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Sodium in PDB 4tof: 1.65A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 1 From Pseudomonas Aeruginosa

Enzymatic activity of 1.65A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 1 From Pseudomonas Aeruginosa

All present enzymatic activity of 1.65A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 1 From Pseudomonas Aeruginosa:
1.16.3.1;

Protein crystallography data

The structure of 1.65A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 1 From Pseudomonas Aeruginosa, PDB code: 4tof was solved by S.Lovell, K.P.Battaile, H.Yao, R.Kumar, K.Eshelman, M.Rivera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.10 / 1.65
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 158.568, 158.568, 152.381, 90.00, 90.00, 120.00
R / Rfree (%) 14.5 / 16.2

Other elements in 4tof:

The structure of 1.65A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 1 From Pseudomonas Aeruginosa also contains other interesting chemical elements:

Potassium (K) 1 atom
Iron (Fe) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the 1.65A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 1 From Pseudomonas Aeruginosa (pdb code 4tof). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the 1.65A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 1 From Pseudomonas Aeruginosa, PDB code: 4tof:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4tof

Go back to Sodium Binding Sites List in 4tof
Sodium binding site 1 out of 4 in the 1.65A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 1 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 1.65A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 1 From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:41.1
occ:1.00
 O A:HOH322 2.3 27.6 1.0
OG1 A:THR136 2.3 19.8 1.0
OD1 A:ASP132 2.4 27.3 1.0
O A:HOH328 3.1 21.2 1.0
O A:ASP132 3.3 16.2 1.0
CG A:ASP132 3.5 26.8 1.0
CB A:THR136 3.7 17.9 1.0
N A:THR136 4.0 16.0 1.0
C A:ASP132 4.1 17.3 1.0
CA A:THR136 4.1 16.2 1.0
OD2 A:ASP132 4.2 38.3 1.0
CA A:ASP132 4.2 14.4 1.0
CB A:ASP132 4.4 16.0 1.0
CG2 A:THR136 4.5 19.0 1.0
O A:HOH348 4.7 32.2 1.0
CB A:GLU135 4.7 16.8 1.0
C A:GLU135 4.8 17.7 1.0
OE1 A:GLU135 4.9 29.1 1.0

Sodium binding site 2 out of 4 in 4tof

Go back to Sodium Binding Sites List in 4tof
Sodium binding site 2 out of 4 in the 1.65A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 1 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 1.65A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 1 From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na205

b:33.5
occ:1.00
 O B:HOH320 2.3 29.0 1.0
OG1 B:THR136 2.4 20.8 1.0
OD1 B:ASP132 2.5 27.6 1.0
O B:HOH312 3.2 24.0 1.0
O B:ASP132 3.3 17.7 1.0
CG B:ASP132 3.6 24.4 1.0
CB B:THR136 3.7 19.4 1.0
N B:THR136 4.0 16.2 1.0
CA B:THR136 4.1 18.3 1.0
C B:ASP132 4.1 18.7 1.0
CA B:ASP132 4.3 16.4 1.0
OD2 B:ASP132 4.4 38.1 1.0
CB B:ASP132 4.5 15.4 1.0
O B:HOH333 4.6 31.0 1.0
CG2 B:THR136 4.6 21.6 1.0
O B:HOH332 4.6 45.2 1.0
CB B:GLU135 4.7 17.9 1.0
C B:GLU135 4.8 17.3 1.0

Sodium binding site 3 out of 4 in 4tof

Go back to Sodium Binding Sites List in 4tof
Sodium binding site 3 out of 4 in the 1.65A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 1 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 1.65A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 1 From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na205

b:38.2
occ:1.00
 O D:HOH474 2.1 22.9 1.0
OG1 C:THR136 2.3 21.2 1.0
O C:HOH341 2.4 30.3 1.0
OD1 C:ASP132 2.4 24.8 1.0
O D:ASP34 3.0 18.9 1.0
O C:HOH360 3.0 22.8 1.0
O C:ASP132 3.2 18.8 1.0
OD1 D:ASP34 3.3 25.5 1.0
O D:HOH302 3.5 28.5 1.0
CG C:ASP132 3.5 29.4 1.0
CB C:THR136 3.7 19.7 1.0
N C:THR136 4.0 19.1 1.0
O D:HOH321 4.0 29.1 1.0
C D:ASP34 4.0 19.3 1.0
C C:ASP132 4.0 19.5 1.0
CA C:THR136 4.1 19.8 1.0
CA C:ASP132 4.2 16.7 1.0
OD2 C:ASP132 4.2 43.4 1.0
CG D:ASP34 4.2 26.0 1.0
CB C:ASP132 4.4 16.7 1.0
CA D:ASP34 4.5 20.1 1.0
CG2 C:THR136 4.5 22.3 1.0
O C:HOH416 4.7 32.4 1.0
CB C:GLU135 4.7 18.5 1.0
C C:GLU135 4.8 23.0 1.0
O C:HOH458 4.8 39.9 1.0
CB D:ASP34 5.0 18.7 1.0
OD2 D:ASP34 5.0 30.1 1.0

Sodium binding site 4 out of 4 in 4tof

Go back to Sodium Binding Sites List in 4tof
Sodium binding site 4 out of 4 in the 1.65A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 1 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 1.65A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 1 From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na205

b:44.8
occ:1.00
 O B:HOH347 2.1 21.7 1.0
O D:HOH475 2.3 28.7 1.0
OD1 D:ASP132 2.3 28.8 1.0
OG1 D:THR136 2.4 21.5 1.0
O B:ASP34 3.0 19.3 1.0
O D:HOH333 3.0 23.2 1.0
OD1 B:ASP34 3.1 27.7 1.0
O B:HOH366 3.2 28.4 1.0
O D:ASP132 3.4 17.3 1.0
CG D:ASP132 3.5 29.8 1.0
CB D:THR136 3.8 17.3 1.0
O B:HOH352 3.8 28.1 1.0
C B:ASP34 4.0 17.3 1.0
C D:ASP132 4.2 18.6 1.0
CG B:ASP34 4.2 22.8 1.0
N D:THR136 4.2 17.9 1.0
CA D:ASP132 4.3 15.5 1.0
OD2 D:ASP132 4.3 36.2 1.0
CA D:THR136 4.3 16.3 1.0
CA B:ASP34 4.4 16.5 1.0
CB D:ASP132 4.5 18.0 1.0
O D:HOH376 4.6 28.2 1.0
CG2 D:THR136 4.6 20.3 1.0
O B:HOH451 4.8 41.4 1.0
O D:HOH354 4.8 44.5 1.0
CB D:GLU135 4.9 19.2 1.0
CB B:ASP34 4.9 21.0 1.0
C D:GLU135 4.9 18.5 1.0

Reference:

H.Yao, H.Rui, R.Kumar, K.Eshelman, S.Lovell, K.P.Battaile, W.Im, M.Rivera. Concerted Motions Networking Pores and Distant Ferroxidase Centers Enable Bacterioferritin Function and Iron Traffic. Biochemistry 2015.
ISSN: ISSN 0006-2960
PubMed: 25640193
DOI: 10.1021/BI501255R
Page generated: Mon Oct 7 18:28:17 2024

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