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Sodium in PDB 1u7h: Structure and A Proposed Mechanism For Ornithine Cyclodeaminase From Pseudomonas Putida

Enzymatic activity of Structure and A Proposed Mechanism For Ornithine Cyclodeaminase From Pseudomonas Putida

All present enzymatic activity of Structure and A Proposed Mechanism For Ornithine Cyclodeaminase From Pseudomonas Putida:
4.3.1.12;

Protein crystallography data

The structure of Structure and A Proposed Mechanism For Ornithine Cyclodeaminase From Pseudomonas Putida, PDB code: 1u7h 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 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.900, 78.600, 119.900, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 18.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure and A Proposed Mechanism For Ornithine Cyclodeaminase From Pseudomonas Putida (pdb code 1u7h). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure and A Proposed Mechanism For Ornithine Cyclodeaminase From Pseudomonas Putida, PDB code: 1u7h:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1u7h

Go back to Sodium Binding Sites List in 1u7h
Sodium binding site 1 out of 2 in the Structure and A Proposed Mechanism For Ornithine Cyclodeaminase From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure and A Proposed Mechanism For Ornithine Cyclodeaminase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na911

b:15.6
occ:1.00
O A:SER293 2.4 5.9 1.0
O A:GLY227 2.4 11.1 1.0
O A:HOH994 2.5 10.3 1.0
O A:HOH992 2.5 14.4 1.0
O A:ALA224 2.5 6.7 1.0
C A:ALA224 3.3 8.0 1.0
C A:VAL225 3.3 8.5 1.0
O A:VAL225 3.4 7.1 1.0
C A:GLY227 3.4 11.2 1.0
N A:GLY227 3.4 10.9 1.0
C A:SER293 3.5 6.9 1.0
CA A:VAL225 3.5 7.2 1.0
N A:VAL225 3.7 7.7 1.0
CA A:GLY227 3.8 11.5 1.0
N A:GLY226 3.9 8.2 1.0
N A:SER293 4.0 7.6 1.0
C A:GLY226 4.2 11.5 1.0
CA A:SER293 4.2 6.8 1.0
OD1 A:ASP292 4.3 8.4 1.0
CB A:ALA224 4.3 7.9 1.0
CA A:ALA224 4.4 7.9 1.0
OE2 A:GLU258 4.4 12.1 1.0
N A:VAL294 4.5 5.3 1.0
CG1 A:VAL294 4.5 4.5 1.0
CA A:GLY226 4.5 9.7 1.0
O A:HOH993 4.6 11.8 1.0
N A:ASP228 4.6 9.6 1.0
OE1 A:GLU234 4.7 10.6 1.0
CB A:SER293 4.7 7.4 1.0
CA A:VAL294 4.7 5.8 1.0
C A:ASP292 4.7 6.8 1.0
CG A:GLU258 4.8 10.0 1.0
N7N A:NAD802 4.8 7.0 1.0
O A:GLY226 5.0 12.8 1.0

Sodium binding site 2 out of 2 in 1u7h

Go back to Sodium Binding Sites List in 1u7h
Sodium binding site 2 out of 2 in the Structure and A Proposed Mechanism For Ornithine Cyclodeaminase From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure and A Proposed Mechanism For Ornithine Cyclodeaminase From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na912

b:15.8
occ:1.00
O B:SER293 2.4 7.0 1.0
O B:HOH1105 2.4 17.2 1.0
O B:GLY227 2.5 14.3 1.0
O B:HOH1104 2.5 12.6 1.0
O B:ALA224 2.5 8.5 1.0
C B:ALA224 3.2 8.2 1.0
C B:VAL225 3.2 9.3 1.0
O B:VAL225 3.2 9.2 1.0
CA B:VAL225 3.4 8.7 1.0
N B:GLY227 3.4 12.8 1.0
C B:GLY227 3.5 12.7 1.0
C B:SER293 3.5 7.1 1.0
N B:VAL225 3.6 8.3 1.0
CA B:GLY227 3.8 13.5 1.0
N B:GLY226 3.8 9.7 1.0
N B:SER293 4.0 8.8 1.0
C B:GLY226 4.1 13.6 1.0
CA B:SER293 4.2 8.7 1.0
CB B:ALA224 4.3 7.4 1.0
CA B:ALA224 4.3 7.7 1.0
OD1 B:ASP292 4.4 10.1 1.0
OE2 B:GLU258 4.4 15.3 1.0
CA B:GLY226 4.5 11.4 1.0
N B:VAL294 4.5 6.0 1.0
OE1 B:GLU234 4.5 11.6 1.0
CG1 B:VAL294 4.6 7.3 1.0
CB B:SER293 4.7 8.8 1.0
N B:ASP228 4.7 10.9 1.0
O B:HOH1106 4.7 13.3 1.0
CA B:VAL294 4.7 6.8 1.0
C B:ASP292 4.8 9.3 1.0
N7N B:NAD801 4.8 6.1 1.0
CG B:GLU258 4.9 13.8 1.0
CB B:VAL225 4.9 9.0 1.0
O B:GLY226 5.0 14.2 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 05:36:47 2020

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