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Magnesium in PDB 4ox9: Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit

Enzymatic activity of Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit

All present enzymatic activity of Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit:
2.1.1.180;

Protein crystallography data

The structure of Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit, PDB code: 4ox9 was solved by J.A.Dunkle, G.L.Conn, C.M.Dunham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.72 / 3.80
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 403.520, 403.520, 176.610, 90.00, 90.00, 90.00
R / Rfree (%) 23.3 / 25.7

Other elements in 4ox9:

The structure of Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit 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 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 120;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit (pdb code 4ox9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 120 binding sites of Magnesium where determined in the Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit, PDB code: 4ox9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 120 in 4ox9

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Magnesium binding site 1 out of 120 in the Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1600

b:63.8
occ:1.00
O6 A:G703 2.5 90.9 1.0
C6 A:G703 3.6 90.9 1.0
O2 A:C701 3.7 90.6 1.0
N1 A:G703 4.1 90.9 1.0
C5 A:G703 4.9 90.9 1.0
C2 A:C701 4.9 90.6 1.0

Magnesium binding site 2 out of 120 in 4ox9

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Magnesium binding site 2 out of 120 in the Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1601

b:42.8
occ:1.00
O6 A:G258 2.6 93.8 1.0
OP2 A:G266 2.7 72.1 1.0
O6 A:G257 3.1 76.5 1.0
C6 A:G258 3.6 93.8 1.0
P A:G266 3.7 72.1 1.0
OP1 A:G266 3.9 72.1 1.0
N7 A:G258 4.1 93.8 1.0
N4 A:C268 4.1 67.9 1.0
C6 A:G257 4.2 76.5 1.0
C5 A:G258 4.2 93.8 1.0
N4 A:C267 4.6 62.7 1.0
O5' A:G266 4.6 72.1 1.0
N1 A:G258 4.7 93.8 1.0
N4 A:C269 4.8 71.5 1.0
N7 A:G257 4.8 76.5 1.0
C5 A:G257 4.8 76.5 1.0
O4 A:U256 4.9 65.8 1.0
O6 A:G259 5.0 78.4 1.0

Magnesium binding site 3 out of 120 in 4ox9

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Magnesium binding site 3 out of 120 in the Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1602

b:22.8
occ:1.00
OP2 A:G731 3.7 35.7 1.0
OP1 A:C1527 3.9 39.1 1.0
N7 A:G731 4.1 35.7 1.0
OP1 A:G730 4.2 35.3 1.0
C8 A:G731 4.4 35.7 1.0
P A:G731 5.0 35.7 1.0
O5' A:G731 5.0 35.7 1.0

Magnesium binding site 4 out of 120 in 4ox9

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Magnesium binding site 4 out of 120 in the Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1603

b:36.2
occ:1.00
OP1 A:G577 3.1 27.2 1.0
OP2 A:U813 3.7 32.4 1.0
N7 A:G577 3.9 27.2 1.0
OP1 A:U813 4.1 32.4 1.0
C8 A:G577 4.3 27.2 1.0
P A:U813 4.4 32.4 1.0
P A:G577 4.5 27.2 1.0
N6 A:A816 4.7 21.4 1.0
O3' A:G576 4.9 41.2 1.0

Magnesium binding site 5 out of 120 in 4ox9

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Magnesium binding site 5 out of 120 in the Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1604

b:70.0
occ:1.00
N7 A:G799 4.0 53.7 1.0
O6 A:G800 4.0 50.5 1.0
O6 A:G798 4.0 57.0 1.0
O6 A:G799 4.2 53.7 1.0
N7 A:G798 4.2 57.0 1.0
OP2 A:A781 4.5 42.3 1.0
C6 A:G800 4.5 50.5 1.0
C6 A:G798 4.7 57.0 1.0
C5 A:G798 4.7 57.0 1.0
N1 A:G800 4.8 50.5 1.0
C5 A:G799 4.8 53.7 1.0
C6 A:G799 4.9 53.7 1.0
C8 A:G799 5.0 53.7 1.0

Magnesium binding site 6 out of 120 in 4ox9

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Magnesium binding site 6 out of 120 in the Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1605

b:8.0
occ:1.00
OP2 A:G21 3.9 39.5 1.0
OP2 A:U20 4.0 33.8 1.0
N7 A:G21 4.3 39.5 1.0
O E:GLY124 4.5 50.1 1.0
P A:U20 4.7 33.8 1.0
OP1 A:U20 4.7 33.8 1.0
C8 A:G21 4.8 39.5 1.0
OP1 A:U561 4.9 37.5 1.0
O5' A:U20 4.9 33.8 1.0
C E:GLY124 4.9 50.1 1.0

Magnesium binding site 7 out of 120 in 4ox9

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Magnesium binding site 7 out of 120 in the Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1606

b:37.6
occ:1.00
N7 A:G758 2.0 33.2 1.0
C8 A:G758 2.9 33.2 1.0
C5 A:G758 3.1 33.2 1.0
N7 A:G581 3.1 41.1 1.0
O6 A:G758 3.5 33.2 1.0
O6 A:G581 3.7 41.1 1.0
C6 A:G758 3.7 33.2 1.0
C5 A:G581 3.9 41.1 1.0
C6 A:G581 4.1 41.1 1.0
C8 A:G581 4.1 41.1 1.0
N9 A:G758 4.1 33.2 1.0
OP2 A:G758 4.1 33.2 1.0
C4 A:G758 4.2 33.2 1.0
C5 A:U757 4.2 35.3 1.0
C6 A:U757 4.5 35.3 1.0
OP2 A:U757 4.7 35.3 1.0
C4 A:U757 4.9 35.3 1.0
O5' A:G758 4.9 33.2 1.0
O5' A:U757 5.0 35.3 1.0

Magnesium binding site 8 out of 120 in 4ox9

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Magnesium binding site 8 out of 120 in the Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1607

b:61.4
occ:1.00
O6 A:G593 2.3 51.0 1.0
O6 A:G592 2.5 54.8 1.0
O4 A:U646 3.1 56.3 1.0
C6 A:G593 3.3 51.0 1.0
C6 A:G592 3.4 54.8 1.0
N7 A:G593 3.7 51.0 1.0
C5 A:G593 3.9 51.0 1.0
O6 A:G594 3.9 58.6 1.0
C4 A:U646 4.1 56.3 1.0
N4 A:C647 4.1 52.4 1.0
N4 A:C645 4.2 31.4 1.0
N1 A:G592 4.2 54.8 1.0
N3 A:U646 4.2 56.3 1.0
C5 A:G592 4.2 54.8 1.0
C6 A:G594 4.4 58.6 1.0
N1 A:G593 4.5 51.0 1.0
N7 A:G592 4.6 54.8 1.0
N3 A:C647 4.8 52.4 1.0
C4 A:C647 4.8 52.4 1.0
C5 A:G594 4.9 58.6 1.0

Magnesium binding site 9 out of 120 in 4ox9

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Magnesium binding site 9 out of 120 in the Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1608

b:56.2
occ:1.00
OP1 A:U387 2.3 63.4 1.0
O3' A:C58 2.5 64.6 1.0
OP1 A:A59 2.9 79.3 1.0
P A:A59 3.3 79.3 1.0
O2' A:C58 3.6 64.6 1.0
C3' A:C58 3.6 64.6 1.0
P A:U387 3.8 63.4 1.0
C4' A:C58 3.9 64.6 1.0
C5' A:A59 3.9 79.3 1.0
O5' A:A59 4.1 79.3 1.0
C2' A:C58 4.2 64.6 1.0
OP2 A:U387 4.5 63.4 1.0
OP2 A:A59 4.5 79.3 1.0
O3' A:C386 4.5 61.5 1.0
C5' A:C58 4.6 64.6 1.0
OP1 A:G388 4.7 65.9 1.0
O5' A:U387 4.8 63.4 1.0

Magnesium binding site 10 out of 120 in 4ox9

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Magnesium binding site 10 out of 120 in the Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of the Aminoglycoside Resistance Methyltransferase Npma Bound to the 30S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1609

b:33.7
occ:1.00
O4 A:U12 2.5 60.4 1.0
O6 A:G11 2.7 46.8 1.0
O6 A:G22 3.5 46.5 1.0
C4 A:U12 3.6 60.4 1.0
O6 A:G21 3.6 39.5 1.0
C6 A:G11 3.8 46.8 1.0
N4 A:C23 3.9 29.8 1.0
N3 A:U12 4.0 60.4 1.0
C6 A:G21 4.2 39.5 1.0
C5 A:G11 4.6 46.8 1.0
N1 A:G21 4.6 39.5 1.0
C6 A:G22 4.6 46.5 1.0
N7 A:G11 4.7 46.8 1.0
N6 A:A10 4.7 48.8 1.0
N1 A:G11 4.8 46.8 1.0
C5 A:U12 4.8 60.4 1.0
C4 A:C23 5.0 29.8 1.0

Reference:

J.A.Dunkle, K.Vinal, P.M.Desai, N.Zelinskaya, M.Savic, D.M.West, G.L.Conn, C.M.Dunham. Molecular Recognition and Modification of the 30S Ribosome By the Aminoglycoside-Resistance Methyltransferase Npma. Proc.Natl.Acad.Sci.Usa V. 111 6275 2014.
ISSN: ESSN 1091-6490
PubMed: 24717845
DOI: 10.1073/PNAS.1402789111
Page generated: Mon Dec 14 19:18:52 2020

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