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Sodium in PDB 1ag9: Flavodoxins That Are Required For Enzyme Activation: the Structure of Oxidized Flavodoxin From Escherichia Coli at 1.8 Angstroms Resolution.

Protein crystallography data

The structure of Flavodoxins That Are Required For Enzyme Activation: the Structure of Oxidized Flavodoxin From Escherichia Coli at 1.8 Angstroms Resolution., PDB code: 1ag9 was solved by D.M.Hoover, M.L.Ludwig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 126.400, 41.100, 68.150, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 25

Other elements in 1ag9:

The structure of Flavodoxins That Are Required For Enzyme Activation: the Structure of Oxidized Flavodoxin From Escherichia Coli at 1.8 Angstroms Resolution. also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Calcium (Ca) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Flavodoxins That Are Required For Enzyme Activation: the Structure of Oxidized Flavodoxin From Escherichia Coli at 1.8 Angstroms Resolution. (pdb code 1ag9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Flavodoxins That Are Required For Enzyme Activation: the Structure of Oxidized Flavodoxin From Escherichia Coli at 1.8 Angstroms Resolution., PDB code: 1ag9:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 1ag9

Go back to Sodium Binding Sites List in 1ag9
Sodium binding site 1 out of 4 in the Flavodoxins That Are Required For Enzyme Activation: the Structure of Oxidized Flavodoxin From Escherichia Coli at 1.8 Angstroms Resolution.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Flavodoxins That Are Required For Enzyme Activation: the Structure of Oxidized Flavodoxin From Escherichia Coli at 1.8 Angstroms Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na400

b:10.5
occ:1.00
O B:HOH1129 2.3 16.5 0.6
O B:HOH1116 2.4 31.3 1.0
O A:HOH474 2.4 15.4 0.6
OE1 A:GLU61 2.5 21.5 1.0
OE2 A:GLU61 2.5 23.5 1.0
O A:HOH512 2.6 32.7 1.0
OD2 B:ASP67 2.6 17.6 1.0
CD A:GLU61 2.8 21.9 1.0
OD1 B:ASP67 2.9 19.0 1.0
CG B:ASP67 3.1 16.3 1.0
CA A:CA200 4.0 16.0 1.0
O B:HOH1036 4.2 16.7 1.0
O B:HOH1073 4.2 30.3 0.8
CG A:GLU61 4.3 18.7 1.0
OE1 B:GLU61 4.4 18.6 1.0
O A:HOH407 4.4 23.2 0.8
CB B:ASP67 4.5 12.2 1.0
O B:HOH1054 4.6 29.6 1.0
O B:HOH1052 4.6 19.4 1.0
O B:HOH1151 4.7 33.3 0.9
CL A:CL405 4.9 20.4 1.0
CL B:CL404 4.9 22.7 1.0
O A:HOH406 5.0 12.0 1.0

Sodium binding site 2 out of 4 in 1ag9

Go back to Sodium Binding Sites List in 1ag9
Sodium binding site 2 out of 4 in the Flavodoxins That Are Required For Enzyme Activation: the Structure of Oxidized Flavodoxin From Escherichia Coli at 1.8 Angstroms Resolution.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Flavodoxins That Are Required For Enzyme Activation: the Structure of Oxidized Flavodoxin From Escherichia Coli at 1.8 Angstroms Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:13.3
occ:1.00
O B:HOH1052 2.4 19.4 1.0
O B:HOH1151 2.4 33.3 0.9
O A:HOH484 2.4 25.4 0.5
OE2 B:GLU61 2.4 21.9 1.0
O B:HOH1074 2.4 30.3 1.0
OE1 B:GLU61 2.5 18.6 1.0
OD2 A:ASP67 2.8 24.0 1.0
CD B:GLU61 2.8 20.3 1.0
OD1 A:ASP67 2.9 21.3 1.0
CG A:ASP67 3.2 21.9 1.0
CA B:CA1000 4.2 21.1 1.0
O A:HOH470 4.2 10.6 1.0
O A:HOH538 4.3 32.2 0.4
CG B:GLU61 4.3 18.4 1.0
OE1 A:GLU61 4.4 21.5 1.0
O B:HOH1003 4.5 26.6 0.7
O B:HOH1116 4.5 31.3 1.0
CB A:ASP67 4.6 20.2 1.0
O A:HOH474 4.7 15.4 0.6
O B:HOH1136 4.9 55.8 1.0
O B:HOH1002 4.9 14.2 1.0
CL A:CL405 4.9 20.4 1.0
CL B:CL404 5.0 22.7 1.0

Sodium binding site 3 out of 4 in 1ag9

Go back to Sodium Binding Sites List in 1ag9
Sodium binding site 3 out of 4 in the Flavodoxins That Are Required For Enzyme Activation: the Structure of Oxidized Flavodoxin From Escherichia Coli at 1.8 Angstroms Resolution.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Flavodoxins That Are Required For Enzyme Activation: the Structure of Oxidized Flavodoxin From Escherichia Coli at 1.8 Angstroms Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:15.1
occ:1.00
O B:HOH1085 2.3 21.8 1.0
O B:HOH1158 2.4 6.8 0.5
OD2 B:ASP43 2.4 20.3 1.0
O B:HOH1075 2.4 31.3 0.8
O B:HOH1076 2.5 10.6 0.6
O B:HOH1070 2.5 27.4 1.0
OD1 B:ASP43 2.7 19.9 1.0
CG B:ASP43 2.9 18.1 1.0
OG B:SER40 4.1 17.9 1.0
O B:HOH1012 4.1 23.5 1.0
O B:LYS38 4.1 22.1 1.0
CB B:ASP43 4.4 16.9 1.0
N B:SER40 4.6 17.3 1.0
CA B:SER39 4.7 19.5 1.0
CB B:SER40 4.8 16.2 1.0

Sodium binding site 4 out of 4 in 1ag9

Go back to Sodium Binding Sites List in 1ag9
Sodium binding site 4 out of 4 in the Flavodoxins That Are Required For Enzyme Activation: the Structure of Oxidized Flavodoxin From Escherichia Coli at 1.8 Angstroms Resolution.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Flavodoxins That Are Required For Enzyme Activation: the Structure of Oxidized Flavodoxin From Escherichia Coli at 1.8 Angstroms Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:17.4
occ:1.00
O B:ALA46 2.4 27.9 1.0
O B:HOH1152 2.4 44.7 1.0
O B:HOH1167 2.4 19.7 0.4
O B:HOH1071 2.5 19.8 1.0
O B:HOH1091 2.6 16.8 0.6
C B:ALA46 3.6 24.9 1.0
O B:ALA2 4.3 25.0 1.0
CA B:ALA46 4.5 25.1 1.0
N B:TYR47 4.6 23.4 1.0
CB B:ALA46 4.6 26.0 1.0
CA B:TYR47 4.6 21.1 1.0
O B:HOH1145 4.7 26.1 0.8
O B:HOH1079 4.7 17.8 1.0
O B:HOH1015 4.7 37.8 1.0
CD2 B:TYR47 4.7 17.7 1.0
O B:HOH1144 4.8 39.7 1.0
O B:HOH1014 4.9 24.0 0.9

Reference:

D.M.Hoover, M.L.Ludwig. A Flavodoxin That Is Required For Enzyme Activation: the Structure of Oxidized Flavodoxin From Escherichia Coli at 1.8 A Resolution. Protein Sci. V. 6 2525 1997.
ISSN: ISSN 0961-8368
PubMed: 9416602
Page generated: Tue Dec 15 05:21:47 2020

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