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Sodium in PDB 4e6k: 2.0 A Resolution Structure of Pseudomonas Aeruginosa Bacterioferritin (Bfrb) in Complex with Bacterioferritin Associated Ferredoxin (Bfd)

Protein crystallography data

The structure of 2.0 A Resolution Structure of Pseudomonas Aeruginosa Bacterioferritin (Bfrb) in Complex with Bacterioferritin Associated Ferredoxin (Bfd), PDB code: 4e6k was solved by S.Lovell, K.P.Battaile, H.Yao, Y.Wang, R.Kumar, A.Ruvinsky, I.Vasker, M.Rivera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.73 / 2.00
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 135.005, 135.005, 200.890, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 18.3

Other elements in 4e6k:

The structure of 2.0 A Resolution Structure of Pseudomonas Aeruginosa Bacterioferritin (Bfrb) in Complex with Bacterioferritin Associated Ferredoxin (Bfd) also contains other interesting chemical elements:

Potassium (K) 3 atoms
Iron (Fe) 12 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the 2.0 A Resolution Structure of Pseudomonas Aeruginosa Bacterioferritin (Bfrb) in Complex with Bacterioferritin Associated Ferredoxin (Bfd) (pdb code 4e6k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the 2.0 A Resolution Structure of Pseudomonas Aeruginosa Bacterioferritin (Bfrb) in Complex with Bacterioferritin Associated Ferredoxin (Bfd), PDB code: 4e6k:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4e6k

Go back to Sodium Binding Sites List in 4e6k
Sodium binding site 1 out of 6 in the 2.0 A Resolution Structure of Pseudomonas Aeruginosa Bacterioferritin (Bfrb) in Complex with Bacterioferritin Associated Ferredoxin (Bfd)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2.0 A Resolution Structure of Pseudomonas Aeruginosa Bacterioferritin (Bfrb) in Complex with Bacterioferritin Associated Ferredoxin (Bfd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:25.9
occ:1.00
 O A:HOH464 2.4 39.0 1.0
OD1 A:ASP132 2.5 31.0 1.0
O A:HOH465 2.7 30.4 1.0
OG1 A:THR136 2.7 19.8 1.0
O A:HOH301 3.4 17.0 1.0
CG A:ASP132 3.7 26.2 1.0
O A:ASP132 3.7 16.6 1.0
CB A:THR136 4.0 18.6 1.0
N A:THR136 4.2 16.9 1.0
CA A:THR136 4.3 13.5 1.0
OD2 A:ASP132 4.3 31.2 1.0
O A:HOH459 4.4 29.2 1.0
C A:ASP132 4.5 15.9 1.0
CA A:ASP132 4.7 15.9 1.0
CG2 A:THR136 4.8 17.9 1.0
CB A:ASP132 4.8 14.9 1.0
O A:HOH415 4.8 38.6 1.0
CB A:GLU135 4.9 17.2 1.0
C A:GLU135 5.0 17.7 1.0

Sodium binding site 2 out of 6 in 4e6k

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Sodium binding site 2 out of 6 in the 2.0 A Resolution Structure of Pseudomonas Aeruginosa Bacterioferritin (Bfrb) in Complex with Bacterioferritin Associated Ferredoxin (Bfd)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 2.0 A Resolution Structure of Pseudomonas Aeruginosa Bacterioferritin (Bfrb) in Complex with Bacterioferritin Associated Ferredoxin (Bfd) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:24.9
occ:1.00
 O C:HOH441 2.4 34.9 1.0
OD1 B:ASP132 2.5 32.3 1.0
O B:HOH307 2.6 29.7 1.0
OG1 B:THR136 2.6 20.1 1.0
O C:ASP34 2.7 15.4 1.0
OD1 C:ASP34 2.9 26.0 1.0
O B:HOH309 3.3 25.5 1.0
O C:HOH405 3.6 33.7 1.0
O B:ASP132 3.7 17.9 1.0
CG B:ASP132 3.7 24.9 1.0
C C:ASP34 3.7 22.9 1.0
O D:HOH301 3.9 30.7 1.0
CG C:ASP34 3.9 31.4 1.0
CB B:THR136 3.9 21.1 1.0
N B:THR136 4.2 18.8 1.0
CA B:THR136 4.2 13.9 1.0
CA C:ASP34 4.3 19.9 1.0
OD2 B:ASP132 4.4 30.4 1.0
O C:HOH442 4.4 32.7 1.0
C B:ASP132 4.5 17.9 1.0
OD2 C:ASP34 4.6 27.8 1.0
CA B:ASP132 4.6 20.3 1.0
CB C:ASP34 4.7 20.6 1.0
O B:HOH428 4.7 35.8 1.0
CG2 B:THR136 4.7 18.1 1.0
CB B:ASP132 4.8 20.6 1.0
N C:TRP35 4.8 17.2 1.0
CB B:GLU135 4.8 20.9 1.0
C B:GLU135 4.9 16.4 1.0

Sodium binding site 3 out of 6 in 4e6k

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Sodium binding site 3 out of 6 in the 2.0 A Resolution Structure of Pseudomonas Aeruginosa Bacterioferritin (Bfrb) in Complex with Bacterioferritin Associated Ferredoxin (Bfd)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 2.0 A Resolution Structure of Pseudomonas Aeruginosa Bacterioferritin (Bfrb) in Complex with Bacterioferritin Associated Ferredoxin (Bfd) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na202

b:25.4
occ:1.00
 O E:HOH446 2.4 32.4 1.0
OD1 C:ASP132 2.4 32.5 1.0
OG1 C:THR136 2.5 21.4 1.0
O C:HOH304 2.6 30.5 1.0
O E:ASP34 2.7 18.7 1.0
OD1 E:ASP34 3.1 26.0 1.0
O C:HOH305 3.2 25.8 1.0
O E:HOH380 3.6 33.4 1.0
O C:ASP132 3.6 16.5 1.0
CG C:ASP132 3.6 26.2 1.0
O E:HOH331 3.8 24.4 1.0
C E:ASP34 3.8 12.0 1.0
CB C:THR136 3.8 24.8 1.0
CG E:ASP34 4.0 29.6 1.0
N C:THR136 4.1 18.6 1.0
CA C:THR136 4.1 18.0 1.0
O E:HOH430 4.3 33.3 1.0
CA E:ASP34 4.3 16.1 1.0
OD2 C:ASP132 4.3 31.2 1.0
C C:ASP132 4.4 18.0 1.0
CG2 C:THR136 4.6 19.9 1.0
CA C:ASP132 4.6 15.2 1.0
CB C:ASP132 4.7 19.2 1.0
CB E:ASP34 4.8 19.8 1.0
OD2 E:ASP34 4.8 31.7 1.0
CB C:GLU135 4.8 22.0 1.0
C C:GLU135 4.8 23.0 1.0
N E:TRP35 4.9 17.3 1.0
O C:HOH392 4.9 38.2 1.0

Sodium binding site 4 out of 6 in 4e6k

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Sodium binding site 4 out of 6 in the 2.0 A Resolution Structure of Pseudomonas Aeruginosa Bacterioferritin (Bfrb) in Complex with Bacterioferritin Associated Ferredoxin (Bfd)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 2.0 A Resolution Structure of Pseudomonas Aeruginosa Bacterioferritin (Bfrb) in Complex with Bacterioferritin Associated Ferredoxin (Bfd) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na201

b:21.2
occ:1.00
 O D:HOH427 2.4 36.4 1.0
OD1 D:ASP132 2.6 34.5 1.0
OG1 D:THR136 2.6 24.4 1.0
O D:HOH428 2.7 28.8 1.0
O D:HOH303 3.5 26.2 1.0
O D:ASP132 3.7 16.4 1.0
CG D:ASP132 3.8 25.0 1.0
CB D:THR136 3.9 26.7 1.0
N D:THR136 4.1 17.4 1.0
CA D:THR136 4.1 17.8 1.0
O D:HOH430 4.3 27.0 1.0
C D:ASP132 4.4 17.4 1.0
OD2 D:ASP132 4.4 30.7 1.0
O D:HOH445 4.6 38.9 1.0
CA D:ASP132 4.6 16.6 1.0
CG2 D:THR136 4.7 21.1 1.0
CB D:GLU135 4.8 19.2 1.0
C D:GLU135 4.8 19.4 1.0
CB D:ASP132 4.8 19.5 1.0

