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Sodium in PDB 2oz3: Crystal Structure of L-Rhamnonate Dehydratase From Azotobacter Vinelandii

Enzymatic activity of Crystal Structure of L-Rhamnonate Dehydratase From Azotobacter Vinelandii

All present enzymatic activity of Crystal Structure of L-Rhamnonate Dehydratase From Azotobacter Vinelandii:
4.2.1.90;

Protein crystallography data

The structure of Crystal Structure of L-Rhamnonate Dehydratase From Azotobacter Vinelandii, PDB code: 2oz3 was solved by Y.Patskovsky, R.Toro, J.M.Sauder, J.C.Freeman, K.Bain, T.Gheyi, B.Wu, S.R.Wasserman, D.Smith, J.Gerlt, S.K.Burley, S.C.Almo, New York Sgxresearch Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 170.772, 115.397, 164.113, 90.00, 96.06, 90.00
R / Rfree (%) 19.6 / 25.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of L-Rhamnonate Dehydratase From Azotobacter Vinelandii (pdb code 2oz3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of L-Rhamnonate Dehydratase From Azotobacter Vinelandii, PDB code: 2oz3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2oz3

Go back to Sodium Binding Sites List in 2oz3
Sodium binding site 1 out of 2 in the Crystal Structure of L-Rhamnonate Dehydratase From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of L-Rhamnonate Dehydratase From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2001

b:62.6
occ:1.00
OE2 B:GLU240 2.2 37.1 1.0
O B:HOH3066 2.3 43.8 1.0
OE1 B:GLU268 2.3 67.6 1.0
OD2 B:ASP214 2.5 59.9 1.0
O B:HOH3132 2.7 32.0 1.0
CG B:ASP214 3.4 43.6 1.0
CD B:GLU240 3.4 37.0 1.0
O B:HOH3200 3.4 33.7 1.0
CD B:GLU268 3.5 68.2 1.0
OD1 B:ASP214 3.7 49.0 1.0
NZ B:LYS177 3.8 43.8 1.0
O B:HOH3232 4.0 47.4 1.0
CG B:GLU240 4.0 23.6 1.0
CD2 B:HIS318 4.1 39.6 1.0
OE2 B:GLU268 4.2 65.8 1.0
CE B:LYS177 4.2 23.0 1.0
OE1 B:GLU240 4.4 27.2 1.0
CG B:GLU268 4.5 55.8 1.0
O B:HOH3053 4.5 29.4 1.0
CB B:ASP214 4.5 25.5 1.0
NE2 B:HIS318 4.7 40.3 1.0
OE2 B:GLU338 4.7 29.0 1.0
CB B:GLU268 4.9 39.7 1.0
OE1 B:GLU241 4.9 38.2 1.0

Sodium binding site 2 out of 2 in 2oz3

Go back to Sodium Binding Sites List in 2oz3
Sodium binding site 2 out of 2 in the Crystal Structure of L-Rhamnonate Dehydratase From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of L-Rhamnonate Dehydratase From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na2002

b:0.3
occ:1.00
OE2 D:GLU240 1.9 50.0 1.0
OD2 D:ASP214 2.1 59.9 1.0
OE1 D:GLU268 2.1 74.7 1.0
CD D:GLU240 2.9 37.5 1.0
CG D:ASP214 3.3 36.3 1.0
CD D:GLU268 3.4 76.1 1.0
CG D:GLU240 3.5 32.1 1.0
O D:HOH3041 3.7 32.9 1.0
OD1 D:ASP214 3.8 47.4 1.0
NZ D:LYS177 3.8 41.7 1.0
OE1 D:GLU240 3.9 35.1 1.0
OE2 D:GLU268 4.1 74.0 1.0
CE D:LYS177 4.3 32.2 1.0
CG D:GLU268 4.4 51.6 1.0
CB D:ASP214 4.5 36.1 1.0
CD2 D:HIS318 4.6 51.9 1.0
OE1 D:GLU241 4.8 56.3 1.0
OE2 D:GLU338 4.8 50.6 1.0
CB D:GLU240 4.9 28.4 1.0
OE1 D:GLN289 4.9 31.5 1.0
O D:HOH3103 4.9 58.5 1.0
CB D:GLU268 4.9 36.8 1.0

Reference:

Y.Patskovsky, R.Toro, J.M.Sauder, J.C.Freeman, K.Bain, B.Wu, T.Gheyi, S.R.Wasserman, D.Smith, J.Gerlt, S.K.Burley, S.C.Almo. Crystal Structure of L-Rhamnonate Dehydratase From Azotobacter Vinelandii To Be Published.
Page generated: Tue Dec 15 05:53:25 2020

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