Nickel in PDB 6dk8: Rets Kinase Region Without Cobalt

The structure of Rets Kinase Region Without Cobalt, PDB code: 6dk8 was solved by J.M.Mancl, F.D.Schubot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.78 / 3.80
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	158.708, 158.708, 243.826, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 24.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Nickel atom in the Rets Kinase Region Without Cobalt (pdb code 6dk8). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 20 binding sites of Nickel where determined in the Rets Kinase Region Without Cobalt, PDB code: 6dk8:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Nickel binding site 1 out of 20 in the Rets Kinase Region Without Cobalt


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Rets Kinase Region Without Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni701 b:71.4 occ:1.00 NE2 A:HIS591 2.2 29.1 1.0 CD2 A:HIS591 2.3 35.2 1.0 CE1 A:HIS591 2.4 39.7 1.0 CG A:HIS591 2.5 52.8 1.0 ND1 A:HIS591 2.6 52.6 1.0 ND1 B:HIS591 3.4 63.5 1.0 CB A:HIS591 3.6 65.8 1.0 CE1 B:HIS591 3.7 96.8 1.0 CA A:HIS591 3.9 86.0 1.0 CG B:HIS591 4.7 70.3 1.0 C A:HIS591 4.9 81.5 1.0 NE2 B:HIS591 4.9 0.6 1.0 N A:HIS591 4.9 85.8 1.0 N B:ALA416 5.0 50.4 1.0

Nickel binding site 2 out of 20 in the Rets Kinase Region Without Cobalt


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Rets Kinase Region Without Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni702 b:88.6 occ:1.00 CE1 A:HIS424 2.1 74.6 1.0 NE2 B:HIS604 2.3 74.0 1.0 NE2 A:HIS424 2.7 0.9 1.0 ND1 A:HIS424 3.1 53.0 1.0 CE1 B:HIS604 3.2 83.6 1.0 CD2 B:HIS604 3.4 73.4 1.0 CD2 A:HIS424 3.9 88.3 1.0 CG A:HIS424 4.1 59.1 1.0 ND1 B:HIS604 4.3 95.8 1.0 CG B:HIS604 4.4 83.3 1.0

Nickel binding site 3 out of 20 in the Rets Kinase Region Without Cobalt


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Rets Kinase Region Without Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni703 b:0.3 occ:1.00 NE2 A:HIS457 2.2 54.2 1.0 CE1 A:HIS457 2.3 60.4 1.0 OE2 A:GLU438 2.7 87.3 1.0 CD2 A:HIS457 3.6 43.2 1.0 ND1 A:HIS457 3.6 56.4 1.0 CD A:GLU438 3.8 80.4 1.0 ND2 A:ASN461 4.0 43.6 1.0 CG A:HIS457 4.2 40.8 1.0 OE1 A:GLU438 4.4 69.7 1.0 CG A:GLU438 5.0 69.7 1.0

Nickel binding site 4 out of 20 in the Rets Kinase Region Without Cobalt


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Rets Kinase Region Without Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni701 b:25.1 occ:1.00 ND1 B:HIS424 2.0 22.4 1.0 CD2 H:HIS424 2.2 28.2 1.0 CE1 B:HIS424 2.9 31.5 1.0 CG H:HIS424 3.0 26.6 1.0 CG B:HIS424 3.1 28.2 1.0 NE2 H:HIS424 3.2 34.3 1.0 CB B:HIS424 3.5 31.7 1.0 CB H:HIS424 3.5 32.8 1.0 ND1 H:HIS424 4.0 27.6 1.0 NE2 B:HIS424 4.1 30.3 1.0 O H:LYS421 4.1 54.2 1.0 CE1 H:HIS424 4.1 31.6 1.0 CD2 B:HIS424 4.1 31.5 1.0 OE1 B:GLU425 4.3 49.4 1.0 OE1 H:GLU425 4.4 54.9 1.0 O B:LYS421 4.5 40.9 1.0 OE2 B:GLU425 4.6 75.6 1.0 N H:HIS424 4.7 31.3 1.0 CA H:HIS424 4.7 33.4 1.0 CA B:HIS424 4.7 33.7 1.0 N B:HIS424 4.7 31.2 1.0 CD B:GLU425 4.8 52.1 1.0 CB G:ALA598 4.9 80.3 1.0

Nickel binding site 5 out of 20 in the Rets Kinase Region Without Cobalt


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Rets Kinase Region Without Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni702 b:0.3 occ:1.00 OE2 B:GLU438 2.1 54.6 1.0 NE2 B:HIS457 2.6 83.0 1.0 CD B:GLU438 2.9 54.8 1.0 OE1 B:GLU438 3.2 49.3 1.0 CE1 B:HIS457 3.4 69.0 1.0 CD2 B:HIS457 3.7 69.7 1.0 CG B:GLU438 4.3 56.5 1.0 ND1 B:HIS457 4.6 50.0 1.0 CG B:HIS457 4.7 57.5 1.0

Nickel binding site 6 out of 20 in the Rets Kinase Region Without Cobalt


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Rets Kinase Region Without Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni703 b:0.9 occ:1.00 CE1 B:HIS575 2.2 81.3 1.0 OD1 B:ASP578 2.7 0.4 1.0 NE2 B:HIS575 2.8 93.7 1.0 OD2 B:ASP578 3.2 0.9 1.0 CG B:ASP578 3.3 0.2 1.0 ND1 B:HIS575 3.4 89.4 1.0 CD2 B:HIS575 4.0 0.2 1.0 CG B:HIS575 4.3 0.8 1.0 CB B:ASP578 4.8 97.7 1.0

Nickel binding site 7 out of 20 in the Rets Kinase Region Without Cobalt


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Rets Kinase Region Without Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni701 b:72.7 occ:1.00 NE2 C:HIS424 2.0 53.9 1.0 NE2 D:HIS604 2.0 74.5 1.0 CD2 D:HIS604 2.7 66.7 1.0 CD2 C:HIS424 2.9 44.9 1.0 CE1 C:HIS424 3.0 75.1 1.0 CE1 D:HIS604 3.0 68.8 1.0 CG D:HIS604 3.8 61.6 1.0 ND1 D:HIS604 3.9 68.1 1.0 CG C:HIS424 4.0 55.4 1.0 ND1 C:HIS424 4.0 76.3 1.0 CG C:GLU425 4.8 51.3 1.0 CD C:GLU425 5.0 49.3 1.0

Nickel binding site 8 out of 20 in the Rets Kinase Region Without Cobalt


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Rets Kinase Region Without Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni702 b:23.0 occ:1.00 CE1 C:HIS575 2.1 59.6 1.0 NE2 C:HIS575 2.5 65.9 1.0 NE2 E:HIS575 2.6 48.0 1.0 OD1 E:ASP578 3.1 77.9 1.0 ND1 C:HIS575 3.4 78.0 1.0 CD2 E:HIS575 3.5 61.2 1.0 CE1 E:HIS575 3.6 57.3 1.0 CD2 C:HIS575 3.8 70.3 1.0 CG E:ASP578 4.1 85.3 1.0 CG C:HIS575 4.2 67.0 1.0 OE1 E:GLU581 4.2 50.9 1.0 OE2 E:GLU581 4.3 51.9 1.0 OD2 E:ASP578 4.3 92.5 1.0 O C:PRO576 4.3 64.3 1.0 O E:PRO576 4.4 51.1 1.0 CG E:HIS575 4.7 66.8 1.0 CD E:GLU581 4.7 57.5 1.0 ND1 E:HIS575 4.7 58.5 1.0 CB C:ASP578 4.8 71.4 1.0

Nickel binding site 9 out of 20 in the Rets Kinase Region Without Cobalt


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Rets Kinase Region Without Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni703 b:42.0 occ:1.00 CD2 C:HIS591 2.1 71.8 1.0 NE2 C:HIS591 2.3 72.9 1.0 CE1 D:HIS591 2.5 90.7 1.0 CG C:HIS591 2.7 82.6 1.0 NE2 D:HIS591 2.8 0.7 1.0 CE1 C:HIS591 2.9 88.8 1.0 ND1 C:HIS591 3.1 90.8 1.0 ND1 D:HIS591 3.3 86.4 1.0 CD2 D:HIS591 3.7 94.3 1.0 CB C:HIS591 3.7 86.6 1.0 CG D:HIS591 3.9 73.4 1.0 CA C:HIS591 4.0 83.5 1.0 N D:ALA416 4.5 38.8 1.0 N C:HIS591 5.0 80.8 1.0

Nickel binding site 10 out of 20 in the Rets Kinase Region Without Cobalt


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of Rets Kinase Region Without Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni701 b:89.9 occ:1.00 OE2 D:GLU438 1.9 46.3 1.0 NE2 D:HIS457 2.0 61.6 1.0 CD D:GLU438 2.7 66.8 1.0 CE1 D:HIS457 2.8 65.3 1.0 CD2 D:HIS457 3.2 58.2 1.0 OE1 D:GLU438 3.3 0.9 1.0 CG D:GLU438 3.6 48.9 1.0 ND1 D:HIS457 4.0 65.5 1.0 CG D:HIS457 4.2 59.5 1.0 ND2 D:ASN461 4.8 55.6 1.0

J.M.Mancl, W.K.Ray, R.F.Helm, F.D.Schubot. Helix Cracking Regulates the Critical Interaction Between Rets and Gacs in Pseudomonas Aeruginosa. Structure V. 27 785 2019.
ISSN: ISSN 0969-2126
PubMed: 30879888
DOI: 10.1016/J.STR.2019.02.006