Atomistry » Magnesium » PDB 7xam-7xqx » 7xd6
Atomistry »
  Magnesium »
    PDB 7xam-7xqx »
      7xd6 »

Magnesium in PDB 7xd6: The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Magnesium atom in the The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon (pdb code 7xd6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 28 binding sites of Magnesium where determined in the The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon, PDB code: 7xd6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 28 in 7xd6

Go back to Magnesium Binding Sites List in 7xd6
Magnesium binding site 1 out of 28 in the The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg501

b:20.7
occ:0.77
N7 N:G111 4.3 27.1 1.0
O6 N:G111 4.3 27.1 1.0
O6 N:G112 4.5 28.7 1.0
N7 N:G112 4.6 28.7 1.0
O6 N:G110 4.9 25.9 1.0
N7 N:G110 5.0 25.9 1.0
C6 N:G111 5.0 27.1 1.0
C5 N:G111 5.0 27.1 1.0

Magnesium binding site 2 out of 28 in 7xd6

Go back to Magnesium Binding Sites List in 7xd6
Magnesium binding site 2 out of 28 in the The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg502

b:29.4
occ:1.00
OP2 N:C262 2.0 33.0 1.0
OP1 N:A207 2.2 31.0 1.0
P N:C262 3.4 33.0 1.0
P N:A207 3.6 31.0 1.0
O5' N:C262 3.7 33.0 1.0
O3' N:A206 4.2 34.3 1.0
OP2 N:A263 4.2 32.2 1.0
OP1 N:C262 4.3 33.0 1.0
OP2 N:A207 4.3 31.0 1.0
O3' N:A261 4.5 24.8 1.0
C3' N:A261 4.5 24.8 1.0
O5' N:A207 4.7 31.0 1.0
O2 N:U305 4.8 21.6 1.0
C5' N:A207 4.9 31.0 1.0
C5' N:C262 5.0 33.0 1.0

Magnesium binding site 3 out of 28 in 7xd6

Go back to Magnesium Binding Sites List in 7xd6
Magnesium binding site 3 out of 28 in the The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg503

b:40.4
occ:0.87
O6 N:G116 4.0 45.3 1.0
O4 N:U205 4.3 40.5 1.0
N7 N:G116 4.4 45.3 1.0
OP2 N:A114 4.4 37.0 1.0
O6 N:G117 4.5 47.4 1.0
OP2 N:A115 4.5 41.8 1.0
N7 N:A115 4.5 41.8 1.0
C6 N:G116 4.9 45.3 1.0
N4 N:C204 4.9 45.0 1.0

Magnesium binding site 4 out of 28 in 7xd6

Go back to Magnesium Binding Sites List in 7xd6
Magnesium binding site 4 out of 28 in the The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg504

b:37.6
occ:0.78
OP2 N:A187 2.0 49.2 1.0
OP1 N:A184 2.0 27.5 1.0
OP1 N:A186 2.3 42.0 1.0
OP2 N:G188 3.1 39.9 1.0
P N:A184 3.4 27.5 1.0
P N:A187 3.4 49.2 1.0
P N:G188 3.7 39.9 1.0
P N:A186 3.8 42.0 1.0
OP1 N:G188 3.8 39.9 1.0
O3' N:A187 3.9 49.2 1.0
O3' N:A183 4.0 30.7 1.0
O5' N:A187 4.0 49.2 1.0
OP2 N:A184 4.1 27.5 1.0
C5' N:A187 4.2 49.2 1.0
OP1 N:A187 4.2 49.2 1.0
O5' N:A184 4.4 27.5 1.0
O3' N:A186 4.5 42.0 1.0
OP2 N:A186 4.5 42.0 1.0
O5' N:A186 4.5 42.0 1.0
C3' N:A186 4.6 42.0 1.0
C5' N:A186 4.7 42.0 1.0
C3' N:A187 4.7 49.2 1.0
C4' N:A187 4.8 49.2 1.0
O3' N:U185 4.8 36.2 1.0
C5' N:A184 4.8 27.5 1.0

Magnesium binding site 5 out of 28 in 7xd6

Go back to Magnesium Binding Sites List in 7xd6
Magnesium binding site 5 out of 28 in the The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg505

b:30.2
occ:0.85
OP2 N:A184 2.1 27.5 1.0
OP2 N:A186 2.2 42.0 1.0
OP1 N:A183 2.2 30.7 1.0
P N:A186 3.6 42.0 1.0
P N:A184 3.6 27.5 1.0
P N:A183 3.6 30.7 1.0
O5' N:A183 4.2 30.7 1.0
OP1 N:A186 4.3 42.0 1.0
C3' N:A183 4.4 30.7 1.0
N7 N:A184 4.4 27.5 1.0
OP2 N:A183 4.4 30.7 1.0
O5' N:A186 4.4 42.0 1.0
O5' N:A184 4.4 27.5 1.0
OP1 N:A184 4.5 27.5 1.0
O3' N:A183 4.5 30.7 1.0
N7 N:A186 4.6 42.0 1.0
C8 N:A186 4.6 42.0 1.0
C8 N:A184 4.6 27.5 1.0
O3' N:U185 4.6 36.2 1.0
O3' N:U182 4.7 42.8 1.0
C5' N:A183 4.8 30.7 1.0
C3' N:U185 4.8 36.2 1.0
C2 N:A139 4.9 45.2 1.0

Magnesium binding site 6 out of 28 in 7xd6

Go back to Magnesium Binding Sites List in 7xd6
Magnesium binding site 6 out of 28 in the The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg506

b:25.9
occ:0.81
N7 N:G188 3.5 39.9 1.0
O6 N:G188 4.0 39.9 1.0
OP2 N:U168 4.2 35.6 1.0
OP1 N:U168 4.3 35.6 1.0
C5 N:G188 4.4 39.9 1.0
OP1 N:C165 4.4 44.7 1.0
OP2 N:A183 4.4 30.7 1.0
C8 N:G188 4.5 39.9 1.0
C6 N:G188 4.6 39.9 1.0
C8 N:A183 4.6 30.7 1.0
N7 N:A183 4.6 30.7 1.0
P N:U168 4.8 35.6 1.0
OP2 N:C166 4.8 44.3 1.0
OP1 N:U182 4.9 42.8 1.0
OP1 N:C166 4.9 44.3 1.0

Magnesium binding site 7 out of 28 in 7xd6

Go back to Magnesium Binding Sites List in 7xd6
Magnesium binding site 7 out of 28 in the The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg507

b:41.1
occ:0.84
O6 N:G164 2.2 46.9 1.0
N7 N:G163 2.7 50.3 1.0
C6 N:G164 3.2 46.9 1.0
C8 N:G163 3.6 50.3 1.0
C5 N:G163 3.7 50.3 1.0
O6 N:G163 3.9 50.3 1.0
C5 N:G164 4.0 46.9 1.0
N7 N:G164 4.1 46.9 1.0
C6 N:G163 4.1 50.3 1.0
OP2 N:G163 4.2 50.3 1.0
N1 N:G164 4.3 46.9 1.0
N7 N:A178 4.5 59.0 1.0
OP2 N:U162 4.5 57.4 1.0
N6 N:A178 4.6 59.0 1.0
N9 N:G163 4.7 50.3 1.0
C4 N:G163 4.8 50.3 1.0

Magnesium binding site 8 out of 28 in 7xd6

Go back to Magnesium Binding Sites List in 7xd6
Magnesium binding site 8 out of 28 in the The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg508

b:47.7
occ:0.78
OP2 N:A140 3.1 46.8 1.0
N7 N:G141 3.4 52.1 1.0
O4 N:U142 3.9 58.6 1.0
P N:A140 4.1 46.8 1.0
O6 N:G141 4.2 52.1 1.0
C8 N:G141 4.2 52.1 1.0
C5 N:G141 4.3 52.1 1.0
O5' N:A140 4.3 46.8 1.0
OP1 N:A140 4.5 46.8 1.0
C6 N:G141 4.6 52.1 1.0
OP2 N:G141 4.6 52.1 1.0
C4 N:U142 4.7 58.6 1.0
C5 N:U142 4.9 58.6 1.0

Magnesium binding site 9 out of 28 in 7xd6

Go back to Magnesium Binding Sites List in 7xd6
Magnesium binding site 9 out of 28 in the The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg509

b:80.3
occ:0.80
O6 N:G148 3.0 78.3 1.0
N7 N:G148 3.3 78.3 1.0
C6 N:G148 3.7 78.3 1.0
C5 N:G148 3.8 78.3 1.0
O6 N:G149 3.9 75.0 1.0
O4 N:U155 4.3 69.0 1.0
O6 N:G147 4.4 80.5 1.0
C8 N:G148 4.5 78.3 1.0
C6 N:G147 4.7 80.5 1.0
N7 N:G149 4.7 75.0 1.0
C6 N:G149 4.8 75.0 1.0
N1 N:G148 5.0 78.3 1.0
N7 N:G147 5.0 80.5 1.0
C5 N:G147 5.0 80.5 1.0

Magnesium binding site 10 out of 28 in 7xd6

Go back to Magnesium Binding Sites List in 7xd6
Magnesium binding site 10 out of 28 in the The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of The Tet-S2 State with A Pseudoknotted 4-Way Junction of Wild-Type Tetrahymena Group I Intron with 30NT 3'/5'-Exon within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg510

b:74.3
occ:0.87
OP2 N:G150 2.0 73.9 1.0
P N:G150 3.2 73.9 1.0
O5' N:G150 3.5 73.9 1.0
OP1 N:G150 4.0 73.9 1.0
C8 N:G150 4.2 73.9 1.0
N7 N:G150 4.3 73.9 1.0
OP2 N:A151 4.3 75.4 1.0
O3' N:G149 4.4 75.0 1.0
C3' N:G149 4.7 75.0 1.0
OP2 N:G149 4.8 75.0 1.0
C5' N:G150 4.9 73.9 1.0

Reference:

B.Luo, C.Zhang, X.Ling, S.Mukherjee, G.Jia, J.Xie, X.Jia, L.Liu, E.F.Baulin, Y.Luo, L.Jiang, H.Dong, X.Wei, J.M.Bujnicki, Z.Su. Cryo-Em Reveals Dynamics of Tetrahymena Group I Intron Self-Splicing Nat Catal 2023.
ISSN: ESSN 2520-1158
DOI: 10.1038/S41929-023-00934-3
Page generated: Thu Oct 3 12:13:46 2024

Last articles

Mg in 8AV7
Mg in 8AV8
Mg in 8AV4
Mg in 8AV3
Mg in 8AV0
Mg in 8AV5
Mg in 8AUY
Mg in 8AU2
Mg in 8ASN
Mg in 8AUS
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy