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Magnesium in PDB 4wcw: Ribosomal Silencing Factor During Starvation or Stationary Phase (Rsfs) From Mycobacterium Tuberculosis

Protein crystallography data

The structure of Ribosomal Silencing Factor During Starvation or Stationary Phase (Rsfs) From Mycobacterium Tuberculosis, PDB code: 4wcw was solved by X.Li, Q.Sun, C.Jiang, K.Yang, L.Hung, J.Zhang, J.Sacchettini, Tb Structuralgenomics Consortium (Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.06 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 50.975, 50.975, 64.546, 110.27, 96.17, 110.59
R / Rfree (%) 21.1 / 25.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ribosomal Silencing Factor During Starvation or Stationary Phase (Rsfs) From Mycobacterium Tuberculosis (pdb code 4wcw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Ribosomal Silencing Factor During Starvation or Stationary Phase (Rsfs) From Mycobacterium Tuberculosis, PDB code: 4wcw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4wcw

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Magnesium binding site 1 out of 6 in the Ribosomal Silencing Factor During Starvation or Stationary Phase (Rsfs) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ribosomal Silencing Factor During Starvation or Stationary Phase (Rsfs) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:10.0
occ:1.00
 OD1 A:ASP39 2.0 5.0 1.0
O A:HOH315 2.2 12.7 1.0
O A:HOH307 2.2 18.2 1.0
O A:HOH306 2.3 10.5 1.0
O A:HOH308 2.5 9.2 1.0
CG A:ASP39 3.0 9.8 1.0
OD2 A:ASP39 3.4 12.0 1.0
O A:ILE37 3.8 12.2 1.0
O A:HOH324 4.2 29.4 1.0
CB A:ASP39 4.3 9.9 1.0
O A:LEU35 4.3 8.7 1.0
O A:VAL36 4.3 13.2 1.0
O A:THR38 4.3 7.6 1.0
CB A:SER32 4.3 16.1 1.0
C A:ILE37 4.4 15.4 1.0
O A:SER32 4.4 10.9 1.0
CA A:SER32 4.5 16.2 1.0
NH1 B:ARG77 4.5 13.2 1.0
C A:VAL36 4.5 15.2 1.0
CA A:ASP39 4.5 11.0 1.0
O A:HOH326 4.6 19.8 1.0
C A:THR38 4.6 14.3 1.0
N A:ASP39 4.7 8.5 1.0
N A:ILE37 4.8 11.8 1.0
CA A:ILE37 4.9 6.3 1.0
C A:SER32 5.0 9.8 1.0

Magnesium binding site 2 out of 6 in 4wcw

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Magnesium binding site 2 out of 6 in the Ribosomal Silencing Factor During Starvation or Stationary Phase (Rsfs) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ribosomal Silencing Factor During Starvation or Stationary Phase (Rsfs) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:28.8
occ:1.00
 O B:HOH317 2.0 18.4 1.0
OD1 B:ASP39 2.0 26.5 1.0
O B:HOH312 2.1 24.4 1.0
O B:HOH330 2.1 33.4 1.0
O B:HOH331 2.1 19.0 1.0
O B:HOH360 2.7 31.5 1.0
CG B:ASP39 2.9 33.0 1.0
OD2 B:ASP39 3.2 29.4 1.0
O B:VAL36 3.9 21.4 1.0
O B:ILE37 3.9 21.8 1.0
CB B:ASP39 4.3 23.4 1.0
CB B:SER32 4.3 24.4 1.0
O B:THR38 4.3 17.5 1.0
O B:SER32 4.4 20.3 1.0
CA B:SER32 4.4 16.9 1.0
O B:LEU35 4.5 13.0 1.0
C B:ILE37 4.5 17.6 1.0
CA B:ASP39 4.5 22.2 1.0
C B:VAL36 4.6 20.8 1.0
C B:THR38 4.7 15.1 1.0
N B:ASP39 4.8 14.2 1.0
C B:SER32 4.9 20.5 1.0
CA B:ILE37 5.0 20.9 1.0

Magnesium binding site 3 out of 6 in 4wcw

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Magnesium binding site 3 out of 6 in the Ribosomal Silencing Factor During Starvation or Stationary Phase (Rsfs) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ribosomal Silencing Factor During Starvation or Stationary Phase (Rsfs) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:30.6
occ:1.00
 O B:HOH308 2.0 21.8 1.0
OD1 B:ASP57 2.1 28.6 1.0
O B:HOH309 2.6 24.8 1.0
CG B:ASP57 3.2 35.7 1.0
OD2 B:ASP57 3.7 37.5 1.0
O B:HOH327 3.9 38.5 1.0
OD1 B:ASN53 4.3 39.0 1.0
CB B:ASP57 4.5 30.7 1.0
O B:ASN53 4.6 20.2 1.0
CA B:ASP57 4.6 24.6 1.0
O B:HOH325 4.6 40.2 1.0
N B:ASP57 4.8 17.9 1.0
CG1 B:VAL56 4.8 26.2 1.0
O B:HOH305 4.8 30.6 1.0

