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Magnesium in PDB 6tnn: Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna

Other elements in 6tnn:

The structure of Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Magnesium Binding Sites:

Magnesium binding site 1 out of 221 in 6tnn

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Magnesium binding site 1 out of 221 in the Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg201

b:42.8
occ:1.00
OP1 U:U1 2.1 64.0 1.0
OE2 I:GLU106 2.3 51.2 1.0
CD I:GLU106 3.2 51.2 1.0
OE1 I:GLU106 3.4 51.2 1.0
P U:U1 3.6 64.0 1.0
OG1 I:THR103 3.7 46.7 1.0
O5' U:U1 4.3 64.0 1.0
C5' U:U1 4.3 64.0 1.0
O3' U:G0 4.4 69.6 1.0
CE1 I:TYR99 4.6 48.5 1.0
OP2 U:U1 4.6 64.0 1.0
CG I:GLU106 4.6 51.2 1.0
CA I:THR103 4.6 46.7 1.0
CB I:THR103 4.6 46.7 1.0
OH I:TYR99 4.7 48.5 1.0
CZ I:TYR99 5.0 48.5 1.0
CB I:GLU106 5.0 51.2 1.0

Magnesium binding site 2 out of 221 in 6tnn

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Magnesium binding site 2 out of 221 in the Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg3001

b:25.4
occ:1.00
OP2 U:G13 2.3 20.8 1.0
OP2 U:A12 3.3 21.7 1.0
P U:G13 3.4 20.8 1.0
OP1 U:G13 3.6 20.8 1.0
O5' U:A12 4.2 21.7 1.0
C5' U:G13 4.2 20.8 1.0
O5' U:G13 4.2 20.8 1.0
P U:A12 4.3 21.7 1.0
C5' U:A12 4.6 21.7 1.0
O3' U:A12 4.6 21.7 1.0

Magnesium binding site 3 out of 221 in 6tnn

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Magnesium binding site 3 out of 221 in the Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg3002

b:21.5
occ:1.00
O4 U:U27 4.5 19.9 1.0
N4 U:C29 4.6 17.8 1.0
C5 U:U27 4.6 19.9 1.0
O6 U:G519 4.6 20.0 1.0
O6 U:G28 4.8 17.5 1.0
OP2 U:A492 4.8 17.9 1.0
OP1 U:U493 4.8 21.4 1.0
O5' U:A492 4.9 17.9 1.0
C4 U:U27 4.9 19.9 1.0
OP2 U:A26 5.0 22.7 1.0

Magnesium binding site 4 out of 221 in 6tnn

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Magnesium binding site 4 out of 221 in the Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg3003

b:26.1
occ:1.00
OP1 U:C29 2.5 17.8 1.0
OP1 U:C1277 3.9 27.2 1.0
P U:C29 3.9 17.8 1.0
OP1 U:U1238 4.3 21.6 1.0
OP1 U:C1239 4.4 25.3 1.0
O3' U:G28 4.5 17.5 1.0
C5' U:C1277 4.7 27.2 1.0
OP2 U:G1278 4.7 33.2 1.0
OP1 U:G1278 4.7 33.2 1.0
OP2 U:C1239 4.7 25.3 1.0
OP2 U:C29 4.8 17.8 1.0
O5' U:C29 4.8 17.8 1.0
P U:C1239 4.9 25.3 1.0
O5' U:C1277 5.0 27.2 1.0
P U:G1278 5.0 33.2 1.0

Magnesium binding site 5 out of 221 in 6tnn

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Magnesium binding site 5 out of 221 in the Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg3004

b:26.6
occ:1.00
O6 U:G80 3.9 63.0 1.0
OP1 U:A100 4.5 71.0 1.0
N7 U:G78 4.5 56.8 1.0
O6 U:G79 4.6 59.5 1.0
C6 U:G80 4.8 63.0 1.0
O6 U:G78 4.9 56.8 1.0
N1 U:G80 4.9 63.0 1.0
N7 U:G79 5.0 59.5 1.0

Magnesium binding site 6 out of 221 in 6tnn

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Magnesium binding site 6 out of 221 in the Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg3005

b:25.0
occ:1.00
OP2 U:U117 2.3 23.6 1.0
P U:U117 3.4 23.6 1.0
O5' U:U117 3.5 23.6 1.0
O3' U:A116 4.0 18.1 1.0
O6 U:G119 4.3 24.4 1.0
O6 U:G120 4.4 20.9 1.0
OP1 U:G118 4.5 28.7 1.0
N7 U:G119 4.6 24.4 1.0
OP1 U:U117 4.8 23.6 1.0
C5' U:U117 4.8 23.6 1.0

Magnesium binding site 7 out of 221 in 6tnn

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Magnesium binding site 7 out of 221 in the Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg3006

b:29.0
occ:1.00
OP2 U:G118 2.9 28.7 1.0
OP2 U:U147 3.2 44.7 1.0
OP2 U:A148 3.5 33.8 1.0
P U:U147 4.0 44.7 1.0
O3' U:U117 4.1 23.6 1.0
P U:G118 4.1 28.7 1.0
O5' U:U147 4.3 44.7 1.0
OP1 U:U147 4.3 44.7 1.0
C5' U:G118 4.7 28.7 1.0
O2' U:U117 4.8 23.6 1.0
P U:A148 4.8 33.8 1.0
C8 U:A148 4.8 33.8 1.0
O6 U:G49 4.9 26.9 1.0
O5' U:G118 5.0 28.7 1.0

Magnesium binding site 8 out of 221 in 6tnn

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Magnesium binding site 8 out of 221 in the Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg3007

b:47.8
occ:1.00
O2' U:G175 2.7 57.7 1.0
OP2 U:A176 2.8 41.8 1.0
N6 U:A177 3.2 31.0 1.0
O2' U:A174 3.4 68.6 1.0
O4' U:A174 3.9 68.6 1.0
C4' U:A174 3.9 68.6 1.0
C2' U:G175 4.0 57.7 1.0
P U:A176 4.2 41.8 1.0
C1' U:A174 4.2 68.6 1.0
C2' U:A174 4.3 68.6 1.0
C6 U:A177 4.4 31.0 1.0
N7 U:A176 4.5 41.8 1.0
O5' U:A176 4.5 41.8 1.0
C8 U:A176 4.5 41.8 1.0
C3' U:A174 4.7 68.6 1.0
C2' U:A47 4.7 26.9 1.0
O2' U:A47 4.7 26.9 1.0
C3' U:G175 4.8 57.7 1.0
N7 U:A177 4.8 31.0 1.0
O3' U:G175 4.9 57.7 1.0
C5' U:A174 5.0 68.6 1.0
O3' U:A174 5.0 68.6 1.0

Magnesium binding site 9 out of 221 in 6tnn

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Magnesium binding site 9 out of 221 in the Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg3008

b:22.9
occ:1.00
O6 U:G179 3.7 28.6 1.0
N7 U:G179 4.4 28.6 1.0
O6 U:G178 4.5 27.2 1.0
N4 U:C180 4.7 34.0 1.0
C6 U:G179 4.7 28.6 1.0
N7 U:G178 4.7 27.2 1.0
OP1 U:A177 4.9 31.0 1.0
C5 U:G179 4.9 28.6 1.0

Magnesium binding site 10 out of 221 in 6tnn

Go back to Magnesium Binding Sites List in 6tnn
Magnesium binding site 10 out of 221 in the Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Mini-Rnase III (Mini-III) Bound to 50S Ribosome with Precursor 23S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg3009

b:19.4
occ:1.00
OP2 U:G189 2.4 22.5 1.0
P U:G189 3.7 22.5 1.0
OP2 U:G188 3.7 21.8 1.0
C3' U:G188 3.9 21.8 1.0
O5' U:G189 4.0 22.5 1.0
C8 U:G189 4.1 22.5 1.0
N7 U:G189 4.3 22.5 1.0
O3' U:G188 4.3 21.8 1.0
C5' U:G188 4.4 21.8 1.0
P U:G188 4.6 21.8 1.0
C8 U:G188 4.7 21.8 1.0
C4' U:G188 4.7 21.8 1.0
O5' U:G188 4.7 21.8 1.0
OP1 U:G188 4.8 21.8 1.0
N7 U:G190 4.8 26.1 1.0
OP1 U:G189 4.9 22.5 1.0
C2' U:G188 4.9 21.8 1.0

Reference:

S.Oerum, T.Dendooven, M.Catala, L.Gilet, C.Degut, A.Trinquier, M.Bourguet, P.Barraud, S.Cianferani, B.F.Luisi, C.Condon, C.Tisne. Structures of B. Subtilis Maturation Rnases Captured on 50S Ribosome with Pre-Rrnas. Mol.Cell V. 80 227 2020.
ISSN: ISSN 1097-2765
PubMed: 32991829
DOI: 10.1016/J.MOLCEL.2020.09.008
Page generated: Tue Oct 1 19:02:09 2024

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