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Sodium in PDB 6ets: Crystal Structure of KDM4D with Tetrazolhydrazide Compound 1

Protein crystallography data

The structure of Crystal Structure of KDM4D with Tetrazolhydrazide Compound 1, PDB code: 6ets was solved by P.H.Malecki, A.Link, M.S.Weiss, U.Heinemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.03 / 1.33
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 71.631, 71.631, 150.770, 90.00, 90.00, 90.00
R / Rfree (%) 12.9 / 15.6

Other elements in 6ets:

The structure of Crystal Structure of KDM4D with Tetrazolhydrazide Compound 1 also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of KDM4D with Tetrazolhydrazide Compound 1 (pdb code 6ets). 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 KDM4D with Tetrazolhydrazide Compound 1, PDB code: 6ets:

Sodium binding site 1 out of 1 in 6ets

Go back to Sodium Binding Sites List in 6ets
Sodium binding site 1 out of 1 in the Crystal Structure of KDM4D with Tetrazolhydrazide Compound 1


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 KDM4D with Tetrazolhydrazide Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:41.3
occ:0.74
HD21 A:ASN262 2.0 13.2 1.0
O A:HOH829 2.3 33.7 0.5
O A:HOH649 2.4 14.8 1.0
ND2 A:ASN262 2.7 11.0 1.0
HD22 A:ASN262 3.1 13.2 1.0
CG A:ASN262 3.5 12.2 1.0
OD1 A:ASN262 3.7 14.0 1.0
O A:PHE261 3.9 9.9 1.0
O A:HOH689 3.9 45.5 1.0
OD1 A:ASN17 4.1 19.7 1.0
HA A:ASN262 4.7 9.6 1.0
HZ1 A:LYS255 4.7 26.5 0.6
O A:HOH708 4.9 13.7 1.0
CB A:ASN262 4.9 10.1 1.0
C A:PHE261 4.9 9.0 1.0
HA A:ASN17 4.9 13.7 1.0
O A:ASN15 4.9 12.0 1.0

Reference:

P.H.Malecki, A.Link, M.S.Weiss, U.Heinemann. Crystal Structure of KDM4D with Tetrazolylhydrazide Ligand To Be Published.
Page generated: Tue Dec 15 12:12:35 2020

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