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Magnesium in PDB 6xt7: TEL25 Hybrid Four-Quartet G-Quadruplex with K+

Protein crystallography data

The structure of TEL25 Hybrid Four-Quartet G-Quadruplex with K+, PDB code: 6xt7 was solved by L.A.Yatsunyk, S.E.Mccarthy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.38 / 1.56
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 29.998, 92.916, 50.081, 90, 99.62, 90
R / Rfree (%) 16.1 / 18.5

Other elements in 6xt7:

The structure of TEL25 Hybrid Four-Quartet G-Quadruplex with K+ also contains other interesting chemical elements:

Potassium (K) 12 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the TEL25 Hybrid Four-Quartet G-Quadruplex with K+ (pdb code 6xt7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the TEL25 Hybrid Four-Quartet G-Quadruplex with K+, PDB code: 6xt7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6xt7

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Magnesium binding site 1 out of 6 in the TEL25 Hybrid Four-Quartet G-Quadruplex with K+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of TEL25 Hybrid Four-Quartet G-Quadruplex with K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1101

b:32.1
occ:1.00
 O A:HOH1227 1.8 33.7 1.0
OP1 A:DT1014 2.0 30.1 1.0
O A:HOH1224 2.0 32.7 1.0
OP1 C:DT1014 2.1 27.9 1.0
O A:HOH1258 2.2 33.7 1.0
O C:HOH1250 2.2 31.7 1.0
P C:DT1014 3.2 28.7 1.0
P A:DT1014 3.3 31.3 1.0
O3' C:DG1013 3.8 26.3 1.0
O3' A:DG1013 3.8 28.8 1.0
OP2 C:DT1014 3.9 29.4 1.0
OP2 A:DT1014 4.0 32.5 1.0
O B:HOH1255 4.1 47.5 1.0
O A:HOH1233 4.1 39.7 1.0
O A:HOH1220 4.2 35.0 1.0
O C:HOH1229 4.3 46.2 1.0
O B:HOH1263 4.3 37.8 1.0
O C:HOH1211 4.4 41.8 1.0
OP1 C:DT1015 4.4 37.8 1.0
O5' C:DT1014 4.5 29.5 1.0
OP1 A:DT1015 4.5 28.1 1.0
O5' A:DT1014 4.5 30.7 1.0
C3' A:DT1014 4.6 30.1 1.0
C3' C:DT1014 4.7 33.1 1.0
C5' A:DT1014 4.8 30.9 1.0
C5' C:DT1014 4.8 29.2 1.0

Magnesium binding site 2 out of 6 in 6xt7

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Magnesium binding site 2 out of 6 in the TEL25 Hybrid Four-Quartet G-Quadruplex with K+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of TEL25 Hybrid Four-Quartet G-Quadruplex with K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1101

b:29.7
occ:0.57
 O D:HOH1234 2.0 32.0 1.0
OP1 B:DG1017 2.1 32.7 1.0
O B:HOH1241 2.1 36.5 1.0
O D:HOH1272 2.2 39.4 1.0
P B:DG1017 3.3 30.6 1.0
O3' B:DG1016 3.5 29.2 1.0
O D:HOH1221 4.0 43.9 1.0
O D:HOH1214 4.3 34.6 1.0
OP2 B:DG1017 4.3 31.5 1.0
OP1 D:DG1013 4.4 30.1 1.0
O5' B:DG1017 4.5 28.8 1.0
C5' B:DG1017 4.5 29.9 1.0
C3' B:DG1016 4.8 28.6 1.0
O B:HOH1230 5.0 47.9 1.0

Magnesium binding site 3 out of 6 in 6xt7

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Magnesium binding site 3 out of 6 in the TEL25 Hybrid Four-Quartet G-Quadruplex with K+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of TEL25 Hybrid Four-Quartet G-Quadruplex with K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1102

b:29.1
occ:1.00
 O D:HOH1236 1.9 32.0 1.0
O B:HOH1228 2.0 30.7 1.0
OP1 B:DT1014 2.0 30.6 1.0
OP1 D:DT1014 2.0 30.1 1.0
O B:HOH1243 2.1 31.6 1.0
O D:HOH1254 2.2 32.9 1.0
P B:DT1014 3.2 31.1 1.0
P D:DT1014 3.3 28.6 1.0
O3' B:DG1013 3.8 29.3 1.0
O3' D:DG1013 3.9 27.0 1.0
OP2 B:DT1014 3.9 32.0 1.0
O B:HOH1215 4.0 36.8 1.0
O A:HOH1259 4.0 49.4 1.0
OP2 D:DT1014 4.1 28.3 1.0
O D:HOH1231 4.1 41.6 1.0
O B:HOH1220 4.1 31.9 1.0
O D:HOH1274 4.1 44.6 1.0
O A:HOH1279 4.1 53.6 1.0
O A:HOH1273 4.3 34.3 1.0
O D:HOH1216 4.5 36.2 1.0
O5' B:DT1014 4.5 29.6 1.0
O5' D:DT1014 4.5 28.5 1.0
OP1 D:DT1015 4.5 33.8 1.0
OP1 B:DT1015 4.6 28.7 1.0
C3' B:DT1014 4.6 28.7 1.0
C3' D:DT1014 4.6 30.1 1.0
C5' D:DT1014 4.8 26.8 1.0
C5' B:DT1014 4.8 30.2 1.0
C2' B:DT1014 4.9 29.5 1.0
C2' D:DT1014 5.0 29.8 1.0

Magnesium binding site 4 out of 6 in 6xt7

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Magnesium binding site 4 out of 6 in the TEL25 Hybrid Four-Quartet G-Quadruplex with K+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of TEL25 Hybrid Four-Quartet G-Quadruplex with K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1101

b:29.6
occ:1.00
 O A:HOH1222 2.0 28.6 1.0
O C:HOH1218 2.0 29.7 1.0
O B:HOH1264 2.1 30.6 1.0
O A:HOH1236 2.1 28.3 1.0
O A:HOH1275 2.2 31.1 1.0
O A:HOH1274 2.2 35.5 1.0
OP2 C:DG1013 3.8 31.6 1.0
O B:HOH1210 4.2 28.9 1.0
OP2 C:DT1014 4.2 29.4 1.0
OP1 A:DG1016 4.3 31.9 1.0
O C:HOH1211 4.3 41.8 1.0
OP1 A:DT1015 4.4 28.1 1.0
O B:HOH1226 4.4 32.2 1.0
O B:HOH1263 4.5 37.8 1.0
C5' C:DG1013 4.5 30.6 1.0
C7 C:DT1014 4.8 35.3 1.0

Magnesium binding site 5 out of 6 in 6xt7

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Magnesium binding site 5 out of 6 in the TEL25 Hybrid Four-Quartet G-Quadruplex with K+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of TEL25 Hybrid Four-Quartet G-Quadruplex with K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1101

b:28.7
occ:1.00
 O B:HOH1265 2.0 30.7 1.0
O B:HOH1222 2.1 27.4 1.0
O B:HOH1266 2.1 29.6 1.0
O D:HOH1222 2.1 27.9 1.0
O D:HOH1211 2.1 28.3 1.0
O A:HOH1263 2.1 27.2 1.0
OP2 D:DG1013 3.9 28.7 1.0
OP1 B:DG1016 4.1 28.9 1.0
O B:HOH1210 4.2 28.9 1.0
O D:HOH1275 4.2 48.0 1.0
OP2 D:DT1014 4.3 28.3 1.0
O A:HOH1267 4.4 41.4 1.0
OP1 B:DT1015 4.4 28.7 1.0
O D:HOH1216 4.5 36.2 1.0
O B:HOH1221 4.5 32.4 1.0
C5' D:DG1013 4.6 27.8 1.0
C2' A:DT1015 4.7 30.1 1.0
O A:HOH1273 4.8 34.3 1.0
C7 D:DT1014 4.8 29.1 1.0
O D:HOH1210 4.9 43.0 1.0

Magnesium binding site 6 out of 6 in 6xt7

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Magnesium binding site 6 out of 6 in the TEL25 Hybrid Four-Quartet G-Quadruplex with K+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of TEL25 Hybrid Four-Quartet G-Quadruplex with K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1102

b:52.2
occ:1.00
 O D:HOH1259 2.2 55.0 1.0
OP1 D:DT1009 2.2 52.0 1.0
O D:HOH1238 2.2 50.1 1.0
OP1 D:DG1007 2.2 48.0 1.0
O D:HOH1262 2.3 59.0 1.0
O D:HOH1267 2.3 56.8 1.0
P D:DT1009 3.6 49.0 1.0
P D:DG1007 3.6 46.2 1.0
C2' D:DT1008 4.0 42.2 1.0
C3' D:DT1008 4.1 42.7 1.0
O3' D:DT1008 4.2 46.5 1.0
OP2 D:DG1007 4.3 46.0 1.0
OP2 D:DT1009 4.4 49.9 1.0
O5' D:DG1007 4.4 43.2 1.0
C5' D:DG1007 4.5 40.6 1.0
O5' D:DT1009 4.5 49.4 1.0
O3' D:DG1006 4.6 47.8 1.0
O D:HOH1204 4.7 46.5 1.0

Reference:

K.Li, L.Yatsunyk, S.Neidle. Water Spines and Networks in G-Quadruplex Structures. Nucleic Acids Res. V. 49 519 2021.
ISSN: ESSN 1362-4962
PubMed: 33290519
DOI: 10.1093/NAR/GKAA1177
Page generated: Tue Oct 1 23:39:34 2024

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