Sodium binding site 5 out of 6 in 4e6k

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Sodium binding site 5 out of 6 in the 2.0 A Resolution Structure of Pseudomonas Aeruginosa Bacterioferritin (Bfrb) in Complex with Bacterioferritin Associated Ferredoxin (Bfd)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of 2.0 A Resolution Structure of Pseudomonas Aeruginosa Bacterioferritin (Bfrb) in Complex with Bacterioferritin Associated Ferredoxin (Bfd) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na202

b:23.5
occ:1.00
 O E:HOH447 2.4 36.8 1.0
OG1 E:THR136 2.5 20.6 1.0
O E:HOH302 2.6 29.8 1.0
OD1 E:ASP132 2.7 33.5 1.0
O E:HOH301 3.6 22.9 1.0
O E:ASP132 3.8 18.0 1.0
CB E:THR136 3.8 16.7 1.0
CG E:ASP132 3.8 25.1 1.0
N E:THR136 4.1 20.8 1.0
CA E:THR136 4.1 15.8 1.0
O E:HOH448 4.2 29.9 1.0
OD2 E:ASP132 4.5 32.4 1.0
CG2 E:THR136 4.5 17.9 1.0
C E:ASP132 4.6 19.3 1.0
CA E:ASP132 4.7 16.8 1.0
CB E:GLU135 4.8 22.9 1.0
C E:GLU135 4.9 25.0 1.0
CB E:ASP132 4.9 18.6 1.0

Sodium binding site 6 out of 6 in 4e6k

Go back to Sodium Binding Sites List in 4e6k
Sodium binding site 6 out of 6 in the 2.0 A Resolution Structure of Pseudomonas Aeruginosa Bacterioferritin (Bfrb) in Complex with Bacterioferritin Associated Ferredoxin (Bfd)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of 2.0 A Resolution Structure of Pseudomonas Aeruginosa Bacterioferritin (Bfrb) in Complex with Bacterioferritin Associated Ferredoxin (Bfd) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na202

b:23.3
occ:1.00
 O F:HOH465 2.4 35.9 1.0
OD1 F:ASP132 2.6 30.7 1.0
OG1 F:THR136 2.6 19.2 1.0
O F:HOH467 2.6 25.9 1.0
O F:HOH301 3.5 18.6 1.0
O F:ASP132 3.8 16.1 1.0
CG F:ASP132 3.8 23.2 1.0
CB F:THR136 3.9 21.2 1.0
N F:THR136 4.1 14.2 1.0
CA F:THR136 4.2 17.8 1.0
O F:HOH468 4.3 30.7 1.0
O F:HOH416 4.4 42.1 1.0
OD2 F:ASP132 4.5 30.8 1.0
C F:ASP132 4.6 15.9 1.0
CG2 F:THR136 4.7 18.0 1.0
CA F:ASP132 4.7 16.0 1.0
CB F:GLU135 4.8 13.5 1.0
C F:GLU135 4.9 16.3 1.0
CB F:ASP132 4.9 15.6 1.0
O F:HOH371 4.9 32.2 1.0

Reference:

H.Yao, Y.Wang, S.Lovell, R.Kumar, A.M.Ruvinsky, K.P.Battaile, I.A.Vakser, M.Rivera. The Structure of the Bfrb-Bfd Complex Reveals Protein-Protein Interactions Enabling Iron Release From Bacterioferritin. J.Am.Chem.Soc. V. 134 13470 2012.
ISSN: ISSN 0002-7863
PubMed: 22812654
DOI: 10.1021/JA305180N
Page generated: Mon Oct 7 15:06:06 2024

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