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Magnesium in PDB 6tpq: Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna

Enzymatic activity of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna

All present enzymatic activity of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna:
3.1.26.8;

Other elements in 6tpq:

The structure of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Magnesium Binding Sites:

Magnesium binding site 1 out of 219 in 6tpq

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Magnesium binding site 1 out of 219 in the Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg201

b:0.5
occ:1.00
OP2 V:G98 2.0 0.3 1.0
P V:G98 3.0 0.3 1.0
O5' V:G98 3.5 0.3 1.0
OP1 V:G98 3.5 0.3 1.0
OP2 V:A99 4.1 0.4 1.0
O3' V:A97 4.4 0.4 1.0
O6 V:G100 4.4 0.7 1.0
N7 V:A99 4.5 0.4 1.0
C5' V:G98 4.8 0.3 1.0
C3' V:A97 4.9 0.4 1.0
OP2 V:A71 5.0 1.0 1.0

Magnesium binding site 2 out of 219 in 6tpq

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Magnesium binding site 2 out of 219 in the Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg3001

b:0.6
occ:1.00
OP2 U:G13 2.0 0.2 1.0
OP1 U:G13 2.2 0.2 1.0
P U:G13 2.2 0.2 1.0
O5' U:G13 2.9 0.2 1.0
C5' U:G13 3.2 0.2 1.0
O3' U:A12 3.8 0.8 1.0
OP2 U:A12 4.2 0.8 1.0
C3' U:A12 4.6 0.8 1.0
C4' U:G13 4.7 0.2 1.0
C5' U:A12 4.9 0.8 1.0
O5' U:A12 5.0 0.8 1.0

Magnesium binding site 3 out of 219 in 6tpq

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Magnesium binding site 3 out of 219 in the Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg3002

b:79.5
occ:1.00
O6 U:G519 4.5 1.0 1.0
O6 U:G28 4.5 0.9 1.0
N4 U:C29 4.6 1.0 1.0
OP2 U:A26 4.7 0.2 1.0
O6 U:G518 4.8 0.4 1.0
O4 U:U27 4.8 0.5 1.0
OP2 U:A492 4.8 0.1 1.0
C5 U:U27 4.9 0.5 1.0

Magnesium binding site 4 out of 219 in 6tpq

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Magnesium binding site 4 out of 219 in the Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg3003

b:0.6
occ:1.00
OP1 U:C29 2.0 1.0 1.0
P U:C29 3.3 1.0 1.0
OP1 U:C1277 3.7 0.1 1.0
O3' U:G28 3.9 0.9 1.0
OP2 U:C29 3.9 1.0 1.0
O5' U:C29 4.5 1.0 1.0
OP1 U:C1239 4.5 0.3 1.0
C5' U:C29 4.8 1.0 1.0
C5' U:C1277 4.8 0.1 1.0

Magnesium binding site 5 out of 219 in 6tpq

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Magnesium binding site 5 out of 219 in the Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg3004

b:0.2
occ:1.00
O6 U:G80 3.6 0.4 1.0
C6 U:G80 4.6 0.4 1.0
OP1 U:A100 4.6 0.5 1.0
N1 U:G80 4.7 0.4 1.0
N7 U:G78 4.7 0.6 1.0
O6 U:G79 4.8 0.7 1.0
N7 U:G79 4.9 0.7 1.0

Magnesium binding site 6 out of 219 in 6tpq

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Magnesium binding site 6 out of 219 in the Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg3005

b:1.0
occ:1.00
OP2 U:U117 1.9 0.1 1.0
P U:U117 3.2 0.1 1.0
O5' U:U117 3.5 0.1 1.0
O3' U:A116 3.8 0.2 1.0
O6 U:G120 4.3 0.5 1.0
OP1 U:G118 4.4 0.3 1.0
OP1 U:U117 4.4 0.1 1.0
O2' U:A116 4.5 0.2 1.0
O6 U:G119 4.5 0.2 1.0
C5' U:U117 4.9 0.1 1.0
C3' U:A116 4.9 0.2 1.0
O6 U:G121 4.9 0.3 1.0
N7 U:G119 5.0 0.2 1.0
C3' U:U117 5.0 0.1 1.0

Magnesium binding site 7 out of 219 in 6tpq

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Magnesium binding site 7 out of 219 in the Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg3006

b:0.3
occ:1.00
OP2 U:G118 2.0 0.3 1.0
P U:G118 3.3 0.3 1.0
O6 U:G49 3.8 0.8 1.0
OP2 U:U147 3.8 0.7 1.0
O3' U:U117 3.9 0.1 1.0
O2' U:U117 3.9 0.1 1.0
OP1 U:G118 4.1 0.3 1.0
O5' U:G118 4.5 0.3 1.0
OP2 U:A148 4.7 0.8 1.0
C5' U:G118 4.8 0.3 1.0
C6 U:G49 4.8 0.8 1.0
C2' U:U117 4.9 0.1 1.0
C3' U:U117 4.9 0.1 1.0

Magnesium binding site 8 out of 219 in 6tpq

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Magnesium binding site 8 out of 219 in the Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg3007

b:0.5
occ:1.00
OP2 U:A176 2.0 0.7 1.0
OP1 U:G175 2.0 0.3 1.0
P U:G175 3.1 0.3 1.0
P U:A176 3.3 0.7 1.0
O3' U:A174 3.4 0.6 1.0
O5' U:G175 3.5 0.3 1.0
OP1 U:A176 3.9 0.7 1.0
O3' U:G175 4.0 0.3 1.0
C3' U:G175 4.3 0.3 1.0
O5' U:A176 4.4 0.7 1.0
OP2 U:G175 4.5 0.3 1.0
C3' U:A174 4.8 0.6 1.0
C5' U:G175 4.8 0.3 1.0
N1 U:A177 4.9 1.0 1.0

Magnesium binding site 9 out of 219 in 6tpq

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Magnesium binding site 9 out of 219 in the Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg3008

b:0.0
occ:1.00
N7 U:G178 4.1 0.8 1.0
O6 U:G178 4.2 0.8 1.0
OP1 U:A177 4.3 1.0 1.0
O6 U:G179 4.3 0.4 1.0
N7 U:G179 4.5 0.4 1.0
C5 U:G178 4.7 0.8 1.0
C6 U:G178 4.7 0.8 1.0
OP2 U:A214 4.9 0.1 1.0
C8 U:G178 5.0 0.8 1.0

Magnesium binding site 10 out of 219 in 6tpq

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Magnesium binding site 10 out of 219 in the Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg3009

b:0.9
occ:1.00
OP2 U:G189 3.5 0.2 1.0
OP2 U:G188 3.6 0.6 1.0
O6 U:G190 4.1 0.1 1.0
N7 U:G190 4.5 0.1 1.0
P U:G188 4.5 0.6 1.0
N7 U:G189 4.6 0.2 1.0
O5' U:G188 4.6 0.6 1.0
C8 U:G189 4.7 0.2 1.0
P U:G189 4.8 0.2 1.0
C6 U:G190 4.9 0.1 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 19:03:45 2024

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