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Cadmium in PDB 3pk1: Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain

Protein crystallography data

The structure of Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain, PDB code: 3pk1 was solved by P.E.Czabotar, P.M.Colman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.14 / 2.49
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 97.923, 81.469, 57.927, 90.00, 124.23, 90.00
R / Rfree (%) 21.2 / 24.5

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain (pdb code 3pk1). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 18 binding sites of Cadmium where determined in the Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain, PDB code: 3pk1:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12; 13; 14; 15; 16; 17; 18;

Cadmium binding site 1 out of 18 in 3pk1

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Cadmium binding site 1 out of 18 in the Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1

b:43.0
occ:1.00
O C:HOH21 2.3 22.1 1.0
ND1 C:HIS277 2.3 44.0 1.0
OE2 A:GLU225 2.3 45.8 1.0
O C:HOH327 2.3 29.0 1.0
OE1 A:GLU225 2.4 47.8 1.0
CD A:GLU225 2.7 45.7 1.0
CE1 C:HIS277 3.2 44.2 1.0
CG C:HIS277 3.3 43.2 1.0
CB C:HIS277 3.7 42.2 1.0
CA C:HIS277 3.9 42.3 1.0
CG A:GLU225 4.2 43.0 1.0
OE1 C:GLN229 4.3 44.9 1.0
NE2 C:HIS277 4.3 43.5 1.0
OG1 C:THR280 4.3 55.4 0.0
CD2 C:LEU232 4.4 41.7 1.0
CD2 C:HIS277 4.4 43.2 1.0
NE2 C:GLN229 4.5 43.4 1.0
CB C:THR280 4.6 55.8 1.0
CG2 C:THR280 4.7 56.7 0.0
N C:HIS277 4.8 41.4 1.0
CD C:GLN229 4.8 43.3 1.0
O C:HIS277 4.9 43.8 1.0
C C:HIS277 5.0 43.7 1.0
CB A:GLU225 5.0 41.1 1.0

Cadmium binding site 2 out of 18 in 3pk1

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Cadmium binding site 2 out of 18 in the Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2

b:46.6
occ:1.00
O C:HOH25 2.2 34.0 1.0
OE2 C:GLU225 2.2 45.6 1.0
OE1 C:GLU225 2.4 47.7 1.0
ND1 A:HIS277 2.5 44.1 1.0
CD C:GLU225 2.6 45.7 1.0
CE1 A:HIS277 3.4 44.3 1.0
CG A:HIS277 3.5 43.2 1.0
CB A:HIS277 3.8 42.1 1.0
CA A:HIS277 3.9 42.3 1.0
O A:HOH327 4.1 33.9 1.0
OG1 A:THR280 4.1 55.4 1.0
CG C:GLU225 4.1 43.1 1.0
OE1 A:GLN229 4.4 44.9 1.0
CB A:THR280 4.5 55.8 1.0
NE2 A:HIS277 4.5 43.6 1.0
CD2 A:HIS277 4.6 43.2 1.0
CG2 A:THR280 4.6 56.9 1.0
CD2 A:LEU232 4.7 41.9 1.0
N A:HIS277 4.7 41.4 1.0
NE2 A:GLN229 4.8 43.4 1.0
O C:HOH43 4.8 19.0 1.0
O A:HIS277 4.9 43.9 1.0
C A:HIS277 4.9 43.6 1.0
CB C:GLU225 5.0 41.0 1.0

Cadmium binding site 3 out of 18 in 3pk1

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Cadmium binding site 3 out of 18 in the Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd5

b:48.1
occ:1.00
NE2 A:HIS224 2.3 44.3 1.0
OE1 B:GLU69 2.4 42.9 1.0
OE2 B:GLU69 2.8 36.9 1.0
O A:HOH23 2.8 22.3 1.0
CD B:GLU69 2.9 40.2 1.0
CE1 A:HIS224 3.2 44.2 1.0
CD2 A:HIS224 3.3 42.7 1.0
ND2 A:ASN223 4.1 48.0 1.0
CB A:ASN223 4.1 44.1 1.0
ND1 A:HIS224 4.3 43.6 1.0
CG A:ASN223 4.4 46.3 1.0
CG B:GLU69 4.4 39.1 1.0
CG A:HIS224 4.4 42.6 1.0
CG2 B:ILE66 4.6 36.8 1.0

Cadmium binding site 4 out of 18 in 3pk1

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Cadmium binding site 4 out of 18 in the Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd12

b:0.0
occ:1.00
SG A:CYS286 3.1 83.6 1.0
CB A:CYS286 3.4 61.4 1.0
CD A:CD14 3.4 0.4 1.0
OE1 A:GLU288 3.7 56.5 1.0
CD A:CD13 4.4 0.8 1.0
CD A:GLU288 4.8 56.5 1.0
CA A:CYS286 4.9 61.4 1.0

Cadmium binding site 5 out of 18 in 3pk1

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Cadmium binding site 5 out of 18 in the Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd13

b:0.8
occ:1.00
OE1 A:GLU288 2.7 56.5 1.0
SG A:CYS286 2.8 83.6 1.0
OE2 A:GLU288 3.0 57.1 1.0
CD A:GLU288 3.2 56.5 1.0
NE A:ARG187 4.0 56.4 1.0
CD A:CD12 4.4 0.0 1.0
CB A:CYS286 4.5 61.4 1.0
CG A:GLU288 4.6 55.6 1.0
CD A:ARG187 4.6 54.7 1.0
CZ A:ARG187 4.9 57.9 1.0
NH2 A:ARG187 5.0 58.0 1.0
CG1 A:ILE287 5.0 47.7 1.0

Cadmium binding site 6 out of 18 in 3pk1

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Cadmium binding site 6 out of 18 in the Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd14

b:0.4
occ:1.00
OE1 A:GLU240 2.6 72.4 1.0
OE2 A:GLU240 2.9 72.4 1.0
CD A:GLU240 3.1 71.6 1.0
CB A:CYS286 3.2 61.4 1.0
CD A:CD12 3.4 0.0 1.0
N A:CYS286 3.6 62.1 1.0
CA A:CYS286 4.0 61.4 1.0
CD A:CD17 4.3 0.8 1.0
SG A:CYS286 4.5 83.6 1.0
C A:SER285 4.5 63.1 1.0
CG A:GLU240 4.6 69.7 1.0
CA A:SER285 4.8 63.5 1.0
C A:CYS286 4.9 60.6 1.0

Cadmium binding site 7 out of 18 in 3pk1

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Cadmium binding site 7 out of 18 in the Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd17

b:0.8
occ:1.00
OD1 A:ASP241 2.5 73.2 1.0
OE2 A:GLU240 3.0 72.4 1.0
CD A:GLU240 3.3 71.6 1.0
CG A:ASP241 3.7 71.2 1.0
CG A:GLU240 3.7 69.7 1.0
OE1 A:GLU240 4.0 72.4 1.0
OD2 A:ASP241 4.1 72.0 1.0
CD A:CD14 4.3 0.4 1.0
CB A:ASP241 4.9 67.8 1.0

Cadmium binding site 8 out of 18 in 3pk1

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Cadmium binding site 8 out of 18 in the Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd18

b:94.9
occ:1.00
OE2 A:GLU180 2.5 60.2 1.0
OE1 A:GLU180 2.9 58.9 1.0
CD A:GLU180 3.1 58.9 1.0
CG A:GLU180 4.5 57.0 1.0

Cadmium binding site 9 out of 18 in 3pk1

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Cadmium binding site 9 out of 18 in the Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd7

b:88.1
occ:0.50
SG B:CYS62 2.8 98.7 1.0
CB B:CYS62 3.6 43.2 1.0
CD B:CD8 3.6 75.8 0.5
CG A:MET231 4.0 46.9 1.0
CD2 B:LEU59 4.6 59.5 1.0
SD A:MET231 4.6 51.8 1.0
O B:LYS58 4.6 64.8 1.0
CE A:MET231 4.8 43.3 1.0
NZ A:LYS234 4.9 56.7 1.0
O A:ALA227 4.9 41.8 1.0
CA B:CYS62 5.0 44.8 1.0

Cadmium binding site 10 out of 18 in 3pk1

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Cadmium binding site 10 out of 18 in the Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd8

b:75.8
occ:0.50
O B:HOH18 2.4 39.1 1.0
SG B:CYS62 2.5 98.7 1.0
CD B:CD7 3.6 88.1 0.5
CB B:CYS62 3.8 43.2 1.0
CA B:CYS62 4.2 44.8 1.0
NH1 B:ARG65 5.0 44.5 0.0
CD B:ARG65 5.0 44.3 0.0
O B:CYS62 5.0 44.1 1.0

Cadmium binding site 11 out of 18 in 3pk1

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Cadmium binding site 11 out of 18 in the Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 11 of Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd3

b:50.3
occ:1.00
NE2 C:HIS224 2.2 44.4 1.0
O C:HOH22 2.5 17.9 1.0
OE1 D:GLU69 2.5 43.0 1.0
OE2 D:GLU69 2.7 37.0 1.0
CD D:GLU69 2.9 40.3 1.0
CE1 C:HIS224 3.0 44.3 1.0
CD2 C:HIS224 3.3 42.8 1.0
CB C:ASN223 4.2 44.2 1.0
ND1 C:HIS224 4.2 43.7 1.0
ND2 C:ASN223 4.3 48.0 1.0
CG C:HIS224 4.4 42.7 1.0
CG D:GLU69 4.4 39.0 1.0
CG C:ASN223 4.5 46.2 1.0
CG2 D:ILE66 4.6 36.8 1.0
CB D:GLU69 5.0 39.5 1.0

