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Cadmium in PDB 3g7d: Native Phpd with Cadmium Atoms

Protein crystallography data

The structure of Native Phpd with Cadmium Atoms, PDB code: 3g7d was solved by S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 85.198, 95.736, 102.163, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 24.6

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Native Phpd with Cadmium Atoms (pdb code 3g7d). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 13 binding sites of Cadmium where determined in the Native Phpd with Cadmium Atoms, PDB code: 3g7d:
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 3g7d

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Cadmium binding site 1 out of 13 in the Native Phpd with Cadmium Atoms


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Native Phpd with Cadmium Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd500

b:43.8
occ:1.00
 O A:HOH772 1.8 30.4 1.0
SG A:CYS180 2.4 29.3 1.0
O A:HOH697 2.4 31.1 1.0
CB A:CYS180 3.3 24.3 1.0
CD A:CD501 3.7 41.5 1.0
O A:HOH561 3.8 31.3 1.0
CA A:CYS180 4.7 24.3 1.0
CG A:PRO177 4.7 21.5 1.0
CB A:PRO177 4.8 21.5 1.0
O A:HOH530 5.0 26.6 1.0

Cadmium binding site 2 out of 13 in 3g7d

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Cadmium binding site 2 out of 13 in the Native Phpd with Cadmium Atoms


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Native Phpd with Cadmium Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd501

b:41.5
occ:1.00
 SG A:CYS180 2.4 29.3 1.0
O A:HOH772 3.5 30.4 1.0
CB A:CYS180 3.6 24.3 1.0
CD A:CD500 3.7 43.8 1.0
CA A:CYS180 3.8 24.3 1.0
N A:CYS180 4.1 23.2 1.0
C A:TYR179 4.6 22.8 1.0
O A:SER178 4.6 21.7 1.0
O A:HOH530 4.7 26.6 1.0
O A:TYR179 4.9 22.5 1.0

Cadmium binding site 3 out of 13 in 3g7d

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Cadmium binding site 3 out of 13 in the Native Phpd with Cadmium Atoms


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Native Phpd with Cadmium Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd502

b:35.2
occ:1.00
 OD2 A:ASP189 2.2 27.1 1.0
CG A:ASP189 3.1 26.2 1.0
OD1 A:ASP189 3.3 29.1 1.0
O A:HOH791 4.3 36.5 1.0
O A:HOH603 4.4 33.2 1.0
CB A:ASP189 4.5 24.5 1.0

Cadmium binding site 4 out of 13 in 3g7d

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Cadmium binding site 4 out of 13 in the Native Phpd with Cadmium Atoms


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Native Phpd with Cadmium Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd503

b:47.2
occ:1.00
 O A:HOH761 2.1 33.8 1.0
OE1 A:GLU80 2.4 23.1 1.0
OE2 A:GLU80 2.5 24.6 1.0
O A:HOH714 2.6 53.6 1.0
CD A:GLU80 2.8 23.6 1.0
CG A:GLU80 4.3 23.4 1.0
O A:HIS75 4.3 20.4 1.0
N A:SER77 4.4 20.5 1.0
ND1 A:HIS75 4.4 24.5 1.0
CE1 A:HIS75 4.6 25.1 1.0
CA A:LYS76 4.6 20.1 1.0
OG A:SER77 4.8 19.6 1.0
CB A:SER77 4.9 20.6 1.0
O A:HOH730 5.0 38.8 1.0
C A:HIS75 5.0 20.5 1.0
O A:HOH637 5.0 30.1 1.0

Cadmium binding site 5 out of 13 in 3g7d

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Cadmium binding site 5 out of 13 in the Native Phpd with Cadmium Atoms


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Native Phpd with Cadmium Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd504

b:26.9
occ:1.00
 O A:HOH758 2.1 25.1 1.0
O A:HOH642 2.2 28.2 1.0
O A:HOH525 2.2 22.9 1.0
OD2 A:ASP309 2.3 20.8 1.0
OD1 A:ASP309 2.5 24.6 1.0
CG A:ASP309 2.7 22.6 1.0
CB A:ASP309 4.2 21.8 1.0
O A:TRP304 4.3 21.8 1.0
OG1 A:THR306 4.4 21.1 1.0
O A:HOH748 4.5 39.5 1.0
NH1 A:ARG312 4.7 37.9 1.0
NH2 A:ARG312 4.7 38.1 1.0
O A:HOH622 4.7 29.0 1.0
OE1 A:GLU308 4.7 28.8 1.0
N A:THR306 4.8 20.8 1.0
CG2 A:THR306 4.8 21.0 1.0

