Atomistry » Magnesium » PDB 3dev-3dtr » 3dll
Atomistry »
  Magnesium »
    PDB 3dev-3dtr »
      3dll »

Magnesium in PDB 3dll: The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning

Protein crystallography data

The structure of The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning, PDB code: 3dll was solved by D.N.Wilson, F.Schluenzen, J.M.Harms, A.L.Starosta, S.R.Connell, P.Fucini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.98 / 3.50
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 169.700, 410.000, 695.000, 90.00, 90.00, 90.00
R / Rfree (%) 25.9 / 28

Other elements in 3dll:

The structure of The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning also contains other interesting chemical elements:

Fluorine (F) 1 atom
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 - 35;

Binding sites:

The binding sites of Magnesium atom in the The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning (pdb code 3dll). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 35 binding sites of Magnesium where determined in the The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning, PDB code: 3dll:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 35 in 3dll

Go back to Magnesium Binding Sites List in 3dll
Magnesium binding site 1 out of 35 in the The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg124

b:11.4
occ:1.00
O6 Z:G99 2.8 50.0 1.0
N4 Z:C98 3.1 68.6 1.0
N7 Z:G99 3.2 50.1 1.0
C6 Z:G99 3.5 50.1 1.0
O6 Z:G100 3.6 47.6 1.0
C5 Z:G99 3.7 50.3 1.0
C4 Z:C98 3.7 67.0 1.0
N3 Z:C98 4.2 66.5 1.0
O4 Z:U82 4.2 40.9 1.0
N7 Z:G100 4.3 49.0 1.0
C8 Z:G99 4.4 50.1 1.0
C6 Z:G100 4.4 48.4 1.0
C5 Z:C98 4.4 66.7 1.0
C5 Z:G100 4.7 49.0 1.0
N3 Z:U82 4.7 40.5 1.0
N1 Z:G99 4.8 49.8 1.0
C4 Z:U82 4.9 39.9 1.0
C4 Z:G99 5.0 50.4 1.0

Magnesium binding site 2 out of 35 in 3dll

Go back to Magnesium Binding Sites List in 3dll
Magnesium binding site 2 out of 35 in the The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg125

b:1.1
occ:1.00
O6 Z:G85 3.7 24.4 1.0
N7 Z:G85 3.8 27.7 1.0
OP2 Z:C83 4.3 38.2 1.0
O6 Z:G84 4.4 26.8 1.0
N7 Z:G84 4.4 29.1 1.0
N6 Z:A86 4.5 44.8 1.0
C6 Z:G85 4.5 25.6 1.0
C5 Z:G85 4.5 25.9 1.0
C6 Z:G84 4.8 27.0 1.0
C5 Z:G84 4.8 28.0 1.0
C8 Z:G85 4.9 27.1 1.0

Magnesium binding site 3 out of 35 in 3dll

Go back to Magnesium Binding Sites List in 3dll
Magnesium binding site 3 out of 35 in the The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg126

b:12.7
occ:1.00
O2' Z:C98 4.1 62.9 1.0
C1' Z:G84 4.8 31.9 1.0
N3 Z:G84 4.8 26.6 1.0
O2 Z:C98 4.9 66.1 1.0
O2 Z:C83 4.9 29.4 1.0
C1' Z:G99 5.0 52.3 1.0

Magnesium binding site 4 out of 35 in 3dll

Go back to Magnesium Binding Sites List in 3dll
Magnesium binding site 4 out of 35 in the The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg127

b:3.9
occ:1.00
OP2 Z:G105 3.7 57.2 1.0
N6 Z:A74 4.2 68.5 1.0
OP1 Z:A104 4.2 59.8 1.0
OP2 Z:C73 4.3 68.7 1.0
N7 Z:A74 4.4 67.7 1.0
P Z:G105 4.9 56.6 1.0
C6 Z:A74 4.9 67.7 1.0
C5 Z:A74 4.9 67.7 1.0

Magnesium binding site 5 out of 35 in 3dll

Go back to Magnesium Binding Sites List in 3dll
Magnesium binding site 5 out of 35 in the The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2881

b:10.7
occ:1.00
OP1 X:G961 3.0 39.6 1.0
OP1 Z:A91 3.7 52.3 1.0
O6 Z:G89 4.1 64.8 1.0
C5' X:G961 4.2 39.3 1.0
P X:G961 4.3 39.5 1.0
O5' X:G961 4.5 39.3 1.0

