Magnesium in PDB 1xpu: Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic 5A-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)

The structure of Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic 5A-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb), PDB code: 1xpu was solved by E.Skordalakes, A.P.Brogan, B.S.Park, H.Kohn, J.M.Berger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.05
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	119.477, 206.935, 148.607, 90.00, 96.95, 90.00
R / Rfree (%)	27.6 / 29.5

The binding sites of Magnesium atom in the Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic 5A-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb) (pdb code 1xpu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic 5A-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb), PDB code: 1xpu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic 5A-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic 5A-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1601 b:54.1 occ:1.00 O2B A:AGS1600 2.3 53.5 1.0 OG1 A:THR185 2.3 53.4 1.0 O2G A:AGS1600 2.4 53.5 1.0 OE1 A:GLU215 3.5 53.5 1.0 NZ A:LYS184 3.6 53.4 1.0 PB A:AGS1600 3.6 53.5 1.0 CE A:LYS184 3.6 53.4 1.0 CB A:THR185 3.6 53.4 1.0 CD A:LYS184 3.7 53.4 1.0 PG A:AGS1600 3.7 53.5 1.0 OE1 A:GLU211 3.7 53.5 1.0 O3B A:AGS1600 3.9 53.5 1.0 OE2 A:GLU215 4.1 53.5 1.0 N A:THR185 4.1 53.4 1.0 CD A:GLU215 4.2 53.5 1.0 CA A:THR185 4.2 53.4 1.0 CG A:LYS184 4.3 53.4 1.0 O1A A:AGS1600 4.3 53.5 1.0 O3A A:AGS1600 4.5 53.5 1.0 CG2 A:THR185 4.6 53.4 1.0 O3G A:AGS1600 4.6 53.5 1.0 CB A:LYS184 4.7 53.4 1.0 O1B A:AGS1600 4.8 53.5 1.0 CD A:GLU211 4.9 53.5 1.0 C A:LYS184 4.9 53.4 1.0 PA A:AGS1600 5.0 53.5 1.0

Magnesium binding site 2 out of 6 in the Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic 5A-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic 5A-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2601 b:54.2 occ:1.00 OG1 B:THR185 2.2 53.4 1.0 O2G B:AGS2600 2.9 53.5 1.0 NZ B:LYS184 2.9 53.4 1.0 O B:HOH2702 3.1 53.4 1.0 O6 B:FPD2701 3.1 53.5 1.0 O2B B:AGS2600 3.2 53.5 1.0 O2 B:FPD2701 3.3 53.5 1.0 CB B:THR185 3.7 53.4 1.0 CE B:LYS184 3.7 53.4 1.0 OD2 B:ASP265 3.9 53.5 1.0 OE2 B:GLU211 4.0 53.5 1.0 C6 B:FPD2701 4.2 53.5 1.0 CG2 B:THR185 4.3 53.4 1.0 PG B:AGS2600 4.3 53.5 1.0 CD B:LYS184 4.4 53.4 1.0 OD1 B:ASP265 4.4 53.5 1.0 C2 B:FPD2701 4.4 53.5 1.0 OE1 B:GLU211 4.4 53.5 1.0 C1 B:FPD2701 4.5 53.5 1.0 CA B:THR185 4.5 53.4 1.0 N B:THR185 4.5 53.4 1.0 PB B:AGS2600 4.6 53.5 1.0 O5 B:FPD2701 4.6 53.5 1.0 CD B:GLU211 4.6 53.5 1.0 CG B:ASP265 4.6 53.5 1.0 O3B B:AGS2600 4.7 53.5 1.0 C5 B:FPD2701 5.0 53.5 1.0 NH1 B:ARG212 5.0 53.4 1.0 O3G B:AGS2600 5.0 53.5 1.0

Magnesium binding site 3 out of 6 in the Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic 5A-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic 5A-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg3601 b:53.8 occ:1.00 OG1 C:THR185 2.7 53.5 1.0 OD2 C:ASP265 2.7 53.5 1.0 CG C:ASP265 3.4 53.5 1.0 O2B C:AGS3600 3.4 53.4 1.0 OD1 C:ASP265 3.4 53.5 1.0 CA C:THR185 3.6 53.4 1.0 N C:THR185 3.6 53.4 1.0 CG C:LYS184 3.6 53.5 1.0 CB C:THR185 3.7 53.4 1.0 CE C:LYS184 3.8 53.5 1.0 CD C:LYS184 4.1 53.5 1.0 C C:LYS184 4.1 53.4 1.0 CG2 C:THR185 4.4 53.5 1.0 CB C:LYS184 4.4 53.4 1.0 O C:LYS184 4.4 53.4 1.0 O6 C:FPD3701 4.5 53.5 1.0 O2 C:FPD3701 4.5 53.5 1.0 C2 C:FPD3701 4.6 53.5 1.0 OE2 C:GLU211 4.6 53.5 1.0 CD1 C:LEU188 4.6 53.5 1.0 O2G C:AGS3600 4.7 53.5 1.0 OE1 C:GLU211 4.8 53.5 1.0 CB C:ASP265 4.8 53.4 1.0 CA C:LYS184 4.9 53.4 1.0 NZ C:LYS184 4.9 53.5 1.0 PB C:AGS3600 5.0 53.4 1.0

