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Sodium in PDB 5h8i: Crystal Structure of Medicago Truncatula N-Carbamoylputrescine Amidohydrolase (Mtcpa) in Complex with N-(Dihydroxymethyl)Putrescine

Enzymatic activity of Crystal Structure of Medicago Truncatula N-Carbamoylputrescine Amidohydrolase (Mtcpa) in Complex with N-(Dihydroxymethyl)Putrescine

All present enzymatic activity of Crystal Structure of Medicago Truncatula N-Carbamoylputrescine Amidohydrolase (Mtcpa) in Complex with N-(Dihydroxymethyl)Putrescine:
3.5.1.53;

Protein crystallography data

The structure of Crystal Structure of Medicago Truncatula N-Carbamoylputrescine Amidohydrolase (Mtcpa) in Complex with N-(Dihydroxymethyl)Putrescine, PDB code: 5h8i was solved by B.Sekula, M.Ruszkowski, M.Malinska, Z.Dauter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.55 / 1.97
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 152.130, 211.060, 208.780, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 19.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Medicago Truncatula N-Carbamoylputrescine Amidohydrolase (Mtcpa) in Complex with N-(Dihydroxymethyl)Putrescine (pdb code 5h8i). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Medicago Truncatula N-Carbamoylputrescine Amidohydrolase (Mtcpa) in Complex with N-(Dihydroxymethyl)Putrescine, PDB code: 5h8i:

Sodium binding site 1 out of 1 in 5h8i

Go back to Sodium Binding Sites List in 5h8i
Sodium binding site 1 out of 1 in the Crystal Structure of Medicago Truncatula N-Carbamoylputrescine Amidohydrolase (Mtcpa) in Complex with N-(Dihydroxymethyl)Putrescine


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 Medicago Truncatula N-Carbamoylputrescine Amidohydrolase (Mtcpa) in Complex with N-(Dihydroxymethyl)Putrescine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na404

b:52.7
occ:1.00
 O L:HOH592 2.4 48.6 1.0
O G:HOH596 2.4 33.1 1.0
O L:HOH593 2.4 39.4 1.0
O L:VAL260 2.4 28.9 1.0
O G:HOH711 2.5 38.6 1.0
O L:HOH765 2.6 41.1 1.0
C L:VAL260 3.5 28.2 1.0
O L:HOH812 3.7 51.2 1.0
O G:HOH685 4.1 53.6 1.0
O L:HOH755 4.1 58.2 1.0
N L:VAL260 4.1 28.7 1.0
O G:HOH617 4.2 55.2 1.0
CA L:VAL260 4.2 28.3 1.0
O G:HOH652 4.3 41.0 1.0
CB L:VAL260 4.3 29.4 1.0
OE1 L:GLN39 4.3 41.4 1.0
O3 G:GOL402 4.4 50.7 1.0
O L:HOH649 4.5 33.4 1.0
N L:LEU261 4.6 26.9 1.0
NE2 L:GLN39 4.6 40.5 1.0
CA L:LEU261 4.8 27.1 1.0
OE1 G:GLU257 4.9 60.0 1.0
CD L:GLN39 4.9 39.6 1.0
CG1 L:VAL260 5.0 29.4 1.0

Reference:

B.Sekula, M.Ruszkowski, M.Malinska, Z.Dauter. Structural Investigations of N-Carbamoylputrescine Amidohydrolase From Medicago Truncatula: Insights Into the Ultimate Step of Putrescine Biosynthesis in Plants. Front Plant Sci V. 7 350 2016.
ISSN: ESSN 1664-462X
PubMed: 27066023
DOI: 10.3389/FPLS.2016.00350
Page generated: Mon Oct 7 21:20:55 2024

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