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Cadmium in PDB 3gbf: Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep)

Protein crystallography data

The structure of Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep), PDB code: 3gbf was solved by H.Zhang, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.92
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 84.974, 94.695, 101.595, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 25.7

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep) (pdb code 3gbf). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 13 binding sites of Cadmium where determined in the Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep), PDB code: 3gbf:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12; 13;

Cadmium binding site 1 out of 13 in 3gbf

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Cadmium binding site 1 out of 13 in the Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep)


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A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd501

b:57.5
occ:1.00
SG A:CYS180 2.4 32.7 1.0
CB A:CYS180 3.3 26.6 1.0
CD A:CD502 3.5 52.8 1.0
CA A:CYS180 4.7 26.2 1.0
CG A:PRO177 4.9 22.9 1.0

Cadmium binding site 2 out of 13 in 3gbf

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Cadmium binding site 2 out of 13 in the Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd502

b:52.8
occ:1.00
SG A:CYS180 2.5 32.7 1.0
O A:HOH672 2.7 41.9 1.0
CD A:CD501 3.5 57.5 1.0
CB A:CYS180 3.7 26.6 1.0
CA A:CYS180 3.8 26.2 1.0
N A:CYS180 4.1 25.3 1.0
O A:HOH652 4.5 30.3 1.0
C A:TYR179 4.5 24.8 1.0
O A:SER178 4.7 22.6 1.0
O A:TYR179 4.8 25.4 1.0

Cadmium binding site 3 out of 13 in 3gbf

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Cadmium binding site 3 out of 13 in the Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd503

b:36.8
occ:1.00
OD2 A:ASP189 2.4 27.2 1.0
CG A:ASP189 3.3 26.7 1.0
OD1 A:ASP189 3.6 29.7 1.0
O A:HOH610 4.3 34.1 1.0
O A:HOH619 4.4 30.6 1.0
CB A:ASP189 4.7 24.6 1.0

Cadmium binding site 4 out of 13 in 3gbf

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Cadmium binding site 4 out of 13 in the Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd504

b:50.1
occ:1.00
O A:HOH531 2.3 30.0 1.0
O A:HOH707 2.3 39.8 1.0
OE2 A:GLU80 2.4 28.6 1.0
OE1 A:GLU80 2.5 26.8 1.0
CD A:GLU80 2.8 25.2 1.0
O A:HOH719 4.1 40.0 1.0
O A:HIS75 4.2 20.3 1.0
CG A:GLU80 4.3 23.9 1.0
N A:SER77 4.3 18.5 1.0
ND1 A:HIS75 4.4 25.1 1.0
CA A:LYS76 4.6 19.1 1.0
CE1 A:HIS75 4.7 24.5 1.0
CB A:SER77 4.8 18.3 1.0
OG A:SER77 4.8 16.2 1.0
O A:HOH563 4.9 24.7 1.0
C A:HIS75 4.9 19.9 1.0
C A:LYS76 5.0 18.7 1.0

Cadmium binding site 5 out of 13 in 3gbf

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Cadmium binding site 5 out of 13 in the Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd505

b:28.3
occ:1.00
O A:HOH705 2.1 20.5 1.0
O A:HOH496 2.2 24.9 1.0
OD2 A:ASP309 2.3 23.1 1.0
OD1 A:ASP309 2.5 25.1 1.0
CG A:ASP309 2.7 23.7 1.0
O A:TRP304 4.1 22.7 1.0
CB A:ASP309 4.2 23.3 1.0
OG1 A:THR306 4.4 20.7 1.0
O A:HOH648 4.4 39.0 1.0
NH1 A:ARG312 4.7 37.9 1.0
N A:THR306 4.7 20.6 1.0
O A:HOH517 4.7 30.8 1.0
NH2 A:ARG312 4.7 37.3 1.0
CG2 A:THR306 4.8 19.8 1.0

