Lead in PDB 1n0y: Crystal Structure of Pb-Bound Calmodulin

The structure of Crystal Structure of Pb-Bound Calmodulin, PDB code: 1n0y was solved by M.A.Wilson, A.T.Brunger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.00 / 1.75
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	100.936, 30.792, 113.084, 90.00, 109.31, 90.00
R / Rfree (%)	21.3 / 22.3

The structure of Crystal Structure of Pb-Bound Calmodulin also contains other interesting chemical elements:

Arsenic

(As)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Lead atom in the Crystal Structure of Pb-Bound Calmodulin (pdb code 1n0y). This binding sites where shown within 5.0 Angstroms radius around Lead atom.
In total 14 binding sites of Lead where determined in the Crystal Structure of Pb-Bound Calmodulin, PDB code: 1n0y:
Jump to Lead binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Lead binding site 1 out of 14 in the Crystal Structure of Pb-Bound Calmodulin


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 1 of Crystal Structure of Pb-Bound Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Pb500 b:17.0 occ:1.00 OD2 A:ASP64 2.4 17.1 1.0 OD2 A:ASP58 2.4 19.2 1.0 OE1 B:GLU114 2.5 20.8 1.0 OE2 B:GLU114 2.5 18.1 1.0 CD B:GLU114 2.8 19.6 1.0 CG A:ASP64 3.1 16.8 1.0 OD1 A:ASP64 3.2 14.1 1.0 OE2 A:GLU67 3.2 21.2 1.0 CG A:ASP58 3.4 21.2 1.0 CD A:GLU67 3.5 16.7 1.0 CG A:GLU67 3.6 17.7 1.0 CB A:ASP58 4.0 23.7 1.0 O B:HOH2004 4.3 14.3 1.0 CG B:GLU114 4.4 16.6 1.0 OD1 A:ASP58 4.4 19.2 1.0 OE1 A:GLU67 4.4 15.5 1.0 PB A:PB501 4.4 19.0 1.0 CB A:ASP64 4.5 14.4 1.0 N A:ASP58 4.7 24.5 1.0 CB A:PRO66 4.7 15.1 1.0 OE2 B:GLU120 4.9 30.5 1.0 CB A:GLU67 5.0 15.6 1.0

Lead binding site 2 out of 14 in the Crystal Structure of Pb-Bound Calmodulin


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 2 of Crystal Structure of Pb-Bound Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Pb501 b:19.0 occ:1.00 OD1 A:ASP56 2.2 25.1 1.0 OD1 A:ASN60 2.4 23.7 1.0 OD1 A:ASP58 2.5 19.2 1.0 O A:THR62 2.5 19.1 1.0 OE1 A:GLU67 2.8 15.5 1.0 OE2 A:GLU67 2.8 21.2 1.0 CD A:GLU67 3.1 16.7 1.0 CG A:ASP58 3.1 21.2 1.0 OD2 A:ASP58 3.1 19.2 1.0 CG A:ASN60 3.1 27.3 1.0 O A:HOH1015 3.2 16.4 1.0 OD2 A:ASP64 3.3 17.1 1.0 CG A:ASP56 3.4 26.6 1.0 ND2 A:ASN60 3.6 28.4 1.0 C A:THR62 3.7 19.0 1.0 CG A:ASP64 4.0 16.8 1.0 N A:ASP64 4.1 13.4 1.0 OD2 A:ASP56 4.2 30.2 1.0 CB A:ASN60 4.3 29.1 1.0 CA A:ILE63 4.3 15.9 1.0 CB A:ASP56 4.4 26.9 1.0 PB A:PB500 4.4 17.0 1.0 N A:ASN60 4.4 31.3 1.0 N A:ILE63 4.4 16.2 1.0 CA A:ASP56 4.5 24.9 1.0 CB A:ASP58 4.5 23.7 1.0 CG A:GLU67 4.5 17.7 1.0 N A:THR62 4.5 23.5 1.0 N A:ASP58 4.5 24.5 1.0 C A:ILE63 4.6 14.6 1.0 OG1 A:THR62 4.6 18.6 1.0 OD1 A:ASP64 4.6 14.1 1.0 CB A:ASP64 4.6 14.4 1.0 CA A:THR62 4.7 21.1 1.0 C A:ASP56 4.8 26.0 1.0 N A:GLY59 4.9 29.3 1.0 CA A:ASN60 4.9 31.7 1.0 N A:ALA57 4.9 24.3 1.0 CA A:ASP58 4.9 25.8 1.0 C A:ASP58 5.0 28.3 1.0 CA A:ASP64 5.0 13.4 1.0

Lead binding site 3 out of 14 in the Crystal Structure of Pb-Bound Calmodulin


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 3 of Crystal Structure of Pb-Bound Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Pb502 b:20.8 occ:1.00 OE2 A:GLU7 2.4 27.2 1.0 OE1 A:GLU7 2.6 21.0 1.0 CD A:GLU7 2.8 19.8 1.0 CG A:GLU7 4.3 17.5 1.0 O A:HOH1011 4.8 28.8 1.0

Lead binding site 4 out of 14 in the Crystal Structure of Pb-Bound Calmodulin


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 4 of Crystal Structure of Pb-Bound Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Pb503 b:18.9 occ:1.00 OD1 A:ASP20 2.3 15.5 1.0 OD1 A:ASP22 2.5 15.9 1.0 OE2 A:GLU31 2.5 17.6 1.0 OE1 A:GLU31 2.6 19.3 1.0 O A:HOH1006 2.6 28.9 1.0 OD1 A:ASP24 2.6 18.2 1.0 O A:THR26 2.7 15.9 1.0 CD A:GLU31 2.9 17.4 1.0 CG A:ASP24 3.4 19.3 1.0 CG A:ASP20 3.4 15.2 1.0 CG A:ASP22 3.4 21.9 1.0 OG1 A:THR26 3.5 17.9 1.0 C A:THR26 3.6 14.8 1.0 OD2 A:ASP22 3.7 26.5 1.0 OD2 A:ASP24 3.8 25.1 1.0 CA A:ASP20 4.0 14.2 1.0 CB A:ASP20 4.1 13.1 1.0 N A:THR26 4.3 14.0 1.0 CG A:GLU31 4.3 22.5 1.0 N A:ASP24 4.4 17.1 1.0 OD2 A:ASP20 4.4 15.8 1.0 CA A:THR26 4.4 14.1 1.0 O A:HOH1026 4.5 41.3 1.0 CB A:ASP24 4.5 19.6 1.0 C A:ASP20 4.5 15.4 1.0 CB A:THR26 4.5 15.1 1.0 N A:ILE27 4.5 14.9 1.0 O A:HOH1013 4.7 22.2 1.0 N A:ASP22 4.7 19.8 1.0 O A:HOH1063 4.7 31.1 1.0 CG2 A:THR28 4.7 24.4 1.0 CA A:ILE27 4.7 16.2 1.0 N A:LYS21 4.8 16.9 1.0 CB A:ASP22 4.8 22.0 1.0 N A:GLY23 4.9 17.4 1.0 CA A:ASP24 4.9 17.5 1.0 N A:THR28 4.9 19.7 1.0

Lead binding site 5 out of 14 in the Crystal Structure of Pb-Bound Calmodulin


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 5 of Crystal Structure of Pb-Bound Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Pb504 b:32.0 occ:1.00 OE1 A:GLU14 2.3 30.8 1.0 OE2 A:GLU11 2.5 23.3 1.0 OE1 A:GLU11 2.7 22.3 1.0 CD A:GLU11 2.9 21.5 1.0 CD A:GLU14 3.0 30.4 1.0 OE2 A:GLU14 3.0 36.7 1.0 CG A:GLU11 4.4 16.7 1.0 CG A:GLU14 4.5 23.8 1.0 O A:HOH1070 4.7 45.7 1.0 O A:HOH1024 4.7 28.7 1.0

Lead binding site 6 out of 14 in the Crystal Structure of Pb-Bound Calmodulin


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 6 of Crystal Structure of Pb-Bound Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Pb507 b:21.2 occ:1.00 O2 A:CAC1001 2.5 24.1 1.0 OE1 A:GLU2 2.5 37.7 1.0 OE2 A:GLU2 2.7 34.4 1.0 O A:HOH1020 2.9 22.5 1.0 CD A:GLU2 2.9 35.8 1.0 OE2 B:GLU84 3.0 18.2 1.0 OE1 B:GLU83 3.1 25.2 1.0 AS A:CAC1001 3.8 22.7 1.0 CD B:GLU84 3.9 17.9 1.0 PB B:PB506 4.0 22.0 1.0 PB B:PB505 4.1 19.3 1.0 CD B:GLU83 4.1 25.2 1.0 C1 A:CAC1001 4.2 25.6 1.0 CG A:GLU2 4.4 34.8 1.0 CB B:GLU83 4.6 21.9 1.0 C2 A:CAC1001 4.6 24.6 1.0 OE1 B:GLU84 4.6 19.6 1.0 CG B:GLU84 4.6 19.4 1.0 OE2 B:GLU83 4.8 27.9 1.0 O A:ALA1 4.8 47.2 1.0 OE1 B:GLU87 4.8 22.8 1.0 O B:ASP80 4.9 21.2 1.0 CG B:GLU83 5.0 24.6 1.0

Lead binding site 7 out of 14 in the Crystal Structure of Pb-Bound Calmodulin


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 7 of Crystal Structure of Pb-Bound Calmodulin within 5.0Å range:

Lead binding site 8 out of 14 in the Crystal Structure of Pb-Bound Calmodulin


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 8 of Crystal Structure of Pb-Bound Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Pb505 b:19.3 occ:1.00 OE2 B:GLU87 2.5 22.0 1.0 OE1 B:GLU84 2.6 19.6 1.0 OE2 B:GLU84 2.6 18.2 1.0 OE1 B:GLU87 2.7 22.8 1.0 O A:HOH1031 2.9 20.4 1.0 CD B:GLU87 2.9 20.2 1.0 CD B:GLU84 2.9 17.9 1.0 OE2 A:GLU2 3.1 34.4 1.0 O A:HOH1055 3.6 25.5 1.0 PB A:PB507 4.1 21.2 1.0 CD A:GLU2 4.3 35.8 1.0 CG B:GLU87 4.4 19.2 1.0 CG B:GLU84 4.4 19.4 1.0 CG A:GLN3 4.5 31.2 1.0 OE1 A:GLN3 4.7 36.2 1.0 N A:GLN3 4.9 31.4 1.0 CB A:GLU2 5.0 33.6 1.0

Lead binding site 9 out of 14 in the Crystal Structure of Pb-Bound Calmodulin


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 9 of Crystal Structure of Pb-Bound Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Pb506 b:22.0 occ:1.00 OE1 B:GLU83 2.4 25.2 1.0 O2 A:CAC1001 2.4 24.1 1.0 OD1 B:ASP80 2.8 19.0 1.0 OE2 B:GLU83 2.9 27.9 1.0 CD B:GLU83 3.0 25.2 1.0 O1 A:CAC1001 3.3 26.8 1.0 AS A:CAC1001 3.4 22.7 1.0 CG B:ASP80 3.8 21.8 1.0 PB A:PB507 4.0 21.2 1.0 PB B:PB509 4.2 22.7 0.7 O A:HOH1034 4.3 27.2 1.0 CG B:GLU83 4.4 24.6 1.0 CA B:ASP80 4.6 22.7 1.0 OD2 B:ASP80 4.6 26.4 1.0 C1 A:CAC1001 4.6 25.6 1.0 CB B:ASP80 4.6 23.0 1.0 O A:HOH1020 4.8 22.5 1.0 NE2 B:GLN79 4.9 37.5 1.0 C2 A:CAC1001 4.9 24.6 1.0

Lead binding site 10 out of 14 in the Crystal Structure of Pb-Bound Calmodulin


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 10 of Crystal Structure of Pb-Bound Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Pb508 b:24.4 occ:1.00 OD1 B:ASP133 2.2 20.5 1.0 OD1 B:ASP129 2.4 20.9 1.0 OD1 B:ASP131 2.5 26.4 1.0 OE1 B:GLU140 2.5 19.3 1.0 O B:HIS135 2.5 15.6 1.0 OE2 B:GLU140 2.8 17.8 1.0 O B:HOH2027 2.8 33.7 1.0 CD B:GLU140 3.0 19.5 1.0 CG B:ASP131 3.1 26.0 1.0 OD2 B:ASP131 3.2 25.8 1.0 CG B:ASP133 3.2 23.0 1.0 CG B:ASP129 3.5 22.8 1.0 C B:HIS135 3.5 14.7 1.0 OD2 B:ASP133 3.8 24.8 1.0 ND2 B:ASN137 4.1 21.4 1.0 CA B:ASP129 4.1 22.9 1.0 CB B:ASP129 4.1 22.4 1.0 N B:ASP133 4.2 25.4 1.0 N B:ILE136 4.3 13.0 1.0 N B:HIS135 4.3 16.3 1.0 CA B:ILE136 4.3 13.5 1.0 N B:ASN137 4.3 14.4 1.0 CB B:ASP133 4.3 24.2 1.0 CA B:HIS135 4.4 14.8 1.0 OD2 B:ASP129 4.4 24.9 1.0 N B:ASP131 4.4 27.6 1.0 CG B:GLU140 4.5 21.9 1.0 N B:ILE130 4.5 25.2 1.0 CB B:ASP131 4.5 28.5 1.0 C B:ASP129 4.6 25.1 1.0 N B:GLY132 4.6 27.5 1.0 CB B:HIS135 4.7 15.0 1.0 CA B:ASP133 4.8 23.7 1.0 C B:ILE136 4.8 13.3 1.0 CG B:ASN137 4.8 17.1 1.0 CA B:ASP131 4.9 28.8 1.0 C B:ASP131 5.0 28.6 1.0

M.A.Wilson, A.T.Brunger. Domain Flexibility in the 1.75 A Resolution Structure of PB2+-Calmodulin. Acta Crystallogr.,Sect.D V. 59 1782 2003.
ISSN: ISSN 0907-4449
PubMed: 14501118
DOI: 10.1107/S0907444903016846