Cadmium binding site 6 out of 13 in 3g7d

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Cadmium binding site 6 out of 13 in the Native Phpd with Cadmium Atoms


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Native Phpd with Cadmium Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd505

b:35.4
occ:1.00
 O A:HOH759 2.1 28.1 1.0
O A:HOH623 2.3 40.2 1.0
ND1 A:HIS94 2.4 24.8 1.0
CE1 A:HIS94 3.3 25.5 1.0
CG A:HIS94 3.4 25.5 1.0
CB A:HIS94 3.7 25.8 1.0
O A:HOH678 4.3 39.0 1.0
O A:HOH765 4.4 46.5 1.0
NE2 A:HIS94 4.5 25.5 1.0
CD2 A:HIS94 4.5 26.0 1.0
CD1 A:LEU116 4.9 21.2 1.0
O A:HOH631 4.9 33.9 1.0

Cadmium binding site 7 out of 13 in 3g7d

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Cadmium binding site 7 out of 13 in the Native Phpd with Cadmium Atoms


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Native Phpd with Cadmium Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd506

b:26.5
occ:1.00
 O A:HOH534 2.3 26.7 1.0
O A:HOH467 2.4 27.2 1.0
ND1 A:HIS10 2.5 27.6 1.0
O A:HOH538 2.8 29.1 1.0
CE1 A:HIS10 3.4 27.1 1.0
CG A:HIS10 3.6 26.6 1.0
CB A:HIS10 3.8 27.2 1.0
CA A:HIS10 3.9 26.8 1.0
O A:HIS10 4.3 26.3 1.0
ND2 A:ASN13 4.3 28.4 1.0
O A:HOH567 4.5 29.6 1.0
C A:HIS10 4.6 26.9 1.0
NE2 A:HIS10 4.6 27.8 1.0
O A:HOH620 4.6 28.0 1.0
CD2 A:HIS10 4.7 27.0 1.0

Cadmium binding site 8 out of 13 in 3g7d

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Cadmium binding site 8 out of 13 in the Native Phpd with Cadmium Atoms


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Native Phpd with Cadmium Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd507

b:24.9
occ:1.00
 NE2 A:HIS163 2.3 26.6 1.0
OD2 A:ASP142 2.3 21.1 1.0
ND1 A:HIS160 2.4 21.2 1.0
OD1 A:ASP142 2.5 18.6 1.0
O A:HOH466 2.5 31.5 1.0
O A:HOH477 2.7 22.3 1.0
CG A:ASP142 2.8 19.4 1.0
CD2 A:HIS163 3.2 25.4 1.0
CE1 A:HIS160 3.2 21.7 1.0
CE1 A:HIS163 3.3 25.7 1.0
CG A:HIS160 3.4 20.4 1.0
CB A:HIS160 3.8 20.7 1.0
O A:ALA161 4.0 21.7 1.0
CB A:ASP142 4.3 19.7 1.0
CG A:HIS163 4.4 25.3 1.0
ND1 A:HIS163 4.4 24.8 1.0
NE2 A:HIS160 4.4 22.3 1.0
CA A:HIS160 4.4 20.3 1.0
O A:HOH573 4.4 28.8 1.0
O A:HOH688 4.4 33.4 1.0
N A:ALA161 4.5 20.8 1.0
CD2 A:HIS160 4.5 21.0 1.0
O A:HOH540 4.6 25.8 1.0
O A:HOH521 4.7 28.8 1.0
O A:HOH698 4.9 40.5 1.0
C A:HIS160 5.0 20.6 1.0

Cadmium binding site 9 out of 13 in 3g7d

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Cadmium binding site 9 out of 13 in the Native Phpd with Cadmium Atoms


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Native Phpd with Cadmium Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd508

b:79.6
occ:1.00
 O A:HOH551 2.5 44.4 1.0
OD2 A:ASP66 2.6 41.1 1.0
OD1 A:ASP66 2.9 41.4 1.0
CG A:ASP66 3.1 41.1 1.0
O A:HOH740 3.9 48.9 1.0
CD A:ARG107 4.4 31.4 1.0
CB A:ASP66 4.6 40.6 1.0
NH1 A:ARG107 4.8 36.7 1.0
CB A:HIS68 4.9 38.9 1.0
N A:HIS68 4.9 39.5 1.0

