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Sodium in PDB 4tog: 1.80A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 2 From Pseudomonas Aeruginosa

Enzymatic activity of 1.80A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 2 From Pseudomonas Aeruginosa

All present enzymatic activity of 1.80A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 2 From Pseudomonas Aeruginosa:
1.16.3.1;

Protein crystallography data

The structure of 1.80A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 2 From Pseudomonas Aeruginosa, PDB code: 4tog 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) 37.27 / 1.80
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 155.134, 155.134, 155.177, 90.00, 90.00, 120.00
R / Rfree (%) 15.3 / 17.8

Other elements in 4tog:

The structure of 1.80A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 2 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 1.80A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 2 From Pseudomonas Aeruginosa (pdb code 4tog). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the 1.80A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 2 From Pseudomonas Aeruginosa, PDB code: 4tog:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4tog

Go back to Sodium Binding Sites List in 4tog
Sodium binding site 1 out of 4 in the 1.80A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 2 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 1.80A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 2 From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:46.5
occ:1.00
 O A:HOH335 2.6 41.1 1.0
O A:HOH343 2.7 40.3 1.0
OG1 A:THR136 3.1 22.8 1.0
CA A:THR136 3.9 20.9 1.0
N A:THR136 4.0 22.2 1.0
CB A:THR136 4.1 24.8 1.0
C A:GLU135 4.4 26.7 1.0
OD1 A:ASP132 4.5 33.7 1.0
O A:HOH321 4.6 40.0 1.0
O A:GLU135 4.6 23.6 1.0
CG2 A:THR136 4.7 24.6 1.0
CB A:GLU135 4.7 23.5 1.0
O A:ASP132 4.8 21.6 1.0

Sodium binding site 2 out of 4 in 4tog

Go back to Sodium Binding Sites List in 4tog
Sodium binding site 2 out of 4 in the 1.80A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 2 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 1.80A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 2 From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na204

b:45.1
occ:1.00
 O B:HOH311 2.3 33.2 1.0
OG1 B:THR136 2.4 23.2 1.0
OD1 B:ASP132 2.4 29.5 1.0
O B:ASP132 3.2 21.4 1.0
CG B:ASP132 3.7 32.3 1.0
CB B:THR136 3.8 26.2 1.0
N B:THR136 3.9 23.8 1.0
C B:ASP132 4.0 19.9 1.0
CA B:ASP132 4.1 19.9 1.0
CA B:THR136 4.1 20.5 1.0
CB B:ASP132 4.5 19.3 1.0
CB B:GLU135 4.5 25.6 1.0
OD2 B:ASP132 4.6 34.8 1.0
O B:HOH333 4.6 35.5 1.0
C B:GLU135 4.6 25.0 1.0
CG2 B:THR136 4.7 25.0 1.0
OE1 B:GLU135 4.9 33.3 1.0

Sodium binding site 3 out of 4 in 4tog

Go back to Sodium Binding Sites List in 4tog
Sodium binding site 3 out of 4 in the 1.80A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 2 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 1.80A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 2 From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na203

b:50.0
occ:1.00
 O D:HOH457 2.2 41.4 1.0
OD1 C:ASP132 2.4 35.2 1.0
OG1 C:THR136 2.4 26.5 1.0
O C:HOH317 2.5 41.2 1.0
O C:ASP132 3.2 24.4 1.0
O D:ASP34 3.2 22.3 1.0
OD1 D:ASP34 3.2 33.2 1.0
O D:HOH303 3.5 36.8 1.0
CG C:ASP132 3.6 34.0 1.0
O C:HOH361 3.6 41.9 1.0
CB C:THR136 3.8 27.9 1.0
C C:ASP132 3.9 23.3 1.0
N C:THR136 3.9 23.9 1.0
CA C:ASP132 4.1 25.6 1.0
CA C:THR136 4.1 23.3 1.0
CG D:ASP34 4.3 31.8 1.0
C D:ASP34 4.3 27.1 1.0
CB C:ASP132 4.4 23.7 1.0
OD2 C:ASP132 4.5 37.1 1.0
CB C:GLU135 4.6 27.0 1.0
O C:HOH405 4.6 41.0 1.0
CA D:ASP34 4.7 23.2 1.0
C C:GLU135 4.7 28.6 1.0
CG2 C:THR136 4.7 28.8 1.0
OE1 C:GLU135 5.0 34.9 1.0
OD2 D:ASP34 5.0 35.0 1.0

Sodium binding site 4 out of 4 in 4tog

Go back to Sodium Binding Sites List in 4tog
Sodium binding site 4 out of 4 in the 1.80A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 2 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 1.80A Resolution Structure of Bfrb (C89S, K96C) Crystal Form 2 From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na204

b:50.5
occ:1.00
 O D:HOH455 2.2 36.9 1.0
O B:HOH454 2.2 39.1 1.0
OD1 D:ASP132 2.4 30.2 1.0
OG1 D:THR136 2.5 26.2 1.0
O B:ASP34 3.2 24.0 1.0
O D:ASP132 3.3 21.4 1.0
OD1 B:ASP34 3.3 31.6 1.0
O B:HOH370 3.3 34.6 1.0
CG D:ASP132 3.6 29.1 1.0
O B:HOH358 3.7 41.4 1.0
O D:HOH404 3.8 36.7 1.0
CB D:THR136 3.9 23.6 1.0
C D:ASP132 4.0 21.5 1.0
N D:THR136 4.0 24.4 1.0
CA D:ASP132 4.1 23.9 1.0
CA D:THR136 4.2 23.3 1.0
CG B:ASP34 4.3 28.2 1.0
C B:ASP34 4.3 22.3 1.0
CB D:ASP132 4.5 23.1 1.0
OD2 D:ASP132 4.5 38.2 1.0
CB D:GLU135 4.5 26.7 1.0
O D:HOH425 4.6 40.2 1.0
CA B:ASP34 4.7 21.7 1.0
C D:GLU135 4.7 23.3 1.0
CG2 D:THR136 4.8 24.9 1.0
OE1 D:GLU135 4.9 33.5 1.0
CD1 A:PHE64 5.0 25.1 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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