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Sodium in PDB 5d8x: 1.50A Resolution Structure of Bfrb (L68A E81A) From Pseudomonas Aeruginosa

Enzymatic activity of 1.50A Resolution Structure of Bfrb (L68A E81A) From Pseudomonas Aeruginosa

All present enzymatic activity of 1.50A Resolution Structure of Bfrb (L68A E81A) From Pseudomonas Aeruginosa:
1.16.3.1;

Protein crystallography data

The structure of 1.50A Resolution Structure of Bfrb (L68A E81A) From Pseudomonas Aeruginosa, PDB code: 5d8x was solved by S.Lovell, K.P.Battaile, Y.Wang, H.Yao, M.Rivera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.01 / 1.50
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 125.273, 125.273, 274.180, 90.00, 90.00, 120.00
R / Rfree (%) 15.2 / 17.3

Other elements in 5d8x:

The structure of 1.50A Resolution Structure of Bfrb (L68A E81A) From Pseudomonas Aeruginosa also contains other interesting chemical elements:

Potassium (K) 6 atoms
Iron (Fe) 12 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Sodium atom in the 1.50A Resolution Structure of Bfrb (L68A E81A) From Pseudomonas Aeruginosa (pdb code 5d8x). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 24 binding sites of Sodium where determined in the 1.50A Resolution Structure of Bfrb (L68A E81A) From Pseudomonas Aeruginosa, PDB code: 5d8x:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 24 in 5d8x

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Sodium binding site 1 out of 24 in the 1.50A Resolution Structure of Bfrb (L68A E81A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.50A Resolution Structure of Bfrb (L68A E81A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:28.4
occ:1.00
 O A:ASP34 2.7 15.3 1.0
O Q:HOH377 2.8 20.0 1.0
OG1 Q:THR136 3.1 15.6 1.0
O A:HOH417 3.1 33.0 1.0
O Q:HOH455 3.1 23.9 1.0
OD1 A:ASP34 3.1 24.2 1.0
O B:HOH391 3.7 24.9 1.0
CG A:ASP34 3.7 20.6 1.0
C A:ASP34 3.7 14.5 1.0
OD1 Q:ASP132 3.9 21.5 1.0
CA Q:THR136 4.0 11.5 1.0
O B:HOH308 4.0 24.4 1.0
N Q:THR136 4.0 12.6 1.0
OD2 A:ASP34 4.0 26.6 1.0
CB Q:THR136 4.1 13.9 1.0
O Q:HOH382 4.3 25.9 1.0
O A:HOH309 4.4 29.5 1.0
C Q:GLU135 4.5 14.4 1.0
O Q:ASP132 4.5 13.4 1.0
CA A:ASP34 4.5 13.0 1.0
N A:TRP35 4.6 11.6 1.0
CB Q:GLU135 4.6 14.5 1.0
CA A:TRP35 4.7 11.2 1.0
CG2 Q:THR136 4.7 14.3 1.0
O Q:GLU135 4.7 15.1 1.0
CB A:ASP34 4.7 17.1 1.0

Sodium binding site 2 out of 24 in 5d8x

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Sodium binding site 2 out of 24 in the 1.50A Resolution Structure of Bfrb (L68A E81A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1.50A Resolution Structure of Bfrb (L68A E81A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:22.7
occ:1.00
 O F:ASP34 2.7 16.1 1.0
O A:HOH398 2.8 21.4 1.0
O F:HOH427 2.9 33.0 1.0
OG1 A:THR136 3.0 15.2 1.0
OD1 F:ASP34 3.1 25.4 1.0
O A:HOH457 3.1 28.2 1.0
C F:ASP34 3.7 14.8 1.0
CG F:ASP34 3.7 21.0 1.0
O E:HOH380 3.8 23.1 1.0
CA A:THR136 3.9 10.7 1.0
O E:HOH305 4.0 19.9 1.0
CB A:THR136 4.0 11.9 1.0
OD2 F:ASP34 4.1 23.1 1.0
N A:THR136 4.1 11.6 1.0
OD1 A:ASP132 4.1 20.2 1.0
O F:HOH301 4.3 27.8 1.0
O E:HOH439 4.4 37.8 1.0
O A:HOH409 4.5 24.7 1.0
CA F:ASP34 4.5 12.2 1.0
N F:TRP35 4.5 12.8 1.0
C A:GLU135 4.5 13.4 1.0
CA F:TRP35 4.6 11.1 1.0
CG2 A:THR136 4.6 12.7 1.0
O A:ASP132 4.7 12.6 1.0
CB F:ASP34 4.7 13.7 1.0
CB A:GLU135 4.7 12.6 1.0
O A:GLU135 4.8 14.2 1.0
O F:HOH343 4.8 18.0 1.0

Sodium binding site 3 out of 24 in 5d8x

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Sodium binding site 3 out of 24 in the 1.50A Resolution Structure of Bfrb (L68A E81A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 1.50A Resolution Structure of Bfrb (L68A E81A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:24.7
occ:1.00
 O B:ASP34 2.6 15.7 1.0
O J:HOH350 2.8 24.6 1.0
O J:HOH441 2.9 28.0 1.0
O B:HOH418 3.0 37.2 1.0
OG1 J:THR136 3.0 18.1 1.0
OD1 B:ASP34 3.1 24.5 1.0
O A:HOH424 3.6 26.2 1.0
C B:ASP34 3.7 14.6 1.0
CG B:ASP34 3.7 18.6 1.0
OD1 J:ASP132 3.8 23.9 1.0
CA J:THR136 4.0 15.9 1.0
CB J:THR136 4.0 17.2 1.0
O B:HOH304 4.0 24.9 1.0
N J:THR136 4.1 15.6 1.0
OD2 B:ASP34 4.1 23.7 1.0
O B:HOH302 4.2 29.6 1.0
O J:HOH406 4.4 24.6 1.0
CA B:ASP34 4.5 15.7 1.0
N B:TRP35 4.6 13.0 1.0
O J:ASP132 4.6 15.1 1.0
C J:GLU135 4.6 17.3 1.0
CG2 J:THR136 4.6 18.5 1.0
CA B:TRP35 4.7 12.4 1.0
CB J:GLU135 4.7 16.8 1.0
CB B:ASP34 4.7 15.9 1.0
O J:GLU135 4.9 16.6 1.0

Sodium binding site 4 out of 24 in 5d8x

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Sodium binding site 4 out of 24 in the 1.50A Resolution Structure of Bfrb (L68A E81A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 1.50A Resolution Structure of Bfrb (L68A E81A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na204

b:27.4
occ:1.00
 O C:ASP34 2.7 16.1 1.0
O B:HOH375 2.7 23.2 1.0
O C:HOH422 2.9 36.9 1.0
O B:HOH443 2.9 29.7 1.0
OG1 B:THR136 3.0 16.6 1.0
OD1 C:ASP34 3.2 24.9 1.0
C C:ASP34 3.7 15.9 1.0
O D:HOH386 3.8 26.4 1.0
CG C:ASP34 3.8 23.6 1.0
CA B:THR136 4.0 16.4 1.0
OD1 B:ASP132 4.0 22.6 1.0
O C:HOH306 4.0 23.8 1.0
CB B:THR136 4.0 17.3 1.0
N B:THR136 4.1 16.0 1.0
OD2 C:ASP34 4.1 27.2 1.0
O B:HOH381 4.4 23.2 1.0
O C:HOH303 4.4 25.6 1.0
C B:GLU135 4.5 18.0 1.0
CA C:ASP34 4.5 16.4 1.0
N C:TRP35 4.5 15.0 1.0
O B:ASP132 4.6 14.0 1.0
CA C:TRP35 4.6 16.1 1.0
CG2 B:THR136 4.6 17.6 1.0
CB B:GLU135 4.7 16.3 1.0
CB C:ASP34 4.8 16.7 1.0
O B:GLU135 4.8 17.6 1.0
O C:HOH353 4.9 22.2 1.0

Sodium binding site 5 out of 24 in 5d8x

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Sodium binding site 5 out of 24 in the 1.50A Resolution Structure of Bfrb (L68A E81A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of 1.50A Resolution Structure of Bfrb (L68A E81A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na203

b:29.6
occ:1.00
 O W:ASP34 2.7 17.7 1.0
O C:HOH359 2.7 26.6 1.0
OD1 W:ASP34 3.0 27.8 1.0
O W:HOH414 3.0 34.6 1.0
OG1 C:THR136 3.0 19.1 1.0
O C:HOH443 3.1 32.8 1.0
O X:HOH415 3.7 24.3 1.0
C W:ASP34 3.7 16.3 1.0
CG W:ASP34 3.7 24.0 1.0
O W:HOH302 3.9 25.6 1.0
OD1 C:ASP132 3.9 23.8 1.0
CA C:THR136 4.0 14.4 1.0
CB C:THR136 4.0 15.9 1.0
N C:THR136 4.1 14.8 1.0
OD2 W:ASP34 4.2 28.4 1.0
O W:HOH306 4.4 30.4 1.0
O C:HOH393 4.5 24.9 1.0
CA W:ASP34 4.5 16.3 1.0
O C:ASP132 4.5 16.2 1.0
C C:GLU135 4.5 18.1 1.0
N W:TRP35 4.5 15.9 1.0
CG2 C:THR136 4.6 18.1 1.0
CB C:GLU135 4.6 17.7 1.0
CA W:TRP35 4.6 15.6 1.0
CB W:ASP34 4.7 19.4 1.0
O C:GLU135 4.8 19.2 1.0

