Magnesium in PDB 1xpo: Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic Bicyclomycin

The structure of Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic Bicyclomycin, PDB code: 1xpo 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 (°)	211.933, 111.370, 161.033, 90.00, 108.79, 90.00
R / Rfree (%)	28.5 / 30.6

The binding sites of Magnesium atom in the Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic Bicyclomycin (pdb code 1xpo). 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 Bicyclomycin, PDB code: 1xpo:
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 Bicyclomycin


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 Bicyclomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1601 b:90.0 occ:1.00 O2G A:AGS1600 2.0 0.6 1.0 OE2 A:GLU215 2.3 90.8 1.0 NH2 A:ARG212 2.5 88.5 1.0 OG1 A:THR185 2.8 99.1 1.0 PG A:AGS1600 3.4 0.4 1.0 CD A:GLU215 3.5 90.9 1.0 CB A:THR185 3.6 99.1 1.0 CZ A:ARG212 3.6 88.5 1.0 CG2 A:THR185 3.7 99.1 1.0 O2B A:AGS1600 3.8 0.8 1.0 NE A:ARG212 4.0 88.4 1.0 OE1 A:GLU215 4.1 90.8 1.0 OE1 A:GLU211 4.1 86.8 1.0 O3B A:AGS1600 4.2 0.7 1.0 S1G A:AGS1600 4.2 0.7 1.0 O1A A:AGS1600 4.4 0.3 1.0 O3G A:AGS1600 4.5 0.6 1.0 CG A:GLU215 4.6 90.9 1.0 PB A:AGS1600 4.7 0.7 1.0 NH1 A:ARG212 4.8 88.5 1.0

Magnesium binding site 2 out of 6 in the Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic Bicyclomycin


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 Bicyclomycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2601 b:85.3 occ:1.00 O2G B:AGS2600 2.5 0.8 1.0 O2A B:BCM2701 2.7 76.7 1.0 OG1 B:THR185 2.7 80.3 1.0 O2B B:AGS2600 2.8 0.9 1.0 NH2 B:ARG212 3.4 72.6 1.0 NZ B:LYS184 3.9 78.7 1.0 C2A B:BCM2701 3.9 76.6 1.0 PG B:AGS2600 3.9 0.7 1.0 O9 B:BCM2701 4.0 76.7 1.0 C3A B:BCM2701 4.0 76.7 1.0 CB B:THR185 4.1 80.3 1.0 OE2 B:GLU215 4.1 76.1 1.0 OE1 B:GLU211 4.1 72.9 1.0 PB B:AGS2600 4.2 0.9 1.0 OE2 B:GLU211 4.2 72.9 1.0 OD2 B:ASP265 4.3 62.9 1.0 O3B B:AGS2600 4.4 0.9 1.0 N B:THR185 4.5 79.7 1.0 C2B B:BCM2701 4.5 76.7 1.0 CZ B:ARG212 4.6 72.6 1.0 CD B:GLU211 4.6 72.9 1.0 O3G B:AGS2600 4.7 0.8 1.0 O2 B:BCM2701 4.7 76.7 1.0 O1A B:AGS2600 4.7 0.6 1.0 CB B:LYS184 4.7 78.7 1.0 CA B:THR185 4.8 80.3 1.0 C9 B:BCM2701 4.9 76.6 1.0 CG2 B:THR185 4.9 80.3 1.0

Magnesium binding site 3 out of 6 in the Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic Bicyclomycin


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 Bicyclomycin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg3601 b:89.7 occ:1.00 OG1 C:THR185 2.3 63.6 1.0 O2B C:AGS3600 2.5 0.4 1.0 O9 C:BCM3701 2.9 77.5 1.0 O2G C:AGS3600 3.0 0.3 1.0 O2A C:BCM3701 3.3 77.1 1.0 CB C:LYS184 3.6 63.2 1.0 C3A C:BCM3701 3.6 77.1 1.0 OD2 C:ASP265 3.7 57.2 1.0 CB C:THR185 3.7 63.5 1.0 NZ C:LYS184 3.9 64.2 1.0 PB C:AGS3600 4.0 0.4 1.0 C9 C:BCM3701 4.1 77.3 1.0 N C:THR185 4.1 63.4 1.0 C2A C:BCM3701 4.1 77.1 1.0 C C:LYS184 4.1 63.2 1.0 PG C:AGS3600 4.1 0.2 1.0 OD1 C:ASP265 4.3 57.1 1.0 CA C:LYS184 4.4 63.1 1.0 O3G C:AGS3600 4.5 0.3 1.0 CA C:THR185 4.5 63.5 1.0 CG C:ASP265 4.5 57.2 1.0 O C:LYS184 4.5 63.3 1.0 O3B C:AGS3600 4.5 0.4 1.0 CG2 C:THR185 4.5 63.5 1.0 O1B C:AGS3600 4.7 0.4 1.0 CD C:LYS184 4.8 63.9 1.0 CG C:LYS184 4.8 63.4 1.0 O3A C:BCM3701 4.9 77.2 1.0 N10 C:BCM3701 4.9 77.4 1.0 CE C:LYS184 5.0 64.1 1.0 N C:LYS184 5.0 62.8 1.0

Magnesium binding site 4 out of 6 in the Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic Bicyclomycin


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 Bicyclomycin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg4601 b:70.5 occ:1.00 OG1 D:THR185 2.2 64.9 1.0 O2G D:AGS4600 2.4 1.0 1.0 O2B D:AGS4600 2.8 0.2 1.0 OE1 D:GLU211 3.3 55.7 1.0 PG D:AGS4600 3.6 0.8 1.0 CB D:THR185 3.6 64.8 1.0 NZ D:LYS184 3.7 63.9 1.0 O2A D:BCM4701 3.7 77.4 1.0 O9 D:BCM4701 3.9 77.8 1.0 S1G D:AGS4600 4.0 0.0 1.0 PB D:AGS4600 4.0 0.1 1.0 O3B D:AGS4600 4.0 0.1 1.0 CD D:GLU211 4.2 55.7 1.0 CG2 D:THR185 4.3 64.9 1.0 NH1 D:ARG212 4.3 55.1 1.0 O1A D:AGS4600 4.3 99.8 1.0 O1A D:BCM4701 4.3 77.5 1.0 N D:THR185 4.4 64.5 1.0 O2 D:BCM4701 4.4 77.8 1.0 OE2 D:GLU211 4.5 55.8 1.0 CA D:THR185 4.5 64.9 1.0 CB D:LYS184 4.8 63.8 1.0 C9 D:BCM4701 4.8 77.7 1.0 OD2 D:ASP265 4.9 60.5 1.0 C2A D:BCM4701 4.9 77.5 1.0 C1A D:BCM4701 4.9 77.6 1.0 O3G D:AGS4600 5.0 0.9 1.0 CG D:GLU215 5.0 58.8 1.0 O3A D:AGS4600 5.0 1.0 1.0

Magnesium binding site 5 out of 6 in the Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic Bicyclomycin


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 Bicyclomycin within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg5601 b:82.3 occ:1.00 OG1 E:THR185 2.4 68.7 1.0 O2G E:AGS5600 2.5 0.9 1.0 NH2 D:ARG366 2.6 82.5 1.0 NH2 E:ARG212 2.7 61.6 1.0 O2A E:BCM5701 2.8 86.6 1.0 O2B E:AGS5600 3.2 0.8 1.0 CB E:THR185 3.6 68.7 1.0 CZ D:ARG366 3.7 82.5 1.0 PG E:AGS5600 3.8 0.7 1.0 CZ E:ARG212 4.0 61.7 1.0 C2A E:BCM5701 4.0 86.5 1.0 O3B E:AGS5600 4.0 0.8 1.0 O1A E:AGS5600 4.1 0.4 1.0 C2B E:BCM5701 4.1 86.5 1.0 OE1 E:GLU211 4.2 63.1 1.0 CG2 E:THR185 4.2 68.7 1.0 NH1 D:ARG366 4.2 82.5 1.0 PB E:AGS5600 4.2 0.8 1.0 O2 E:BCM5701 4.4 86.5 1.0 CG E:GLU215 4.5 65.0 1.0 NE E:ARG212 4.5 61.8 1.0 O9 E:BCM5701 4.6 86.5 1.0 C3A E:BCM5701 4.7 86.5 1.0 NE D:ARG366 4.7 82.4 1.0 CA E:THR185 4.8 68.7 1.0 O3G E:AGS5600 4.8 0.8 1.0 CD E:GLU215 4.8 65.1 1.0 CD E:GLU211 4.8 63.0 1.0 OE2 E:GLU215 4.9 65.2 1.0 NH1 E:ARG212 4.9 61.6 1.0 OE2 E:GLU211 4.9 63.0 1.0 OD2 E:ASP265 5.0 61.9 1.0

Magnesium binding site 6 out of 6 in the Structural Mechanism of Inhibition of the Rho Transcription Termination Factor By the Antibiotic Bicyclomycin


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 Bicyclomycin within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg6601 b:69.0 occ:1.00 O2G F:AGS6600 2.3 0.1 1.0 OG1 F:THR185 2.4 70.0 1.0 O2B F:AGS6600 3.0 0.3 1.0 OE1 F:GLU215 3.0 68.9 1.0 O2A F:BCM6701 3.3 79.1 1.0 CB F:THR185 3.6 70.0 1.0 OE2 F:GLU211 3.7 65.5 1.0 PG F:AGS6600 3.8 1.0 1.0 NH2 F:ARG212 3.8 66.6 1.0 NH1 F:ARG212 4.0 66.7 1.0 CD F:GLU215 4.1 68.9 1.0 O1A F:AGS6600 4.2 99.8 1.0 OE1 F:GLU211 4.2 65.6 1.0 PB F:AGS6600 4.2 0.2 1.0 O3B F:AGS6600 4.2 0.2 1.0 CG2 F:THR185 4.2 70.0 1.0 CZ F:ARG212 4.3 66.6 1.0 CD F:GLU211 4.4 65.5 1.0 C3A F:BCM6701 4.5 79.1 1.0 C2A F:BCM6701 4.5 79.0 1.0 O9 F:BCM6701 4.5 78.2 1.0 CG F:GLU215 4.5 68.6 1.0 OD2 F:ASP265 4.5 66.5 1.0 CA F:THR185 4.8 70.0 1.0 S1G F:AGS6600 4.8 0.2 1.0 O3G F:AGS6600 4.8 0.1 1.0 N F:THR185 4.9 69.7 1.0 O2 F:BCM6701 4.9 78.1 1.0 NZ F:LYS184 4.9 69.5 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