Cadmium binding site 12 out of 18 in 3pk1

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Cadmium binding site 12 out of 18 in the Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 12 of Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd4

b:0.6
occ:1.00
NE2 C:HIS252 2.7 71.8 1.0
O C:HOH34 2.9 46.8 1.0
CD2 C:HIS252 3.6 70.4 1.0
CE1 C:HIS252 3.6 70.6 1.0
ND1 C:HIS252 4.8 68.9 1.0
CG C:HIS252 4.8 67.5 1.0

Cadmium binding site 13 out of 18 in 3pk1

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Cadmium binding site 13 out of 18 in the Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 13 of Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd10

b:1.0
occ:1.00
CD C:CD15 2.9 0.3 1.0
CD C:CD11 3.2 0.7 1.0
OE1 C:GLU240 3.9 72.4 1.0
CB C:CYS286 3.9 61.5 1.0
CD C:CD16 4.3 0.2 1.0
CD C:GLU240 4.6 71.6 1.0
CD C:PRO289 4.6 49.5 1.0
OE2 C:GLU240 4.7 72.4 1.0
OE1 C:GLU288 4.8 56.5 0.0
SG C:CYS286 4.8 83.7 1.0

Cadmium binding site 14 out of 18 in 3pk1

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Cadmium binding site 14 out of 18 in the Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 14 of Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd11

b:0.7
occ:1.00
SG C:CYS286 2.6 83.7 1.0
OE1 C:GLU288 2.8 56.5 0.0
CB C:CYS286 3.0 61.5 1.0
CD C:CD10 3.2 1.0 1.0
CD C:GLU288 3.8 56.4 0.0
CG C:GLU288 4.5 55.7 1.0
CD C:CD15 4.5 0.3 1.0
CA C:CYS286 4.5 61.5 1.0
CB C:GLU288 4.7 54.9 1.0
OE2 C:GLU288 4.7 57.0 0.0

Cadmium binding site 15 out of 18 in 3pk1

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Cadmium binding site 15 out of 18 in the Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 15 of Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd15

b:0.3
occ:1.00
OE2 C:GLU240 2.6 72.4 1.0
OE1 C:GLU240 2.7 72.4 1.0
CD C:CD10 2.9 1.0 1.0
CD C:GLU240 3.0 71.6 1.0
N C:CYS286 3.7 62.0 1.0
CB C:CYS286 3.7 61.5 1.0
CD C:CD16 4.0 0.2 1.0
CA C:CYS286 4.4 61.5 1.0
C C:SER285 4.4 63.1 1.0
CA C:SER285 4.5 63.5 1.0
CD C:CD11 4.5 0.7 1.0
CG C:GLU240 4.5 69.8 1.0
O C:GLU284 4.8 64.5 1.0

Cadmium binding site 16 out of 18 in 3pk1

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Cadmium binding site 16 out of 18 in the Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 16 of Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd16

b:0.2
occ:1.00
OD1 C:ASP241 2.5 73.2 1.0
OE2 C:GLU240 3.0 72.4 1.0
CD C:GLU240 3.2 71.6 1.0
CG C:ASP241 3.6 71.2 1.0
OE1 C:GLU240 3.6 72.4 1.0
CG C:GLU240 3.7 69.8 1.0
OD2 C:ASP241 3.9 72.0 1.0
CD C:CD15 4.0 0.3 1.0
CD C:CD10 4.3 1.0 1.0
CG C:PRO289 4.9 48.6 1.0
CB C:ASP241 4.9 67.8 1.0

Cadmium binding site 17 out of 18 in 3pk1

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Cadmium binding site 17 out of 18 in the Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 17 of Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd6

b:71.9
occ:0.50
SG D:CYS62 2.7 98.7 1.0
CD D:CD9 3.9 94.0 0.5
CB D:CYS62 4.0 43.1 1.0
CA D:CYS62 4.2 44.7 1.0
CD D:ARG65 4.7 44.3 0.0
NH1 D:ARG65 4.7 44.5 0.0
O D:CYS62 4.9 44.1 1.0

Cadmium binding site 18 out of 18 in 3pk1

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Cadmium binding site 18 out of 18 in the Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 18 of Crystal Structure of Mcl-1 in Complex with the BAXBH3 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd9

b:94.0
occ:0.50
SG D:CYS62 2.9 98.7 1.0
CB D:CYS62 3.5 43.1 1.0
CD D:CD6 3.9 71.9 0.5
O D:LYS58 4.2 64.8 1.0
CG C:MET231 4.4 46.9 1.0
CD2 D:LEU59 4.5 59.4 1.0
CA D:CYS62 4.8 44.7 1.0
NZ C:LYS234 4.9 56.7 0.0
SD C:MET231 5.0 52.0 1.0

Reference:

P.E.Czabotar, E.F.Lee, G.V.Thompson, A.Z.Wardak, W.D.Fairlie, P.M.Colman. Mutation to Bax Beyond the BH3 Domain Disrupts Interactions with Pro-Survival Proteins and Promotes Apoptosis J.Biol.Chem. V. 286 7123 2011.
ISSN: ISSN 0021-9258
PubMed: 21199865
DOI: 10.1074/JBC.M110.161281
Page generated: Fri Aug 28 13:54:46 2020
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