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Nickel in PDB 4x3k: Crystal Structure of Chromobox Homolog 7 (CBX7) Chromodomain with H3K27ME3 Peptide

Protein crystallography data

The structure of Crystal Structure of Chromobox Homolog 7 (CBX7) Chromodomain with H3K27ME3 Peptide, PDB code: 4x3k was solved by C.Ren, M.M.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.71 / 1.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.460, 33.230, 46.160, 90.00, 95.80, 90.00
R / Rfree (%) 18.9 / 23.2

Other elements in 4x3k:

The structure of Crystal Structure of Chromobox Homolog 7 (CBX7) Chromodomain with H3K27ME3 Peptide also contains other interesting chemical elements:

Potassium (K) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Chromobox Homolog 7 (CBX7) Chromodomain with H3K27ME3 Peptide (pdb code 4x3k). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Chromobox Homolog 7 (CBX7) Chromodomain with H3K27ME3 Peptide, PDB code: 4x3k:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 4x3k

Go back to Nickel Binding Sites List in 4x3k
Nickel binding site 1 out of 2 in the Crystal Structure of Chromobox Homolog 7 (CBX7) Chromodomain with H3K27ME3 Peptide


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 Chromobox Homolog 7 (CBX7) Chromodomain with H3K27ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni101

b:10.6
occ:1.00
OE1 A:GLU8 2.0 19.1 1.0
NE2 A:HIS47 2.1 9.1 1.0
ND1 A:HIS5 2.1 13.0 1.0
CD A:GLU8 2.9 17.1 1.0
CE1 A:HIS5 2.9 14.8 1.0
OE2 A:GLU8 3.0 17.8 1.0
CE1 A:HIS47 3.0 9.8 1.0
CD2 A:HIS47 3.1 9.2 1.0
CG A:HIS5 3.1 17.0 1.0
CB A:HIS5 3.5 16.4 1.0
NE2 A:HIS5 4.1 18.1 1.0
ND1 A:HIS47 4.1 8.3 1.0
CA A:HIS5 4.1 20.4 1.0
CD2 A:HIS5 4.2 16.1 1.0
CG A:HIS47 4.2 9.5 1.0
CG A:GLU8 4.3 24.1 1.0
O C:HOH101 4.5 19.9 1.0
O A:SER4 4.8 29.0 1.0
CB A:GLU8 4.8 22.6 1.0
CG A:PRO44 4.9 12.0 1.0

Nickel binding site 2 out of 2 in 4x3k

Go back to Nickel Binding Sites List in 4x3k
Nickel binding site 2 out of 2 in the Crystal Structure of Chromobox Homolog 7 (CBX7) Chromodomain with H3K27ME3 Peptide


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Chromobox Homolog 7 (CBX7) Chromodomain with H3K27ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni101

b:10.5
occ:1.00
OE1 B:GLU8 1.8 16.8 1.0
NE2 B:HIS47 2.0 8.3 1.0
ND1 B:HIS5 2.1 21.3 1.0
CD B:GLU8 2.7 12.9 1.0
OE2 B:GLU8 2.9 13.4 1.0
CE1 B:HIS5 3.0 24.8 1.0
CE1 B:HIS47 3.0 8.2 1.0
CD2 B:HIS47 3.1 10.3 1.0
CG B:HIS5 3.2 21.2 1.0
CB B:HIS5 3.6 21.7 1.0
CA B:HIS5 3.9 27.9 1.0
ND1 B:HIS47 4.1 8.5 1.0
CG B:GLU8 4.1 15.6 1.0
NE2 B:HIS5 4.1 26.7 1.0
CG B:HIS47 4.2 9.1 1.0
CD2 B:HIS5 4.3 24.8 1.0
CD D:ARG4 4.5 9.7 0.5
CB B:GLU8 4.6 18.0 1.0
CD D:ARG4 4.7 11.4 0.5
O B:HOH218 4.7 19.7 1.0
N B:HIS5 4.8 32.7 1.0
C B:HIS5 4.8 29.6 1.0

Reference:

C.Ren, K.Morohashi, A.N.Plotnikov, J.Jakoncic, S.G.Smith, J.Li, L.Zeng, Y.Rodriguez, V.Stojanoff, M.Walsh, M.M.Zhou. Small-Molecule Modulators of Methyl-Lysine Binding For the CBX7 Chromodomain. Chem.Biol. V. 22 161 2015.
ISSN: ISSN 1074-5521
PubMed: 25660273
DOI: 10.1016/J.CHEMBIOL.2014.11.021
Page generated: Wed Dec 16 01:37:38 2020

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