30.5 1.0
OP1 A:C6 4.5 32.0 1.0
P B:LCG4 4.8 30.0 1.0
P B:A5 4.8 33.2 1.0
OP2 B:LCG4 4.8 28.1 1.0
OP1 A:U7 4.9 41.8 1.0

Magnesium binding site 7 out of 9 in 6c8d

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Magnesium binding site 7 out of 9 in the Rna-Dgmp Complex with Mg Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Rna-Dgmp Complex with Mg Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg104

b:42.4
occ:1.00
 O B:HOH234 1.9 42.8 1.0
O B:HOH226 2.0 36.0 1.0
O B:HOH230 2.0 41.0 1.0
O B:HOH235 2.1 33.9 1.0
O B:HOH207 2.2 38.3 1.0
O B:HOH203 2.3 38.9 1.0
O B:HOH231 4.2 40.1 1.0
N7 B:A10 4.2 36.4 1.0
O A:HOH227 4.3 34.4 1.0
O B:HOH216 4.4 38.4 1.0
N6 B:A10 4.4 33.2 1.0
O6 B:G11 4.4 33.3 1.0
N7 B:G11 4.6 35.2 1.0
C5 B:A10 4.9 36.6 1.0

Magnesium binding site 8 out of 9 in 6c8d

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Magnesium binding site 8 out of 9 in the Rna-Dgmp Complex with Mg Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Rna-Dgmp Complex with Mg Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg105

b:62.8
occ:1.00
 O A:HOH224 1.9 59.7 1.0
O A:HOH226 2.1 56.9 1.0
O B:HOH205 2.1 44.1 1.0
O B:HOH217 2.2 47.5 1.0
O B:HOH233 2.3 52.8 1.0
N7 A:DG101 2.4 31.1 1.0
C8 A:DG101 3.2 30.6 1.0
C5 A:DG101 3.6 32.7 1.0
O A:HOH222 3.7 46.6 1.0
O6 A:DG101 3.8 37.8 1.0
O6 B:G14 3.9 34.1 1.0
C6 A:DG101 4.2 31.7 1.0
N7 B:G14 4.3 33.8 1.0
N9 A:DG101 4.4 32.2 1.0
C6 B:G14 4.6 28.0 1.0
OP2 A:DG101 4.6 72.7 1.0
C4 A:DG101 4.7 30.7 1.0
C5 B:G14 4.8 30.8 1.0
N7 A:DG102 4.9 32.4 1.0

Magnesium binding site 9 out of 9 in 6c8d

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Magnesium binding site 9 out of 9 in the Rna-Dgmp Complex with Mg Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Rna-Dgmp Complex with Mg Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg106

b:70.1
occ:0.33
 O A:HOH202 2.4 24.5 0.5
O3' A:DG101 4.2 50.9 1.0
C2' A:DG101 4.4 42.3 1.0
C3' A:DG101 4.9 43.3 1.0

Reference:

W.Zhang, T.Walton, L.Li, J.W.Szostak. Crystallographic Observation of Nonenzymatic Rna Primer Extension. Elife V. 7 2018.
ISSN: ESSN 2050-084X
PubMed: 29851379
DOI: 10.7554/ELIFE.36422
Page generated: Mon Dec 14 22:26:47 2020

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