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Sodium in PDB 5ucq: The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate

Enzymatic activity of The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate

All present enzymatic activity of The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate:
3.6.1.1;

Protein crystallography data

The structure of The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate, PDB code: 5ucq was solved by N.Inoguchi, R.C.Hughes, E.J.Meehan, J.D.Ng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.37 / 1.40
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.161, 100.161, 97.801, 90.00, 90.00, 120.00
R / Rfree (%) 10.9 / 14

Other elements in 5ucq:

The structure of The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate also contains other interesting chemical elements:

Calcium (Ca) 9 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate (pdb code 5ucq). 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 The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate, PDB code: 5ucq:

Sodium binding site 1 out of 1 in 5ucq

Go back to Sodium Binding Sites List in 5ucq
Sodium binding site 1 out of 1 in the The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na209

b:16.7
occ:1.00
 O1 B:EDO206 2.3 16.7 0.2
O5 B:POP208 2.3 9.0 0.4
O2 B:EDO205 2.3 51.5 0.7
O1 B:POP208 2.4 13.8 0.4
C1 B:EDO205 2.5 17.7 0.3
OE2 B:GLU32 2.6 12.5 0.6
O5 B:POP208 2.7 9.2 0.6
C1 B:EDO205 2.8 52.5 0.7
C2 B:EDO205 2.8 51.5 0.7
O1 B:EDO205 3.2 17.6 0.3
O B:POP208 3.2 6.5 0.6
C1 B:EDO206 3.3 20.6 0.2
P2 B:POP208 3.4 10.7 0.4
P2 B:POP208 3.5 6.3 0.6
CD B:GLU32 3.6 13.9 0.6
P1 B:POP208 3.7 12.5 0.4
O4 B:POP208 3.8 9.4 0.4
O1 B:EDO206 3.8 71.2 0.8
O B:POP208 3.8 7.3 0.4
O B:HOH326 3.8 41.8 1.0
C2 B:EDO206 3.8 21.4 0.2
C2 B:EDO205 3.9 23.8 0.3
OE1 B:GLU32 3.9 14.1 0.6
O1 B:EDO207 3.9 14.0 0.3
O1 B:EDO205 4.0 54.1 0.7
NZ B:LYS30 4.1 9.3 1.0
O2 B:EDO205 4.2 24.9 0.3
O4 B:POP208 4.2 6.5 0.6
O2 B:EDO206 4.2 71.5 0.8
C2 B:EDO206 4.3 71.3 0.8
OE1 B:GLU32 4.4 20.9 0.4
NH2 B:ARG44 4.4 9.8 1.0
OD1 B:ASP43 4.4 15.9 1.0
P1 B:POP208 4.4 7.7 0.6
C1 B:EDO207 4.4 12.5 0.3
CG B:ASP43 4.5 11.4 1.0
O2 B:POP208 4.6 11.1 0.4
O3 B:POP208 4.6 8.3 0.6
OD2 B:ASP43 4.6 13.9 1.0
O3 B:POP208 4.6 14.3 0.4
O6 B:POP208 4.7 11.3 0.4
O2 B:POP208 4.7 8.6 0.6
C1 B:EDO206 4.7 70.7 0.8
CE B:LYS30 4.7 9.2 1.0
OD2 B:ASP68 4.7 34.6 0.7
O6 B:POP208 4.8 6.0 0.6
CG B:GLU32 4.9 11.2 0.6
OD2 B:ASP68 5.0 25.8 0.3

Reference:

N.Inoguchi, R.C.Hughes, E.J.Meehan, J.D.Ng. The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Pyrophosphate To Be Published.
Page generated: Tue Oct 8 00:28:11 2024

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