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Cadmium in PDB 2r1f: Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli

Protein crystallography data

The structure of Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli, PDB code: 2r1f was solved by Y.Patskovsky, U.A.Ramagopal, R.Toro, A.J.Meyer, M.Rutter, C.Lau, M.Maletic, D.Smith, T.Gheyi, S.Wasserman, J.M.Sauder, S.K.Burley, S.C.Almo, New Yorksgx Research Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.21
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 92.783, 92.783, 181.931, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 25.7

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli (pdb code 2r1f). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 15 binding sites of Cadmium where determined in the Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli, PDB code: 2r1f:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12; 13; 14; 15;

Cadmium binding site 1 out of 15 in 2r1f

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Cadmium binding site 1 out of 15 in the Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli


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A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1

b:51.3
occ:1.00
OE2 A:GLU116 2.2 55.7 1.0
OD2 A:ASP290 2.3 40.2 1.0
OE1 A:GLU216 2.5 26.2 1.0
OD1 A:ASP290 2.5 32.2 1.0
O A:HOH436 2.6 38.9 1.0
OE2 A:GLU216 2.6 26.7 1.0
CG A:ASP290 2.7 41.5 1.0
CD A:GLU216 2.9 40.9 1.0
O A:HOH361 3.1 62.8 1.0
CD A:GLU116 3.4 44.9 1.0
OG A:SER291 3.9 50.7 1.0
CG A:GLU116 4.0 37.5 1.0
CB A:ASP290 4.3 36.6 1.0
O A:HOH380 4.3 53.7 1.0
O A:HOH442 4.4 48.6 1.0
O A:HOH402 4.4 55.3 1.0
CG A:GLU216 4.4 30.7 1.0
OE1 A:GLU116 4.4 48.2 1.0
CA A:GLY288 4.5 37.6 1.0
N A:GLY288 4.6 36.3 1.0
CB A:GLU116 4.8 40.6 1.0
N A:SER291 4.8 39.8 1.0
O A:HOH363 4.9 33.4 1.0
CB A:SER291 5.0 41.7 1.0

Cadmium binding site 2 out of 15 in 2r1f

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Cadmium binding site 2 out of 15 in the Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli


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A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd341

b:74.4
occ:0.50
O A:HOH460 2.2 49.5 1.0
ND1 A:HIS297 2.6 60.9 1.0
CE1 A:HIS297 3.3 63.3 1.0
CG A:HIS297 3.6 53.9 1.0
CB A:HIS297 4.0 49.3 1.0
O A:HOH407 4.2 70.3 1.0
CB A:ALA197 4.4 57.9 1.0
O A:HOH437 4.4 65.3 1.0
NE2 A:HIS297 4.5 59.6 1.0
CD2 A:HIS297 4.6 60.3 1.0
CA A:HIS297 4.7 48.6 1.0
CA A:ALA197 4.8 61.0 1.0

Cadmium binding site 3 out of 15 in 2r1f

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Cadmium binding site 3 out of 15 in the Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli


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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 Predicted Aminodeoxychorismate Lyase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd342

b:61.9
occ:1.00
NE2 A:HIS314 2.2 41.5 1.0
O A:HOH465 2.3 79.7 1.0
O A:HOH462 2.3 68.9 1.0
O A:HOH461 2.4 56.5 1.0
O A:HOH450 2.4 37.0 1.0
O A:HOH451 2.6 62.2 1.0
CE1 A:HIS314 3.2 47.0 1.0
CD2 A:HIS314 3.3 45.5 1.0
O A:HOH452 4.0 63.4 1.0
ND1 A:HIS314 4.3 52.2 1.0
O A:HOH453 4.3 61.1 1.0
CG A:HIS314 4.4 44.6 1.0
O A:HOH374 4.4 43.4 1.0
O A:HOH376 4.8 67.2 1.0
O A:GLU218 4.8 66.7 1.0
OE2 A:GLU218 4.9 75.0 1.0
CB A:ALA308 4.9 47.7 1.0

Cadmium binding site 4 out of 15 in 2r1f

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Cadmium binding site 4 out of 15 in the Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli


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A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd343

b:60.2
occ:0.50
O A:HOH489 2.2 56.7 1.0
O A:HOH479 2.4 51.0 1.0
O A:HOH418 2.5 52.2 1.0
OE1 A:GLU150 2.5 80.2 1.0
O A:HOH438 2.5 56.9 1.0
CD A:GLU150 3.5 79.9 1.0
OE2 A:GLU150 3.9 83.3 1.0
NZ A:LYS179 4.8 75.7 1.0
CG A:GLU150 4.8 76.7 1.0

Cadmium binding site 5 out of 15 in 2r1f

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Cadmium binding site 5 out of 15 in the Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli


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A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd344

b:72.5
occ:1.00
O A:HOH445 2.2 79.1 1.0
O A:HOH463 2.3 50.1 1.0
O A:HOH444 2.4 68.9 1.0
NE2 A:HIS135 2.4 52.9 1.0
CE1 A:HIS135 3.2 55.6 1.0
CD2 A:HIS135 3.5 56.0 1.0
O A:ALA130 3.9 66.1 1.0
O A:ILE133 4.0 60.3 1.0
O A:HOH395 4.3 56.5 1.0
O A:ARG128 4.4 62.2 1.0
ND1 A:HIS135 4.4 56.8 1.0
CG A:HIS135 4.5 57.9 1.0
N A:ILE133 4.9 58.9 1.0
C A:ALA130 5.0 66.8 1.0

Cadmium binding site 6 out of 15 in 2r1f

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Cadmium binding site 6 out of 15 in the Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd345

b:78.8
occ:0.50
O A:HOH413 2.2 48.9 1.0
OD2 A:ASP164 2.3 54.8 1.0
O A:HOH464 2.5 53.0 1.0
CG A:ASP164 3.0 51.9 1.0
OD1 A:ASP164 3.0 51.2 1.0
NZ A:LYS184 4.4 66.6 1.0
O A:HOH471 4.4 57.8 1.0
O A:HOH466 4.4 57.3 1.0
CB A:ASP164 4.5 49.7 1.0
NE1 A:TRP162 4.7 44.8 1.0
O A:HOH382 4.8 55.2 1.0

Cadmium binding site 7 out of 15 in 2r1f

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Cadmium binding site 7 out of 15 in the Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd346

b:0.3
occ:1.00
OE2 A:GLU103 2.3 98.3 1.0
NE2 A:HIS81 2.4 92.7 1.0
CD A:GLU103 3.1 94.9 1.0
CE1 A:HIS81 3.2 97.0 1.0
CD2 A:HIS81 3.3 95.9 1.0
OE1 A:GLU103 3.3 94.8 1.0
ND1 A:HIS81 4.2 99.1 1.0
CG A:HIS81 4.3 98.4 1.0
CG A:GLU103 4.5 87.2 1.0

Cadmium binding site 8 out of 15 in 2r1f

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Cadmium binding site 8 out of 15 in the Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd347

b:79.4
occ:0.50
O2 A:SO4349 2.3 56.0 0.5
NE2 A:HIS182 2.4 50.1 1.0
OE1 A:GLU152 3.1 96.5 1.0
CD2 A:HIS182 3.3 51.2 1.0
CE1 A:HIS182 3.4 44.8 1.0
S A:SO4349 3.4 64.0 0.5
O3 A:SO4349 3.7 59.1 0.5
O1 A:SO4349 3.8 61.2 0.5
CD2 A:LEU151 3.9 64.2 1.0
CD A:GLU152 4.0 99.2 1.0
CG2 A:VAL186 4.2 40.5 1.0
OE2 A:GLU152 4.2 0.6 1.0
CG A:HIS182 4.5 49.1 1.0
ND1 A:HIS182 4.5 50.8 1.0
O4 A:SO4349 4.6 51.6 0.5
CA A:LEU151 4.8 72.3 1.0
CB A:LEU151 4.8 69.6 1.0

Cadmium binding site 9 out of 15 in 2r1f

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Cadmium binding site 9 out of 15 in the Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd348

b:0.7
occ:0.25
OE2 A:GLU155 2.2 73.5 0.5
CD A:GLU155 3.1 75.6 0.5
OE1 A:GLU155 3.3 76.7 0.5
CG A:GLU155 4.5 74.5 0.5
CG A:GLU155 4.7 66.6 0.5
OD1 A:ASN153 4.8 73.5 0.5

Cadmium binding site 10 out of 15 in 2r1f

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Cadmium binding site 10 out of 15 in the Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1

b:50.8
occ:1.00
OE2 B:GLU216 2.3 34.1 1.0
OE1 B:GLU216 2.3 31.5 1.0
OE2 B:GLU116 2.3 66.0 1.0
OD2 B:ASP290 2.3 23.0 1.0
OD1 B:ASP290 2.5 28.3 1.0
O B:HOH411 2.5 30.2 1.0
CD B:GLU216 2.6 41.5 1.0
CG B:ASP290 2.8 37.9 1.0
CD B:GLU116 3.5 55.2 1.0
OG B:SER291 3.8 49.3 1.0
O B:HOH394 3.8 66.1 1.0
CG B:GLU116 4.0 39.8 1.0
CG B:GLU216 4.1 42.9 1.0
CB B:ASP290 4.3 28.5 1.0
CA B:GLY288 4.3 47.7 1.0
O B:HOH377 4.4 49.1 1.0
N B:GLY288 4.4 51.0 1.0
O B:HOH352 4.5 66.7 1.0
OE1 B:GLU116 4.5 63.6 1.0
CB B:GLU116 4.7 39.9 1.0
O B:HOH369 4.7 36.7 1.0
CB B:GLU216 4.8 44.3 1.0
N B:SER291 4.9 36.5 1.0
CB B:SER291 5.0 39.5 1.0

