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Magnesium in PDB 5no3: Rsga-Gdpnp Bound to the 30S Ribosomal Subunit (Rsga Assembly Intermediate Without US3)

Other elements in 5no3:

The structure of Rsga-Gdpnp Bound to the 30S Ribosomal Subunit (Rsga Assembly Intermediate Without US3) also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 71;

Binding sites:

The binding sites of Magnesium atom in the Rsga-Gdpnp Bound to the 30S Ribosomal Subunit (Rsga Assembly Intermediate Without US3) (pdb code 5no3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 71 binding sites of Magnesium where determined in the Rsga-Gdpnp Bound to the 30S Ribosomal Subunit (Rsga Assembly Intermediate Without US3), PDB code: 5no3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 71 in 5no3

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Magnesium binding site 1 out of 71 in the Rsga-Gdpnp Bound to the 30S Ribosomal Subunit (Rsga Assembly Intermediate Without US3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rsga-Gdpnp Bound to the 30S Ribosomal Subunit (Rsga Assembly Intermediate Without US3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1601

b:0.7
occ:1.00
N7 A:G742 4.4 0.7 1.0
O6 A:G742 4.6 0.7 1.0

Magnesium binding site 2 out of 71 in 5no3

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Magnesium binding site 2 out of 71 in the Rsga-Gdpnp Bound to the 30S Ribosomal Subunit (Rsga Assembly Intermediate Without US3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rsga-Gdpnp Bound to the 30S Ribosomal Subunit (Rsga Assembly Intermediate Without US3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1602

b:0.2
occ:1.00
O6 A:G38 3.9 0.6 1.0
C6 A:G38 4.9 0.6 1.0

Magnesium binding site 3 out of 71 in 5no3

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Magnesium binding site 3 out of 71 in the Rsga-Gdpnp Bound to the 30S Ribosomal Subunit (Rsga Assembly Intermediate Without US3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Rsga-Gdpnp Bound to the 30S Ribosomal Subunit (Rsga Assembly Intermediate Without US3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1603

b:0.1
occ:1.00
O4 A:U677 2.2 0.0 1.0
N6 A:A676 2.3 0.5 1.0
C6 A:A676 2.4 0.5 1.0
C5 A:A676 2.4 0.5 1.0
N7 A:A676 2.5 0.5 1.0
C4 A:U677 2.6 0.0 1.0
C5 A:U677 2.8 0.0 1.0
N1 A:A676 3.4 0.5 1.0
C4 A:A676 3.5 0.5 1.0
C8 A:A676 3.5 0.5 1.0
N3 A:U677 3.8 0.0 1.0
N9 A:A676 4.0 0.5 1.0
C6 A:U677 4.0 0.0 1.0
C2 A:A676 4.2 0.5 1.0
O6 A:G713 4.3 0.7 1.0
N3 A:A676 4.3 0.5 1.0
O4 A:U678 4.5 0.1 1.0
C2 A:U677 4.9 0.0 1.0
N7 A:A675 4.9 0.7 1.0
N1 A:U677 4.9 0.0 1.0

Magnesium binding site 4 out of 71 in 5no3

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Magnesium binding site 4 out of 71 in the Rsga-Gdpnp Bound to the 30S Ribosomal Subunit (Rsga Assembly Intermediate Without US3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Rsga-Gdpnp Bound to the 30S Ribosomal Subunit (Rsga Assembly Intermediate Without US3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1604

b:0.9
occ:1.00
OP1 A:A16 3.9 0.8 1.0
C5 A:U14 3.9 0.8 1.0
OP2 A:A16 4.0 0.8 1.0
OP1 A:U13 4.1 0.8 1.0
C4 A:U14 4.4 0.8 1.0
C6 A:U14 4.4 0.8 1.0
P A:A16 4.5 0.8 1.0
OP2 A:U14 4.5 0.8 1.0
O4 A:U14 4.6 0.8 1.0
O5' A:U13 4.9 0.8 1.0
OP2 A:G15 4.9 0.2 1.0

Magnesium binding site 5 out of 71 in 5no3

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Magnesium binding site 5 out of 71 in the Rsga-Gdpnp Bound to the 30S Ribosomal Subunit (Rsga Assembly Intermediate Without US3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Rsga-Gdpnp Bound to the 30S Ribosomal Subunit (Rsga Assembly Intermediate Without US3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1605

b:0.8
occ:1.00
OP1 A:A621 2.2 0.2 1.0
P A:A621 2.9 0.2 1.0
OP2 A:A621 3.3 0.2 1.0
O3' A:C620 3.3 0.8 1.0
C5' A:C620 4.4 0.8 1.0
C3' A:C620 4.4 0.8 1.0
O5' A:A621 4.4 0.2 1.0
C4' A:C620 4.6 0.8 1.0
N4 A:C618 4.9 0.6 1.0
CE1 D:TYR135 5.0 0.6 1.0

Magnesium binding site 6 out of 71 in 5no3

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Magnesium binding site 6 out of 71 in the Rsga-Gdpnp Bound to the 30S Ribosomal Subunit (Rsga Assembly Intermediate Without US3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Rsga-Gdpnp Bound to the 30S Ribosomal Subunit (Rsga Assembly Intermediate Without US3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1606

b:0.3
occ:1.00
OP2 A:G450 3.4 0.8 1.0
OP2 A:G449 3.5 0.2 1.0
O5' A:G449 4.1 0.2 1.0
O6 A:G481 4.2 0.8 1.0
N7 A:G450 4.3 0.8 1.0
P A:G449 4.4 0.2 1.0
N7 A:G481 4.6 0.8 1.0
C8 A:G449 4.7 0.2 1.0
N7 A:G449 4.7 0.2 1.0
O2' A:A451 4.7 0.3 1.0
C8 A:G450 4.8 0.8 1.0
P A:G450 4.9 0.8 1.0
OP1 A:G449 5.0 0.2 1.0

Magnesium binding site 7 out of 71 in 5no3

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Magnesium binding site 7 out of 71 in the Rsga-Gdpnp Bound to the 30S Ribosomal Subunit (Rsga Assembly Intermediate Without US3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Rsga-Gdpnp Bound to the 30S Ribosomal Subunit (Rsga Assembly Intermediate Without US3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1607

b:0.1
occ:1.00
OP2 A:C175 2.2 0.2 1.0
OP1 A:A174 2.2 0.9 1.0
P A:C175 3.3 0.2 1.0
P A:A174 3.6 0.9 1.0
C5' A:A174 3.8 0.9 1.0
O3' A:A174 3.8 0.9 1.0
OP1 A:C175 3.9 0.2 1.0
O5' A:A174 4.2 0.9 1.0
C3' A:A174 4.2 0.9 1.0
O3' A:U173 4.4 0.7 1.0
C4' A:A174 4.5 0.9 1.0
O5' A:C175 4.6 0.2 1.0
OP2 A:A174 4.7 0.9 1.0

Magnesium binding site 8 out of 71 in 5no3

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Magnesium binding site 8 out of 71 in the Rsga-Gdpnp Bound to the 30S Ribosomal Subunit (Rsga Assembly Intermediate Without US3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Rsga-Gdpnp Bound to the 30S Ribosomal Subunit (Rsga Assembly Intermediate Without US3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1608

b:0.3
occ:1.00
OP2 A:A197 2.2 0.9 1.0
O6 A:G145 2.5 0.4 1.0
P A:A197 3.1 0.9 1.0
OP1 A:A197 3.3 0.9 1.0
O6 A:G177 3.7 0.9 1.0
C6 A:G145 3.7 0.4 1.0
C5' A:A197 4.0 0.9 1.0
O5' A:A197 4.1 0.9 1.0
O3' A:A196 4.4 0.2 1.0
O6 A:G144 4.4 0.7 1.0
N1 A:G145 4.5 0.4 1.0
O6 A:G146 4.5 0.6 1.0
C3' A:A196 4.6 0.2 1.0
C6 A:G177 4.7 0.9 1.0
C5 A:G145 4.7 0.4 1.0
N7 A:G146 4.8 0.6 1.0

Magnesium binding site 9 out of 71 in 5no3

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Magnesium binding site 9 out of 71 in the Rsga-Gdpnp Bound to the 30S Ribosomal Subunit (Rsga Assembly Intermediate Without US3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Rsga-Gdpnp Bound to the 30S Ribosomal Subunit (Rsga Assembly Intermediate Without US3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1609

b:0.9
occ:1.00
O5' A:C440 2.2 0.5 1.0
C6 A:C440 2.5 0.5 1.0
C3' A:C440 2.6 0.5 1.0
OP2 A:A441 3.0 0.3 1.0
C5' A:C440 3.0 0.5 1.0
C4' A:C440 3.1 0.5 1.0
N1 A:C440 3.2 0.5 1.0
C5 A:C440 3.2 0.5 1.0
O4' A:C440 3.3 0.5 1.0
OP2 A:C440 3.3 0.5 1.0
P A:C440 3.4 0.5 1.0
C2' A:C440 3.4 0.5 1.0
C1' A:C440 3.5 0.5 1.0
N7 A:A441 3.5 0.3 1.0
O3' A:C440 3.6 0.5 1.0
C8 A:A441 3.6 0.3 1.0
P A:A441 3.8 0.3 1.0
OP1 A:C440 4.2 0.5 1.0
O5' A:A441 4.3 0.3 1.0
C2 A:C440 4.3 0.5 1.0
C4 A:C440 4.3 0.5 1.0
O3' A:U439 4.5 0.6 1.0
C3' A:U439 4.7 0.6 1.0
O2' A:C440 4.7 0.5 1.0
N3 A:C440 4.8 0.5 1.0
C5 A:A441 4.9 0.3 1.0
N9 A:A441 5.0 0.3 1.0

Magnesium binding site 10 out of 71 in 5no3

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Magnesium binding site 10 out of 71 in the Rsga-Gdpnp Bound to the 30S Ribosomal Subunit (Rsga Assembly Intermediate Without US3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Rsga-Gdpnp Bound to the 30S Ribosomal Subunit (Rsga Assembly Intermediate Without US3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1610

b:0.6
occ:1.00
OP1 A:G113 2.5 0.4 1.0
OP1 A:C308 2.7 0.0 1.0
P A:G113 3.6 0.4 1.0
P A:C308 3.7 0.0 1.0
OP2 A:C308 3.9 0.0 1.0
OP2 A:G113 3.9 0.4 1.0
O3' A:C307 4.3 0.3 1.0
O3' A:G112 4.3 0.2 1.0
OP1 A:U390 4.7 0.7 1.0
O5' A:G113 4.9 0.4 1.0

Reference:

J.P.Lopez-Alonso, T.Kaminishi, T.Kikuchi, Y.Hirata, I.Iturrioz, N.Dhimole, A.Schedlbauer, Y.Hase, S.Goto, D.Kurita, A.Muto, S.Zhou, C.Naoe, D.J.Mills, D.Gil-Carton, C.Takemoto, H.Himeno, P.Fucini, S.R.Connell. Rsga Couples the Maturation State of the 30S Ribosomal Decoding Center to Activation of Its Gtpase Pocket. Nucleic Acids Res. V. 45 6945 2017.
ISSN: ESSN 1362-4962
PubMed: 28482099
DOI: 10.1093/NAR/GKX324
Page generated: Mon Dec 14 20:56:21 2020

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