Magnesium in PDB 1xpr: Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic 5A-Formylbicyclomycin (Fb)

The structure of Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic 5A-Formylbicyclomycin (Fb), PDB code: 1xpr 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 / 3.15
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	210.526, 109.679, 160.046, 90.00, 108.16, 90.00
R / Rfree (%)	27.4 / 29.6

The binding sites of Magnesium atom in the Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic 5A-Formylbicyclomycin (Fb) (pdb code 1xpr). 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-Formylbicyclomycin (Fb), PDB code: 1xpr:
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-Formylbicyclomycin (Fb)


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-Formylbicyclomycin (Fb) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1601 b:62.4 occ:1.00 O2G A:AGS1600 2.0 89.1 1.0 OG1 A:THR185 2.3 64.4 1.0 OE2 A:GLU215 2.9 57.5 1.0 O2B A:AGS1600 3.0 87.3 1.0 PG A:AGS1600 3.4 89.0 1.0 CB A:THR185 3.7 64.4 1.0 O3B A:AGS1600 3.7 88.2 1.0 PB A:AGS1600 4.0 87.2 1.0 NZ A:LYS184 4.0 64.0 1.0 CG2 A:THR185 4.1 64.5 1.0 O1A A:AGS1600 4.1 84.9 1.0 CD A:GLU215 4.1 57.4 1.0 OE2 A:GLU211 4.2 54.4 1.0 O3G A:AGS1600 4.5 89.0 1.0 NH2 A:ARG212 4.5 55.4 1.0 S1G A:AGS1600 4.6 89.2 1.0 OE1 A:GLU211 4.6 54.3 1.0 CA A:THR185 4.7 64.5 1.0 CD A:GLU211 4.7 54.4 1.0 O3A A:AGS1600 4.8 86.1 1.0 N A:THR185 4.9 64.3 1.0 CG A:GLU215 4.9 57.2 1.0 CE A:LYS184 5.0 64.0 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-Formylbicyclomycin (Fb)


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-Formylbicyclomycin (Fb) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2601 b:59.1 occ:1.00 O2G B:AGS2600 1.9 88.5 1.0 O2B B:AGS2600 2.0 86.4 1.0 OG1 B:THR185 2.3 47.1 1.0 PG B:AGS2600 3.2 88.3 1.0 PB B:AGS2600 3.2 86.4 1.0 O3B B:AGS2600 3.5 87.5 1.0 O1A B:AGS2600 3.6 84.2 1.0 CB B:THR185 3.7 47.0 1.0 O2A B:FB2701 3.7 53.0 1.0 NH2 B:ARG212 4.0 37.6 1.0 O3A B:AGS2600 4.1 85.3 1.0 CE B:LYS184 4.2 46.5 1.0 N B:THR185 4.2 46.8 1.0 O9 B:FB2701 4.3 53.4 1.0 S1G B:AGS2600 4.4 88.6 1.0 NZ B:LYS184 4.4 46.6 1.0 O3G B:AGS2600 4.4 88.4 1.0 O1B B:AGS2600 4.5 86.5 1.0 CG2 B:THR185 4.5 47.0 1.0 CA B:THR185 4.5 47.0 1.0 PA B:AGS2600 4.5 84.1 1.0 OD2 B:ASP265 4.7 39.3 1.0 NH1 B:ARG212 4.8 37.6 1.0 CZ B:ARG212 4.9 37.6 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-Formylbicyclomycin (Fb)


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-Formylbicyclomycin (Fb) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg3601 b:77.6 occ:1.00 O2G C:AGS3600 1.9 88.3 1.0 O2B C:AGS3600 2.5 86.4 1.0 OG1 C:THR185 2.7 35.5 1.0 O2A C:FB3701 2.8 43.5 1.0 O9 C:FB3701 3.2 43.9 1.0 PG C:AGS3600 3.2 88.1 1.0 O3G C:AGS3600 3.6 88.2 1.0 CB C:THR185 3.6 35.5 1.0 CE C:LYS184 3.6 35.0 1.0 PB C:AGS3600 3.7 86.3 1.0 O3B C:AGS3600 3.8 87.3 1.0 NZ C:LYS184 4.0 35.0 1.0 C2A C:FB3701 4.1 43.4 1.0 C3A C:FB3701 4.2 43.1 1.0 C9 C:FB3701 4.3 43.6 1.0 OD2 C:ASP265 4.4 21.7 1.0 CG2 C:THR185 4.5 35.4 1.0 N C:THR185 4.5 35.2 1.0 O2 C:FB3701 4.6 43.4 1.0 O1B C:AGS3600 4.7 86.4 1.0 O1A C:AGS3600 4.7 84.0 1.0 CA C:THR185 4.7 35.5 1.0 NH1 C:ARG212 4.8 27.9 1.0 OE1 C:GLU211 4.8 28.6 1.0 O3A C:AGS3600 4.9 85.2 1.0 S1G C:AGS3600 4.9 88.3 1.0 C1 C:FB3701 4.9 43.5 1.0 C2B C:FB3701 4.9 43.4 1.0 CD C:LYS184 5.0 34.9 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-Formylbicyclomycin (Fb)


