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Magnesium in PDB 5lmq: Structure of Bacterial 30S-IF1-IF3-Mrna-Trna Translation Pre- Initiation Complex, Open Form (State-2A)

Other elements in 5lmq:

The structure of Structure of Bacterial 30S-IF1-IF3-Mrna-Trna Translation Pre- Initiation Complex, Open Form (State-2A) 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 - 64;

Binding sites:

The binding sites of Magnesium atom in the Structure of Bacterial 30S-IF1-IF3-Mrna-Trna Translation Pre- Initiation Complex, Open Form (State-2A) (pdb code 5lmq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 64 binding sites of Magnesium where determined in the Structure of Bacterial 30S-IF1-IF3-Mrna-Trna Translation Pre- Initiation Complex, Open Form (State-2A), PDB code: 5lmq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 64 in 5lmq

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Magnesium binding site 1 out of 64 in the Structure of Bacterial 30S-IF1-IF3-Mrna-Trna Translation Pre- Initiation Complex, Open Form (State-2A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Bacterial 30S-IF1-IF3-Mrna-Trna Translation Pre- Initiation Complex, Open Form (State-2A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1601

b:50.0
occ:1.00
OP2 A:G317 2.3 50.0 1.0
OP1 A:A315 2.9 50.0 1.0
C5' A:A315 3.2 50.0 1.0
OP1 A:G316 3.5 50.0 1.0
C4' A:A315 3.6 50.0 1.0
P A:G317 3.7 50.0 1.0
O5' A:G317 4.0 50.0 1.0
N7 A:G317 4.0 50.0 1.0
P A:A315 4.1 50.0 1.0
O5' A:A315 4.1 50.0 1.0
C8 A:G317 4.2 50.0 1.0
C3' A:A315 4.3 50.0 1.0
O3' A:A315 4.4 50.0 1.0
N7 A:G318 4.4 50.0 1.0
P A:G316 4.4 50.0 1.0
OP1 A:G317 4.6 50.0 1.0
O5' A:G316 4.6 50.0 1.0
OP2 A:G318 4.6 50.0 1.0
O3' A:G316 4.8 50.0 1.0
C3' A:G316 4.8 50.0 1.0
C8 A:G318 4.8 50.0 1.0
O4' A:A315 4.9 50.0 1.0
O3' A:C314 4.9 50.0 1.0

Magnesium binding site 2 out of 64 in 5lmq

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Magnesium binding site 2 out of 64 in the Structure of Bacterial 30S-IF1-IF3-Mrna-Trna Translation Pre- Initiation Complex, Open Form (State-2A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Bacterial 30S-IF1-IF3-Mrna-Trna Translation Pre- Initiation Complex, Open Form (State-2A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1602

b:50.0
occ:1.00
OP2 A:A172 2.7 50.0 1.0
P A:A172 3.5 50.0 1.0
OP1 A:A172 3.5 50.0 1.0
O6 A:G148 3.7 50.0 1.0
O5' A:A172 4.2 50.0 1.0
N4 A:C174 4.4 50.0 1.0
N7 A:G148 4.5 50.0 1.0
C6 A:G148 4.6 50.0 1.0
C5 A:G148 4.9 50.0 1.0
O3' A:A171 4.9 50.0 1.0

Magnesium binding site 3 out of 64 in 5lmq

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Magnesium binding site 3 out of 64 in the Structure of Bacterial 30S-IF1-IF3-Mrna-Trna Translation Pre- Initiation Complex, Open Form (State-2A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Bacterial 30S-IF1-IF3-Mrna-Trna Translation Pre- Initiation Complex, Open Form (State-2A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1603

b:50.0
occ:1.00
OP1 A:U793 2.4 50.0 1.0
O6 A:G785 3.3 50.0 1.0
O6 A:G786 3.5 50.0 1.0
P A:U793 3.8 50.0 1.0
C6 A:G785 4.1 50.0 1.0
N6 A:A787 4.2 50.0 1.0
N7 A:G786 4.3 50.0 1.0
N7 A:G785 4.3 50.0 1.0
OP2 A:U793 4.4 50.0 1.0
C6 A:G786 4.5 50.0 1.0
C5 A:G785 4.5 50.0 1.0
O3' A:A792 4.6 50.0 1.0
C5 A:G786 4.8 50.0 1.0
O5' A:U793 4.9 50.0 1.0

Magnesium binding site 4 out of 64 in 5lmq

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Magnesium binding site 4 out of 64 in the Structure of Bacterial 30S-IF1-IF3-Mrna-Trna Translation Pre- Initiation Complex, Open Form (State-2A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Bacterial 30S-IF1-IF3-Mrna-Trna Translation Pre- Initiation Complex, Open Form (State-2A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1604

b:50.0
occ:1.00
OP2 A:A119 3.4 50.0 1.0
OP1 A:A119 3.8 50.0 1.0
P A:A119 4.0 50.0 1.0
O4 A:U287 4.2 50.0 1.0
OP2 A:G285 4.4 50.0 1.0
O5' A:A119 4.7 50.0 1.0
N7 A:G286 5.0 50.0 1.0

Magnesium binding site 5 out of 64 in 5lmq

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Magnesium binding site 5 out of 64 in the Structure of Bacterial 30S-IF1-IF3-Mrna-Trna Translation Pre- Initiation Complex, Open Form (State-2A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Bacterial 30S-IF1-IF3-Mrna-Trna Translation Pre- Initiation Complex, Open Form (State-2A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1605

b:50.0
occ:1.00
OP1 A:A1500 2.0 50.0 1.0
OP1 A:G1508 2.0 50.0 1.0
OP1 A:G1505 2.6 50.0 1.0
O3' A:G1504 2.9 50.0 1.0
P A:G1508 3.1 50.0 1.0
O3' A:A1507 3.2 50.0 1.0
P A:A1500 3.3 50.0 1.0
P A:G1505 3.3 50.0 1.0
OP2 A:A1500 3.9 50.0 1.0
C5' A:G1508 4.1 50.0 1.0
C5' A:G1505 4.1 50.0 1.0
O5' A:G1505 4.1 50.0 1.0
O5' A:G1508 4.1 50.0 1.0
C3' A:G1504 4.1 50.0 1.0
O5' A:G1504 4.1 50.0 1.0
O5' A:A1500 4.2 50.0 1.0
OP2 A:G1508 4.2 50.0 1.0
O3' A:A1499 4.4 50.0 1.0
OP1 A:G1504 4.4 50.0 1.0
O2' A:U1506 4.5 50.0 1.0
OP2 A:G1505 4.6 50.0 1.0
C3' A:A1507 4.6 50.0 1.0
C5' A:A1500 4.6 50.0 1.0
C2' A:U1506 4.7 50.0 1.0
OP2 A:C1501 5.0 50.0 1.0
P A:G1504 5.0 50.0 1.0

Magnesium binding site 6 out of 64 in 5lmq

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Magnesium binding site 6 out of 64 in the Structure of Bacterial 30S-IF1-IF3-Mrna-Trna Translation Pre- Initiation Complex, Open Form (State-2A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Bacterial 30S-IF1-IF3-Mrna-Trna Translation Pre- Initiation Complex, Open Form (State-2A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1606

b:50.0
occ:1.00
O4 A:U125 2.2 50.0 1.0
N3 A:C121 2.2 50.0 1.0
O2 A:C121 2.6 50.0 1.0
O6 A:G124 2.7 50.0 1.0
C2 A:C121 2.8 50.0 1.0
O6 A:G236 3.1 50.0 1.0
C4 A:U125 3.1 50.0 1.0
C4 A:C121 3.3 50.0 1.0
O6 A:G126 3.3 50.0 1.0
N3 A:U125 3.5 50.0 1.0
N4 A:C121 3.6 50.0 1.0
C6 A:G124 3.6 50.0 1.0
N4 A:C237 3.7 50.0 1.0
N4 A:C235 3.8 50.0 1.0
C6 A:G126 4.1 50.0 1.0
N1 A:C121 4.1 50.0 1.0
C6 A:G236 4.2 50.0 1.0
C5 A:U125 4.4 50.0 1.0
C4 A:C235 4.4 50.0 1.0
C5 A:G124 4.5 50.0 1.0
N1 A:G124 4.5 50.0 1.0
C5 A:C121 4.5 50.0 1.0
N1 A:G126 4.5 50.0 1.0
N7 A:G124 4.7 50.0 1.0
C2 A:U125 4.8 50.0 1.0
C6 A:C121 4.8 50.0 1.0
C4 A:C237 4.8 50.0 1.0
N7 A:G236 4.9 50.0 1.0
C5 A:C235 4.9 50.0 1.0
C5 A:G236 5.0 50.0 1.0

Magnesium binding site 7 out of 64 in 5lmq

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Magnesium binding site 7 out of 64 in the Structure of Bacterial 30S-IF1-IF3-Mrna-Trna Translation Pre- Initiation Complex, Open Form (State-2A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Bacterial 30S-IF1-IF3-Mrna-Trna Translation Pre- Initiation Complex, Open Form (State-2A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1607

b:50.0
occ:1.00
OP2 A:A195 2.1 50.0 1.0
O4 A:U180 2.8 50.0 1.0
C5' A:A195 3.3 50.0 1.0
P A:A195 3.4 50.0 1.0
O5' A:A195 3.5 50.0 1.0
O6 A:G181 3.8 50.0 1.0
N7 A:A179 3.8 50.0 1.0
C4 A:U180 3.8 50.0 1.0
C5 A:U180 4.3 50.0 1.0
OP1 A:A195 4.4 50.0 1.0
O3' A:C194 4.4 50.0 1.0
C3' A:C194 4.5 50.0 1.0
C8 A:A179 4.5 50.0 1.0
OP2 A:A179 4.6 50.0 1.0
N6 A:A179 4.6 50.0 1.0
C5 A:A179 4.6 50.0 1.0
O5' A:C194 4.8 50.0 1.0
C4' A:A195 4.8 50.0 1.0
C6 A:G181 5.0 50.0 1.0
C5 A:C178 5.0 50.0 1.0

Magnesium binding site 8 out of 64 in 5lmq

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Magnesium binding site 8 out of 64 in the Structure of Bacterial 30S-IF1-IF3-Mrna-Trna Translation Pre- Initiation Complex, Open Form (State-2A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Bacterial 30S-IF1-IF3-Mrna-Trna Translation Pre- Initiation Complex, Open Form (State-2A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1608

b:50.0
occ:1.00
OP2 A:C749 2.1 50.0 1.0
OP2 A:G750 2.5 50.0 1.0
P A:C749 3.5 50.0 1.0
N7 A:G750 3.5 50.0 1.0
O2' A:C748 3.6 50.0 1.0
P A:G750 3.9 50.0 1.0
C8 A:G750 4.0 50.0 1.0
O5' A:C749 4.1 50.0 1.0
O5' A:G750 4.3 50.0 1.0
O6 A:G752 4.3 50.0 1.0
OP1 A:C749 4.3 50.0 1.0
O3' A:C748 4.5 50.0 1.0
C2' A:C748 4.5 50.0 1.0
C3' A:C749 4.5 50.0 1.0
C5 A:G750 4.6 50.0 1.0
O3' A:C749 4.7 50.0 1.0
OP1 A:G750 5.0 50.0 1.0

Magnesium binding site 9 out of 64 in 5lmq

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Magnesium binding site 9 out of 64 in the Structure of Bacterial 30S-IF1-IF3-Mrna-Trna Translation Pre- Initiation Complex, Open Form (State-2A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of Bacterial 30S-IF1-IF3-Mrna-Trna Translation Pre- Initiation Complex, Open Form (State-2A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1609

b:50.0
occ:1.00
OP2 A:G309 4.5 50.0 1.0
N7 A:G309 4.7 50.0 1.0
N7 A:G310 4.8 50.0 1.0
NZ P:LYS27 4.9 50.0 1.0
O6 A:G309 5.0 50.0 1.0
OP2 A:C308 5.0 50.0 1.0
O6 A:G310 5.0 50.0 1.0

Magnesium binding site 10 out of 64 in 5lmq

Go back to Magnesium Binding Sites List in 5lmq
Magnesium binding site 10 out of 64 in the Structure of Bacterial 30S-IF1-IF3-Mrna-Trna Translation Pre- Initiation Complex, Open Form (State-2A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of Bacterial 30S-IF1-IF3-Mrna-Trna Translation Pre- Initiation Complex, Open Form (State-2A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1610

b:50.0
occ:1.00
OP1 A:C370 4.0 50.0 1.0
OP2 A:C370 4.0 50.0 1.0
OP1 A:G371 4.2 50.0 1.0
P A:C370 4.3 50.0 1.0
OP2 A:G371 4.4 50.0 1.0
O5' A:C370 4.4 50.0 1.0
P A:G371 4.8 50.0 1.0

Reference:

T.Hussain, J.L.Llacer, B.T.Wimberly, J.S.Kieft, V.Ramakrishnan. Large-Scale Movements of IF3 and Trna During Bacterial Translation Initiation. Cell V. 167 133 2016.
ISSN: ISSN 1097-4172
PubMed: 27662086
DOI: 10.1016/J.CELL.2016.08.074
Page generated: Mon Dec 14 20:48:18 2020

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