Atomistry » Cadmium » PDB 4qe1-5ai3 » 4yar
Atomistry »
  Cadmium »
    PDB 4qe1-5ai3 »
      4yar »

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

Go back to Cadmium Binding Sites List in 4yar
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

Go back to Cadmium Binding Sites List in 4yar
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

Go back to Cadmium Binding Sites List in 4yar
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

Go back to Cadmium Binding Sites List in 4yar
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

Go back to Cadmium Binding Sites List in 4yar
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

Go back to Cadmium Binding Sites List in 4yar
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

Go back to Cadmium Binding Sites List in 4yar
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

Go back to Cadmium Binding Sites List in 4yar
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

Go back to Cadmium Binding Sites List in 4yar
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

Go back to Cadmium Binding Sites List in 4yar
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy