Atomistry » Magnesium » PDB 4b3m-4be7 » 4b3t
Atomistry »
  Magnesium »
    PDB 4b3m-4be7 »
      4b3t »

Magnesium in PDB 4b3t: Crystal Structure of the 30S Ribosome in Complex with Compound 39

Protein crystallography data

The structure of Crystal Structure of the 30S Ribosome in Complex with Compound 39, PDB code: 4b3t was solved by C.L.Ng, K.Lang, D.Shcherbakov, T.Matt, D.Perez-Fernandez, R.Patak, M.Meyer, S.Duscha, R.Akbergenov, H.Boukari, P.Freihofer, I.Kudyba, M.S.K.Reddy, R.S.Nandurikar, V.Ramakrishnan, A.Vasella, E.C.Bottger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 3.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 401.730, 401.730, 173.910, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 24.3

Other elements in 4b3t:

The structure of Crystal Structure of the 30S Ribosome in Complex with Compound 39 also contains other interesting chemical elements:

Potassium (K) 17 atoms
Chlorine (Cl) 1 atom
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

Magnesium binding site 1 out of 219 in 4b3t

Go back to Magnesium Binding Sites List in 4b3t
Magnesium binding site 1 out of 219 in the Crystal Structure of the 30S Ribosome in Complex with Compound 39


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 30S Ribosome in Complex with Compound 39 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2545

b:78.7
occ:1.00
O6 A:G703 2.6 81.2 1.0
O2 A:C701 2.7 81.5 1.0
O2' A:C701 3.4 72.2 1.0
C6 A:G703 3.4 79.5 1.0
C1' A:C701 3.8 70.6 1.0
C2 A:C701 3.8 81.2 1.0
N1 A:G703 4.0 79.1 1.0
O3' A:C701 4.1 70.6 1.0
C2' A:C701 4.1 70.3 1.0
OP2 A:A702 4.2 77.4 1.0
C5 A:G703 4.3 78.0 1.0
N1 A:C701 4.3 80.0 1.0
N7 A:G703 4.7 78.3 1.0
C3' A:C701 4.8 70.0 1.0
P A:A702 4.8 76.6 1.0
O4' A:C701 4.9 69.7 1.0
N3 A:C701 4.9 82.5 1.0

Magnesium binding site 2 out of 219 in 4b3t

Go back to Magnesium Binding Sites List in 4b3t
Magnesium binding site 2 out of 219 in the Crystal Structure of the 30S Ribosome in Complex with Compound 39


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 30S Ribosome in Complex with Compound 39 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2546

b:94.5
occ:1.00
O6 A:G77 3.2 67.2 1.0
O6 A:G78 3.6 67.2 1.0
N7 A:G77 3.9 64.2 1.0
C6 A:G77 4.0 64.7 1.0
N7 A:G78 4.1 64.3 1.0
C5 A:G77 4.2 63.6 1.0
C6 A:G78 4.5 65.4 1.0
C5 A:G78 4.7 64.2 1.0
C8 A:G77 5.0 64.7 1.0

Magnesium binding site 3 out of 219 in 4b3t

Go back to Magnesium Binding Sites List in 4b3t
Magnesium binding site 3 out of 219 in the Crystal Structure of the 30S Ribosome in Complex with Compound 39


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 30S Ribosome in Complex with Compound 39 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2547

b:81.3
occ:1.00
OP2 A:G731 3.5 58.0 1.0
OP1 A:G730 4.0 61.3 1.0
OP1 A:C1527 4.1 54.8 1.0
N7 A:G731 4.1 50.6 1.0
C8 A:G731 4.5 50.9 1.0
C5' A:G730 4.7 63.4 1.0
P A:G730 4.8 58.8 1.0
O5' A:G730 4.8 61.8 1.0
P A:G731 4.9 58.0 1.0

Magnesium binding site 4 out of 219 in 4b3t

Go back to Magnesium Binding Sites List in 4b3t
Magnesium binding site 4 out of 219 in the Crystal Structure of the 30S Ribosome in Complex with Compound 39


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 30S Ribosome in Complex with Compound 39 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2548

b:48.5
occ:1.00
MG A:MG2707 1.6 48.3 1.0
N7 A:G581 2.1 49.8 1.0
C8 A:G581 2.8 53.1 1.0
N7 A:G758 2.9 60.8 1.0
O6 A:G758 3.3 62.1 1.0
C5 A:G581 3.3 51.4 1.0
C5 A:G758 3.6 61.5 1.0
OP2 A:G581 3.8 65.1 1.0
C6 A:G758 3.8 61.2 1.0
O6 A:G581 3.9 54.8 1.0
C8 A:G758 4.0 60.1 1.0
C6 A:G581 4.0 51.0 1.0
N9 A:G581 4.0 55.1 1.0
C4 A:G581 4.3 52.1 1.0
OP2 A:U580 4.5 65.8 1.0
O5' A:G581 4.5 62.4 1.0
P A:G581 4.8 65.7 1.0
C4 A:G758 4.9 61.1 1.0
C5 A:U580 5.0 52.4 1.0

Magnesium binding site 5 out of 219 in 4b3t

Go back to Magnesium Binding Sites List in 4b3t
Magnesium binding site 5 out of 219 in the Crystal Structure of the 30S Ribosome in Complex with Compound 39


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 30S Ribosome in Complex with Compound 39 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2549

b:61.1
occ:1.00
O6 A:G260 2.6 72.2 1.0
OP1 A:U264 2.8 58.4 1.0
O4 A:U261 2.9 69.0 1.0
NH2 T:ARG76 3.2 89.1 1.0
C6 A:G260 3.6 71.7 1.0
OP2 A:U264 3.6 60.3 1.0
P A:U264 3.7 60.1 1.0
C4 A:U261 3.9 69.3 1.0
N1 A:G260 4.2 70.6 1.0
N3 A:U261 4.4 69.1 1.0
CZ T:ARG76 4.5 89.8 1.0
C5 A:G260 4.7 72.1 1.0
O5' A:U264 4.7 60.2 1.0
O3' A:A263 4.9 60.2 1.0
N1 A:G189G 4.9 65.9 1.0
OP2 A:G265 4.9 73.3 1.0

Magnesium binding site 6 out of 219 in 4b3t

Go back to Magnesium Binding Sites List in 4b3t
Magnesium binding site 6 out of 219 in the Crystal Structure of the 30S Ribosome in Complex with Compound 39


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 30S Ribosome in Complex with Compound 39 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2550

b:63.6
occ:1.00
OP1 A:U387 2.5 62.1 1.0
O2' A:C58 2.9 67.0 1.0
OP1 A:G388 3.5 56.1 1.0
O3' A:C58 3.6 66.8 1.0
C5' A:A59 3.6 67.2 1.0
P A:U387 3.6 61.8 1.0
C5' A:U387 4.1 76.8 1.0
O5' A:U387 4.1 75.9 1.0
OP2 A:U387 4.1 60.4 1.0
C2' A:C58 4.1 67.4 1.0
MG A:MG2633 4.1 72.3 1.0
OP1 A:A59 4.2 74.5 1.0
C3' A:C58 4.3 66.9 1.0
P A:A59 4.4 75.1 1.0
O5' A:A59 4.5 67.4 1.0
C8 A:G388 4.5 68.3 1.0
C4' A:C58 4.6 67.8 1.0
P A:G388 4.6 60.2 1.0
C4' A:A59 4.7 66.5 1.0
N7 A:G388 4.8 68.7 1.0
OP2 A:G388 4.8 61.1 1.0
O3' A:C386 5.0 63.5 1.0

Magnesium binding site 7 out of 219 in 4b3t

Go back to Magnesium Binding Sites List in 4b3t
Magnesium binding site 7 out of 219 in the Crystal Structure of the 30S Ribosome in Complex with Compound 39


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 30S Ribosome in Complex with Compound 39 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2551

b:39.0
occ:1.00
O4 A:U12 2.7 57.7 1.0
O6 A:G22 2.7 59.8 1.0
O6 A:G21 3.1 68.3 1.0
O6 A:G11 3.1 56.4 1.0
N4 A:C23 3.6 56.1 1.0
C4 A:U12 3.6 54.8 1.0
C6 A:G21 3.6 65.1 1.0
N3 A:U12 3.8 55.7 1.0
C6 A:G22 3.9 58.7 1.0
N1 A:G21 4.1 65.2 1.0
C6 A:G11 4.1 56.7 1.0
C5 A:G21 4.4 63.7 1.0
N7 A:G22 4.6 57.2 1.0
C5 A:G22 4.6 57.8 1.0
C4 A:C23 4.7 54.1 1.0
N7 A:G21 4.9 64.2 1.0
N1 A:G22 4.9 59.0 1.0
C5 A:U12 5.0 54.6 1.0
N1 A:G11 5.0 56.0 1.0

Magnesium binding site 8 out of 219 in 4b3t

Go back to Magnesium Binding Sites List in 4b3t
Magnesium binding site 8 out of 219 in the Crystal Structure of the 30S Ribosome in Complex with Compound 39


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 30S Ribosome in Complex with Compound 39 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2552

b:75.5
occ:1.00
OP2 A:G667 2.8 66.4 1.0
O3' A:A665 2.8 63.4 1.0
O2' A:A665 2.9 57.6 1.0
O5' A:G666 2.9 57.3 1.0
P A:G666 3.4 70.0 1.0
OP1 A:G666 3.7 69.3 1.0
C3' A:A665 3.9 61.3 1.0
C2' A:A665 3.9 59.2 1.0
C5' A:G666 4.0 56.7 1.0
P A:G667 4.2 67.3 1.0
C3' A:G666 4.3 57.9 1.0
C4' A:A665 4.4 62.4 1.0
O2' A:C732 4.6 67.7 1.0
O3' A:G666 4.6 58.6 1.0
C8 A:G666 4.7 64.8 1.0
C4' A:G666 4.7 57.4 1.0
OP2 A:G666 4.8 70.3 1.0
N7 A:G667 4.9 58.3 1.0
N7 A:G666 4.9 64.9 1.0

Magnesium binding site 9 out of 219 in 4b3t

Go back to Magnesium Binding Sites List in 4b3t
Magnesium binding site 9 out of 219 in the Crystal Structure of the 30S Ribosome in Complex with Compound 39


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 30S Ribosome in Complex with Compound 39 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2553

b:0.3
occ:1.00
OP1 A:C883 3.0 54.6 1.0
O3' A:C882 3.5 43.6 1.0
P A:C883 3.8 52.3 1.0
O6 A:G890 4.5 68.7 1.0
OP2 A:G906 4.6 56.0 1.0
C3' A:C882 4.6 43.6 1.0
C4' A:C882 4.6 43.5 1.0
C5' A:C883 4.8 47.0 1.0
O5' A:C883 4.8 45.1 1.0
C5' A:C882 4.9 44.5 1.0
OP2 A:C883 5.0 52.5 1.0

Magnesium binding site 10 out of 219 in 4b3t

Go back to Magnesium Binding Sites List in 4b3t
Magnesium binding site 10 out of 219 in the Crystal Structure of the 30S Ribosome in Complex with Compound 39


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 30S Ribosome in Complex with Compound 39 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2554

b:67.2
occ:1.00
O6 A:G584 3.5 57.8 1.0
N2 A:G758 3.6 61.4 1.0
OP2 A:A583 3.7 64.5 1.0
O4 A:U757 3.8 66.0 1.0
N7 A:G584 3.9 52.3 1.0
N4 A:C756 3.9 56.4 1.0
O6 A:G585 4.0 57.1 1.0
C2 A:G758 4.2 62.3 1.0
C6 A:G584 4.3 55.4 1.0
N1 A:G758 4.5 61.8 1.0
C5 A:G584 4.5 54.5 1.0
C4 A:U757 4.7 63.1 1.0
N3 A:U757 4.9 62.1 1.0
OP2 A:U582 4.9 73.3 1.0

Reference:

D.Perez-Fernandez, D.Shcherbakov, T.Matt, N.C.Leong, I.Kudyba, S.Duscha, H.Boukari, R.Patak, S.R.Dubakka, K.Lang, M.Meyer, R.Akbergenov, P.Freihofer, S.Vaddi, P.Thommes, V.Ramakrishnan, A.Vasella, E.C.Bottger. 4'-O-Substitutions Determine Selectivity of Aminoglycoside Antibiotics Nat.Commun. V. 5 3112 2014.
ISSN: ESSN 2041-1723
PubMed: 24473108
DOI: 10.1038/NCOMMS4112
Page generated: Thu Aug 15 15:16:25 2024

Last articles

Ca in 2W0D
Ca in 2W0Q
Ca in 2W1Q
Ca in 2W0C
Ca in 2W08
Ca in 2VZR
Ca in 2VZQ
Ca in 2VZP
Ca in 2VYP
Ca in 2VYO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy