Atomistry » Magnesium » PDB 1xoq-1xyc » 1xpu
Atomistry »
  Magnesium »
    PDB 1xoq-1xyc »
      1xpu »

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

Go back to Magnesium Binding Sites List in 1xpu
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

Go back to Magnesium Binding Sites List in 1xpu
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

Go back to Magnesium Binding Sites List in 1xpu
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

Go back to Magnesium Binding Sites List in 1xpu
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

Go back to Magnesium Binding Sites List in 1xpu
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy