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Magnesium in PDB 4aqy: Structure of Ribosome-Apramycin Complexes

Protein crystallography data

The structure of Structure of Ribosome-Apramycin Complexes, PDB code: 4aqy was solved by T.Matt, C.L.Ng, K.Lang, S.H.Sha, R.Akbergenov, D.Shcherbakov, M.Meyer, S.Duscha, J.Xie, S.R.Dubbaka, D.Perez-Fernandez, A.Vasella, V.Ramakrishnan, J.Schacht, E.C.Bottger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 3.50
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 402.180, 402.180, 175.000, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.5

Other elements in 4aqy:

The structure of Structure of Ribosome-Apramycin Complexes also contains other interesting chemical elements:

Potassium (K) 15 atoms
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

Magnesium binding site 1 out of 203 in 4aqy

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Magnesium binding site 1 out of 203 in the Structure of Ribosome-Apramycin Complexes


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Ribosome-Apramycin Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2545

b:0.0
occ:1.00
O6 A:G1482 2.4 0.7 1.0
O6 A:G1417 2.9 0.7 1.0
N7 A:G1482 3.1 0.3 1.0
C6 A:G1482 3.2 0.6 1.0
C5 A:G1482 3.5 0.2 1.0
C6 A:G1417 3.6 0.0 1.0
C5 A:G1417 4.3 0.1 1.0
C8 A:G1482 4.4 0.9 1.0
N1 A:G1417 4.5 0.2 1.0
N7 A:G1417 4.5 0.4 1.0
NC4 A:AM23005 4.5 0.8 1.0
N1 A:G1482 4.5 0.2 1.0
C4 A:G1482 4.9 0.9 1.0
C5 A:U1481 4.9 0.8 1.0

Magnesium binding site 2 out of 203 in 4aqy

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Magnesium binding site 2 out of 203 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Ribosome-Apramycin Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2546

b:0.7
occ:1.00
OP2 A:G1120 1.9 0.5 1.0
N7 A:G1120 3.1 0.6 1.0
P A:G1120 3.2 0.2 1.0
C8 A:G1120 3.2 0.7 1.0
O5' A:G1120 3.5 0.1 1.0
MG A:MG2743 3.6 0.5 1.0
C5' A:C1119 3.6 0.9 1.0
C3' A:C1119 3.6 0.1 1.0
O3' A:C1119 3.9 0.4 1.0
C4' A:C1119 4.2 0.1 1.0
OP1 A:G1120 4.4 0.4 1.0
C5 A:G1120 4.4 0.6 1.0
N9 A:G1120 4.6 1.0 1.0
C6 A:C1119 4.7 0.7 1.0
C2' A:C1119 4.8 0.7 1.0
O5' A:C1119 4.8 0.0 1.0
C5' A:G1120 4.9 0.6 1.0
O4' A:C1119 5.0 0.7 1.0

Magnesium binding site 3 out of 203 in 4aqy

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Magnesium binding site 3 out of 203 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Ribosome-Apramycin Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2547

b:0.3
occ:1.00
OP1 A:G758 1.8 0.2 1.0
C5' A:G758 2.1 87.9 1.0
P A:G758 2.2 0.7 1.0
O5' A:G758 2.3 90.7 1.0
O3' A:U757 2.4 87.3 1.0
N2 A:G821 3.1 99.2 1.0
C4' A:G758 3.6 87.3 1.0
C3' A:U757 3.6 83.7 1.0
OP2 A:G758 3.7 0.5 1.0
O2 A:C880 3.7 94.2 1.0
O2' A:U757 3.9 80.2 1.0
O6 A:G576 3.9 94.6 1.0
C2 A:G821 4.1 98.1 1.0
C2' A:U757 4.1 81.4 1.0
C1' A:C880 4.1 86.6 1.0
N3 A:G821 4.1 98.1 1.0
O4' A:G758 4.3 86.3 1.0
C3' A:G758 4.5 88.1 1.0
C2 A:C880 4.5 92.0 1.0
O4' A:C880 4.6 84.7 1.0
O2 A:C879 4.7 87.4 1.0
C4' A:U757 4.7 82.4 1.0
N1 A:C880 4.7 91.4 1.0
O2' A:C880 4.8 88.0 1.0
O3' A:G758 4.9 90.4 1.0

Magnesium binding site 4 out of 203 in 4aqy

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Magnesium binding site 4 out of 203 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Ribosome-Apramycin Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2548

b:0.0
occ:1.00
OP2 A:C307 3.1 0.5 1.0
O6 A:G309 3.3 92.0 1.0
OP2 A:G306 3.6 0.5 1.0
C6 A:G309 4.2 92.3 1.0
N4 A:C308 4.3 0.8 1.0
N7 A:G309 4.4 95.0 1.0
C5 A:C308 4.5 0.6 1.0
O6 A:G310 4.5 82.9 1.0
P A:C307 4.5 0.9 1.0
C5 A:G309 4.6 94.3 1.0
C4 A:C308 4.8 0.3 1.0
P A:G306 4.8 0.6 1.0
N4 A:C291 5.0 0.7 1.0

Magnesium binding site 5 out of 203 in 4aqy

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Magnesium binding site 5 out of 203 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Ribosome-Apramycin Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2549

b:0.9
occ:1.00
O6 A:G592 2.4 0.6 1.0
O4 A:U646 2.9 0.1 1.0
O6 A:G593 3.1 0.2 1.0
C6 A:G592 3.5 1.0 1.0
N4 A:C647 3.9 0.2 1.0
C4 A:U646 4.1 0.8 1.0
C6 A:G593 4.1 0.9 1.0
N4 A:C645 4.2 0.7 1.0
C5 A:G592 4.3 0.8 1.0
N7 A:G592 4.4 0.2 1.0
N1 A:G592 4.4 0.1 1.0
N7 A:G593 4.5 0.9 1.0
N3 A:U646 4.5 0.9 1.0
O6 A:G594 4.6 0.7 1.0
C5 A:G593 4.7 0.8 1.0
C4 A:C647 5.0 0.9 1.0

Magnesium binding site 6 out of 203 in 4aqy

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Magnesium binding site 6 out of 203 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Ribosome-Apramycin Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2550

b:0.7
occ:1.00
O N:ALA2 2.9 0.0 1.0
OP1 A:U1049 3.2 0.4 1.0
OP1 A:G1048 3.4 0.7 1.0
MG A:MG2693 3.8 89.3 1.0
C N:ALA2 4.1 0.0 1.0
P A:G1048 4.2 0.0 1.0
OP1 A:C1203 4.3 0.2 1.0
OP2 A:G1048 4.3 0.4 1.0
P A:U1049 4.5 0.7 1.0
OP2 A:A1204 4.5 0.2 1.0
CA N:ARG3 4.5 0.3 1.0
O5' A:G1048 4.5 0.5 1.0
OP1 A:A1204 4.6 0.8 1.0
OP2 A:U1049 4.8 0.4 1.0
N N:ARG3 4.8 0.3 1.0

Magnesium binding site 7 out of 203 in 4aqy

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Magnesium binding site 7 out of 203 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Ribosome-Apramycin Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2551

b:0.1
occ:1.00
O4 A:U261 2.6 94.1 1.0
O6 A:G260 2.6 0.2 1.0
OP1 A:U264 3.0 92.6 1.0
OP2 A:U264 3.5 93.8 1.0
C6 A:G260 3.5 0.8 1.0
C4 A:U261 3.7 93.4 1.0
P A:U264 3.7 92.4 1.0
NH2 T:ARG83 4.0 1.0 1.0
N3 A:U261 4.1 93.8 1.0
N1 A:G260 4.1 1.0 1.0
C5 A:G260 4.6 0.8 1.0
OP2 A:G265 4.7 0.7 1.0
O5' A:U264 4.8 91.5 1.0
O3' A:A263 4.9 87.9 1.0
C5 A:U261 4.9 93.9 1.0

Magnesium binding site 8 out of 203 in 4aqy

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Magnesium binding site 8 out of 203 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Ribosome-Apramycin Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2552

b:84.8
occ:1.00
OP1 A:U387 2.8 99.1 1.0
OP1 A:G388 3.0 0.6 1.0
O2' A:C58 3.3 0.3 1.0
O3' A:C58 3.8 0.7 1.0
MG A:MG2736 3.8 0.1 0.9
P A:U387 3.9 0.3 1.0
O5' A:A59 4.1 0.8 1.0
OP2 A:U387 4.2 0.6 1.0
P A:G388 4.3 0.1 1.0
C2' A:C58 4.4 0.6 1.0
C3' A:C58 4.5 0.2 1.0
P A:A59 4.5 1.0 1.0
C4' A:C58 4.6 0.3 1.0
O5' A:U387 4.7 0.2 1.0
OP2 A:G388 4.7 0.5 1.0
OP1 A:A59 4.8 0.4 1.0
N7 A:G388 4.8 0.4 1.0

Magnesium binding site 9 out of 203 in 4aqy

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Magnesium binding site 9 out of 203 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of Ribosome-Apramycin Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2553

b:69.3
occ:1.00
O6 A:G22 2.8 95.3 1.0
O6 A:G11 3.2 0.8 1.0
O6 A:G21 3.2 98.6 1.0
O4 A:U12 3.3 0.1 1.0
N4 A:C23 3.3 83.0 1.0
C6 A:G21 3.7 98.4 1.0
C6 A:G22 3.9 95.0 1.0
N3 A:U12 4.0 0.1 1.0
C4 A:U12 4.1 0.6 1.0
N1 A:G21 4.1 97.3 1.0
N7 A:G22 4.2 95.7 1.0
C6 A:G11 4.3 0.3 1.0
C5 A:G22 4.4 95.1 1.0
C5 A:G21 4.5 98.7 1.0
C4 A:C23 4.5 84.8 1.0
N7 A:G21 5.0 0.4 1.0

Magnesium binding site 10 out of 203 in 4aqy

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Magnesium binding site 10 out of 203 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of Ribosome-Apramycin Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2554

b:0.2
occ:1.00
O6 A:G474 3.7 0.6 1.0
N7 A:G474 4.0 0.8 1.0
O6 A:G475 4.3 0.2 1.0
C6 A:G474 4.4 0.1 1.0
C5 A:G474 4.5 0.5 1.0
O6 A:G473 4.8 0.6 1.0

Reference:

T.Matt, C.L.Ng, K.Lang, S.H.Sha, R.Akbergenov, D.Shcherbakov, M.Meyer, S.Duscha, J.Xie, S.R.Dubbaka, D.Perez-Fernandez, A.Vasella, V.Ramakrishnan, J.Schacht, E.C.Bottger. Dissociation of Antibacterial Activity and Aminoglycoside Ototoxicity in the 4-Monosubstituted 2-Deoxystreptamine Apramycin. Proc.Natl.Acad.Sci.Usa V. 109 10984 2012.
ISSN: ISSN 0027-8424
PubMed: 22699498
DOI: 10.1073/PNAS.1204073109
Page generated: Mon Dec 14 09:08:43 2020

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