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

Protein crystallography data

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

Nickel Binding Sites:

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 2be6

Go back to Nickel Binding Sites List in 2be6
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 2be6

Go back to Nickel Binding Sites List in 2be6
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 2be6

Go back to Nickel Binding Sites List in 2be6
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

Reference:

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
Page generated: Fri Sep 25 08:06:22 2020
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