Nickel in PDB 2be6: 2.0 A Crystal Structure of the CAV1.2 Iq Domain-Ca/Cam Complex

The structure of 2.0 A Crystal Structure of the CAV1.2 Iq Domain-Ca/Cam Complex, PDB code: 2be6 was solved by F.Van Petegem, F.C.Chatelain, D.L.Minor Jr., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	84.731, 37.241, 86.860, 90.00, 97.77, 90.00
R / Rfree (%)	20.2 / 25.5

The structure of 2.0 A Crystal Structure of the CAV1.2 Iq Domain-Ca/Cam Complex also contains other interesting chemical elements:

Calcium

(Ca)

12 atoms

The binding sites of Nickel atom in the 2.0 A Crystal Structure of the CAV1.2 Iq Domain-Ca/Cam Complex (pdb code 2be6). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the 2.0 A Crystal Structure of the CAV1.2 Iq Domain-Ca/Cam Complex, PDB code: 2be6:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the 2.0 A Crystal Structure of the CAV1.2 Iq Domain-Ca/Cam Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of 2.0 A Crystal Structure of the CAV1.2 Iq Domain-Ca/Cam Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni505 b:38.6 occ:1.00 O A:HOH569 2.0 40.4 1.0 NE2 A:HIS107 2.1 18.5 0.7 NE2 A:HIS107 2.1 23.8 0.3 O A:HOH564 2.2 40.3 1.0 O A:HOH565 2.4 42.4 1.0 O A:HOH572 2.4 39.9 1.0 O A:HOH570 2.5 43.8 1.0 CE1 A:HIS107 2.8 24.7 0.3 CE1 A:HIS107 3.0 20.4 0.7 O A:HOH576 3.2 55.9 1.0 CD2 A:HIS107 3.2 19.8 0.7 CD2 A:HIS107 3.4 25.5 0.3 O A:HOH558 3.9 34.7 1.0 ND1 A:HIS107 4.0 26.1 0.3 O A:HOH571 4.1 54.4 1.0 ND1 A:HIS107 4.1 21.3 0.7 OD1 A:ASN111 4.3 33.9 1.0 CG A:HIS107 4.3 21.3 0.7 CG A:HIS107 4.3 24.5 0.3 O A:SER38 4.4 30.6 1.0 O A:HOH559 4.8 37.4 1.0

Nickel binding site 2 out of 3 in the 2.0 A Crystal Structure of the CAV1.2 Iq Domain-Ca/Cam Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of 2.0 A Crystal Structure of the CAV1.2 Iq Domain-Ca/Cam Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni510 b:57.1 occ:0.60 O B:HOH546 2.0 42.1 1.0 O B:HOH544 2.2 55.1 1.0 O B:HOH547 2.3 45.6 1.0 NE2 B:HIS107 2.3 29.8 0.3 CE1 B:HIS107 2.5 29.3 0.3 NE2 B:HIS107 2.7 32.8 0.7 O B:HOH543 2.9 77.8 1.0 O B:HOH529 3.1 53.8 1.0 CD2 B:HIS107 3.3 30.6 0.7 CD2 B:HIS107 3.6 30.2 0.3 CE1 B:HIS107 3.7 32.6 0.7 ND1 B:HIS107 3.8 29.1 0.3 OD1 B:ASN111 4.0 31.4 1.0 CG B:HIS107 4.4 29.4 0.3 CG B:HIS107 4.5 30.1 0.7 ND1 B:HIS107 4.7 30.8 0.7 CG B:ASN111 4.9 33.2 1.0 ND2 B:ASN111 5.0 33.5 1.0

Nickel binding site 3 out of 3 in the 2.0 A Crystal Structure of the CAV1.2 Iq Domain-Ca/Cam Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of 2.0 A Crystal Structure of the CAV1.2 Iq Domain-Ca/Cam Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni515 b:44.2 occ:1.00 O C:HOH594 1.9 36.0 1.0 NE2 C:HIS107 2.1 26.7 1.0 O C:HOH584 2.2 45.0 1.0 O C:HOH596 2.4 50.7 1.0 O C:HOH595 2.4 40.6 1.0 O C:HOH583 2.5 41.4 1.0 CE1 C:HIS107 2.8 28.3 1.0 O C:HOH599 2.8 57.3 1.0 CD2 C:HIS107 3.2 27.0 1.0 O C:HOH601 3.3 62.4 1.0 O C:HOH606 3.7 60.9 1.0 OD1 C:ASN111 3.9 31.0 1.0 ND1 C:HIS107 4.0 30.3 1.0 O C:HOH603 4.3 52.3 1.0 CG C:HIS107 4.3 26.5 1.0 ND2 C:ASN111 4.3 23.9 1.0 CG C:ASN111 4.5 29.0 1.0 CE C:LYS94 4.6 36.0 1.0

F.Van Petegem, F.C.Chatelain, D.L.Minor Jr.. Insights Into Voltage-Gated Calcium Channel Regulation From the Structure of the Ca(V)1.2 Iq Domain-Ca(2+)/Calmodulin Complex Nat.Struct.Mol.Biol. V. 12 1108 2005.
ISSN: ISSN 1545-9993
PubMed: 16299511
DOI: 10.1038/NSMB1027