Magnesium binding site 6 out of 35 in 3dll

Go back to Magnesium Binding Sites List in 3dll
Magnesium binding site 6 out of 35 in the The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2882

b:49.4
occ:1.00
OP1 X:G2466 3.3 34.4 1.0
N1 Z:A91 3.8 40.7 1.0
C2 Z:A91 3.9 40.2 1.0
P X:G2466 4.5 33.5 1.0
O3' X:G2465 4.7 34.2 1.0
O2' X:A1039 4.8 55.3 1.0
N4 Z:C90 4.8 47.3 1.0
C6 Z:A91 4.8 40.4 1.0
N3 Z:A91 5.0 39.5 1.0

Magnesium binding site 7 out of 35 in 3dll

Go back to Magnesium Binding Sites List in 3dll
Magnesium binding site 7 out of 35 in the The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2883

b:1.1
occ:1.00
O4 X:U2222 3.3 22.4 1.0
O4 X:U2057 3.4 6.7 1.0
O4 X:U2058 4.0 11.7 1.0
O6 X:G2221 4.1 9.9 1.0
N6 X:A2060 4.3 23.1 1.0
C4 X:U2222 4.3 21.0 1.0
C4 X:U2057 4.3 6.2 1.0
N7 X:G2217 4.4 29.6 1.0
C5 X:U2057 4.7 6.5 1.0
C8 X:G2217 4.8 29.7 1.0
C5 X:U2222 4.9 20.4 1.0
N7 X:G2221 5.0 12.0 1.0

Magnesium binding site 8 out of 35 in 3dll

Go back to Magnesium Binding Sites List in 3dll
Magnesium binding site 8 out of 35 in the The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2884

b:19.4
occ:1.00
OP1 X:G2415 2.7 8.2 1.0
OP2 X:G2415 3.2 7.9 1.0
P X:G2415 3.3 8.3 1.0
O2' X:U2224 4.2 18.0 1.0
C5' X:G2415 4.2 8.2 1.0
O5' X:G2415 4.2 8.2 1.0
OP2 X:G2225 4.5 21.1 1.0
O3' X:A2414 4.7 7.3 1.0

Magnesium binding site 9 out of 35 in 3dll

Go back to Magnesium Binding Sites List in 3dll
Magnesium binding site 9 out of 35 in the The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2885

b:45.2
occ:1.00
OP2 X:C1385 3.1 39.7 1.0
OP2 X:A1386 3.2 55.0 1.0
O4 X:U1370 3.6 42.0 1.0
N2 X:G1371 3.6 60.9 1.0
OP1 X:C1385 3.6 39.3 1.0
P X:C1385 3.8 39.5 1.0
N1 X:G1371 3.9 60.1 1.0
C2 X:G1371 4.3 60.7 1.0
O5' X:C1385 4.4 41.6 1.0
P X:A1386 4.7 54.7 1.0
C4 X:U1370 4.8 41.9 1.0
O6 X:G1387 4.9 36.0 1.0
O6 X:G1369 4.9 41.2 1.0
C6 X:G1371 5.0 59.3 1.0

Magnesium binding site 10 out of 35 in 3dll

Go back to Magnesium Binding Sites List in 3dll
Magnesium binding site 10 out of 35 in the The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2886

b:15.4
occ:1.00
OP1 X:A747 2.9 9.0 1.0
O3' X:G746 3.4 8.6 1.0
P X:A747 3.6 9.8 1.0
OP2 X:A747 4.0 8.9 1.0
C5' X:G746 4.1 10.2 1.0
C3' X:G746 4.4 8.4 1.0
C4' X:G746 4.4 9.3 1.0
C5' X:A1753 4.6 16.2 1.0
OP1 X:A1753 4.7 7.6 1.0
OP2 X:G1754 4.7 15.0 1.0
OP1 X:G746 4.9 10.0 1.0

Reference:

D.N.Wilson, F.Schluenzen, J.M.Harms, A.L.Starosta, S.R.Connell, P.Fucini. The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl-Transferase Center and Effect Trna Positioning Proc.Natl.Acad.Sci.Usa V. 105 13339 2008.
ISSN: ISSN 0027-8424
PubMed: 18757750
DOI: 10.1073/PNAS.0804276105
Page generated: Mon Dec 14 08:04:31 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy