Cadmium in PDB 5jpd: Metal Abc Transporter From Listeria Monocytogenes with Cadmium

The structure of Metal Abc Transporter From Listeria Monocytogenes with Cadmium, PDB code: 5jpd was solved by J.Osipiuk, M.Zhou, S.Grimshaw, W.F.Anderson, A.Joachimiak, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.20 / 1.72
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.316, 62.341, 75.987, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 20.7

The structure of Metal Abc Transporter From Listeria Monocytogenes with Cadmium also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Cadmium atom in the Metal Abc Transporter From Listeria Monocytogenes with Cadmium (pdb code 5jpd). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 13 binding sites of Cadmium where determined in the Metal Abc Transporter From Listeria Monocytogenes with Cadmium, PDB code: 5jpd:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 13 in the Metal Abc Transporter From Listeria Monocytogenes with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Metal Abc Transporter From Listeria Monocytogenes with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd501 b:16.3 occ:1.00 NE2 A:HIS140 2.2 12.8 1.0 OE1 A:GLU206 2.2 14.1 1.0 OD2 A:ASP281 2.3 15.2 1.0 NE2 A:HIS67 2.3 15.0 1.0 OE2 A:GLU206 2.6 15.1 1.0 OD1 A:ASP281 2.6 17.3 1.0 CD A:GLU206 2.8 14.9 1.0 CG A:ASP281 2.8 15.3 1.0 CD2 A:HIS140 3.2 13.1 1.0 CE1 A:HIS67 3.2 15.3 1.0 CE1 A:HIS140 3.2 14.0 1.0 CD2 A:HIS67 3.3 15.6 1.0 ND2 A:ASN227 3.7 17.1 1.0 CG A:ASN227 4.2 16.5 1.0 O A:HOH646 4.2 17.1 1.0 CG A:GLU206 4.3 14.7 1.0 CB A:ASP281 4.3 15.3 1.0 ND1 A:HIS140 4.3 14.0 1.0 ND1 A:HIS67 4.3 16.0 1.0 CG A:HIS140 4.3 13.9 1.0 CG A:HIS67 4.4 15.9 1.0 O A:HOH659 4.4 17.0 1.0 OD1 A:ASN227 4.6 15.7 1.0 CB A:ALA208 4.6 17.1 1.0 CB A:ASN227 4.8 16.8 1.0 CD1 A:LEU92 4.8 18.4 1.0

Cadmium binding site 2 out of 13 in the Metal Abc Transporter From Listeria Monocytogenes with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Metal Abc Transporter From Listeria Monocytogenes with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd502 b:18.7 occ:0.50 O A:HOH602 2.1 27.9 1.0 OD1 A:ASP65 2.2 25.1 1.0 O A:HOH798 2.3 24.9 1.0 O A:HOH774 2.3 31.8 1.0 O A:HOH776 2.6 17.6 1.0 O A:HOH615 2.8 36.9 1.0 CG A:ASP65 3.1 23.8 1.0 OD2 A:ASP65 3.4 20.1 1.0 O A:HOH781 3.9 28.1 1.0 O A:GLU68 4.1 22.6 1.0 O A:HOH745 4.1 24.7 1.0 O A:ASP65 4.3 19.8 1.0 CB A:ASP65 4.4 22.5 1.0 O A:HOH813 4.6 37.6 1.0 N A:ASP65 4.8 21.0 1.0 C A:ASP65 4.8 19.4 1.0 N A:GLU68 4.9 18.7 1.0 CA A:ASP65 4.9 21.2 1.0

Cadmium binding site 3 out of 13 in the Metal Abc Transporter From Listeria Monocytogenes with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Metal Abc Transporter From Listeria Monocytogenes with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd503 b:43.1 occ:0.60 CD A:CD503 0.0 43.1 0.6 CD A:CD503 1.8 25.9 0.4 O A:HOH809 2.3 37.4 1.0 OE2 A:GLU118 2.3 24.5 1.0 OE1 A:GLU118 2.5 28.9 1.0 O A:HOH786 2.7 25.5 1.0 O A:HOH795 2.7 38.9 1.0 O A:HOH694 2.7 24.5 1.0 CD A:GLU118 2.7 24.6 1.0 O A:HOH759 3.3 23.7 0.6 CG A:GLU118 4.1 22.4 1.0 CD A:LYS121 4.2 25.1 0.4 NZ A:LYS121 4.2 25.6 0.4 CE A:LYS121 4.3 25.9 0.4 O A:HOH759 4.5 23.7 0.4 N A:LEU90 4.5 21.1 1.0 OG A:SER120 4.6 20.8 1.0 O A:HOH666 4.7 34.1 1.0 O A:HOH769 4.9 27.8 1.0

Cadmium binding site 4 out of 13 in the Metal Abc Transporter From Listeria Monocytogenes with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Metal Abc Transporter From Listeria Monocytogenes with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd503 b:25.9 occ:0.40 CD A:CD503 0.0 25.9 0.4 O A:HOH759 1.5 23.7 0.6 CD A:CD503 1.8 43.1 0.6 O A:HOH795 2.1 38.9 1.0 OE2 A:GLU118 2.3 24.5 1.0 O A:HOH786 2.4 25.5 1.0 OE1 A:GLU118 2.6 28.9 1.0 O A:HOH759 2.8 23.7 0.4 CD A:GLU118 2.8 24.6 1.0 O A:HOH809 3.7 37.4 1.0 O A:HOH775 4.2 29.2 1.0 CG A:GLU118 4.3 22.4 1.0 N A:LEU90 4.3 21.1 1.0 O A:HOH694 4.3 24.5 1.0 NZ A:LYS121 4.7 25.6 0.4 CA A:GLY89 4.8 19.4 1.0 OH A:TYR87 5.0 23.6 1.0

Cadmium binding site 5 out of 13 in the Metal Abc Transporter From Listeria Monocytogenes with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Metal Abc Transporter From Listeria Monocytogenes with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd504 b:43.3 occ:0.60 CD A:CD504 0.0 43.3 0.6 CD A:CD504 2.2 39.8 0.4 OD2 A:ASP291 2.2 21.3 1.0 O A:HOH789 2.4 39.8 1.0 OD1 A:ASP291 2.8 20.8 1.0 CG A:ASP291 2.8 20.2 1.0 O A:HOH793 2.9 27.7 0.6 O A:HOH617 3.4 19.4 1.0 N A:GLY287 4.1 22.5 1.0 CB A:ASP291 4.3 18.6 1.0 CA A:GLY287 4.4 23.3 1.0 OE2 A:GLU295 4.5 36.6 1.0 CG2 A:THR292 4.8 18.5 1.0 O A:GLU288 4.8 19.5 1.0 C A:GLY287 5.0 24.6 1.0 O A:HOH761 5.0 49.0 1.0 OE1 A:GLU295 5.0 31.0 1.0

Cadmium binding site 6 out of 13 in the Metal Abc Transporter From Listeria Monocytogenes with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Metal Abc Transporter From Listeria Monocytogenes with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd504 b:39.8 occ:0.40 CD A:CD504 0.0 39.8 0.4 O A:HOH617 1.9 19.4 1.0 CD A:CD504 2.2 43.3 0.6 OD1 A:ASP291 2.4 20.8 1.0 OE2 A:GLU295 2.5 36.6 1.0 OE1 A:GLU295 3.0 31.0 1.0 CD A:GLU295 3.1 31.6 1.0 CG A:ASP291 3.2 20.2 1.0 OD2 A:ASP291 3.3 21.3 1.0 O A:HOH806 3.8 40.1 1.0 O A:HOH789 3.9 39.8 1.0 O A:HOH761 4.1 49.0 1.0 O A:GLU288 4.2 19.5 1.0 CG A:GLU295 4.6 27.5 1.0 CB A:ASP291 4.6 18.6 1.0 CG2 A:THR292 4.6 18.5 1.0 N A:ASP291 4.8 17.0 1.0 O A:HOH793 4.9 27.7 0.6

Cadmium binding site 7 out of 13 in the Metal Abc Transporter From Listeria Monocytogenes with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Metal Abc Transporter From Listeria Monocytogenes with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd505 b:31.3 occ:0.50 CD A:CD505 0.0 31.3 0.5 OD1 A:ASP70 2.2 32.9 1.0 O A:HOH674 2.3 24.1 1.0 O A:HOH763 2.3 26.9 0.6 O A:HOH681 2.3 31.3 0.6 O A:HOH777 2.6 23.8 1.0 CD A:CD505 3.3 48.0 0.4 CG A:ASP70 3.3 29.1 1.0 OD2 A:ASP70 3.8 32.7 1.0 O A:HOH811 4.0 28.7 1.0 O A:HOH603 4.1 15.2 0.6 O A:HOH683 4.2 26.4 1.0 O A:HOH704 4.5 34.5 1.0 O A:PRO71 4.5 18.0 1.0 CD A:PRO71 4.5 19.1 1.0 CB A:ASP70 4.6 24.8 1.0 CA A:ASP70 4.7 22.0 1.0 N A:PRO71 4.8 19.2 1.0 CD A:ARG101 4.9 25.0 1.0 C A:ASP70 4.9 20.3 1.0

Cadmium binding site 8 out of 13 in the Metal Abc Transporter From Listeria Monocytogenes with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Metal Abc Transporter From Listeria Monocytogenes with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd505 b:48.0 occ:0.40 CD A:CD505 0.0 48.0 0.4 O A:HOH603 1.0 15.2 0.6 O A:HOH763 1.9 26.9 0.6 OD2 A:ASP70 2.3 32.7 1.0 O A:HOH681 2.3 31.3 0.6 CG A:ASP70 3.1 29.1 1.0 OD1 A:ASP70 3.2 32.9 1.0 CD A:CD505 3.3 31.3 0.5 O A:HOH704 4.3 34.5 1.0 CB A:ASP70 4.5 24.8 1.0 O A:HOH674 5.0 24.1 1.0

Cadmium binding site 9 out of 13 in the Metal Abc Transporter From Listeria Monocytogenes with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Metal Abc Transporter From Listeria Monocytogenes with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd506 b:60.4 occ:0.60 O A:HOH782 2.3 45.7 1.0 OD1 A:ASP165 2.7 40.3 1.0 OD2 A:ASP165 2.7 40.8 1.0 CG A:ASP165 3.0 40.2 1.0 CB A:ASP165 4.5 38.5 1.0

Cadmium binding site 10 out of 13 in the Metal Abc Transporter From Listeria Monocytogenes with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Metal Abc Transporter From Listeria Monocytogenes with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd507 b:55.6 occ:0.60 CD A:CD507 0.0 55.6 0.6 CD A:CD507 1.2 24.1 0.3 O A:HOH779 2.3 19.6 1.0 O A:HOH805 2.4 30.2 1.0 ND1 A:HIS57 2.9 25.3 1.0 O A:HOH783 3.0 22.4 1.0 OG A:SER78 3.0 21.1 1.0 CB A:HIS57 3.5 22.7 1.0 CG A:HIS57 3.6 24.5 1.0 CB A:SER78 3.8 19.8 1.0 CE1 A:HIS57 4.0 26.2 1.0 O A:ALA74 4.4 16.9 1.0 CA A:HIS57 4.5 21.1 1.0 ND2 A:ASN75 4.5 17.3 1.0 CD2 A:HIS57 4.8 23.8 1.0 C A:ALA74 4.8 16.9 1.0 N A:SER58 4.9 18.7 1.0 NE2 A:HIS57 5.0 25.5 1.0 CB A:ALA74 5.0 17.3 1.0

J.Osipiuk, M.Zhou, S.Grimshaw, W.F.Anderson, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). Metal Abc Transporter From Listeria Monocytogenes with Cadmium To Be Published.