Sodium binding site 6 out of 24 in 5d8x

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Sodium binding site 6 out of 24 in the 1.50A Resolution Structure of Bfrb (L68A E81A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of 1.50A Resolution Structure of Bfrb (L68A E81A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na203

b:27.0
occ:1.00
 O D:ASP34 2.5 16.2 1.0
O T:HOH393 2.5 24.4 1.0
O D:HOH368 2.9 36.0 1.0
OG1 T:THR136 3.0 17.4 1.0
OD1 D:ASP34 3.1 25.3 1.0
O T:HOH449 3.3 29.3 1.0
C D:ASP34 3.6 15.7 1.0
CG D:ASP34 3.6 21.5 1.0
O C:HOH402 3.6 28.1 1.0
OD1 T:ASP132 3.7 21.9 1.0
O D:HOH305 3.9 23.6 1.0
OD2 D:ASP34 4.0 26.9 1.0
CA T:THR136 4.0 14.0 1.0
CB T:THR136 4.0 16.0 1.0
O D:HOH301 4.1 30.7 1.0
N T:THR136 4.1 14.9 1.0
O T:HOH363 4.2 25.4 1.0
CA D:ASP34 4.4 15.6 1.0
O T:ASP132 4.5 14.4 1.0
N D:TRP35 4.5 14.5 1.0
C T:GLU135 4.6 15.3 1.0
CB D:ASP34 4.6 16.2 1.0
CG2 T:THR136 4.6 15.9 1.0
CA D:TRP35 4.6 15.3 1.0
CB T:GLU135 4.7 17.1 1.0
CG T:ASP132 4.9 21.5 1.0
O T:GLU135 4.9 17.7 1.0

Sodium binding site 7 out of 24 in 5d8x

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Sodium binding site 7 out of 24 in the 1.50A Resolution Structure of Bfrb (L68A E81A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of 1.50A Resolution Structure of Bfrb (L68A E81A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na204

b:28.5
occ:1.00
 O R:ASP34 2.7 16.2 1.0
O D:HOH360 2.7 22.1 1.0
O R:HOH3427 2.7 38.8 1.0
OG1 D:THR136 3.0 15.6 1.0
OD1 R:ASP34 3.0 25.2 1.0
O D:HOH449 3.2 30.1 1.0
C R:ASP34 3.7 14.2 1.0
CG R:ASP34 3.7 20.7 1.0
O Q:HOH424 3.7 24.6 1.0
OD1 D:ASP132 3.8 20.8 1.0
O Q:HOH304 4.0 22.8 1.0
CA D:THR136 4.0 15.6 1.0
CB D:THR136 4.0 14.8 1.0
OD2 R:ASP34 4.1 25.5 1.0
N D:THR136 4.1 13.7 1.0
O D:HOH376 4.2 25.4 1.0
CA R:ASP34 4.5 14.9 1.0
O D:ASP132 4.5 14.4 1.0
N R:TRP35 4.5 14.4 1.0
C D:GLU135 4.6 15.3 1.0
CG2 D:THR136 4.6 14.7 1.0
CA R:TRP35 4.6 13.5 1.0
CB D:GLU135 4.7 15.2 1.0
CB R:ASP34 4.7 19.0 1.0
O D:GLU135 4.8 15.7 1.0

Sodium binding site 8 out of 24 in 5d8x

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Sodium binding site 8 out of 24 in the 1.50A Resolution Structure of Bfrb (L68A E81A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of 1.50A Resolution Structure of Bfrb (L68A E81A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na205