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-Formylbicyclomycin (Fb) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg4601 b:36.7 occ:1.00 O2G D:AGS4600 1.9 87.3 1.0 OG1 D:THR185 2.1 38.6 1.0 O2B D:AGS4600 2.5 85.5 1.0 O2A D:FB4701 3.1 43.7 1.0 PG D:AGS4600 3.4 87.1 1.0 CB D:THR185 3.4 38.5 1.0 O9 D:FB4701 3.7 43.8 1.0 PB D:AGS4600 3.8 85.5 1.0 O3B D:AGS4600 3.8 86.5 1.0 CG2 D:THR185 4.0 38.6 1.0 CE D:LYS184 4.2 37.9 1.0 C2A D:FB4701 4.3 43.4 1.0 OE1 D:GLU211 4.3 29.3 1.0 OE2 D:GLU211 4.3 29.1 1.0 O1A D:AGS4600 4.4 83.7 1.0 O3G D:AGS4600 4.4 87.3 1.0 C3A D:FB4701 4.5 12.0 1.0 NH1 D:ARG212 4.5 29.1 1.0 S1G D:AGS4600 4.5 87.3 1.0 CA D:THR185 4.5 38.5 1.0 N D:THR185 4.6 38.2 1.0 OD2 D:ASP265 4.6 41.0 1.0 CD D:GLU211 4.7 29.2 1.0 NZ D:LYS184 4.7 38.2 1.0 O3A D:AGS4600 4.8 84.6 1.0 C9 D:FB4701 4.8 43.5 1.0 CG D:LYS184 4.8 37.7 1.0 O1B D:AGS4600 4.9 85.5 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-Formylbicyclomycin (Fb)


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-Formylbicyclomycin (Fb) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg5601 b:60.1 occ:1.00 O2G E:AGS5600 1.9 87.8 1.0 OG1 E:THR185 2.4 38.4 1.0 OE2 E:GLU211 3.3 30.9 1.0 O2A E:FB5701 3.3 53.1 1.0 NH1 E:ARG212 3.3 31.0 1.0 O2B E:AGS5600 3.3 86.0 1.0 PG E:AGS5600 3.4 87.7 1.0 CB E:THR185 3.5 38.4 1.0 O1A E:AGS5600 3.9 84.0 1.0 O3B E:AGS5600 4.0 86.9 1.0 CG2 E:THR185 4.0 38.5 1.0 CZ E:ARG212 4.1 31.0 1.0 S1G E:AGS5600 4.1 87.9 1.0 PB E:AGS5600 4.2 86.0 1.0 CD E:GLU211 4.3 30.8 1.0 CG E:GLU215 4.3 31.2 1.0 O9 E:FB5701 4.4 53.3 1.0 OE1 E:GLU211 4.5 30.9 1.0 OE1 E:GLU215 4.5 31.8 1.0 O3G E:AGS5600 4.5 87.8 1.0 CD E:GLU215 4.5 31.5 1.0 CD E:ARG212 4.6 30.8 1.0 C2A E:FB5701 4.6 43.8 1.0 NE E:ARG212 4.7 30.9 1.0 CA E:THR185 4.8 38.4 1.0 NH2 E:ARG212 4.9 31.2 1.0 N E:THR185 5.0 38.2 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-Formylbicyclomycin (Fb)


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-Formylbicyclomycin (Fb) within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg6601 b:63.0 occ:1.00 O2G F:AGS6600 1.9 88.2 1.0 OG1 F:THR185 2.3 47.9 1.0 OE1 F:GLU215 2.4 41.0 1.0 O2B F:AGS6600 2.8 86.3 1.0 O2A F:FB6701 3.3 53.1 1.0 NH2 F:ARG212 3.3 38.8 1.0 PG F:AGS6600 3.4 88.1 1.0 CD F:GLU215 3.5 41.0 1.0 CB F:THR185 3.6 47.8 1.0 O3B F:AGS6600 3.8 87.3 1.0 PB F:AGS6600 3.9 86.3 1.0 O1A F:AGS6600 3.9 84.0 1.0 NZ F:LYS184 4.0 47.4 1.0 OE2 F:GLU215 4.0 41.1 1.0 O9 F:FB6701 4.1 53.7 1.0 OE2 F:GLU211 4.2 39.7 1.0 CZ F:ARG212 4.2 38.9 1.0 CG2 F:THR185 4.2 47.8 1.0 NH1 F:ARG212 4.3 38.9 1.0 O3G F:AGS6600 4.3 88.2 1.0 OE1 F:GLU211 4.5 39.9 1.0 C2A F:FB6701 4.6 53.0 1.0 CA F:THR185 4.7 47.8 1.0 N F:THR185 4.7 47.7 1.0 S1G F:AGS6600 4.7 88.3 1.0 CG F:GLU215 4.7 40.8 1.0 O3A F:AGS6600 4.7 85.2 1.0 CD F:GLU211 4.8 39.6 1.0 C3A F:FB6701 4.9 43.7 1.0 PA F:AGS6600 5.0 83.9 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