Atomistry » Sodium » PDB 131d-1b7r » 1ag9
Atomistry »
  Sodium »
    PDB 131d-1b7r »
      1ag9 »

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

Last articles

Zn in 8PFC
Zn in 8SF0
Zn in 8SOJ
Zn in 8SOK
Zn in 8SYI
Zn in 8SLG
Zn in 8SEX
Zn in 8SEZ
Zn in 8SJG
Zn in 8SEY
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy