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Cadmium in PDB 3oeo: The Crystal Structure E. Coli Spy

Protein crystallography data

The structure of The Crystal Structure E. Coli Spy, PDB code: 3oeo was solved by E.Kwon, D.Y.Kim, C.A.Gross, J.D.Gross, K.K.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.70
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 69.195, 69.195, 126.347, 90.00, 90.00, 120.00
R / Rfree (%) 25.2 / 30

Cadmium Binding Sites:

The binding sites of Cadmium atom in the The Crystal Structure E. Coli Spy (pdb code 3oeo). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 22 binding sites of Cadmium where determined in the The Crystal Structure E. Coli Spy, PDB code: 3oeo:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12; 13; 14; 15; 16; 17; 18; 19; 20; 21; 22;

Cadmium binding site 1 out of 22 in 3oeo

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Cadmium binding site 1 out of 22 in the The Crystal Structure E. Coli Spy


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of The Crystal Structure E. Coli Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd5

b:68.4
occ:1.00
O A:HOH167 2.1 85.7 1.0
O A:HOH180 2.1 16.0 1.0
OD1 A:ASP59 2.7 0.1 1.0
OD2 A:ASP59 2.8 0.9 1.0
CG A:ASP59 3.1 0.9 1.0
O A:HOH168 3.5 20.9 1.0
O A:HOH164 4.0 41.5 1.0
CB A:ASP59 4.6 0.1 1.0
NZ A:LYS62 4.9 0.3 1.0

Cadmium binding site 2 out of 22 in 3oeo

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Cadmium binding site 2 out of 22 in the The Crystal Structure E. Coli Spy


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of The Crystal Structure E. Coli Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd14

b:0.2
occ:1.00
O C:HOH179 2.1 61.4 1.0
O A:HOH181 2.6 43.7 1.0
OE1 A:GLN123 4.5 77.7 1.0
NE2 A:GLN123 4.7 78.7 1.0

Cadmium binding site 3 out of 22 in 3oeo

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Cadmium binding site 3 out of 22 in the The Crystal Structure E. Coli Spy


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of The Crystal Structure E. Coli Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd18

b:76.5
occ:1.00
O C:HOH185 2.4 35.0 1.0
OD1 A:ASP89 2.5 85.4 1.0
O C:HOH183 2.6 36.4 1.0
CG A:ASP89 3.3 85.0 1.0
CD C:CD19 3.6 69.5 1.0
OD2 A:ASP89 3.7 85.5 1.0
CD C:CD20 4.0 99.7 1.0
CG A:ARG85 4.3 0.3 1.0
CB A:ASP89 4.4 82.5 1.0
CD A:ARG85 4.5 0.9 1.0
CA A:ASP89 4.7 81.6 1.0

Cadmium binding site 4 out of 22 in 3oeo

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Cadmium binding site 4 out of 22 in the The Crystal Structure E. Coli Spy


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of The Crystal Structure E. Coli Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd22

b:94.7
occ:1.00
O C:HOH187 2.7 63.8 1.0
CD C:CD21 3.0 0.6 1.0
OE1 A:GLU143 3.2 97.1 1.0
CD A:CD23 3.2 0.2 1.0
OE2 A:GLU143 3.6 92.9 1.0
O A:HOH188 3.6 11.7 1.0
O C:HOH186 3.7 30.6 1.0
NE2 C:HIS88 3.8 97.7 1.0
CD A:GLU143 3.8 95.5 1.0
CE1 C:HIS88 4.1 97.7 1.0
CG C:ARG85 4.2 0.3 1.0
CD C:ARG85 4.6 0.7 1.0
OD1 C:ASP89 4.6 90.9 1.0
CB C:ARG85 4.6 99.0 1.0
OD2 C:ASP89 4.9 91.2 1.0

Cadmium binding site 5 out of 22 in 3oeo

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Cadmium binding site 5 out of 22 in the The Crystal Structure E. Coli Spy


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of The Crystal Structure E. Coli Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd23

b:0.2
occ:1.00
O A:HOH188 2.2 11.7 1.0
O C:HOH186 2.8 30.6 1.0
CD C:CD21 3.2 0.6 1.0
CD A:CD22 3.2 94.7 1.0
OE2 A:GLU143 3.7 92.9 1.0
OE1 A:GLU143 4.1 97.1 1.0
O C:HOH187 4.2 63.8 1.0
CD A:GLU143 4.3 95.5 1.0

Cadmium binding site 6 out of 22 in 3oeo

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Cadmium binding site 6 out of 22 in the The Crystal Structure E. Coli Spy


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of The Crystal Structure E. Coli Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd162

b:91.3
occ:1.00
OE1 A:GLU82 2.6 0.4 1.0
OE2 A:GLU82 2.6 0.8 1.0
O A:HOH182 2.7 18.0 1.0
CD A:GLU82 2.7 0.8 1.0
CG A:GLU82 3.9 0.2 1.0
O A:HOH178 4.8 2.0 1.0
NZ A:LYS107 4.8 79.1 1.0

Cadmium binding site 7 out of 22 in 3oeo

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Cadmium binding site 7 out of 22 in the The Crystal Structure E. Coli Spy


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of The Crystal Structure E. Coli Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd7

b:51.1
occ:1.00
O B:HOH178 2.0 9.3 1.0
OD2 B:ASP59 2.8 0.3 1.0
OD1 B:ASP59 3.0 0.6 1.0
CG B:ASP59 3.2 0.2 1.0
O B:HOH165 3.4 33.0 1.0
O B:HOH166 4.7 49.8 1.0
CB B:ASP59 4.7 0.4 1.0
NZ B:LYS62 4.8 0.4 1.0

Cadmium binding site 8 out of 22 in 3oeo

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Cadmium binding site 8 out of 22 in the The Crystal Structure E. Coli Spy


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of The Crystal Structure E. Coli Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd8

b:46.4
occ:1.00
OD2 B:ASP97 2.0 69.4 1.0
O B:HOH179 2.5 15.3 1.0
CG B:ASP97 3.0 69.7 1.0
O B:HOH3 3.2 3.4 1.0
CG1 B:VAL99 3.4 74.1 1.0
OD1 B:ASP97 3.5 69.5 1.0
CB B:ASP97 4.1 68.7 1.0
O C:HOH189 4.5 2.0 1.0
O C:HOH163 4.7 2.0 1.0
CD B:LYS100 4.7 74.7 1.0
CD C:CD162 4.8 42.7 1.0
CE B:LYS100 4.8 77.2 1.0
CB B:VAL99 4.9 74.0 1.0
NZ B:LYS100 4.9 78.9 1.0

Cadmium binding site 9 out of 22 in 3oeo

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Cadmium binding site 9 out of 22 in the The Crystal Structure E. Coli Spy


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of The Crystal Structure E. Coli Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd12

b:0.8
occ:1.00
O B:HOH173 4.4 36.5 1.0
O B:HOH180 4.5 69.0 1.0
O D:HOH177 4.5 45.1 1.0
ND1 B:HIS119 4.6 57.2 1.0

Cadmium binding site 10 out of 22 in 3oeo

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Cadmium binding site 10 out of 22 in the The Crystal Structure E. Coli Spy


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of The Crystal Structure E. Coli Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd15

b:0.2
occ:1.00
OE1 B:GLU82 2.6 97.9 1.0
O B:HOH181 2.8 27.0 1.0
CD B:GLU82 3.6 0.5 1.0
OE2 B:GLU82 4.0 0.5 1.0
CG B:GLU82 4.9 99.2 1.0

Cadmium binding site 11 out of 22 in 3oeo

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Cadmium binding site 11 out of 22 in the The Crystal Structure E. Coli Spy


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 11 of The Crystal Structure E. Coli Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd162

b:70.6
occ:1.00
OE1 C:GLU109 2.0 76.0 1.0
OE2 B:GLU109 2.0 83.5 1.0
OE1 A:GLU109 2.3 80.5 1.0
OE1 D:GLU109 2.4 80.4 1.0
CD B:GLU109 2.8 83.0 1.0
CD C:GLU109 2.8 75.0 1.0
O B:HOH182 2.8 36.6 1.0
O C:HOH167 2.9 23.3 1.0
OE2 D:GLU109 2.9 84.0 1.0
OE1 B:GLU109 2.9 82.6 1.0
OE2 C:GLU109 3.0 73.9 1.0
CD D:GLU109 3.0 81.1 1.0
CD A:GLU109 3.4 80.7 1.0
OE2 A:GLU109 3.9 83.4 1.0
NZ C:LYS113 4.2 77.5 1.0
NZ B:LYS113 4.2 80.4 1.0
CE C:LYS113 4.2 78.9 1.0
CG B:GLU109 4.3 81.4 1.0
CG C:GLU109 4.3 74.1 1.0
CG D:GLU109 4.4 79.3 1.0
CG A:GLU109 4.7 77.5 1.0
CB A:GLU109 4.8 74.4 1.0
CB D:GLU109 5.0 76.5 1.0