Cadmium binding site 10 out of 13 in 3g7d

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Cadmium binding site 10 out of 13 in the Native Phpd with Cadmium Atoms


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Native Phpd with Cadmium Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd509

b:83.7
occ:1.00
 NE2 A:HIS75 2.5 25.9 1.0
CE1 A:HIS75 3.1 25.1 1.0
CD2 A:HIS75 3.7 24.3 1.0
ND1 A:HIS75 4.3 24.5 1.0
O A:HOH518 4.5 24.7 1.0
CG A:HIS75 4.7 22.0 1.0

Cadmium binding site 11 out of 13 in 3g7d

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Cadmium binding site 11 out of 13 in the Native Phpd with Cadmium Atoms


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 11 of Native Phpd with Cadmium Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd510

b:62.9
occ:1.00
 O A:HOH773 2.2 40.2 1.0
CE1 A:HIS410 2.5 23.5 1.0
ND1 A:HIS410 3.3 24.6 1.0
NE2 A:HIS410 3.5 26.9 1.0
CG A:HIS410 4.5 23.8 1.0
CD2 A:HIS410 4.6 23.8 1.0
O A:HOH689 4.9 34.7 1.0
CB A:ALA409 5.0 22.1 1.0

Cadmium binding site 12 out of 13 in 3g7d

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Cadmium binding site 12 out of 13 in the Native Phpd with Cadmium Atoms


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 12 of Native Phpd with Cadmium Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd511

b:55.8
occ:1.00
 ND1 A:HIS330 2.1 22.1 1.0
CE1 A:HIS330 2.2 21.7 1.0
O A:HOH444 2.4 11.0 1.0
OE1 A:GLN296 2.6 42.1 1.0
O A:HOH704 3.1 34.5 1.0
CG A:HIS330 3.1 20.2 1.0
NE2 A:HIS330 3.2 22.4 1.0
CD A:GLN296 3.4 42.0 1.0
CD2 A:HIS330 3.7 22.4 1.0
O A:HOH556 3.8 39.8 1.0
CB A:HIS330 4.1 18.7 1.0
NE2 A:GLN296 4.1 41.6 1.0
NZ A:LYS302 4.2 36.2 1.0
CG A:GLN296 4.4 41.9 1.0
OD1 A:ASP294 4.5 39.8 1.0
CD A:LYS302 4.6 33.9 1.0
CB A:ALA328 4.7 19.2 1.0
CE A:LYS302 4.8 35.4 1.0
N A:HIS330 4.8 18.1 1.0
O A:HOH610 4.8 32.9 1.0
O A:HOH708 4.9 39.4 1.0

Cadmium binding site 13 out of 13 in 3g7d

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Cadmium binding site 13 out of 13 in the Native Phpd with Cadmium Atoms


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 13 of Native Phpd with Cadmium Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd512

b:21.7
occ:1.00
 O A:HOH793 2.0 25.9 1.0
O A:HOH795 2.2 23.7 1.0
O A:HOH794 2.2 17.9 1.0
NE2 A:HIS129 2.3 21.5 1.0
OE1 A:GLU176 2.3 14.9 1.0
NE2 A:HIS182 2.3 22.2 1.0
CD A:GLU176 3.2 18.7 1.0
CE1 A:HIS182 3.2 21.6 1.0
CE1 A:HIS129 3.2 21.8 1.0
CD2 A:HIS129 3.2 21.4 1.0
CD2 A:HIS182 3.3 21.8 1.0
OE2 A:GLU176 3.4 18.2 1.0
OG A:SER196 4.2 21.5 1.0
ND1 A:HIS182 4.3 22.1 1.0
ND1 A:HIS129 4.3 21.3 1.0
O A:HOH690 4.4 35.8 1.0
CG A:HIS129 4.4 20.8 1.0
ND2 A:ASN126 4.4 22.3 1.0
CG A:HIS182 4.4 22.2 1.0
CG A:GLU176 4.6 17.6 1.0
CB A:GLU176 4.9 18.9 1.0

Reference:

R.M.Cicchillo, H.Zhang, J.A.Blodgett, J.T.Whitteck, G.Li, S.K.Nair, W.A.Van Der Donk, W.W.Metcalf. An Unusual Carbon-Carbon Bond Cleavage Reaction During Phosphinothricin Biosynthesis. Nature V. 459 871 2009.
ISSN: ISSN 0028-0836
PubMed: 19516340
DOI: 10.1038/NATURE07972
Page generated: Fri Aug 28 13:40:39 2020
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