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Cadmium in PDB 4yar: 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H

Enzymatic activity of 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H

All present enzymatic activity of 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H:
1.13.11.72;

Protein crystallography data

The structure of 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H, PDB code: 4yar was solved by J.R.Chekan, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.75 / 1.75
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 85.286, 95.953, 101.142, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 23.8

Other elements in 4yar:

The structure of 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H also contains other interesting chemical elements:

Sodium (Na) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H (pdb code 4yar). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 10 binding sites of Cadmium where determined in the 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H, PDB code: 4yar:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 10 in 4yar

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Cadmium binding site 1 out of 10 in the 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd501

b:30.0
occ:1.00
 O A:HOH695 2.2 31.5 1.0
NE2 A:HIS129 2.3 23.4 1.0
O A:HOH728 2.4 39.7 1.0
O A:HOH696 2.4 27.2 1.0
NE2 A:HIS182 2.4 27.3 1.0
O A:HOH697 2.5 24.6 1.0
CD2 A:HIS129 3.2 25.7 1.0
CE1 A:HIS182 3.3 25.1 1.0
CE1 A:HIS129 3.3 26.3 1.0
CD2 A:HIS182 3.4 22.0 1.0
NE2 A:HIS176 3.7 33.8 0.5
OG A:SER196 4.1 34.0 1.0
ND2 A:ASN126 4.3 25.4 1.0
CG A:HIS129 4.4 25.4 1.0
ND1 A:HIS129 4.4 24.7 1.0
ND1 A:HIS182 4.5 28.6 1.0
CD2 A:HIS176 4.5 32.1 0.5
CG A:HIS182 4.5 26.6 1.0
CE1 A:HIS176 4.6 32.7 0.5

Cadmium binding site 2 out of 10 in 4yar

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Cadmium binding site 2 out of 10 in the 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd502

b:79.5
occ:1.00
 NH2 A:ARG107 2.4 52.9 1.0
OD2 A:ASP66 2.7 65.5 1.0
OD1 A:ASP66 2.7 58.2 1.0
CZ A:ARG107 2.8 51.0 1.0
CG A:ASP66 2.9 54.3 1.0
NE A:ARG107 3.4 46.3 1.0
NH1 A:ARG107 3.4 51.8 1.0
CB A:ASP66 4.2 53.3 1.0
O A:HOH782 4.2 42.9 1.0
CB A:HIS68 4.3 85.6 1.0
CD A:ARG107 4.5 39.5 1.0
N A:HIS68 4.8 71.8 1.0
ND1 A:HIS68 4.9 99.5 1.0

Cadmium binding site 3 out of 10 in 4yar

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Cadmium binding site 3 out of 10 in the 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd503

b:89.7
occ:1.00
 NE2 A:HIS75 2.5 25.7 1.0
CE1 A:HIS75 3.1 24.8 1.0
CD2 A:HIS75 3.7 25.5 1.0
ND1 A:HIS75 4.4 27.4 1.0
O A:HOH735 4.5 23.8 1.0
CG A:HIS75 4.7 24.4 1.0
CH2 A:TRP369 4.9 21.1 1.0

Cadmium binding site 4 out of 10 in 4yar

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Cadmium binding site 4 out of 10 in the 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd504

b:26.8
occ:1.00
 OE1 A:GLU131 2.4 24.4 1.0
OE2 A:GLU131 2.5 25.4 1.0
CD A:GLU131 2.7 25.8 1.0
O A:HOH652 4.2 25.2 1.0
CG A:GLU131 4.2 25.0 1.0
CB A:LEU130 4.3 25.2 1.0
N A:LEU130 4.6 22.1 1.0
N A:GLU131 4.7 23.6 1.0

Cadmium binding site 5 out of 10 in 4yar

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Cadmium binding site 5 out of 10 in the 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd505

b:24.6
occ:1.00
 O A:HOH601 1.9 43.8 1.0
O A:HOH611 2.0 26.4 1.0
O A:HOH624 2.3 27.1 1.0
OD1 A:ASP32 2.3 19.0 1.0
OD2 A:ASP32 2.5 29.4 1.0
CG A:ASP32 2.7 24.0 1.0
OE1 A:GLU43 3.8 89.4 1.0
CB A:ASP32 4.2 25.7 1.0
CG A:PRO29 4.5 27.6 1.0
OD1 A:ASP31 4.5 33.6 1.0
O A:HOH688 4.6 37.7 1.0
NH2 A:ARG35 4.6 49.9 1.0
CB A:PRO29 4.7 29.4 1.0
O A:HOH627 4.8 34.5 1.0
CD A:GLU43 4.9 97.2 1.0

Cadmium binding site 6 out of 10 in 4yar

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Cadmium binding site 6 out of 10 in the 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd506

b:28.9
occ:1.00
 CD2 A:HIS94 2.3 17.3 1.0
O A:HOH711 2.4 36.4 1.0
CG A:HIS94 3.3 19.4 1.0
NE2 A:HIS94 3.4 20.8 1.0
CB A:HIS94 3.7 19.9 1.0
ND1 A:HIS94 4.4 21.3 1.0
O A:HOH785 4.4 42.3 1.0
CE1 A:HIS94 4.4 17.6 1.0
O A:HOH626 4.8 29.5 1.0

Cadmium binding site 7 out of 10 in 4yar

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Cadmium binding site 7 out of 10 in the 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd507

b:20.6
occ:1.00
 O A:ACT513 1.8 33.1 1.0
NE2 A:HIS163 2.2 22.2 1.0
OD1 A:ASP142 2.4 20.1 1.0
ND1 A:HIS160 2.4 22.0 1.0
OD2 A:ASP142 2.4 20.9 1.0
C A:ACT513 2.6 24.7 1.0
OXT A:ACT513 2.6 19.6 1.0
O A:HOH803 2.6 20.0 1.0
CG A:ASP142 2.8 20.6 1.0
CE1 A:HIS163 3.1 18.6 1.0
CE1 A:HIS160 3.2 23.2 1.0
CD2 A:HIS163 3.2 19.2 1.0
CG A:HIS160 3.4 20.1 1.0
CB A:HIS160 3.8 19.1 1.0
CH3 A:ACT513 4.0 38.4 1.0
O A:ALA161 4.0 18.6 1.0
CB A:ASP142 4.3 21.3 1.0
ND1 A:HIS163 4.3 18.7 1.0
CG A:HIS163 4.3 18.6 1.0
CA A:HIS160 4.4 19.2 1.0
NE2 A:HIS160 4.4 25.8 1.0
O A:HOH759 4.5 20.9 1.0
CD2 A:HIS160 4.5 20.6 1.0
N A:ALA161 4.5 19.7 1.0
O A:HOH686 4.5 20.8 1.0
O A:HOH617 4.6 23.6 1.0
C A:HIS160 5.0 18.6 1.0

Cadmium binding site 8 out of 10 in 4yar

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Cadmium binding site 8 out of 10 in the 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd508

b:1.0
occ:1.00
 CD A:CD510 2.4 31.4 1.0
OD2 A:ASP189 3.3 25.2 1.0
CG A:ASP189 3.9 26.2 1.0
OD1 A:ASP189 4.0 30.6 1.0
N A:ASP189 4.7 21.6 1.0
CA A:GLY188 4.8 22.4 1.0
OG A:SER119 5.0 25.2 1.0

Cadmium binding site 9 out of 10 in 4yar

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Cadmium binding site 9 out of 10 in the 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd509

b:51.4
occ:1.00
 OE1 A:GLU80 2.4 25.2 1.0
O A:HOH802 2.5 31.4 1.0
OE2 A:GLU80 2.6 29.3 1.0
CD A:GLU80 2.9 26.6 1.0
O A:HIS75 4.2 18.4 1.0
CG A:GLU80 4.3 24.0 1.0
N A:SER77 4.4 18.1 1.0
ND1 A:HIS75 4.5 27.4 1.0
CA A:LYS76 4.6 18.9 1.0
CE1 A:HIS75 4.7 24.8 1.0
CB A:SER77 4.9 21.4 1.0
OG A:SER77 4.9 19.9 1.0
C A:HIS75 4.9 18.6 1.0
C A:LYS76 5.0 18.8 1.0

Cadmium binding site 10 out of 10 in 4yar

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Cadmium binding site 10 out of 10 in the 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd510

b:31.4
occ:1.00
 OD2 A:ASP189 2.4 25.2 1.0
CD A:CD508 2.4 1.0 1.0
CG A:ASP189 3.2 26.2 1.0
OD1 A:ASP189 3.4 30.6 1.0
CB A:ASP189 4.6 22.3 1.0

Reference:

S.C.Peck, J.R.Chekan, E.C.Ulrich, S.K.Nair, W.A.Van Der Donk. A Common Late-Stage Intermediate in Catalysis By 2-Hydroxyethylphosphonate Dioxygenase and Methylphosphonate Synthase. J.Am.Chem.Soc. 2015.
ISSN: ESSN 1520-5126
PubMed: 25699631
DOI: 10.1021/JACS.5B00282
Page generated: Fri Jul 19 18:05:38 2024

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