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Zinc 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

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning, PDB code: 3dll:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3dll

Go back to Zinc Binding Sites List in 3dll
Zinc binding site 1 out of 2 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 Zinc with other atoms in the Zn 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
Y:Zn61

b:89.0
occ:1.00
SG Y:CYS36 2.2 29.5 1.0
CB Y:CYS33 2.2 32.6 1.0
O Y:GLY38 2.5 22.5 1.0
SG Y:CYS46 2.6 7.9 1.0
SG Y:CYS33 3.0 33.6 1.0
N Y:GLY38 3.4 27.9 1.0
C Y:GLY38 3.5 22.9 1.0
CA Y:CYS33 3.6 31.5 1.0
CB Y:CYS36 3.7 30.1 1.0
CB Y:CYS46 3.7 4.9 1.0
CA Y:GLY38 3.8 25.1 1.0
N Y:HIS37 3.8 27.9 1.0
N Y:CYS33 3.9 30.8 1.0
C Y:CYS36 4.1 28.0 1.0
C Y:HIS37 4.1 28.6 1.0
CA Y:CYS36 4.3 29.0 1.0
CB Y:LYS40 4.3 14.1 1.0
CA Y:HIS37 4.4 29.1 1.0
N Y:CYS36 4.4 30.3 1.0
C Y:CYS33 4.5 31.4 1.0
SG Y:CYS49 4.5 10.4 1.0
O Y:CYS36 4.7 27.0 1.0
CB Y:ASN48 4.7 9.0 1.0
N Y:LYS40 4.7 13.8 1.0
N Y:LYS39 4.7 20.2 1.0
ND2 Y:ASN48 4.8 12.5 1.0
O Y:CYS33 4.9 31.8 1.0
C Y:LYS39 4.9 15.3 1.0
CG Y:LYS40 4.9 15.6 1.0
CA Y:CYS46 4.9 4.1 1.0

Zinc binding site 2 out of 2 in 3dll

Go back to Zinc Binding Sites List in 3dll
Zinc binding site 2 out of 2 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 Zinc with other atoms in the Zn 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
4:Zn38

b:78.3
occ:1.00
CB 4:CYS27 2.3 53.9 1.0
SG 4:CYS27 2.4 51.1 1.0
ND1 4:HIS32 2.8 66.8 1.0
SG 4:CYS11 2.9 70.4 1.0
CG 4:HIS32 2.9 66.8 1.0
SG 4:CYS14 3.1 73.0 1.0
CB 4:HIS32 3.2 65.3 1.0
CE1 4:HIS32 3.5 67.4 1.0
CA 4:CYS14 3.5 68.7 1.0
N 4:CYS14 3.6 68.4 1.0
CD2 4:HIS32 3.6 67.1 1.0
CA 4:CYS27 3.8 54.4 1.0
CB 4:CYS14 3.8 70.1 1.0
NE2 4:HIS32 3.9 67.3 1.0
CB 4:CYS11 4.1 71.0 1.0
C 4:ASN13 4.3 68.3 1.0
N 4:CYS11 4.4 71.8 1.0
CA 4:HIS32 4.5 64.1 1.0
O 4:HIS32 4.5 64.5 1.0
N 4:MET10 4.6 72.4 1.0
N 4:CYS27 4.6 54.0 1.0
C 4:CYS27 4.7 55.2 1.0
CB 4:ASN13 4.7 68.8 1.0
C 4:MET10 4.7 72.2 1.0
CA 4:CYS11 4.7 71.5 1.0
C 4:HIS32 4.8 64.7 1.0
N 4:ASN13 4.8 69.0 1.0
N 4:SER28 4.9 55.9 1.0
O 4:ASN13 4.9 67.7 1.0
C 4:CYS14 4.9 67.7 1.0
CA 4:ASN13 5.0 68.7 1.0
C 4:CYS11 5.0 71.7 1.0
CG1 4:VAL25 5.0 56.5 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: Sat Sep 26 06:01:27 2020
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