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Nickel in PDB 6h0w: Crystal Structure of KDM4D with Tetrazolylhydrazide Ligand NS035

Protein crystallography data

The structure of Crystal Structure of KDM4D with Tetrazolylhydrazide Ligand NS035, PDB code: 6h0w was solved by P.H.Malecki, M.S.Weiss, U.Heinemann, A.Link, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.74 / 1.23
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 71.482, 71.482, 150.707, 90.00, 90.00, 90.00
R / Rfree (%) 12 / 13.6

Other elements in 6h0w:

The structure of Crystal Structure of KDM4D with Tetrazolylhydrazide Ligand NS035 also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of KDM4D with Tetrazolylhydrazide Ligand NS035 (pdb code 6h0w). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Crystal Structure of KDM4D with Tetrazolylhydrazide Ligand NS035, PDB code: 6h0w:

Nickel binding site 1 out of 1 in 6h0w

Go back to Nickel Binding Sites List in 6h0w
Nickel binding site 1 out of 1 in the Crystal Structure of KDM4D with Tetrazolylhydrazide Ligand NS035


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of KDM4D with Tetrazolylhydrazide Ligand NS035 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni413

b:10.5
occ:0.96
OAI A:I1L417 2.0 17.3 0.2
OE2 A:GLU194 2.0 10.8 1.0
OAI A:I1L417 2.0 16.8 0.2
O A:HOH648 2.1 30.0 0.5
NAJ A:I1L417 2.1 6.2 0.2
NAJ A:I1L417 2.1 14.5 0.2
NAP A:FHW415 2.1 19.3 0.5
NE2 A:HIS192 2.1 11.2 1.0
OAN A:FHW415 2.1 13.7 0.5
NE2 A:HIS280 2.1 9.9 1.0
O A:HOH648 2.3 30.0 0.5
CAG A:I1L417 2.7 17.9 0.2
CAG A:I1L417 2.7 17.9 0.2
N A:I1L417 2.8 15.6 0.2
N A:I1L417 2.8 15.9 0.2
CAM A:FHW415 2.8 14.7 0.5
NAO A:FHW415 2.9 14.2 0.5
CE1 A:HIS192 3.0 11.9 1.0
CE1 A:HIS280 3.0 9.6 1.0
CD A:GLU194 3.0 11.3 1.0
CD2 A:HIS192 3.2 10.7 1.0
CD2 A:HIS280 3.2 10.0 1.0
OE1 A:GLU194 3.4 19.3 1.0
ND1 A:HIS192 4.1 11.3 1.0
CAF A:I1L417 4.1 19.5 0.2
O1 A:EDO411 4.1 28.4 1.0
ND1 A:HIS280 4.2 9.5 1.0
O A:HOH813 4.2 30.0 0.5
CAF A:I1L417 4.2 19.6 0.2
CG A:HIS192 4.3 10.0 1.0
CG A:HIS280 4.3 8.7 1.0
CG A:GLU194 4.4 10.3 1.0
CAL A:FHW415 4.4 17.1 0.5
O A:HOH622 4.4 53.5 1.0
OG A:SER200 4.4 12.2 1.0
O A:HOH853 4.6 30.0 0.5
NAC A:I1L417 4.8 21.1 0.2
CAE A:I1L417 4.9 20.6 0.2

Reference:

P.H.Malecki, M.S.Weiss, U.Heinemann, A.Link. Crystal Structure of KDM4D with Tetrazolylhydrazide Ligand NS035 To Be Published.
Page generated: Wed Dec 16 01:51:27 2020

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