Magnesium binding site 4 out of 6 in the Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic 5A-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic 5A-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg4601 b:53.4 occ:1.00 O2G D:AGS4600 2.2 53.5 1.0 OG1 D:THR185 2.4 53.4 1.0 O2B D:AGS4600 2.8 53.4 1.0 PG D:AGS4600 3.6 53.5 1.0 CB D:THR185 3.7 53.4 1.0 NH2 D:ARG212 3.7 53.4 1.0 NZ D:LYS184 3.8 53.4 1.0 O3B D:AGS4600 3.9 53.5 1.0 PB D:AGS4600 3.9 53.5 1.0 O6 D:FPD4701 4.0 53.5 1.0 O1A D:AGS4600 4.0 53.5 1.0 O2 D:FPD4701 4.1 53.4 1.0 CG2 D:THR185 4.5 53.4 1.0 OE2 D:GLU211 4.5 53.5 1.0 CE D:LYS184 4.5 53.4 1.0 O3G D:AGS4600 4.6 53.5 1.0 N D:THR185 4.6 53.4 1.0 CA D:THR185 4.6 53.4 1.0 CZ D:ARG212 4.7 53.4 1.0 O3A D:AGS4600 4.7 53.5 1.0 OE1 D:GLU211 4.7 53.5 1.0 CG D:GLU215 4.8 53.4 1.0 NH1 D:ARG212 4.8 53.4 1.0 PA D:AGS4600 4.9 53.5 1.0 S1G D:AGS4600 4.9 53.5 1.0 OD2 D:ASP265 4.9 53.4 1.0 CD D:GLU215 5.0 53.5 1.0 C6 D:FPD4701 5.0 53.5 1.0

Magnesium binding site 5 out of 6 in the Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic 5A-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic 5A-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg5601 b:53.9 occ:1.00 OG1 E:THR185 2.4 53.5 1.0 OE1 E:GLU211 3.2 53.5 1.0 NZ E:LYS184 3.2 53.5 1.0 OE2 E:GLU211 3.2 53.5 1.0 CD E:GLU211 3.6 53.5 1.0 O2G E:AGS5600 3.6 53.5 1.0 CB E:THR185 3.7 53.4 1.0 CG E:GLU215 3.7 53.4 1.0 O2 E:FPD5701 3.7 53.5 1.0 CG2 E:THR185 3.7 53.4 1.0 OD2 E:ASP265 3.7 53.5 1.0 CE E:LYS184 3.9 53.5 1.0 O2B E:AGS5600 4.1 53.5 1.0 CD E:GLU215 4.3 53.5 1.0 OE2 E:GLU215 4.4 53.5 1.0 NH2 E:ARG212 4.5 53.4 1.0 O6 E:FPD5701 4.6 53.5 1.0 CA E:THR185 4.6 53.4 1.0 CG E:ASP265 4.8 53.4 1.0 C2 E:FPD5701 4.8 53.5 1.0 CB E:GLU215 4.8 53.4 1.0 C1 E:FPD5701 4.9 53.5 1.0

Magnesium binding site 6 out of 6 in the Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic 5A-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic 5A-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb) within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg6601 b:53.9 occ:1.00 OG1 F:THR185 2.2 53.4 1.0 O2G E:AGS6600 2.5 53.5 1.0 O2B E:AGS6600 2.6 53.5 1.0 O6 F:FPD6701 3.1 53.5 1.0 NZ F:LYS184 3.6 53.5 1.0 CB F:THR185 3.6 53.4 1.0 C2 F:FPD6701 3.9 53.5 1.0 PG E:AGS6600 3.9 53.5 1.0 PB E:AGS6600 3.9 53.5 1.0 O2 F:FPD6701 3.9 53.5 1.0 CE F:LYS184 4.1 53.5 1.0 O3B E:AGS6600 4.1 53.5 1.0 CD F:LYS184 4.1 53.4 1.0 N F:THR185 4.2 53.4 1.0 CA F:THR185 4.2 53.4 1.0 CG2 F:THR185 4.3 53.4 1.0 C6 F:FPD6701 4.3 53.5 1.0 C1 F:FPD6701 4.5 53.5 1.0 OD2 F:ASP265 4.6 53.5 1.0 O3G E:AGS6600 4.7 53.5 1.0 OE1 F:GLU211 4.7 53.5 1.0 O3A E:AGS6600 4.8 53.5 1.0 O1A E:AGS6600 4.9 53.5 1.0 OE2 F:GLU211 4.9 53.5 1.0 CB F:LYS184 4.9 53.4 1.0 C F:LYS184 5.0 53.4 1.0 OD1 F:ASP265 5.0 53.5 1.0 O1 F:FPD6701 5.0 53.5 1.0

E.Skordalakes, A.P.Brogan, B.S.Park, H.Kohn, J.M.Berger. Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic Bicyclomycin Structure V. 13 99 2005.
ISSN: ISSN 0969-2126
PubMed: 15642265
DOI: 10.1016/J.STR.2004.10.013