Atomistry » Sodium » PDB 4tmw-4u9k » 4tof
Atomistry »
  Sodium »
    PDB 4tmw-4u9k »
      4tof »

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: Tue Dec 15 07:31:28 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy