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Cadmium in PDB 6k5p: Structure of Mosquito-Larvicidal Binary Toxin Receptor, CQM1

Protein crystallography data

The structure of Structure of Mosquito-Larvicidal Binary Toxin Receptor, CQM1, PDB code: 6k5p was solved by V.Kumar, M.Sharma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.83 / 1.81
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.181, 191.486, 205.332, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 22.7

Other elements in 6k5p:

The structure of Structure of Mosquito-Larvicidal Binary Toxin Receptor, CQM1 also contains other interesting chemical elements:

Cobalt (Co) 2 atoms
Magnesium (Mg) 4 atoms
Calcium (Ca) 4 atoms

Cadmium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Cadmium atom in the Structure of Mosquito-Larvicidal Binary Toxin Receptor, CQM1 (pdb code 6k5p). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 14 binding sites of Cadmium where determined in the Structure of Mosquito-Larvicidal Binary Toxin Receptor, CQM1, PDB code: 6k5p:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 14 in 6k5p

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Cadmium binding site 1 out of 14 in the Structure of Mosquito-Larvicidal Binary Toxin Receptor, CQM1


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Mosquito-Larvicidal Binary Toxin Receptor, CQM1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd602

b:29.9
occ:0.80
 O A:ILE31 2.3 19.9 1.0
OD1 A:ASN27 2.3 22.1 1.0
OD2 A:ASP33 2.5 26.3 1.0
OD1 A:ASP25 2.5 28.2 1.0
OD1 A:ASP29 2.5 27.7 1.0
O A:HOH704 2.6 39.3 1.0
CG A:ASN27 3.3 33.3 1.0
CG A:ASP29 3.3 31.3 1.0
CG A:ASP25 3.4 24.8 1.0
C A:ILE31 3.5 25.5 1.0
OD2 A:ASP29 3.5 30.9 1.0
CG A:ASP33 3.5 25.4 1.0
ND2 A:ASN27 3.7 39.8 1.0
CB A:ASP33 3.9 25.3 1.0
CB A:ASP25 4.0 22.1 1.0
CA A:ASP25 4.1 21.6 1.0
N A:ASN27 4.1 25.8 1.0
N A:ILE31 4.1 28.0 1.0
OD2 A:ASP25 4.2 27.8 1.0
N A:SER26 4.2 22.4 1.0
CA A:ILE31 4.2 31.1 1.0
C A:GLY32 4.3 18.1 1.0
O A:GLY32 4.3 21.5 1.0
CB A:ILE31 4.3 32.1 1.0
O A:GLU78 4.5 26.5 1.0
N A:ASP29 4.5 25.5 1.0
N A:ASP33 4.5 18.3 1.0
N A:GLY32 4.5 22.4 1.0
C A:ASP25 4.5 22.5 1.0
CB A:ASN27 4.5 28.2 1.0
CB A:ASP29 4.6 30.1 1.0
OD1 A:ASP33 4.6 23.5 1.0
CA A:GLY32 4.6 19.1 1.0
CA A:ASN27 4.7 26.4 1.0
N A:GLY28 4.8 32.2 1.0
CA A:ASP33 4.8 26.9 1.0
C A:ASN27 4.8 32.9 1.0
CG2 A:ILE31 5.0 28.4 1.0
CA A:ASP29 5.0 27.5 1.0

Cadmium binding site 2 out of 14 in 6k5p

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Cadmium binding site 2 out of 14 in the Structure of Mosquito-Larvicidal Binary Toxin Receptor, CQM1


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Mosquito-Larvicidal Binary Toxin Receptor, CQM1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd604

b:42.8
occ:0.88
 OE2 A:GLU269 2.6 31.8 1.0
OE1 A:GLU269 2.6 21.5 1.0
O A:HOH841 2.7 28.8 1.0
O A:HOH1186 2.7 32.1 1.0
O A:HOH1140 2.8 39.0 1.0
CD A:GLU269 2.9 29.2 1.0
O A:HOH1091 3.1 51.4 1.0
OD1 A:ASP203 3.2 30.8 1.0
CG A:ASP203 4.0 22.7 1.0
OD2 A:ASP337 4.0 26.6 1.0
NH2 A:ARG201 4.1 26.6 1.0
O A:HOH1304 4.2 43.7 1.0
N A:ALA204 4.3 22.9 1.0
O A:HOH743 4.3 23.4 1.0
OD2 A:ASP203 4.3 26.9 1.0
O A:HOH952 4.4 19.5 1.0
CG A:GLU269 4.4 26.5 1.0
CB A:ALA204 4.5 26.0 1.0
CA A:ALA204 4.6 25.6 1.0
O A:HOH873 4.8 27.7 1.0
O A:HOH997 5.0 38.1 1.0

Cadmium binding site 3 out of 14 in 6k5p

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Cadmium binding site 3 out of 14 in the Structure of Mosquito-Larvicidal Binary Toxin Receptor, CQM1


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Mosquito-Larvicidal Binary Toxin Receptor, CQM1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd605

b:30.3
occ:0.84
 O A:HOH1174 2.3 35.5 1.0
NE2 A:HIS438 2.4 25.7 1.0
O A:HOH788 2.5 35.3 1.0
ND1 A:HIS434 2.5 31.6 1.0
O A:HOH976 2.6 38.0 1.0
O A:HOH1277 2.9 39.9 1.0
CD2 A:HIS438 3.3 29.1 1.0
CE1 A:HIS438 3.4 28.8 1.0
CG A:HIS434 3.4 29.7 1.0
CE1 A:HIS434 3.5 34.0 1.0
CB A:HIS434 3.6 26.6 1.0
O A:HOH1241 4.3 46.0 1.0
CA A:HIS434 4.4 22.9 1.0
O A:HOH1084 4.4 40.5 1.0
O A:HIS434 4.4 27.5 1.0
CG A:HIS438 4.5 25.0 1.0
ND1 A:HIS438 4.5 21.0 1.0
O A:PRO429 4.6 32.1 1.0
NE2 A:HIS434 4.6 29.4 1.0
CD2 A:HIS434 4.6 29.9 1.0
C A:HIS434 4.7 25.0 1.0

Cadmium binding site 4 out of 14 in 6k5p

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Cadmium binding site 4 out of 14 in the Structure of Mosquito-Larvicidal Binary Toxin Receptor, CQM1


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Mosquito-Larvicidal Binary Toxin Receptor, CQM1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd606

b:35.7
occ:0.93
 O A:HOH973 2.1 33.7 1.0
O A:HOH1172 2.4 39.4 1.0
OE2 A:GLU472 2.4 29.7 1.0
O A:HOH1132 2.5 42.4 1.0
OE1 A:GLU472 2.7 29.3 1.0
CD A:GLU472 2.9 29.0 1.0
O A:HOH1113 4.2 33.6 1.0
CG A:GLU472 4.4 20.3 1.0
O A:HOH848 4.5 21.1 1.0
NH1 A:ARG446 4.6 37.6 1.0
CD A:ARG446 4.7 36.2 1.0
O A:HOH937 4.7 47.2 1.0

Cadmium binding site 5 out of 14 in 6k5p

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Cadmium binding site 5 out of 14 in the Structure of Mosquito-Larvicidal Binary Toxin Receptor, CQM1


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of Mosquito-Larvicidal Binary Toxin Receptor, CQM1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd608

b:67.3
occ:0.98
 OE2 A:GLU227 2.6 44.2 1.0
OE1 A:GLU227 2.7 46.4 1.0
O D:HOH1073 2.7 44.4 1.0
OE1 D:GLU227 2.7 64.5 1.0
OD2 D:ASP229 2.8 55.1 1.0
CD A:GLU227 2.8 45.1 1.0
OD2 A:ASP229 2.9 40.3 1.0
OD1 D:ASP229 2.9 55.4 1.0
OE2 D:GLU227 2.9 66.9 1.0
CD D:GLU227 3.0 63.2 1.0
CG D:ASP229 3.2 52.8 1.0
OD1 A:ASP229 3.5 45.7 1.0
CG A:ASP229 3.6 46.9 1.0
CA D:GLY223 3.7 56.0 1.0
CA A:GLY223 3.9 56.1 1.0
CG A:GLU227 4.0 48.3 1.0
CG D:GLU227 4.1 58.2 1.0
CB D:GLU227 4.3 46.9 1.0
N A:GLN224 4.3 59.8 1.0
CB A:GLU227 4.4 41.0 1.0
N D:GLN224 4.4 55.9 1.0
O D:HOH821 4.5 34.8 1.0
N D:GLY223 4.6 61.5 1.0
C D:GLY223 4.7 56.2 1.0
C A:GLY223 4.7 57.6 1.0
O D:HOH838 4.7 37.2 1.0
CB D:ASP229 4.7 44.0 1.0
N A:GLY223 4.9 60.1 1.0

Cadmium binding site 6 out of 14 in 6k5p

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Cadmium binding site 6 out of 14 in the Structure of Mosquito-Larvicidal Binary Toxin Receptor, CQM1


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structure of Mosquito-Larvicidal Binary Toxin Receptor, CQM1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd602

b:25.4
occ:0.84
 O B:ILE31 2.3 16.8 1.0
OD1 B:ASN27 2.4 22.1 1.0
O B:HOH713 2.4 33.5 1.0
OD1 B:ASP29 2.4 22.0 1.0
OD2 B:ASP33 2.4 20.0 1.0
OD1 B:ASP25 2.5 21.6 1.0
CG B:ASP29 3.2 27.2 1.0
CG B:ASN27 3.2 28.8 1.0
CG B:ASP25 3.3 20.1 1.0
OD2 B:ASP29 3.4 23.6 1.0
C B:ILE31 3.5 23.9 1.0
ND2 B:ASN27 3.5 34.1 1.0
CG B:ASP33 3.5 18.6 1.0
CB B:ASP33 4.0 20.1 1.0
OD2 B:ASP25 4.0 23.8 1.0
CB B:ASP25 4.1 16.9 1.0
N B:ILE31 4.1 20.0 1.0
CA B:ASP25 4.1 25.4 1.0
N B:SER26 4.1 17.0 1.0
N B:ASN27 4.1 20.7 1.0
CA B:ILE31 4.2 22.9 1.0
CB B:ILE31 4.3 17.0 1.0
C B:GLY32 4.3 18.3 1.0
O B:GLY32 4.4 18.6 1.0
N B:ASP29 4.4 18.7 1.0
CB B:ASP29 4.5 23.8 1.0
N B:ASP33 4.5 17.9 1.0
N B:GLY32 4.5 17.7 1.0
CB B:ASN27 4.5 20.7 1.0
C B:ASP25 4.5 25.1 1.0
O B:GLU78 4.6 21.7 1.0
OD1 B:ASP33 4.6 22.3 1.0
CA B:GLY32 4.7 18.9 1.0
CA B:ASN27 4.7 22.8 1.0
N B:GLY28 4.7 19.9 1.0
CA B:ASP33 4.9 19.6 1.0
C B:ASN27 4.9 24.6 1.0
CA B:ASP29 4.9 24.5 1.0
N B:GLY30 5.0 18.1 1.0

Cadmium binding site 7 out of 14 in 6k5p

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Cadmium binding site 7 out of 14 in the Structure of Mosquito-Larvicidal Binary Toxin Receptor, CQM1


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structure of Mosquito-Larvicidal Binary Toxin Receptor, CQM1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd604

b:42.5
occ:0.92
 OE2 B:GLU269 2.5 19.0 1.0
OE1 B:GLU269 2.5 27.2 1.0
O B:HOH1060 2.7 40.3 1.0
O B:HOH1185 2.7 32.3 1.0
O B:HOH990 2.7 37.1 1.0
CD B:GLU269 2.9 28.8 1.0
O B:HOH899 3.0 45.3 1.0
OD1 B:ASP203 3.3 27.3 1.0
CG B:ASP203 4.0 26.1 1.0
OD2 B:ASP337 4.1 26.1 1.0
NH2 B:ARG201 4.2 25.4 1.0
OD2 B:ASP203 4.2 30.8 1.0
O B:HOH1294 4.3 47.1 1.0
N B:ALA204 4.3 17.9 1.0
CG B:GLU269 4.4 26.0 1.0
O B:HOH866 4.4 22.6 1.0
O B:HOH765 4.4 27.3 1.0
CB B:ALA204 4.5 24.5 1.0
CA B:ALA204 4.6 25.0 1.0
O B:HOH745 4.8 23.8 1.0
O B:HOH879 4.9 31.2 1.0
CE1 B:TYR271 4.9 23.0 1.0

Cadmium binding site 8 out of 14 in 6k5p

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Cadmium binding site 8 out of 14 in the Structure of Mosquito-Larvicidal Binary Toxin Receptor, CQM1


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Structure of Mosquito-Larvicidal Binary Toxin Receptor, CQM1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd605

b:31.7
occ:0.77
 O B:HOH725 2.3 39.2 1.0
O B:ACT607 2.5 20.4 1.0
ND1 B:HIS434 2.5 25.6 1.0
O B:HOH749 2.5 31.8 1.0
NE2 B:HIS438 2.6 32.2 1.0
OXT B:ACT607 2.6 40.1 1.0
C B:ACT607 2.8 28.9 1.0
O B:HOH751 3.0 49.5 1.0
CE1 B:HIS434 3.4 35.4 1.0
CG B:HIS434 3.4 31.4 1.0
CD2 B:HIS438 3.5 32.1 1.0
CE1 B:HIS438 3.6 35.8 1.0
CB B:HIS434 3.7 22.9 1.0
O B:HIS434 4.4 23.7 1.0
O B:HOH1081 4.4 43.9 1.0
CH3 B:ACT607 4.4 19.7 1.0
CA B:HIS434 4.4 18.2 1.0
NE2 B:HIS434 4.5 30.2 1.0
CD2 B:HIS434 4.6 29.6 1.0
CG B:HIS438 4.6 23.4 1.0
ND1 B:HIS438 4.6 22.4 1.0
O B:PRO429 4.6 36.0 1.0
C B:HIS434 4.7 19.3 1.0
O B:HOH729 4.8 37.3 1.0
CB B:PRO429 4.9 35.1 1.0
CA B:PRO429 4.9 33.0 1.0

Cadmium binding site 9 out of 14 in 6k5p

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Cadmium binding site 9 out of 14 in the Structure of Mosquito-Larvicidal Binary Toxin Receptor, CQM1


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Structure of Mosquito-Larvicidal Binary Toxin Receptor, CQM1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd606

b:68.1
occ:0.98
 OD2 B:ASP229 2.6 45.4 1.0
OE2 B:GLU227 2.7 61.4 1.0
OE2 C:GLU227 2.7 61.4 1.0
OE1 B:GLU227 2.8 64.4 1.0
OD2 C:ASP229 2.8 45.9 1.0
OE1 C:GLU227 2.8 60.6 1.0
CD B:GLU227 2.9 61.1 1.0
OD1 B:ASP229 2.9 50.5 1.0
CD C:GLU227 2.9 57.6 1.0
CG B:ASP229 3.2 48.8 1.0
OD1 C:ASP229 3.4 49.7 1.0
CG C:ASP229 3.5 44.1 1.0
CA B:GLY223 3.5 59.9 1.0
CA C:GLY223 4.0 56.1 1.0
CG B:GLU227 4.1 56.6 1.0
CG C:GLU227 4.1 51.1 1.0
N B:GLN224 4.2 58.5 1.0
CB B:GLU227 4.2 49.0 1.0
C B:GLY223 4.4 58.4 1.0
CB C:GLU227 4.4 41.5 1.0
N B:GLY223 4.5 64.8 1.0
O C:HOH723 4.6 40.0 1.0
N C:GLN224 4.6 50.7 1.0
CB B:ASP229 4.7 42.7 1.0
O C:HOH899 4.8 34.7 1.0
C C:GLY223 4.9 54.5 1.0
N C:GLY223 5.0 63.8 1.0
CB C:ASP229 5.0 40.7 1.0

Cadmium binding site 10 out of 14 in 6k5p

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Cadmium binding site 10 out of 14 in the Structure of Mosquito-Larvicidal Binary Toxin Receptor, CQM1


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Structure of Mosquito-Larvicidal Binary Toxin Receptor, CQM1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd602

b:39.6
occ:0.80
 O C:ILE31 2.3 27.0 1.0
OD1 C:ASN27 2.5 34.1 1.0
OD1 C:ASP29 2.5 38.7 1.0
OD2 C:ASP33 2.6 37.6 1.0
OD1 C:ASP25 2.6 33.5 1.0
O C:HOH701 2.6 42.0 1.0
CG C:ASP29 3.2 41.9 1.0
CG C:ASP25 3.3 36.1 1.0
OD2 C:ASP29 3.4 40.9 1.0
C C:ILE31 3.4 33.5 1.0
CG C:ASN27 3.5 43.7 1.0
CG C:ASP33 3.6 38.2 1.0
CB C:ASP33 3.9 34.7 1.0
ND2 C:ASN27 4.0 50.5 1.0
CB C:ASP25 4.0 30.0 1.0
CA C:ASP25 4.0 34.5 1.0
N C:ILE31 4.1 35.0 1.0
N C:ASN27 4.1 37.8 1.0
OD2 C:ASP25 4.1 30.4 1.0
CA C:ILE31 4.2 36.5 1.0
N C:SER26 4.2 32.3 1.0
CB C:ILE31 4.3 34.6 1.0
C C:GLY32 4.3 29.0 1.0
O C:GLY32 4.5 36.5 1.0
N C:GLY32 4.5 27.1 1.0
N C:ASP33 4.5 25.2 1.0
N C:ASP29 4.5 39.3 1.0
C C:ASP25 4.5 36.5 1.0
O C:GLU78 4.5 42.1 1.0
CB C:ASP29 4.6 37.1 1.0
CA C:GLY32 4.6 28.2 1.0
N C:GLY28 4.6 38.1 1.0
CB C:ASN27 4.7 40.8 1.0
CA C:ASN27 4.7 42.1 1.0
OD1 C:ASP33 4.7 37.5 1.0
C C:ASN27 4.8 41.2 1.0
CA C:ASP33 4.8 29.9 1.0
CA C:ASP29 5.0 34.7 1.0

Reference:

M.Sharma, V.Kumar. Crystal Structure of Binab Toxin Receptor (CQM1) Protein and Molecular Dynamics Simulations Reveal the Role of Unique Ca(II) Ion. Int.J.Biol.Macromol. 2019.
ISSN: ISSN 0141-8130
PubMed: 31449868
DOI: 10.1016/J.IJBIOMAC.2019.08.126
Page generated: Fri Jul 19 19:28:10 2024

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