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

Protein crystallography data

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

Magnesium Binding Sites:

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 1xpu

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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 1xpu

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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 1xpu

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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 1xpu

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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 1xpu

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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 1xpu

Go back to Magnesium Binding Sites List in 1xpu
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

Reference:

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
Page generated: Tue Aug 13 18:20:18 2024

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