Nickel in PDB 6v2h: Crystal Structure of CDYL2 in Complex with H3TK27ME3

The structure of Crystal Structure of CDYL2 in Complex with H3TK27ME3, PDB code: 6v2h was solved by C.Dong, W.Tempel, J.R.Walker, C.Bountra, C.H.Arrowsmith, A.M.Edwards, J.Min, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.14 / 2.60
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	210.750, 210.750, 67.200, 90.00, 90.00, 120.00
R / Rfree (%)	21.7 / 23.7

The binding sites of Nickel atom in the Crystal Structure of CDYL2 in Complex with H3TK27ME3 (pdb code 6v2h). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Crystal Structure of CDYL2 in Complex with H3TK27ME3, PDB code: 6v2h:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in the Crystal Structure of CDYL2 in Complex with H3TK27ME3


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 CDYL2 in Complex with H3TK27ME3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni101 b:0.1 occ:1.00 N A:GLY1 2.1 0.4 1.0 O A:GLY1 2.1 94.9 1.0 NE2 A:HIS44 2.2 75.7 1.0 NE2 A:HIS43 2.2 86.1 1.0 C A:GLY1 2.7 96.0 1.0 CA A:GLY1 2.9 0.9 1.0 CE1 A:HIS43 3.0 83.2 1.0 CD2 A:HIS44 3.1 68.9 1.0 CE1 A:HIS44 3.2 69.3 1.0 CD2 A:HIS43 3.3 80.4 1.0 ND1 A:HIS43 4.2 81.0 1.0 CG A:HIS44 4.3 63.8 1.0 ND1 A:HIS44 4.3 64.6 1.0 CG A:HIS43 4.4 78.0 1.0 CG A:PRO41 5.0 66.8 1.0

Nickel binding site 2 out of 6 in the Crystal Structure of CDYL2 in Complex with H3TK27ME3


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 CDYL2 in Complex with H3TK27ME3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni101 b:0.2 occ:1.00 NE2 C:HIS44 2.1 89.7 1.0 O C:GLY1 2.1 0.9 1.0 N C:GLY1 2.1 0.8 1.0 NE2 C:HIS43 2.2 97.9 1.0 C C:GLY1 2.8 0.5 1.0 CA C:GLY1 2.8 0.8 1.0 CE1 C:HIS43 3.0 93.5 1.0 CD2 C:HIS44 3.0 83.9 1.0 CE1 C:HIS44 3.2 83.9 1.0 CD2 C:HIS43 3.3 94.7 1.0 N C:ALA2 4.1 0.9 1.0 ND1 C:HIS43 4.2 91.1 1.0 CG C:HIS44 4.2 78.2 1.0 ND1 C:HIS44 4.2 78.8 1.0 CG C:HIS43 4.3 90.2 1.0 O C:SER3 4.9 1.0 1.0 CA C:ALA2 4.9 0.5 1.0 CG C:PRO41 5.0 72.0 1.0

Nickel binding site 3 out of 6 in the Crystal Structure of CDYL2 in Complex with H3TK27ME3


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of CDYL2 in Complex with H3TK27ME3 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni101 b:62.1 occ:1.00 NE2 E:HIS44 2.1 51.7 1.0 O E:GLY1 2.1 61.3 1.0 N E:GLY1 2.1 66.9 1.0 NE2 E:HIS43 2.2 55.1 1.0 C E:GLY1 2.8 67.8 1.0 CA E:GLY1 2.8 68.9 1.0 CD2 E:HIS44 3.0 48.4 1.0 CE1 E:HIS43 3.0 51.5 1.0 CE1 E:HIS44 3.1 49.5 1.0 CD2 E:HIS43 3.3 51.0 1.0 N E:ALA2 4.1 75.8 1.0 ND1 E:HIS43 4.2 48.8 1.0 CG E:HIS44 4.2 44.4 1.0 ND1 E:HIS44 4.2 46.1 1.0 CG E:HIS43 4.3 47.9 1.0 UNK E:UNX108 4.7 34.3 1.0 O E:SER3 4.8 72.3 1.0 CA E:ALA2 4.9 74.3 1.0 CG E:PRO41 4.9 42.9 1.0

Nickel binding site 4 out of 6 in the Crystal Structure of CDYL2 in Complex with H3TK27ME3


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of CDYL2 in Complex with H3TK27ME3 within 5.0Å range: probe atom residue distance (Å) B Occ G:Ni101 b:94.0 occ:1.00 N G:GLY1 2.1 98.4 1.0 O G:GLY1 2.1 93.0 1.0 NE2 G:HIS44 2.2 68.1 1.0 NE2 G:HIS43 2.2 74.8 1.0 C G:GLY1 2.7 0.7 1.0 CA G:GLY1 2.8 0.1 1.0 CE1 G:HIS43 3.0 68.3 1.0 CD2 G:HIS44 3.0 60.2 1.0 CE1 G:HIS44 3.2 61.4 1.0 CD2 G:HIS43 3.3 68.6 1.0 N G:ALA2 4.1 1.0 1.0 ND1 G:HIS43 4.2 64.4 1.0 CG G:HIS44 4.2 55.0 1.0 ND1 G:HIS44 4.3 56.2 1.0 CG G:HIS43 4.3 63.4 1.0 CA G:ALA2 4.9 0.3 1.0 O G:SER3 4.9 99.0 1.0

Nickel binding site 5 out of 6 in the Crystal Structure of CDYL2 in Complex with H3TK27ME3


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of CDYL2 in Complex with H3TK27ME3 within 5.0Å range: probe atom residue distance (Å) B Occ I:Ni101 b:70.7 occ:1.00 O I:GLY1 2.1 70.2 1.0 N I:GLY1 2.1 76.7 1.0 NE2 I:HIS44 2.1 63.2 1.0 NE2 I:HIS43 2.2 67.7 1.0 C I:GLY1 2.8 75.6 1.0 CA I:GLY1 2.8 77.0 1.0 CE1 I:HIS43 3.0 67.9 1.0 CD2 I:HIS44 3.0 58.0 1.0 CE1 I:HIS44 3.2 62.5 1.0 CD2 I:HIS43 3.3 63.3 1.0 N I:ALA2 4.1 78.4 1.0 ND1 I:HIS43 4.2 64.8 1.0 CG I:HIS44 4.2 55.4 1.0 ND1 I:HIS44 4.3 58.5 1.0 CG I:HIS43 4.3 61.5 1.0 UNK I:UNX102 4.5 49.4 1.0 O I:SER3 4.8 79.8 1.0 UNK A:UNX105 4.9 42.4 1.0 CA I:ALA2 4.9 76.6 1.0 CG I:PRO41 5.0 58.2 1.0

Nickel binding site 6 out of 6 in the Crystal Structure of CDYL2 in Complex with H3TK27ME3


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of CDYL2 in Complex with H3TK27ME3 within 5.0Å range: probe atom residue distance (Å) B Occ K:Ni101 b:0.9 occ:1.00 N K:GLY1 2.1 0.1 1.0 O K:GLY1 2.1 1.0 1.0 NE2 K:HIS44 2.2 93.3 1.0 NE2 K:HIS43 2.2 99.4 1.0 CA K:GLY1 2.7 0.3 1.0 C K:GLY1 2.7 0.3 1.0 CE1 K:HIS43 3.0 95.1 1.0 CD2 K:HIS44 3.1 86.2 1.0 CE1 K:HIS44 3.2 87.6 1.0 CD2 K:HIS43 3.3 95.3 1.0 ND1 K:HIS43 4.2 93.1 1.0 CG K:HIS44 4.3 80.8 1.0 ND1 K:HIS44 4.3 82.7 1.0 CG K:HIS43 4.4 91.3 1.0 CG K:PRO41 5.0 75.0 1.0

C.Dong, W.Tempel, J.R.Walker, C.Bountra, C.H.Arrowsmith, A.M.Edwards, J.Min. Crystal Structure of CDYL2 in Complex with H3TK27ME3 To Be Published.