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Magnesium in PDB 3f79: Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb

Protein crystallography data

The structure of Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb, PDB code: 3f79 was solved by I.Levchenko, R.A.Grant, R.T.Sauer, T.A.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.80
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 124.872, 124.872, 92.900, 90.00, 90.00, 120.00
R / Rfree (%) 24.3 / 29.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb (pdb code 3f79). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb, PDB code: 3f79:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 3f79

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Magnesium binding site 1 out of 7 in the Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1

b:61.1
occ:1.00
 OD2 B:ASP210 2.7 28.5 1.0
OD1 B:ASP382 2.8 54.1 1.0
OD1 B:ASP210 2.8 0.2 1.0
O B:GLY213 2.9 0.4 1.0
OD2 B:ASP382 3.0 49.2 1.0
CG B:ASP210 3.1 55.0 1.0
CG B:ASP382 3.2 74.6 1.0
OD2 B:ASP336 3.3 45.5 1.0
O B:VAL211 3.5 83.0 1.0
C B:GLY213 3.8 0.8 1.0
N B:GLY213 3.9 0.2 1.0
CA B:GLY213 4.1 0.8 1.0
CG B:ASP336 4.3 78.0 1.0
OD1 B:ASP192 4.4 0.2 1.0
CB B:ASP336 4.5 94.9 1.0
CB B:ASP210 4.6 72.6 1.0
C B:VAL211 4.6 83.8 1.0
CB B:ASP382 4.7 59.2 1.0
C B:SER212 4.8 0.1 1.0
N B:HIS214 5.0 0.1 1.0

Magnesium binding site 2 out of 7 in 3f79

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Magnesium binding site 2 out of 7 in the Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg5

b:50.1
occ:1.00
 OD1 C:ASP336 2.8 65.0 1.0
CG C:ASP336 3.6 0.4 1.0
CB C:ASP382 3.9 91.4 1.0
O C:ASP336 4.2 0.8 1.0
OD2 C:ASP336 4.2 61.7 1.0
CG C:ASP382 4.2 83.8 1.0
OD2 C:ASP382 4.2 93.0 1.0
C C:ASP336 4.6 68.9 1.0
CB C:ASP336 4.6 0.1 1.0
OD1 C:ASP382 4.9 57.0 1.0
N C:GLY337 5.0 39.4 1.0

Magnesium binding site 3 out of 7 in 3f79

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Magnesium binding site 3 out of 7 in the Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg6

b:78.6
occ:1.00
 OD2 D:ASP336 2.9 36.5 1.0
OD2 D:ASP210 3.0 62.3 1.0
OD2 D:ASP382 3.0 47.9 1.0
OD1 D:ASP210 3.2 91.8 1.0
CG D:ASP210 3.4 83.7 1.0
N D:GLY213 3.6 99.1 1.0
O D:VAL211 3.6 81.1 1.0
O D:GLY213 3.7 96.3 1.0
CG D:ASP382 3.9 87.2 1.0
OD1 D:ASP382 3.9 92.8 1.0
CG D:ASP336 3.9 61.1 1.0
MG D:MG7 4.2 41.0 1.0
CA D:GLY213 4.2 86.1 1.0
CB D:ASP336 4.2 46.2 1.0
C D:GLY213 4.4 95.2 1.0
C D:SER212 4.4 88.5 1.0
CA D:SER212 4.5 97.3 1.0
C D:VAL211 4.6 79.9 1.0
CB D:ASP210 4.9 67.2 1.0
N D:SER212 4.9 68.2 1.0

Magnesium binding site 4 out of 7 in 3f79

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Magnesium binding site 4 out of 7 in the Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg7

b:41.0
occ:1.00
 O D:GLY213 2.7 96.3 1.0
OD1 D:ASP210 2.7 91.8 1.0
OD1 D:ASP192 3.0 66.4 1.0
O D:VAL211 3.3 81.1 1.0
CA D:GLY191 3.3 46.2 1.0
C D:GLY191 3.5 66.2 1.0
N D:GLY191 3.5 97.3 1.0
N D:ASP192 3.6 79.1 1.0
CG D:ASP210 3.8 83.7 1.0
CG D:ASP192 3.8 0.3 1.0
C D:GLY213 3.9 95.2 1.0
OD1 D:ASP382 3.9 92.8 1.0
CB D:ASP383 4.1 91.7 1.0
CB D:HIS214 4.1 0.4 1.0
O D:GLY191 4.2 0.5 1.0
CA D:HIS214 4.2 0.5 1.0
MG D:MG6 4.2 78.6 1.0
N D:VAL211 4.3 71.0 1.0
OD2 D:ASP210 4.3 62.3 1.0
OD2 D:ASP192 4.3 0.4 1.0
C D:VAL211 4.4 79.9 1.0
CA D:ASP192 4.5 94.4 1.0
N D:HIS214 4.5 0.8 1.0
CB D:ASP192 4.7 60.6 1.0
OG D:SER218 4.8 0.4 1.0
C D:ASP210 4.8 38.1 1.0
CA D:ASP210 4.8 26.1 1.0
C D:SER190 4.8 99.7 1.0
CB D:ASP210 4.8 67.2 1.0
CA D:VAL211 4.8 43.3 1.0
N D:ASP383 4.9 85.0 1.0
CG D:ASP382 4.9 87.2 1.0