Cadmium binding site 11 out of 15 in 2r1f

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Cadmium binding site 11 out of 15 in the Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 11 of Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd341

b:84.9
occ:1.00
O B:HOH415 2.2 42.0 1.0
NE2 B:HIS135 2.5 82.2 1.0
CE1 B:HIS135 3.3 80.0 1.0
CD2 B:HIS135 3.5 82.8 1.0
O B:ARG128 4.0 73.8 1.0
O B:ALA130 4.1 73.8 1.0
O B:ILE133 4.2 71.4 1.0
ND1 B:HIS135 4.5 80.9 1.0
CG B:HIS135 4.6 80.1 1.0
N B:ILE133 5.0 67.8 1.0

Cadmium binding site 12 out of 15 in 2r1f

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Cadmium binding site 12 out of 15 in the Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli


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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 Predicted Aminodeoxychorismate Lyase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd342

b:69.9
occ:1.00
O B:HOH431 2.3 89.4 1.0
O B:HOH426 2.3 50.3 1.0
O B:HOH424 2.3 58.4 1.0
O B:HOH440 2.3 64.2 1.0
NE2 B:HIS314 2.4 51.6 1.0
O B:HOH425 2.9 56.9 1.0
CE1 B:HIS314 3.1 52.0 1.0
CD2 B:HIS314 3.5 51.8 1.0
O B:THR219 3.8 83.1 1.0
O B:HOH443 4.3 58.9 1.0
ND1 B:HIS314 4.3 55.3 1.0
CG B:HIS314 4.5 47.5 1.0
OE2 B:GLU218 4.6 75.7 1.0
C B:THR219 4.9 81.7 1.0
CB B:ALA308 5.0 58.9 1.0

Cadmium binding site 13 out of 15 in 2r1f

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Cadmium binding site 13 out of 15 in the Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 13 of Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd343

b:78.5
occ:0.50
OD2 B:ASP164 2.2 54.7 1.0
O B:HOH429 2.4 57.3 1.0
OD1 B:ASP164 2.8 53.3 1.0
CG B:ASP164 2.9 53.8 1.0
O B:HOH395 3.1 63.6 1.0
O B:HOH372 4.4 55.7 1.0
CB B:ASP164 4.4 49.6 1.0
NZ B:LYS184 4.7 73.9 1.0
NE1 B:TRP162 4.9 42.7 1.0

Cadmium binding site 14 out of 15 in 2r1f

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Cadmium binding site 14 out of 15 in the Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 14 of Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd344

b:88.9
occ:0.50
ND1 B:HIS297 2.3 66.0 1.0
CE1 B:HIS297 3.1 70.3 1.0
CG B:HIS297 3.3 65.6 1.0
CB B:HIS297 3.7 64.1 1.0
NE2 B:HIS297 4.3 71.1 1.0
CB B:ALA197 4.3 62.8 1.0
CD2 B:HIS297 4.4 68.7 1.0
O B:HOH404 4.5 58.1 1.0
CA B:HIS297 4.6 60.1 1.0
CA B:ALA197 5.0 66.1 1.0

Cadmium binding site 15 out of 15 in 2r1f

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Cadmium binding site 15 out of 15 in the Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli


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 Predicted Aminodeoxychorismate Lyase From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd345

b:90.4
occ:0.50
NE2 B:HIS182 2.4 68.3 1.0
O B:HOH434 2.6 62.9 1.0
O B:HOH416 2.9 60.2 1.0
OE1 B:GLU152 2.9 0.8 1.0
CE1 B:HIS182 3.3 68.9 1.0
CD2 B:HIS182 3.4 65.7 1.0
CD2 B:LEU151 3.8 81.9 1.0
CD B:GLU152 3.8 0.6 1.0
OE2 B:GLU152 3.9 0.4 1.0
O B:HOH376 4.1 68.0 1.0
CG2 B:VAL186 4.2 49.4 1.0
ND1 B:HIS182 4.4 64.2 1.0
CG B:HIS182 4.5 62.9 1.0
CA B:LEU151 4.9 91.4 1.0
N B:GLU152 4.9 93.0 1.0

Reference:

Y.Patskovsky, U.A.Ramagopal, R.Toro, A.J.Meyer, M.Rutter, C.Lau, M.Maletic, T.Gheyi, D.Smith, S.Wasserman, J.M.Sauder, S.K.Burley, S.C.Almo. Crystal Structure of Predicted Aminodeoxychorismate Lyase From Escherichia Coli. To Be Published.
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