Cadmium binding site 12 out of 22 in 3oeo

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Cadmium binding site 12 out of 22 in the The Crystal Structure E. Coli Spy


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 12 of The Crystal Structure E. Coli Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd9

b:78.0
occ:1.00
O C:HOH175 1.9 25.7 1.0
OD1 C:ASP59 2.1 0.6 1.0
OD2 C:ASP59 2.5 0.1 1.0
CG C:ASP59 2.7 0.6 1.0
O C:HOH180 2.7 30.3 1.0
O C:HOH172 3.1 9.9 1.0
CB C:ASP59 4.2 0.1 1.0
CA C:ASP59 4.8 0.2 1.0

Cadmium binding site 13 out of 22 in 3oeo

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Cadmium binding site 13 out of 22 in the The Crystal Structure E. Coli Spy


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 13 of The Crystal Structure E. Coli Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd11

b:0.8
occ:1.00
NE2 C:HIS119 2.2 73.4 1.0
O C:HOH181 2.7 48.0 1.0
CD2 C:HIS119 2.8 72.3 1.0
CE1 C:HIS119 3.3 74.1 1.0
OE1 C:GLN123 3.9 77.5 1.0
CG C:HIS119 4.0 72.3 1.0
ND1 C:HIS119 4.2 74.0 1.0
CD C:GLN123 4.8 77.2 1.0
O C:HOH171 4.9 37.8 1.0

Cadmium binding site 14 out of 22 in 3oeo

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Cadmium binding site 14 out of 22 in the The Crystal Structure E. Coli Spy


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 14 of The Crystal Structure E. Coli Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd17

b:87.1
occ:1.00
O C:HOH182 2.0 42.6 1.0
OE1 C:GLU82 3.7 0.5 1.0
CD C:GLU82 3.8 0.5 1.0
OE2 C:GLU82 3.8 0.7 1.0
NZ C:LYS107 3.9 90.6 1.0
CB C:GLU82 4.5 0.6 1.0
CG C:GLU82 4.6 0.7 1.0

Cadmium binding site 15 out of 22 in 3oeo

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Cadmium binding site 15 out of 22 in the The Crystal Structure E. Coli Spy


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 15 of The Crystal Structure E. Coli Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd19

b:69.5
occ:1.00
O C:HOH183 2.2 36.4 1.0
OE2 C:GLU143 2.4 0.1 1.0
O C:HOH184 2.4 17.4 1.0
CD C:CD20 3.1 99.7 1.0
CD C:GLU143 3.1 0.9 1.0
CG A:ARG85 3.3 0.3 1.0
CG C:GLU143 3.6 0.8 1.0
CD A:CD18 3.6 76.5 1.0
O C:HOH185 3.9 35.0 1.0
CD A:ARG85 4.0 0.9 1.0
OE1 C:GLU143 4.1 0.4 1.0
OD1 A:ASP89 4.4 85.4 1.0
CB A:ARG85 4.4 98.3 1.0
ND1 A:HIS88 4.4 92.3 1.0
NE A:ARG85 4.6 0.6 1.0
CA A:ARG85 4.8 95.0 1.0

Cadmium binding site 16 out of 22 in 3oeo

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Cadmium binding site 16 out of 22 in the The Crystal Structure E. Coli Spy


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 16 of The Crystal Structure E. Coli Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd20

b:99.7
occ:1.00
O C:HOH185 2.4 35.0 1.0
CD C:CD19 3.1 69.5 1.0
O C:HOH183 3.1 36.4 1.0
CG C:GLU143 3.5 0.8 1.0
CD A:CD18 4.0 76.5 1.0
CD C:GLU143 4.1 0.9 1.0
OE2 C:GLU143 4.2 0.1 1.0
CB C:GLU143 4.5 0.9 1.0
O C:HOH184 4.6 17.4 1.0
OE1 C:GLU143 4.9 0.4 1.0
ND1 A:HIS88 4.9 92.3 1.0
ND2 C:ASN139 5.0 95.9 1.0

Cadmium binding site 17 out of 22 in 3oeo

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Cadmium binding site 17 out of 22 in the The Crystal Structure E. Coli Spy


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 17 of The Crystal Structure E. Coli Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd21

b:0.6
occ:1.00
OD1 C:ASP89 2.2 90.9 1.0
O C:HOH186 2.4 30.6 1.0
OD2 C:ASP89 2.8 91.2 1.0
CG C:ASP89 2.9 89.8 1.0
CD A:CD22 3.0 94.7 1.0
O C:HOH187 3.1 63.8 1.0
CD A:CD23 3.2 0.2 1.0
O A:HOH188 4.0 11.7 1.0
CE1 C:HIS88 4.3 97.7 1.0
CB C:ASP89 4.4 86.2 1.0
NE2 C:HIS88 4.6 97.7 1.0
O C:ARG85 4.7 93.4 1.0
O C:HOH178 4.7 2.0 1.0

Cadmium binding site 18 out of 22 in 3oeo

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Cadmium binding site 18 out of 22 in the The Crystal Structure E. Coli Spy


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 18 of The Crystal Structure E. Coli Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd162

b:42.7
occ:1.00
OD2 C:ASP97 2.2 61.6 1.0
O C:HOH163 2.6 2.0 1.0
CG C:ASP97 2.9 63.9 1.0
O C:HOH189 2.9 2.0 1.0
OD1 C:ASP97 3.0 63.9 1.0
O B:HOH3 4.1 3.4 1.0
CB C:LYS100 4.2 62.2 1.0
CB C:ASP97 4.4 63.9 1.0
N C:LYS100 4.5 61.7 1.0
CA C:LYS100 4.8 61.8 1.0
CD B:CD8 4.8 46.4 1.0
CE B:LYS100 4.9 77.2 1.0
CG C:LYS100 4.9 63.5 1.0

Cadmium binding site 19 out of 22 in 3oeo

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Cadmium binding site 19 out of 22 in the The Crystal Structure E. Coli Spy


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 19 of The Crystal Structure E. Coli Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd10

b:66.6
occ:1.00
OD2 D:ASP59 2.1 0.6 1.0
O D:HOH184 2.2 16.8 1.0
O D:HOH20 2.3 58.8 1.0
CG D:ASP59 3.0 0.9 1.0
OD1 D:ASP59 3.4 0.5 1.0
O D:HOH166 3.5 28.8 1.0
O D:HOH173 4.1 38.5 1.0
CB D:ASP59 4.2 0.4 1.0

Cadmium binding site 20 out of 22 in 3oeo

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Cadmium binding site 20 out of 22 in the The Crystal Structure E. Coli Spy


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 20 of The Crystal Structure E. Coli Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd13

b:0.9
occ:1.00
NE2 D:HIS119 2.2 69.8 1.0
O D:HOH180 2.5 44.7 1.0
CE1 D:HIS119 2.6 70.2 1.0
O D:HOH164 3.2 46.1 1.0
CD2 D:HIS119 3.4 68.1 1.0
ND1 D:HIS119 3.8 70.4 1.0
NE2 D:GLN123 3.8 69.8 1.0
CG D:HIS119 4.2 68.6 1.0
CD D:GLN123 5.0 70.8 1.0

Cadmium binding site 21 out of 22 in 3oeo

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Cadmium binding site 21 out of 22 in the The Crystal Structure E. Coli Spy


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 21 of The Crystal Structure E. Coli Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd16

b:89.8
occ:1.00
OE1 D:GLU82 2.7 0.8 1.0
O D:HOH181 3.5 12.2 1.0
CB D:GLU82 3.8 0.8 1.0
CD D:GLU82 3.8 0.5 1.0
CG D:GLU82 4.3 0.5 1.0
OE2 D:GLU82 4.8 0.2 1.0

Cadmium binding site 22 out of 22 in 3oeo

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Cadmium binding site 22 out of 22 in the The Crystal Structure E. Coli Spy


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 22 of The Crystal Structure E. Coli Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd162

b:77.5
occ:1.00
OE1 D:GLU110 2.0 95.5 1.0
CD D:GLU110 2.6 93.4 1.0
OE2 D:GLU110 2.7 94.6 1.0
O D:HOH182 2.7 33.4 1.0
O D:HOH179 3.5 26.1 1.0
CG C:GLU110 3.6 82.9 1.0
CG D:GLU110 4.0 89.3 1.0
CD C:GLU110 4.3 82.7 1.0
OE2 C:GLU110 4.4 81.9 1.0
CB C:GLU110 4.8 81.0 1.0
CB D:GLU110 4.9 86.1 1.0

Reference:

E.Kwon, D.Y.Kim, C.A.Gross, J.D.Gross, K.K.Kim. The Crystal Structure Escherichia Coli Spy. Protein Sci. V. 19 2252 2010.
ISSN: ISSN 0961-8368
PubMed: 20799348
DOI: 10.1002/PRO.489
Page generated: Wed Oct 28 10:03:58 2020
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