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Sodium in PDB 3umc: Crystal Structure of the L-2-Haloacid Dehalogenase PA0810

Enzymatic activity of Crystal Structure of the L-2-Haloacid Dehalogenase PA0810

All present enzymatic activity of Crystal Structure of the L-2-Haloacid Dehalogenase PA0810:
3.8.1.2;

Protein crystallography data

The structure of Crystal Structure of the L-2-Haloacid Dehalogenase PA0810, PDB code: 3umc was solved by P.Petit, P.W.Y.Chan, A.Savchenko, A.F.Yakunin, E.A.Edwards, E.F.Pai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.38 / 2.15
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 73.424, 123.867, 125.599, 90.00, 90.97, 90.00
R / Rfree (%) 19 / 23.6

Other elements in 3umc:

The structure of Crystal Structure of the L-2-Haloacid Dehalogenase PA0810 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the L-2-Haloacid Dehalogenase PA0810 (pdb code 3umc). 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 the L-2-Haloacid Dehalogenase PA0810, PDB code: 3umc:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3umc

Go back to Sodium Binding Sites List in 3umc
Sodium binding site 1 out of 2 in the Crystal Structure of the L-2-Haloacid Dehalogenase PA0810


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 the L-2-Haloacid Dehalogenase PA0810 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na235

b:37.3
occ:1.00
O C:HOH456 2.0 30.0 1.0
O C:HOH558 2.0 33.9 1.0
O C:HOH556 2.1 34.7 1.0
OE1 C:GLN46 2.2 24.1 1.0
CD C:GLN46 3.3 26.3 1.0
NE2 C:GLN46 3.7 21.9 1.0
O C:HOH270 4.1 24.1 1.0
OE1 C:GLU78 4.2 30.8 1.0
CG C:GLN46 4.6 31.7 1.0
CA C:GLN46 4.6 33.5 1.0
OE2 C:GLU78 4.6 32.6 1.0
CB C:GLN46 4.7 32.6 1.0
CD C:GLU78 4.7 38.5 1.0
O C:ARG42 4.9 33.3 1.0
N C:GLN46 5.0 34.9 1.0

Sodium binding site 2 out of 2 in 3umc

Go back to Sodium Binding Sites List in 3umc
Sodium binding site 2 out of 2 in the Crystal Structure of the L-2-Haloacid Dehalogenase PA0810


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 the L-2-Haloacid Dehalogenase PA0810 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na235

b:45.3
occ:1.00
O D:HOH557 2.0 43.5 1.0
OE1 D:GLN46 2.0 36.5 1.0
O D:HOH555 2.1 39.2 1.0
O D:HOH457 2.1 36.5 1.0
CD D:GLN46 3.0 36.3 1.0
NE2 D:GLN46 3.6 34.5 1.0
CA D:GLN46 4.2 36.7 1.0
CG D:GLN46 4.3 36.6 1.0
OE2 D:GLU78 4.3 41.1 1.0
O D:HOH407 4.3 37.2 1.0
CB D:GLN46 4.3 36.5 1.0
O D:HOH447 4.4 36.0 1.0
OE1 D:GLU78 4.4 40.9 1.0
N D:GLN46 4.7 36.8 1.0
O D:ARG42 4.7 41.0 1.0
CD D:GLU78 4.7 42.3 1.0
CD2 D:LEU75 4.8 44.1 1.0

Reference:

P.W.Y.Chan, T.K.W.To, P.Petit, C.Tran, M.Waelti, A.Savchenko, A.F.Yakunin, E.A.Edwards, E.F.Pai. Structural Adaptations of L-2-Haloacid Dehalogenases That Enable Hydrolytic Defluorination To Be Published.
Page generated: Mon Oct 7 13:29:05 2024

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