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Sodium in PDB 5m1y: The Case of 1LKR Held at the Pdb and Its Variable Amino Acid Occupancies; Re Refinement of 4OW9 to Correct This

Enzymatic activity of The Case of 1LKR Held at the Pdb and Its Variable Amino Acid Occupancies; Re Refinement of 4OW9 to Correct This

All present enzymatic activity of The Case of 1LKR Held at the Pdb and Its Variable Amino Acid Occupancies; Re Refinement of 4OW9 to Correct This:
3.2.1.17;

Protein crystallography data

The structure of The Case of 1LKR Held at the Pdb and Its Variable Amino Acid Occupancies; Re Refinement of 4OW9 to Correct This, PDB code: 5m1y was solved by J.R.Helliwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.00 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 27.251, 62.537, 58.981, 90.00, 90.92, 90.00
R / Rfree (%) 21.6 / 26.2

Other elements in 5m1y:

The structure of The Case of 1LKR Held at the Pdb and Its Variable Amino Acid Occupancies; Re Refinement of 4OW9 to Correct This also contains other interesting chemical elements:

Iodine (I) 26 atoms
Platinum (Pt) 3 atoms
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Case of 1LKR Held at the Pdb and Its Variable Amino Acid Occupancies; Re Refinement of 4OW9 to Correct This (pdb code 5m1y). 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 Case of 1LKR Held at the Pdb and Its Variable Amino Acid Occupancies; Re Refinement of 4OW9 to Correct This, PDB code: 5m1y:

Sodium binding site 1 out of 1 in 5m1y

Go back to Sodium Binding Sites List in 5m1y
Sodium binding site 1 out of 1 in the The Case of 1LKR Held at the Pdb and Its Variable Amino Acid Occupancies; Re Refinement of 4OW9 to Correct This


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Case of 1LKR Held at the Pdb and Its Variable Amino Acid Occupancies; Re Refinement of 4OW9 to Correct This within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na213

b:16.5
occ:1.00
CL B:CL212 2.5 21.9 1.0
HZ1 B:LYS96 3.6 22.9 1.0
HZ3 B:LYS96 3.9 22.9 1.0
O B:HIS15 4.1 17.1 1.0
HA3 B:GLY16 4.1 22.3 1.0
NZ B:LYS96 4.1 19.1 1.0
HZ2 B:LYS96 4.3 22.9 1.0
HA B:HIS15 4.3 22.6 1.0
C B:HIS15 4.4 18.6 1.0
PT B:PT201 4.5 28.2 0.7
N B:GLY16 4.9 19.2 1.0
CA B:GLY16 4.9 18.6 1.0
CA B:HIS15 4.9 18.8 1.0
O B:ARG14 5.0 20.1 1.0

Reference:

J.R.Helliwell, S.W.M.Tanley. The Case of 1LKR Held at the Pdb and Its Variable Amino Acid Occupancies; Re Refinement of 4OW9 to Correct This Zenodo 2016.
DOI: 10.5281/ZENODO.160328
Page generated: Tue Dec 15 11:15:11 2020

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