Cadmium binding site 6 out of 13 in 3gbf

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Cadmium binding site 6 out of 13 in the Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd506

b:36.6
occ:1.00
ND1 A:HIS94 2.4 22.9 1.0
CE1 A:HIS94 3.3 24.0 1.0
CG A:HIS94 3.5 25.5 1.0
CB A:HIS94 3.8 26.3 1.0
O A:HOH686 4.1 38.1 1.0
NE2 A:HIS94 4.5 23.5 1.0
CD2 A:HIS94 4.6 24.9 1.0
O A:HOH655 4.8 44.5 1.0
CD1 A:LEU116 4.9 23.6 1.0

Cadmium binding site 7 out of 13 in 3gbf

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Cadmium binding site 7 out of 13 in the Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd507

b:26.1
occ:1.00
O A:HOH704 2.1 24.7 1.0
O A:HOH481 2.3 29.6 1.0
ND1 A:HIS10 2.4 27.5 1.0
O A:HOH561 2.5 40.5 1.0
CE1 A:HIS10 3.4 26.2 1.0
CG A:HIS10 3.4 26.2 1.0
CB A:HIS10 3.6 26.1 1.0
CA A:HIS10 3.8 25.8 1.0
O A:HOH649 4.2 32.4 1.0
ND2 A:ASN13 4.3 26.3 1.0
O A:HIS10 4.3 24.9 1.0
O A:HOH568 4.5 31.6 1.0
C A:HIS10 4.5 25.6 1.0
NE2 A:HIS10 4.5 25.8 1.0
CD2 A:HIS10 4.5 27.1 1.0
N A:HIS10 4.9 25.4 1.0

Cadmium binding site 8 out of 13 in 3gbf

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Cadmium binding site 8 out of 13 in the Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd508

b:26.4
occ:1.00
OD2 A:ASP142 2.1 20.9 1.0
ND1 A:HIS160 2.3 23.5 1.0
O A:HOH451 2.4 25.2 1.0
NE2 A:HIS163 2.5 23.9 1.0
O A:HOH464 2.5 23.5 1.0
OD1 A:ASP142 2.6 23.2 1.0
CG A:ASP142 2.7 21.6 1.0
CD2 A:HIS163 3.1 23.9 1.0
CE1 A:HIS160 3.2 22.9 1.0
CG A:HIS160 3.4 21.9 1.0
CE1 A:HIS163 3.6 24.4 1.0
CB A:HIS160 3.7 21.8 1.0
O A:ALA161 4.0 20.6 1.0
CB A:ASP142 4.2 20.9 1.0
NE2 A:HIS160 4.3 23.4 1.0
O A:HOH527 4.4 23.5 1.0
CA A:HIS160 4.4 21.2 1.0
CG A:HIS163 4.4 24.7 1.0
CD2 A:HIS160 4.4 21.7 1.0
O A:HOH478 4.5 28.7 1.0
N A:ALA161 4.6 21.3 1.0
ND1 A:HIS163 4.6 22.4 1.0
O A:HOH551 4.9 30.2 1.0
C A:HIS160 5.0 21.4 1.0

Cadmium binding site 9 out of 13 in 3gbf

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Cadmium binding site 9 out of 13 in the Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd509

b:70.4
occ:1.00
O A:HOH519 2.6 42.5 1.0
OD2 A:ASP66 2.6 41.2 1.0
OD1 A:ASP66 2.7 43.4 1.0
CG A:ASP66 3.0 42.3 1.0
CB A:ASP66 4.5 41.9 1.0
CD A:ARG107 4.5 34.5 1.0
CB A:HIS68 4.8 40.4 1.0
NH1 A:ARG107 4.8 39.9 1.0
N A:HIS68 4.9 40.9 1.0

Cadmium binding site 10 out of 13 in 3gbf

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Cadmium binding site 10 out of 13 in the Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd510

b:65.7
occ:1.00
O A:HOH698 2.2 29.3 1.0
NE2 A:HIS75 2.4 24.5 1.0
CE1 A:HIS75 3.0 24.5 1.0
CD2 A:HIS75 3.7 24.3 1.0
ND1 A:HIS75 4.3 25.1 1.0
O A:HOH542 4.6 24.4 1.0
CG A:HIS75 4.6 21.8 1.0
CH2 A:TRP369 5.0 24.2 1.0

Cadmium binding site 11 out of 13 in 3gbf

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Cadmium binding site 11 out of 13 in the Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 11 of Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd511

b:68.0
occ:1.00
CE1 A:HIS410 2.4 24.5 1.0
O A:HOH717 2.4 35.7 1.0
ND1 A:HIS410 3.3 25.3 1.0
NE2 A:HIS410 3.4 24.9 1.0
CG A:HIS410 4.5 22.4 1.0
CD2 A:HIS410 4.5 23.2 1.0
O A:HOH706 4.7 44.1 1.0

Cadmium binding site 12 out of 13 in 3gbf

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Cadmium binding site 12 out of 13 in the Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 12 of Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd512

b:77.8
occ:1.00
ND1 A:HIS330 1.8 19.9 1.0
OD1 A:ASP294 2.4 39.2 1.0
CE1 A:HIS330 2.7 2.0 1.0
CG A:HIS330 3.0 18.7 1.0
CG A:ASP294 3.0 40.0 1.0
CB A:HIS330 3.5 18.2 1.0
NZ A:LYS302 3.5 37.5 1.0
CB A:ASP294 3.5 38.6 1.0
O A:ASP294 3.7 40.2 1.0
OE1 A:GLN296 3.8 49.8 1.0
OD2 A:ASP294 3.8 40.3 1.0
O A:ASP295 3.8 44.5 1.0
NE2 A:HIS330 3.8 21.7 1.0
CD2 A:HIS330 4.0 17.5 1.0
N A:HIS330 4.0 18.1 1.0
NE2 A:GLN296 4.1 48.6 1.0
O A:HOH578 4.1 41.2 1.0
CD A:GLN296 4.1 48.6 1.0
C A:ASP294 4.1 39.9 1.0
CA A:HIS330 4.3 18.1 1.0
CA A:ASP294 4.3 38.5 1.0
C A:ASP295 4.7 44.2 1.0
N A:ASP294 4.8 36.0 1.0
CE A:LYS302 4.9 37.1 1.0
C A:ALA329 4.9 18.4 1.0

Cadmium binding site 13 out of 13 in 3gbf

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Cadmium binding site 13 out of 13 in the Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 13 of Phpd with Cadmium Complexed with Hydroethylphosphonate (Hep) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd513

b:21.8
occ:1.00
O4 A:2HE550 2.0 32.8 1.0
NE2 A:HIS129 2.3 20.4 1.0
NE2 A:HIS182 2.3 22.7 1.0
O A:HOH725 2.3 28.0 1.0
OE1 A:GLU176 2.3 12.4 1.0
O2 A:2HE550 2.5 35.5 1.0
CE1 A:HIS182 3.2 22.2 1.0
CE1 A:HIS129 3.2 19.2 1.0
CB A:2HE550 3.2 36.3 1.0
CD A:GLU176 3.3 18.7 1.0
CD2 A:HIS129 3.3 19.3 1.0
CD2 A:HIS182 3.4 21.3 1.0
OE2 A:GLU176 3.5 17.8 1.0
CA A:2HE550 3.7 36.5 1.0
P A:2HE550 3.7 39.3 1.0
OG A:SER196 4.1 21.0 1.0
ND2 A:ASN126 4.2 20.3 1.0
ND1 A:HIS182 4.3 21.5 1.0
ND1 A:HIS129 4.3 19.0 1.0
CG A:HIS129 4.4 19.8 1.0
CG A:HIS182 4.4 22.2 1.0
O A:HOH500 4.5 29.6 1.0
O3 A:2HE550 4.6 38.2 1.0
CG A:GLU176 4.6 16.8 1.0
O1 A:2HE550 4.8 36.8 1.0
CB A:GLU176 4.9 18.4 1.0

Reference:

R.M.Cicchillio, H.Zhang, J.A.V.Blodgett, J.T.Whitteck, G.Li, S.K.Nair, W.A.Van Der Donk, W.W.Metcalf. An Unusual Carbon-Carbon Bond Cleavage Reaction in the Biosynthesis of the Herbicide Phosphinothricin To Be Published.
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