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Zinc in PDB 6etg: Crystal Structure of KDM4D with Tetrazolhydrazide Compound 6

Protein crystallography data

The structure of Crystal Structure of KDM4D with Tetrazolhydrazide Compound 6, PDB code: 6etg 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) 35.93 / 1.28
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 71.854, 71.854, 151.531, 90.00, 90.00, 90.00
R / Rfree (%) 12.4 / 15.8

Other elements in 6etg:

The structure of Crystal Structure of KDM4D with Tetrazolhydrazide Compound 6 also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of KDM4D with Tetrazolhydrazide Compound 6 (pdb code 6etg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of KDM4D with Tetrazolhydrazide Compound 6, PDB code: 6etg:

Zinc binding site 1 out of 1 in 6etg

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of KDM4D with Tetrazolhydrazide Compound 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:22.6
occ:1.00
NE2 A:HIS244 2.1 20.3 1.0
SG A:CYS238 2.2 24.8 1.0
SG A:CYS310 2.2 25.4 1.0
SG A:CYS312 2.3 24.8 1.0
HB2 A:CYS238 2.8 32.0 1.0
CB A:CYS238 3.0 26.7 1.0
CE1 A:HIS244 3.0 20.4 1.0
CD2 A:HIS244 3.1 19.6 1.0
H A:CYS312 3.1 31.9 1.0
HB3 A:CYS312 3.2 31.7 1.0
HE1 A:HIS244 3.2 24.5 1.0
HB2 A:GLU314 3.2 65.2 1.0
HD2 A:HIS244 3.3 23.5 1.0
HB3 A:CYS238 3.3 32.0 1.0
HB2 A:CYS310 3.4 28.4 1.0
CB A:CYS312 3.4 26.4 1.0
CB A:CYS310 3.4 23.7 1.0
H A:ALA315 3.9 65.5 1.0
H A:GLU314 3.9 58.8 1.0
N A:CYS312 3.9 26.6 1.0
HA A:CYS310 3.9 27.6 1.0
HA A:PHE241 3.9 23.0 1.0
HB2 A:CYS312 4.1 31.7 1.0
CA A:CYS312 4.2 28.0 1.0
ND1 A:HIS244 4.2 19.7 1.0
CB A:GLU314 4.2 54.3 1.0
CA A:CYS310 4.2 23.0 1.0
HB3 A:CYS310 4.2 28.4 1.0
CG A:HIS244 4.2 18.7 1.0
O A:HOH672 4.3 29.0 1.0
H A:SER311 4.3 30.3 1.0
CA A:CYS238 4.4 27.5 1.0
N A:GLU314 4.5 49.0 1.0
HA A:CYS238 4.6 33.0 1.0
O A:HOH842 4.6 45.7 1.0
H A:GLY313 4.6 44.8 1.0
N A:SER311 4.6 25.3 1.0
HB2 A:ARG243 4.6 18.2 0.6
C A:CYS310 4.6 24.9 1.0
HB3 A:GLU314 4.7 65.2 1.0
HB2 A:ALA315 4.7 65.6 1.0
N A:ALA315 4.7 54.6 1.0
C A:CYS312 4.7 33.2 1.0
HG2 A:GLU314 4.7 67.5 1.0
HG3 A:GLU314 4.7 67.5 1.0
O A:ALA240 4.7 19.6 1.0
H A:ALA240 4.7 29.4 1.0
N A:GLY313 4.8 37.3 1.0
CG A:GLU314 4.8 56.3 1.0
CA A:PHE241 4.8 19.2 1.0
HB3 A:ALA315 4.9 65.6 1.0
CA A:GLU314 4.9 52.3 1.0
HB3 A:ALA240 4.9 28.1 1.0
O A:HOH642 4.9 38.7 1.0
C A:ALA240 4.9 20.1 1.0
HD1 A:HIS244 5.0 23.7 1.0

Reference:

P.H.Malecki, M.S.Weiss, U.Heinemann. Crystal Structure of KDM4D with Tetrazolhydrazide Compound 6 To Be Published.
Page generated: Wed Dec 16 11:44:09 2020

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