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Magnesium in PDB 1k01: Structural Basis For the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria

Protein crystallography data

The structure of Structural Basis For the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria, PDB code: 1k01 was solved by F.Schluenzen, R.Zarivach, J.Harms, A.Bashan, A.Tocilj, R.Albrecht, A.Yonath, F.Franceschi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.50
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 171.100, 409.300, 696.900, 90.00, 90.00, 90.00
R / Rfree (%) 27.5 / 32.1

Other elements in 1k01:

The structure of Structural Basis For the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structural Basis For the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria (pdb code 1k01). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structural Basis For the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria, PDB code: 1k01:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 1k01

Go back to Magnesium Binding Sites List in 1k01
Magnesium binding site 1 out of 3 in the Structural Basis For the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Basis For the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2881

b:48.2
occ:1.00
OP1 A:C2420 3.9 67.0 1.0
N3 A:A2045 3.9 71.9 1.0
O2' A:A2045 4.0 62.9 1.0
C1' A:A2045 4.4 62.9 1.0
OP1 A:C2421 4.5 63.5 1.0
C2 A:A2045 4.6 71.9 1.0
C2' A:A2045 4.6 62.9 1.0
C4 A:A2045 4.7 71.9 1.0
P A:C2420 4.9 75.3 1.0
O3' A:C2420 4.9 75.3 1.0
C5' A:C2420 4.9 75.3 1.0
OP2 A:C2420 4.9 67.0 1.0
N9 A:A2045 4.9 71.9 1.0

Magnesium binding site 2 out of 3 in 1k01

Go back to Magnesium Binding Sites List in 1k01
Magnesium binding site 2 out of 3 in the Structural Basis For the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Basis For the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2882

b:57.3
occ:1.00
O2' A:G2484 2.6 61.3 1.0
C5 A:U2485 3.2 73.1 1.0
O4 A:CLM2884 3.2 80.6 1.0
C6 A:U2485 3.2 73.1 1.0
C2' A:G2484 3.5 61.3 1.0
C1' A:G2484 3.5 61.3 1.0
C3 A:CLM2884 4.1 80.6 1.0
N3 A:G2484 4.1 73.0 1.0
C4 A:CLM2884 4.2 80.6 1.0
O5 A:CLM2884 4.3 80.6 1.0
O4' A:G2484 4.5 61.3 1.0
N9 A:G2484 4.5 73.0 1.0
O4' A:U2485 4.5 59.0 1.0
C4 A:U2485 4.5 73.1 1.0
N1 A:U2485 4.5 73.1 1.0
C4 A:G2484 4.7 73.0 1.0
C5' A:U2485 4.7 59.0 1.0
C5 A:CLM2884 4.8 80.6 1.0
C3' A:G2484 4.9 61.3 1.0

Magnesium binding site 3 out of 3 in 1k01

Go back to Magnesium Binding Sites List in 1k01
Magnesium binding site 3 out of 3 in the Structural Basis For the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Basis For the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2883

b:68.7
occ:1.00
O9B A:CLM2884 2.5 80.6 1.0
N4 A:C2431 3.1 80.5 1.0
C2 A:A2432 3.2 90.2 1.0
N1 A:A2432 3.3 90.2 1.0
C4 A:U2483 3.3 74.0 1.0
N3 A:C2431 3.3 80.5 1.0
O4 A:U2483 3.4 74.0 1.0
O2 A:U2479 3.4 78.7 1.0
C5 A:U2483 3.6 74.0 1.0
N3 A:A2432 3.6 90.2 1.0
C6 A:A2432 3.6 90.2 1.0
N3 A:U2483 3.7 74.0 1.0
C4 A:C2431 3.7 80.5 1.0
N9 A:CLM2884 3.8 80.6 1.0
C4 A:A2432 3.9 90.2 1.0
C5 A:A2432 4.0 90.2 1.0
C2 A:U2479 4.1 78.7 1.0
C6 A:U2483 4.2 74.0 1.0
N3 A:U2479 4.2 78.7 1.0
C2 A:U2483 4.3 74.0 1.0
N6 A:A2432 4.3 90.2 1.0
N1 A:U2483 4.5 74.0 1.0
C2 A:C2431 4.5 80.5 1.0
O9A A:CLM2884 4.6 80.6 1.0
C9 A:CLM2884 4.6 80.6 1.0
C10 A:CLM2884 4.8 80.6 1.0
O2 A:C2431 4.9 80.5 1.0
N9 A:A2432 4.9 90.2 1.0
N7 A:A2432 4.9 90.2 1.0

Reference:

F.Schlunzen, R.Zarivach, J.Harms, A.Bashan, A.Tocilj, R.Albrecht, A.Yonath, F.Franceschi. Structural Basis For the Interaction of Antibiotics with the Peptidyl Transferase Centre in Eubacteria. Nature V. 413 814 2001.
ISSN: ISSN 0028-0836
PubMed: 11677599
DOI: 10.1038/35101544
Page generated: Mon Dec 14 06:12:45 2020

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