Atomistry » Magnesium » PDB 6xmq-6xz7 » 6xt7
Atomistry »
  Magnesium »
    PDB 6xmq-6xz7 »
      6xt7 »

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

Go back to Magnesium Binding Sites List in 6xt7
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

Go back to Magnesium Binding Sites List in 6xt7
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

Go back to Magnesium Binding Sites List in 6xt7
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

Go back to Magnesium Binding Sites List in 6xt7
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

Go back to Magnesium Binding Sites List in 6xt7
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

Go back to Magnesium Binding Sites List in 6xt7
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy