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Sodium in PDB 8w06: Crystal Structure of the Reconstruction of the Ancestral Triosephosphate Isomerase of the Last Opisthokont Common Ancestor Obtained By Maximum Likelihood with Pgh

Enzymatic activity of Crystal Structure of the Reconstruction of the Ancestral Triosephosphate Isomerase of the Last Opisthokont Common Ancestor Obtained By Maximum Likelihood with Pgh

All present enzymatic activity of Crystal Structure of the Reconstruction of the Ancestral Triosephosphate Isomerase of the Last Opisthokont Common Ancestor Obtained By Maximum Likelihood with Pgh:
5.3.1.1;

Protein crystallography data

The structure of Crystal Structure of the Reconstruction of the Ancestral Triosephosphate Isomerase of the Last Opisthokont Common Ancestor Obtained By Maximum Likelihood with Pgh, PDB code: 8w06 was solved by J.A.Perez-Nino, A.Rodriguez-Romero, Y.Guerra-Borrego, D.A.Fernandez-Velasco, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.45 / 2.06
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 111.642, 83.222, 127.865, 90, 103.49, 90
R / Rfree (%) 19.5 / 23.5

Other elements in 8w06:

The structure of Crystal Structure of the Reconstruction of the Ancestral Triosephosphate Isomerase of the Last Opisthokont Common Ancestor Obtained By Maximum Likelihood with Pgh also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Reconstruction of the Ancestral Triosephosphate Isomerase of the Last Opisthokont Common Ancestor Obtained By Maximum Likelihood with Pgh (pdb code 8w06). 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 the Reconstruction of the Ancestral Triosephosphate Isomerase of the Last Opisthokont Common Ancestor Obtained By Maximum Likelihood with Pgh, PDB code: 8w06:

Sodium binding site 1 out of 1 in 8w06

Go back to Sodium Binding Sites List in 8w06
Sodium binding site 1 out of 1 in the Crystal Structure of the Reconstruction of the Ancestral Triosephosphate Isomerase of the Last Opisthokont Common Ancestor Obtained By Maximum Likelihood with Pgh


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 Reconstruction of the Ancestral Triosephosphate Isomerase of the Last Opisthokont Common Ancestor Obtained By Maximum Likelihood with Pgh within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na301

b:21.9
occ:1.00
 N D:LEU130 3.1 31.9 1.0
O A:HOH449 3.4 34.6 1.0
O A:HOH465 3.6 30.0 1.0
NE2 A:GLN52 3.6 42.2 1.0
N D:TRP169 3.6 22.6 1.0
CB D:LEU130 3.7 36.8 1.0
CA D:TRP169 3.7 27.6 1.0
CG1 D:VAL168 3.8 26.6 1.0
CA D:THR129 3.9 28.2 1.0
C D:VAL168 3.9 23.1 1.0
CB D:TRP169 3.9 23.8 1.0
CG A:GLN52 4.0 51.3 1.0
C D:THR129 4.0 32.9 1.0
CA D:LEU130 4.0 32.0 1.0
CB D:VAL168 4.0 29.1 1.0
CB D:THR129 4.0 28.2 1.0
CD A:GLN52 4.3 46.2 1.0
O D:VAL168 4.3 27.4 1.0
CA D:VAL168 4.6 26.6 1.0
O A:GLN52 4.7 39.6 1.0
CG2 D:THR129 4.7 30.4 1.0
CD1 D:TRP169 4.8 26.8 1.0
CG D:TRP169 4.8 23.8 1.0

Reference:

J.A.Perez-Nino, Y.Guerra, A.J.Diaz-Salazar, M.Costas, A.Rodriguez-Romero, D.A.Fernandez-Velasco. Stable Monomers in the Ancestral Sequence Reconstruction of the Last Opisthokont Common Ancestor of Dimeric Triosephosphate Isomerase. Protein Sci. V. 33 E5134 2024.
ISSN: ESSN 1469-896X
PubMed: 39145435
DOI: 10.1002/PRO.5134
Page generated: Mon Aug 18 16:13:00 2025

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