Magnesium binding site 5 out of 7 in 3f79

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Magnesium binding site 5 out of 7 in the Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg2

b:39.8
occ:1.00
 O E:GLY213 2.6 0.6 1.0
OD1 E:ASP210 2.7 89.7 1.0
OD1 E:ASP192 2.7 0.1 1.0
O E:VAL211 2.9 73.8 1.0
OD1 E:ASP382 3.0 41.6 1.0
OD2 E:ASP336 3.4 48.5 1.0
CG E:ASP210 3.5 16.9 1.0
OD2 E:ASP383 3.8 26.7 1.0
C E:GLY213 3.8 0.1 1.0
CG E:ASP192 3.9 0.8 1.0
OD2 E:ASP210 3.9 73.2 1.0
CG E:ASP382 4.0 65.6 1.0
C E:VAL211 4.1 76.1 1.0
OD2 E:ASP382 4.3 0.1 1.0
OD2 E:ASP192 4.3 0.8 1.0
N E:VAL211 4.3 68.1 1.0
C E:GLY191 4.4 53.2 1.0
CA E:GLY191 4.4 35.5 1.0
N E:GLY213 4.4 0.6 1.0
CG E:ASP336 4.5 67.1 1.0
C E:ASP210 4.5 41.6 1.0
N E:ASP192 4.6 72.1 1.0
CB E:ASP383 4.6 0.2 1.0
CG E:ASP383 4.6 33.7 1.0
CA E:GLY213 4.6 92.8 1.0
CB E:ASP210 4.7 16.3 1.0
N E:GLY191 4.7 90.1 1.0
O E:GLY191 4.7 99.3 1.0
N E:ASP383 4.7 84.4 1.0
N E:HIS214 4.7 0.5 1.0
CA E:ASP210 4.8 27.1 1.0
CA E:HIS214 4.8 0.5 1.0
CA E:VAL211 4.8 38.1 1.0
C E:SER212 4.8 85.7 1.0
CB E:HIS214 4.8 88.7 1.0

Magnesium binding site 6 out of 7 in 3f79

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Magnesium binding site 6 out of 7 in the Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg3

b:47.6
occ:1.00
 O F:GLY213 2.8 0.4 1.0
OD1 F:ASP210 3.0 28.6 1.0
OD1 F:ASP382 3.2 51.9 1.0
OD2 F:ASP210 3.2 28.8 1.0
O F:VAL211 3.3 74.0 1.0
OD2 F:ASP382 3.4 0.1 1.0
N F:GLY213 3.4 0.2 1.0
CG F:ASP210 3.5 63.0 1.0
C F:GLY213 3.6 0.6 1.0
CG F:ASP382 3.7 89.8 1.0
MG F:MG4 3.7 94.5 1.0
CA F:GLY213 3.7 0.5 1.0
OD2 F:ASP336 4.2 83.4 1.0
C F:SER212 4.3 0.1 1.0
C F:VAL211 4.4 71.7 1.0
OD1 F:ASP192 4.6 0.5 1.0
CA F:SER212 4.7 0.0 1.0
N F:HIS214 4.7 0.8 1.0
CB F:ASP210 5.0 59.8 1.0

Magnesium binding site 7 out of 7 in 3f79

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Magnesium binding site 7 out of 7 in the Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Pseudo-Centered Cell Crystal Form of the C-Terminal Phosphatase Domain of P. Aeruginosa Rssb within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg4

b:94.5
occ:1.00
 OD2 F:ASP210 2.7 28.8 1.0
O F:ASP383 2.8 74.8 1.0
OD2 F:ASP382 2.8 0.1 1.0
OD2 F:ASP192 3.1 0.0 1.0
OD1 F:ASP382 3.2 51.9 1.0
CG F:ASP382 3.2 89.8 1.0
CG F:ASP210 3.3 63.0 1.0
CB F:ASP336 3.3 66.9 1.0
N F:ASP336 3.5 0.6 1.0
OD1 F:ASP192 3.5 0.5 1.0
OD1 F:ASP210 3.6 28.6 1.0
MG F:MG3 3.7 47.6 1.0
CG F:ASP192 3.7 0.2 1.0
C F:ASP383 3.9 98.9 1.0
CA F:ASP336 3.9 75.0 1.0
CB F:SER335 3.9 0.8 1.0
OD2 F:ASP336 4.1 83.4 1.0
CG F:ASP336 4.1 69.5 1.0
N F:ASP383 4.2 84.2 1.0
CB F:ASP210 4.4 59.8 1.0
CB F:ASP382 4.4 0.7 1.0
N F:GLY337 4.4 56.4 1.0
CA F:ASP383 4.4 93.2 1.0
C F:SER335 4.5 62.6 1.0
CB F:ASP383 4.5 63.9 1.0
C F:ASP336 4.7 69.5 1.0
C F:ASP382 4.7 94.2 1.0
OG F:SER335 4.7 0.5 1.0
CA F:SER335 4.8 76.0 1.0
N F:ILE384 5.0 94.9 1.0

Reference:

I.Levchenko, R.A.Grant, R.T.Sauer, T.A.Baker. The Structure of Rssb, A Clpx Adaptor Protein That Regulates Sigma S To Be Published.
Page generated: Wed Aug 14 13:35:15 2024

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