b:28.6
occ:1.00
 O O:HOH344 2.6 28.1 1.0
O E:ASP34 2.7 17.9 1.0
OD1 E:ASP34 3.0 26.9 1.0
OG1 O:THR136 3.0 18.6 1.0
O E:HOH426 3.0 38.5 1.0
O O:HOH449 3.3 29.1 1.0
O F:HOH398 3.6 26.2 1.0
OD1 O:ASP132 3.7 23.7 1.0
CG E:ASP34 3.7 19.7 1.0
C E:ASP34 3.7 15.2 1.0
CA O:THR136 4.0 14.2 1.0
CB O:THR136 4.0 19.0 1.0
O E:HOH307 4.1 24.5 1.0
N O:THR136 4.1 16.8 1.0
O E:HOH309 4.2 29.6 1.0
OD2 E:ASP34 4.2 26.1 1.0
O O:HOH402 4.3 25.4 1.0
O O:ASP132 4.5 15.7 1.0
CA E:ASP34 4.5 18.6 1.0
C O:GLU135 4.6 18.1 1.0
N E:TRP35 4.6 14.5 1.0
CG2 O:THR136 4.6 17.1 1.0
CB O:GLU135 4.7 18.0 1.0
CB E:ASP34 4.7 19.6 1.0
CA E:TRP35 4.7 17.8 1.0
O O:GLU135 4.9 17.5 1.0
CG O:ASP132 4.9 21.4 1.0

Sodium binding site 9 out of 24 in 5d8x

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Sodium binding site 9 out of 24 in the 1.50A Resolution Structure of Bfrb (L68A E81A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of 1.50A Resolution Structure of Bfrb (L68A E81A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na206

b:26.7
occ:1.00
 O E:HOH389 2.6 23.1 1.0
O I:ASP34 2.7 19.2 1.0
O I:HOH417 3.0 33.0 1.0
O E:HOH456 3.0 30.8 1.0
OD1 I:ASP34 3.1 25.3 1.0
OG1 E:THR136 3.1 17.6 1.0
C I:ASP34 3.7 17.4 1.0
O J:HOH385 3.7 25.4 1.0
CG I:ASP34 3.8 25.8 1.0
OD1 E:ASP132 4.0 22.6 1.0
CA E:THR136 4.0 15.0 1.0
O I:HOH302 4.0 22.7 1.0
CB E:THR136 4.1 17.4 1.0
N E:THR136 4.1 14.6 1.0
OD2 I:ASP34 4.2 25.5 1.0
O I:HOH301 4.4 30.2 1.0
O E:HOH428 4.4 25.7 1.0
C E:GLU135 4.5 17.1 1.0
CA I:ASP34 4.6 18.1 1.0
N I:TRP35 4.6 14.1 1.0
O E:ASP132 4.6 15.5 1.0
CA I:TRP35 4.6 15.4 1.0
CB E:GLU135 4.6 16.2 1.0
CG2 E:THR136 4.7 17.4 1.0
CB I:ASP34 4.8 15.2 1.0
O E:GLU135 4.8 16.6 1.0
O I:HOH339 4.9 22.9 1.0

Sodium binding site 10 out of 24 in 5d8x

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Sodium binding site 10 out of 24 in the 1.50A Resolution Structure of Bfrb (L68A E81A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of 1.50A Resolution Structure of Bfrb (L68A E81A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na202

b:27.3
occ:1.00
 O F:HOH376 2.6 24.7 1.0
O H:ASP34 2.7 17.0 1.0
OG1 F:THR136 3.0 17.0 1.0
O H:HOH430 3.0 40.6 1.0
O F:HOH441 3.1 27.9 1.0
OD1 H:ASP34 3.1 26.4 1.0
O G:HOH411 3.7 26.4 1.0
C H:ASP34 3.7 16.2 1.0
CG H:ASP34 3.7 21.8 1.0
O H:HOH302 3.9 25.3 1.0
CA F:THR136 4.0 13.5 1.0
OD1 F:ASP132 4.0 23.1 1.0
CB F:THR136 4.0 16.7 1.0
N F:THR136 4.1 15.1 1.0
OD2 H:ASP34 4.1 24.5 1.0
O F:HOH392 4.5 27.8 1.0
C F:GLU135 4.5 14.5 1.0
O F:ASP132 4.5 15.8 1.0
CA H:ASP34 4.5 17.1 1.0
N H:TRP35 4.6 14.4 1.0
CB F:GLU135 4.6 17.9 1.0
CA H:TRP35 4.6 14.5 1.0
CG2 F:THR136 4.7 16.6 1.0
O F:GLU135 4.7 17.1 1.0
CB H:ASP34 4.7 14.6 1.0

Reference:

Y.Wang, H.Yao, Y.Cheng, S.Lovell, K.P.Battaile, C.R.Midaugh, M.Rivera. Characterization of the Bacterioferritin/Bacterioferritin Associated Ferredoxin Protein-Protein Interaction in Solution and Determination of Binding Energy Hot Spots. Biochemistry V. 54 6162 2015.
ISSN: ISSN 0006-2960
PubMed: 26368531
DOI: 10.1021/ACS.BIOCHEM.5B00937
Page generated: Mon Oct 7 20:31:35 2024

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