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Sodium in PDB 4a9v: Pseudomonas Fluorescens Phox

Enzymatic activity of Pseudomonas Fluorescens Phox

All present enzymatic activity of Pseudomonas Fluorescens Phox:
3.1.3.1;

Protein crystallography data

The structure of Pseudomonas Fluorescens Phox, PDB code: 4a9v was solved by S.C.Yong, P.Roversi, J.E.D.Lillington, O.B.Zeldin, E.F.Garman, S.M.Lea, B.C.Berks, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.30 / 1.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.820, 75.980, 114.970, 90.00, 90.00, 90.00
R / Rfree (%) 13.7 / 11.7

Other elements in 4a9v:

The structure of Pseudomonas Fluorescens Phox also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Calcium (Ca) 2 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Pseudomonas Fluorescens Phox (pdb code 4a9v). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Pseudomonas Fluorescens Phox, PDB code: 4a9v:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4a9v

Go back to Sodium Binding Sites List in 4a9v
Sodium binding site 1 out of 2 in the Pseudomonas Fluorescens Phox


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pseudomonas Fluorescens Phox within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na614

b:12.6
occ:1.00
H A:ASN555 2.4 13.1 1.0
H A:GLY557 2.6 17.0 1.0
O A:HOH2867 3.1 20.8 1.0
N A:ASN555 3.2 13.3 1.0
O A:HOH2891 3.2 28.0 1.0
N A:GLY557 3.3 16.3 1.0
H A:GLY556 3.3 13.2 1.0
CA A:GLY553 3.5 9.6 1.0
N A:GLY556 3.5 14.8 1.0
C A:ASN555 3.6 15.9 1.0
C A:GLY553 3.6 10.6 1.0
CA A:GLY530 3.6 10.4 1.0
CA A:ASN555 3.6 15.0 1.0
CB A:ASN555 3.7 19.0 1.0
N A:GLU554 3.7 10.3 1.0
CG2 A:ILE529 3.8 11.6 1.0
H A:GLU554 3.8 10.1 1.0
CA A:GLY557 3.9 16.6 1.0
H A:GLY553 3.9 9.6 1.0
O A:GLY553 4.1 10.8 1.0
N A:GLY530 4.1 9.6 1.0
N A:GLY553 4.2 9.3 1.0
O A:ASN555 4.3 19.3 1.0
O A:ILE529 4.3 9.7 1.0
C A:GLU554 4.3 12.5 1.0
C A:ILE529 4.3 8.9 1.0
C A:GLY556 4.3 21.7 1.0
C A:GLY557 4.4 14.7 1.0
CA A:GLY556 4.5 18.8 1.0
H A:GLY530 4.5 9.7 1.0
CA A:GLU554 4.6 11.9 1.0
CG A:ASN555 4.7 21.2 1.0
H A:SER558 4.7 11.8 1.0
N A:SER558 4.7 11.5 1.0
CG A:GLU554 4.8 13.2 1.0
ND2 A:ASN555 4.8 27.5 1.0
C A:GLY530 4.9 9.5 1.0
CB A:ILE529 5.0 10.3 1.0

Sodium binding site 2 out of 2 in 4a9v

Go back to Sodium Binding Sites List in 4a9v
Sodium binding site 2 out of 2 in the Pseudomonas Fluorescens Phox


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pseudomonas Fluorescens Phox within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na615

b:10.6
occ:1.00
H A:ASP541 2.4 9.6 1.0
O A:HOH2221 3.0 13.8 1.0
O A:HOH2892 3.1 30.3 1.0
N A:ASP541 3.1 9.2 1.0
NH2 A:ARG126 3.3 14.0 1.0
CG A:ASP541 3.3 10.0 1.0
NH1 A:ARG126 3.4 16.0 1.0
CD A:PRO540 3.5 10.0 1.0
CB A:ASP541 3.5 10.7 1.0
OD2 A:ASP541 3.6 13.2 1.0
OD1 A:ASP541 3.6 10.8 1.0
N A:PRO540 3.6 8.6 1.0
CZ A:ARG126 3.7 13.5 1.0
CB A:PRO540 3.7 10.5 1.0
CZ2 A:TRP131 3.8 10.1 1.0
CA A:ASP541 3.9 9.8 1.0
CG A:PRO540 4.0 11.4 1.0
C A:PRO540 4.0 9.1 1.0
CA A:PRO540 4.0 9.8 1.0
CB A:SER539 4.0 9.8 1.0
C A:SER539 4.3 8.3 1.0
OG A:SER539 4.4 9.6 1.0
O A:LYS80 4.5 8.5 0.5
O A:LYS80 4.6 10.6 0.5
CE2 A:TRP131 4.6 9.1 1.0
O A:HOH2324 4.7 12.1 1.0
CA A:SER539 4.7 8.4 1.0
NE1 A:TRP131 4.7 10.1 1.0
CH2 A:TRP131 4.8 10.8 1.0
O A:HOH2858 4.8 24.4 1.0
H A:GLN542 4.9 9.2 1.0
NE A:ARG126 4.9 15.7 1.0
HA A:PRO540 5.0 9.4 1.0

Reference:

S.C.Yong, P.Roversi, J.Lillington, F.Rodriguez, M.Krehenbrink, O.B.Zeldin, E.F.Garman, S.M.Lea, B.C.Berks. A Complex Iron-Calcium Cofactor Catalyzing Phosphotransfer Chemistry Science V. 345 1170 2014.
ISSN: ISSN 0036-8075
PubMed: 25190793
DOI: 10.1126/SCIENCE.1254237
Page generated: Tue Dec 15 06:32:37 2020

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