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Cadmium in PDB 2ev0: Bacillus Subtilis Manganese Transport Regulator (Mntr) Bound to Cadmium

Protein crystallography data

The structure of Bacillus Subtilis Manganese Transport Regulator (Mntr) Bound to Cadmium, PDB code: 2ev0 was solved by J.I.Kliegman, S.L.Griner, J.D.Helmann, R.G.Brennan, A.Glasfeld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.95 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.900, 46.200, 74.900, 90.00, 93.00, 90.00
R / Rfree (%) 20.7 / 22.9

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Bacillus Subtilis Manganese Transport Regulator (Mntr) Bound to Cadmium (pdb code 2ev0). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Bacillus Subtilis Manganese Transport Regulator (Mntr) Bound to Cadmium, PDB code: 2ev0:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 2ev0

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Cadmium binding site 1 out of 5 in the Bacillus Subtilis Manganese Transport Regulator (Mntr) Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Bacillus Subtilis Manganese Transport Regulator (Mntr) Bound to Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1150

b:17.2
occ:1.00
 OE2 A:GLU99 2.3 19.3 1.0
ND1 A:HIS77 2.3 16.0 1.0
OE2 A:GLU11 2.4 23.8 1.0
OE2 A:GLU102 2.4 18.7 1.0
OE1 A:GLU102 2.4 16.7 1.0
O A:HOH3002 2.5 31.5 1.0
OE1 A:GLU11 2.5 31.1 1.0
CD A:GLU11 2.8 22.8 1.0
CD A:GLU102 2.8 12.8 1.0
O A:HOH3003 2.9 39.5 1.0
CE1 A:HIS77 3.2 16.0 1.0
CD A:GLU99 3.2 15.9 1.0
CG A:HIS77 3.3 15.9 1.0
OE1 A:GLU99 3.6 15.7 1.0
CB A:HIS77 3.7 15.0 1.0
O A:HOH3006 4.2 22.4 1.0
CG A:GLU11 4.3 20.1 1.0
O A:HOH3022 4.3 26.9 1.0
CG A:GLU102 4.3 16.2 1.0
CD A:CD1151 4.3 19.4 1.0
NE2 A:HIS77 4.4 15.0 1.0
O A:HOH3007 4.4 17.2 1.0
CD2 A:HIS77 4.4 18.2 1.0
CG A:GLU99 4.5 16.2 1.0
O A:HOH3019 4.5 22.3 1.0
OD2 A:ASP8 4.6 20.9 1.0
CA A:GLU99 4.8 16.7 1.0
CA A:HIS77 4.8 14.2 1.0

Cadmium binding site 2 out of 5 in 2ev0

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Cadmium binding site 2 out of 5 in the Bacillus Subtilis Manganese Transport Regulator (Mntr) Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Bacillus Subtilis Manganese Transport Regulator (Mntr) Bound to Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1151

b:19.4
occ:1.00
 O A:HOH3004 2.2 26.0 1.0
NE2 A:HIS103 2.3 19.9 1.0
OE2 A:GLU102 2.3 18.7 1.0
OE1 A:GLU99 2.3 15.7 1.0
OD2 A:ASP8 2.3 20.9 1.0
O A:GLU99 2.4 17.3 1.0
CG A:ASP8 3.1 22.6 1.0
OD1 A:ASP8 3.2 26.2 1.0
CE1 A:HIS103 3.2 21.5 1.0
CD2 A:HIS103 3.2 20.8 1.0
CD A:GLU99 3.3 15.9 1.0
C A:GLU99 3.3 16.9 1.0
CD A:GLU102 3.3 12.8 1.0
CA A:GLU99 3.5 16.7 1.0
O A:HOH3002 3.5 31.5 1.0
CG A:GLU102 3.7 16.2 1.0
CB A:GLU99 3.9 15.4 1.0
OE2 A:GLU99 4.0 19.3 1.0
CG A:GLU99 4.2 16.2 1.0
O A:HOH3041 4.2 30.2 1.0
CD A:CD1150 4.3 17.2 1.0
ND1 A:HIS103 4.3 20.0 1.0
CG A:HIS103 4.4 21.7 1.0
O A:HOH3057 4.4 29.3 1.0
O A:HOH3120 4.4 46.4 1.0
O A:HOH3087 4.4 45.4 1.0
OE1 A:GLU102 4.5 16.7 1.0
N A:GLY100 4.6 17.1 1.0
CB A:ASP8 4.6 20.0 1.0
O A:HOH3006 4.8 22.4 1.0
N A:GLU99 4.9 15.0 1.0
O A:VAL98 5.0 15.0 1.0

Cadmium binding site 3 out of 5 in 2ev0

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Cadmium binding site 3 out of 5 in the Bacillus Subtilis Manganese Transport Regulator (Mntr) Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Bacillus Subtilis Manganese Transport Regulator (Mntr) Bound to Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd3001

b:48.5
occ:0.50
 NE2 A:HIS104 2.4 23.4 1.0
NE2 B:HIS104 2.4 21.7 1.0
O A:HOH3036 2.9 26.2 1.0
O B:HOH2226 3.0 28.7 1.0
CE1 B:HIS104 3.2 26.1 1.0
CE1 A:HIS104 3.3 26.7 1.0
CD2 A:HIS104 3.3 23.5 1.0
CD2 B:HIS104 3.3 22.2 1.0
ND1 B:HIS104 4.3 22.6 1.0
ND1 A:HIS104 4.4 24.7 1.0
CG B:HIS104 4.4 20.0 1.0
CG A:HIS104 4.4 21.4 1.0
O A:GLY100 4.6 19.5 1.0
O B:GLY100 4.7 18.8 1.0
O A:HOH3057 4.9 29.3 1.0

Cadmium binding site 4 out of 5 in 2ev0

Go back to Cadmium Binding Sites List in 2ev0
Cadmium binding site 4 out of 5 in the Bacillus Subtilis Manganese Transport Regulator (Mntr) Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Bacillus Subtilis Manganese Transport Regulator (Mntr) Bound to Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd2150

b:17.1
occ:1.00
 ND1 B:HIS77 2.3 15.8 1.0
OE2 B:GLU99 2.3 18.4 1.0
OE1 B:GLU11 2.3 21.8 0.5
OE2 B:GLU11 2.4 22.7 0.5
OE2 B:GLU11 2.4 21.5 0.5
OE1 B:GLU102 2.4 15.8 1.0
OE2 B:GLU102 2.5 14.8 1.0
CD B:GLU11 2.7 20.9 0.5
OE1 B:GLU11 2.7 18.6 0.5
CD B:GLU102 2.8 14.0 1.0
CD B:GLU11 2.8 17.1 0.5
CE1 B:HIS77 3.1 15.4 1.0
CD B:GLU99 3.3 16.7 1.0
CG B:HIS77 3.3 14.1 1.0
O B:HOH2219 3.6 33.1 1.0
OE1 B:GLU99 3.7 18.0 1.0
CB B:HIS77 3.7 15.2 1.0
O B:HOH2155 4.1 21.7 1.0
CG B:GLU11 4.2 18.0 0.5
NE2 B:HIS77 4.3 13.7 1.0
O B:HOH2153 4.3 17.4 1.0
CG B:GLU11 4.3 17.4 0.5
CD B:CD2151 4.3 18.6 1.0
CG B:GLU102 4.3 14.5 1.0
CD2 B:HIS77 4.4 14.3 1.0
O B:HOH2168 4.4 25.4 1.0
CG B:GLU99 4.5 16.7 1.0
OD2 B:ASP8 4.6 15.9 1.0
O B:HOH2171 4.6 27.2 1.0
CA B:HIS77 4.8 15.4 1.0
CA B:GLU99 4.8 15.8 1.0
CB B:GLU11 5.0 18.4 0.5
CB B:GLU11 5.0 18.1 0.5

Cadmium binding site 5 out of 5 in 2ev0

Go back to Cadmium Binding Sites List in 2ev0
Cadmium binding site 5 out of 5 in the Bacillus Subtilis Manganese Transport Regulator (Mntr) Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Bacillus Subtilis Manganese Transport Regulator (Mntr) Bound to Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd2151

b:18.6
occ:1.00
 NE2 B:HIS103 2.2 18.8 1.0
O B:HOH2152 2.3 24.3 1.0
OE2 B:GLU102 2.3 14.8 1.0
OD2 B:ASP8 2.3 15.9 1.0
O B:GLU99 2.4 16.5 1.0
OE1 B:GLU99 2.4 18.0 1.0
CE1 B:HIS103 3.1 20.6 1.0
CG B:ASP8 3.2 20.4 1.0
CD2 B:HIS103 3.2 18.3 1.0
CD B:GLU99 3.3 16.7 1.0
C B:GLU99 3.3 15.9 1.0
OD1 B:ASP8 3.3 21.7 1.0
CD B:GLU102 3.3 14.0 1.0
CA B:GLU99 3.6 15.8 1.0
CG B:GLU102 3.7 14.5 1.0
CB B:GLU99 3.9 16.2 1.0
OE2 B:GLU99 4.0 18.4 1.0
CG B:GLU99 4.2 16.7 1.0
ND1 B:HIS103 4.3 19.0 1.0
O B:HOH2247 4.3 33.0 1.0
O B:HOH2179 4.3 23.6 1.0
CG B:HIS103 4.3 20.1 1.0
CD B:CD2150 4.3 17.1 1.0
OE1 B:GLU102 4.4 15.8 1.0
N B:GLY100 4.5 16.0 1.0
CB B:ASP8 4.6 17.8 1.0
O B:HOH2155 4.7 21.7 1.0
OE1 B:GLU11 4.9 21.8 0.5
N B:GLU99 4.9 15.3 1.0
O B:VAL98 5.0 15.8 1.0

Reference:

J.I.Kliegman, S.L.Griner, J.D.Helmann, R.G.Brennan, A.Glasfeld. Structural Basis For the Metal-Selective Activation of the Manganese Transport Regulator of Bacillus Subtilis. Biochemistry V. 45 3493 2006.
ISSN: ISSN 0006-2960
PubMed: 16533030
DOI: 10.1021/BI0524215
Page generated: Fri Jul 19 14:49:04 2024

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