Magnesium binding site 4 out of 6 in 4wcw

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Magnesium binding site 4 out of 6 in the Ribosomal Silencing Factor During Starvation or Stationary Phase (Rsfs) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ribosomal Silencing Factor During Starvation or Stationary Phase (Rsfs) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:11.9
occ:1.00
 O C:HOH358 1.9 7.5 1.0
O C:HOH357 2.0 9.1 1.0
O C:HOH356 2.0 16.3 1.0
OD1 C:ASP39 2.1 7.1 1.0
O A:HOH336 2.2 15.3 1.0
O C:HOH355 2.4 12.4 1.0
CG C:ASP39 3.0 6.4 1.0
OD2 C:ASP39 3.4 11.5 1.0
O C:ILE37 3.9 14.0 1.0
OD1 A:ASP97 4.1 16.6 1.0
O C:VAL36 4.1 13.0 1.0
O C:LEU35 4.2 9.8 1.0
O C:THR38 4.2 7.2 1.0
O A:HOH340 4.3 18.4 1.0
CB C:ASP39 4.3 12.8 1.0
CB C:SER32 4.3 12.2 1.0
CA C:SER32 4.4 15.9 1.0
O C:SER32 4.4 12.7 1.0
C C:ILE37 4.4 13.4 1.0
C C:VAL36 4.5 13.6 1.0
NH1 D:ARG77 4.6 19.0 1.0
O A:ASP97 4.6 18.5 1.0
CA C:ASP39 4.6 13.8 1.0
C C:THR38 4.6 14.8 1.0
CA A:ASP97 4.7 11.7 1.0
O C:HOH369 4.7 17.9 1.0
N C:ILE37 4.8 16.8 1.0
N C:ASP39 4.8 11.0 1.0
CA C:ILE37 4.8 4.8 1.0
CG A:ASP97 4.9 17.1 1.0
C C:SER32 4.9 11.1 1.0

Magnesium binding site 5 out of 6 in 4wcw

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Magnesium binding site 5 out of 6 in the Ribosomal Silencing Factor During Starvation or Stationary Phase (Rsfs) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ribosomal Silencing Factor During Starvation or Stationary Phase (Rsfs) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg201

b:30.6
occ:1.00
 O D:HOH303 2.1 34.5 1.0
O D:THR38 2.2 15.2 1.0
OD1 D:ASP39 2.2 31.0 1.0
C D:THR38 2.8 14.4 1.0
O D:HOH366 2.9 29.6 1.0
O D:ILE37 3.1 15.9 1.0
O D:HOH319 3.1 27.7 1.0
C D:ILE37 3.2 23.2 1.0
O D:LEU35 3.3 11.4 1.0
N D:ASP39 3.4 11.3 1.0
CG D:ASP39 3.4 28.6 1.0
CA D:ASP39 3.5 20.5 1.0
N D:THR38 3.5 15.2 1.0
O D:HOH310 3.5 22.7 1.0
CA D:THR38 3.7 18.1 1.0
O D:VAL36 3.8 16.0 1.0
CA D:SER32 3.8 20.4 1.0
N D:ILE37 3.9 15.5 1.0
C D:VAL36 3.9 17.7 1.0
CA D:ILE37 4.0 21.0 1.0
CB D:ASP39 4.0 24.8 1.0
C D:LEU35 4.0 11.1 1.0
CB D:SER32 4.3 21.0 1.0
O D:SER32 4.3 20.8 1.0
OD2 D:ASP39 4.4 30.6 1.0
C D:SER32 4.5 19.2 1.0
N D:VAL36 4.7 12.8 1.0
O D:HOH312 4.7 33.7 1.0
N D:SER32 4.7 18.2 1.0
CA D:VAL36 4.7 17.3 1.0
CB D:LEU35 4.8 16.9 1.0
O D:VAL31 4.8 12.7 1.0
C D:ASP39 4.8 20.8 1.0
CA D:LEU35 4.9 11.0 1.0
CB D:THR38 4.9 15.8 1.0

Magnesium binding site 6 out of 6 in 4wcw

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Magnesium binding site 6 out of 6 in the Ribosomal Silencing Factor During Starvation or Stationary Phase (Rsfs) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ribosomal Silencing Factor During Starvation or Stationary Phase (Rsfs) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:43.2
occ:1.00
 O D:HOH354 2.0 40.0 1.0
OD1 D:ASP57 2.1 38.3 1.0
O A:HOH405 2.2 36.8 1.0
O D:HOH349 2.3 34.6 1.0
CG D:ASP57 2.9 36.9 1.0
OD2 D:ASP57 3.0 48.8 1.0
O A:LEU22 3.7 20.4 1.0
OD1 A:ASP24 3.7 36.6 1.0
CB A:LEU22 4.1 18.1 1.0
C A:LEU22 4.2 11.7 1.0
CA A:LEU22 4.3 12.7 1.0
CB D:ASP57 4.3 27.3 1.0
O A:ALA23 4.4 11.3 1.0
CD2 A:LEU22 4.5 15.1 1.0
OD1 D:ASN53 4.7 33.1 1.0
OE2 D:GLU60 4.7 45.0 1.0
CA D:ASP57 4.8 26.6 1.0
CG A:LEU22 4.9 22.4 1.0
CG A:ASP24 4.9 31.0 1.0

Reference:

X.Li, Q.Sun, C.Jiang, K.Yang, L.Hung, J.Zhang, J.Sacchettini, Tb Structural Genomics Consortium (Tbsgc). Mechanism of Ribosomal Silencing in the Mycobacterium Tuberculosis To Be Published.
Page generated: Tue Aug 20 13:10:53 2024

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