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Sodium in PDB 1x7d: Crystal Structure Analysis of Ornithine Cyclodeaminase Complexed with Nad and Ornithine to 1.6 Angstroms

Enzymatic activity of Crystal Structure Analysis of Ornithine Cyclodeaminase Complexed with Nad and Ornithine to 1.6 Angstroms

All present enzymatic activity of Crystal Structure Analysis of Ornithine Cyclodeaminase Complexed with Nad and Ornithine to 1.6 Angstroms:
4.3.1.12;

Protein crystallography data

The structure of Crystal Structure Analysis of Ornithine Cyclodeaminase Complexed with Nad and Ornithine to 1.6 Angstroms, PDB code: 1x7d was solved by S.Alam, J.L.Goodman, S.Wang, F.J.Ruzicka, P.A.Frey, J.E.Wedekind, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.95 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.880, 78.620, 119.940, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 19

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure Analysis of Ornithine Cyclodeaminase Complexed with Nad and Ornithine to 1.6 Angstroms (pdb code 1x7d). 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 Analysis of Ornithine Cyclodeaminase Complexed with Nad and Ornithine to 1.6 Angstroms, PDB code: 1x7d:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1x7d

Go back to Sodium Binding Sites List in 1x7d
Sodium binding site 1 out of 2 in the Crystal Structure Analysis of Ornithine Cyclodeaminase Complexed with Nad and Ornithine to 1.6 Angstroms


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure Analysis of Ornithine Cyclodeaminase Complexed with Nad and Ornithine to 1.6 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1501

b:12.8
occ:1.00
O A:SER293 2.4 8.3 1.0
O A:GLY227 2.4 13.6 1.0
O A:HOH1513 2.5 10.8 1.0
O A:ALA224 2.6 8.8 1.0
O A:HOH1879 2.6 16.8 1.0
C A:ALA224 3.3 7.3 1.0
C A:VAL225 3.4 8.9 1.0
O A:VAL225 3.4 8.0 1.0
C A:GLY227 3.5 11.6 1.0
C A:SER293 3.5 7.5 1.0
N A:GLY227 3.5 10.0 1.0
CA A:VAL225 3.5 8.2 1.0
N A:VAL225 3.7 8.7 1.0
CA A:GLY227 3.9 12.2 1.0
N A:GLY226 3.9 8.7 1.0
N A:SER293 4.0 8.6 1.0
CA A:SER293 4.2 7.7 1.0
C A:GLY226 4.3 11.9 1.0
OD1 A:ASP292 4.3 10.0 1.0
CB A:ALA224 4.3 8.6 1.0
CA A:ALA224 4.4 8.3 1.0
OE2 A:GLU258 4.4 12.2 1.0
N A:VAL294 4.5 7.1 1.0
CG1 A:VAL294 4.5 6.2 1.0
O A:HOH1530 4.6 14.3 1.0
CA A:GLY226 4.6 10.4 1.0
CB A:SER293 4.6 8.1 1.0
N A:ASP228 4.6 10.9 1.0
CA A:VAL294 4.7 7.3 1.0
C A:ASP292 4.7 7.9 1.0
OE1 A:GLU234 4.7 9.7 1.0
CG A:GLU258 4.8 10.4 1.0
N7N A:NAD1302 4.8 8.6 1.0
CA A:ASP228 5.0 10.1 1.0

Sodium binding site 2 out of 2 in 1x7d

Go back to Sodium Binding Sites List in 1x7d
Sodium binding site 2 out of 2 in the Crystal Structure Analysis of Ornithine Cyclodeaminase Complexed with Nad and Ornithine to 1.6 Angstroms


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure Analysis of Ornithine Cyclodeaminase Complexed with Nad and Ornithine to 1.6 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1502

b:13.7
occ:1.00
O B:SER293 2.4 9.2 1.0
O B:GLY227 2.5 13.3 1.0
O B:ALA224 2.6 10.1 1.0
O B:HOH3176 2.6 15.4 1.0
O B:HOH3315 2.6 20.8 1.0
C B:ALA224 3.3 9.5 1.0
O B:VAL225 3.3 9.8 1.0
C B:VAL225 3.3 10.2 1.0
C B:GLY227 3.5 12.5 1.0
N B:GLY227 3.5 11.7 1.0
C B:SER293 3.5 9.1 1.0
CA B:VAL225 3.5 9.3 1.0
N B:VAL225 3.7 9.1 1.0
CA B:GLY227 3.8 12.4 1.0
N B:GLY226 3.9 10.3 1.0
N B:SER293 4.0 9.9 1.0
CA B:SER293 4.2 9.4 1.0
C B:GLY226 4.2 12.5 1.0
OD1 B:ASP292 4.2 12.5 1.0
CB B:ALA224 4.3 9.7 1.0
CA B:ALA224 4.4 9.3 1.0
OE2 B:GLU258 4.4 16.5 1.0
N B:VAL294 4.5 8.8 1.0
CG1 B:VAL294 4.5 8.8 1.0
O B:HOH3184 4.6 14.2 1.0
CA B:GLY226 4.6 11.6 1.0
OE1 B:GLU234 4.7 11.9 1.0
N B:ASP228 4.7 11.6 1.0
CB B:SER293 4.7 11.3 1.0
CA B:VAL294 4.7 9.0 1.0
C B:ASP292 4.7 10.4 1.0
CG B:GLU258 4.8 15.1 1.0
N7N B:NAD1301 4.8 7.3 1.0

Reference:

J.L.Goodman, S.Wang, S.Alam, F.J.Ruzicka, P.A.Frey, J.E.Wedekind. Ornithine Cyclodeaminase: Structure, Mechanism of Action, and Implications For the U-Crystallin Family Biochemistry V. 43 13883 2004.
ISSN: ISSN 0006-2960
PubMed: 15518536
DOI: 10.1021/BI048207I
Page generated: Tue Dec 15 05:41:31 2020

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