Cadmium in PDB 3rzz: Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant

The structure of Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant, PDB code: 3rzz was solved by H.A.Cooke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.00 / 2.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	84.747, 94.964, 101.396, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 26.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Cadmium atom in the Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant (pdb code 3rzz). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 15 binding sites of Cadmium where determined in the Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant, PDB code: 3rzz:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 15 in the Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd444 b:36.7 occ:1.00 NE2 A:HIS182 2.5 27.9 1.0 O A:HOH563 2.5 29.6 1.0 NE2 A:HIS129 2.5 39.2 1.0 O A:HOH574 2.6 33.1 1.0 OE1 A:GLU176 2.6 30.5 1.0 O A:HOH555 2.9 26.5 1.0 CE1 A:HIS182 3.4 27.4 1.0 CD2 A:HIS129 3.4 38.4 1.0 CD A:GLU176 3.4 31.6 1.0 CD2 A:HIS182 3.5 28.0 1.0 CE1 A:HIS129 3.5 38.9 1.0 OE2 A:GLU176 3.5 29.1 1.0 O A:HOH680 4.1 46.5 1.0 OG A:SER196 4.2 40.4 1.0 ND2 A:ASN126 4.5 35.0 1.0 ND1 A:HIS182 4.5 28.1 1.0 CG A:HIS129 4.6 39.1 1.0 CG A:HIS182 4.6 30.0 1.0 ND1 A:HIS129 4.6 40.5 1.0 CG A:GLU176 4.8 32.9 1.0

Cadmium binding site 2 out of 15 in the Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd445 b:42.0 occ:1.00 O A:HOH637 2.5 34.5 1.0 O A:HOH638 2.6 39.5 1.0 OE1 A:GLU131 2.6 30.4 1.0 O A:HOH579 2.6 34.5 1.0 OE2 A:GLU131 2.7 36.0 1.0 CD A:GLU131 3.0 32.8 1.0 CB A:LEU130 4.4 32.8 1.0 CG A:GLU131 4.4 33.1 1.0 N A:LEU130 4.7 33.3 1.0 N A:GLU131 4.8 33.4 1.0

Cadmium binding site 3 out of 15 in the Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd446 b:37.5 occ:1.00 ND1 A:HIS160 2.4 36.8 1.0 O A:HOH558 2.5 62.2 1.0 OD2 A:ASP142 2.5 31.2 1.0 NE2 A:HIS163 2.6 38.8 1.0 OD1 A:ASP142 2.7 34.2 1.0 O A:HOH517 2.7 34.5 1.0 CG A:ASP142 2.9 30.7 1.0 O A:HOH639 2.9 41.6 1.0 CD2 A:HIS163 3.1 38.5 1.0 CE1 A:HIS160 3.2 38.5 1.0 CG A:HIS160 3.6 35.0 1.0 CE1 A:HIS163 3.7 40.6 1.0 CB A:HIS160 4.0 35.0 1.0 O A:ALA161 4.1 33.7 1.0 CB A:ASP142 4.3 30.7 1.0 CG A:HIS163 4.4 39.3 1.0 NE2 A:HIS160 4.4 39.5 1.0 N A:ALA161 4.5 34.3 1.0 O A:HOH702 4.5 33.9 1.0 CA A:HIS160 4.6 35.7 1.0 CD2 A:HIS160 4.6 37.1 1.0 ND1 A:HIS163 4.7 37.8 1.0 O A:HOH694 4.7 33.0 1.0 O A:HOH508 4.9 43.4 1.0

Cadmium binding site 4 out of 15 in the Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd447 b:56.0 occ:0.50 O A:HOH586 2.3 38.4 1.0 O A:HOH617 2.4 53.1 1.0 O A:HOH568 2.5 71.2 1.0 O A:HOH470 2.9 46.4 1.0 O A:HOH678 2.9 57.0 1.0 CG A:HIS82 3.5 52.4 1.0 CD2 A:HIS82 3.5 53.2 1.0 ND1 A:HIS82 3.8 55.3 1.0 CB A:HIS82 3.8 46.0 1.0 NE2 A:HIS82 3.9 57.2 1.0 O A:HOH700 4.1 48.7 1.0 CE1 A:HIS82 4.1 55.7 1.0

Cadmium binding site 5 out of 15 in the Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd448 b:81.0 occ:0.50 OE1 A:GLN296 2.2 72.8 1.0 ND1 A:HIS330 2.3 43.4 1.0 CE1 A:HIS330 2.4 43.3 1.0 O A:HOH567 2.6 28.8 1.0 O A:HOH679 2.8 56.7 1.0 CD A:GLN296 3.0 72.5 1.0 O A:HOH560 3.2 66.7 1.0 CG A:HIS330 3.2 39.9 1.0 NE2 A:HIS330 3.4 43.2 1.0 NE2 A:GLN296 3.4 72.9 1.0 NZ A:LYS302 3.6 55.0 1.0 CE A:LYS302 3.6 55.9 1.0 OD2 A:ASP294 3.8 64.7 1.0 CD2 A:HIS330 3.8 41.5 1.0 CB A:HIS330 4.1 36.8 1.0 O A:ASP295 4.2 68.7 1.0 CG A:GLN296 4.2 71.8 1.0 O A:HOH471 4.4 36.9 1.0 CA A:GLN296 4.5 69.0 1.0 N A:HIS330 4.9 33.3 1.0 CB A:GLN296 4.9 69.7 1.0 O A:HOH696 4.9 73.1 1.0 O A:ASP294 5.0 62.9 1.0 CG A:ASP294 5.0 64.2 1.0

Cadmium binding site 6 out of 15 in the Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd449 b:71.5 occ:1.00 SG A:CYS180 2.4 52.7 1.0 O A:HOH577 2.6 62.3 1.0 O A:ASP298 2.8 73.1 1.0 O A:HOH580 3.0 44.4 1.0 O A:HOH629 3.0 50.9 1.0 OD1 A:ASP298 3.4 77.5 1.0 CB A:CYS180 3.5 43.5 1.0 CD A:CD457 3.7 57.3 1.0 CG A:ASP298 3.7 76.3 1.0 OD2 A:ASP298 3.9 78.0 1.0 C A:ASP298 3.9 72.0 1.0 CA A:ASP298 4.5 73.2 1.0 CB A:ASP298 4.6 74.3 1.0 CB A:PRO177 4.9 39.0 1.0 CA A:CYS180 4.9 42.1 1.0

Cadmium binding site 7 out of 15 in the Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd450 b:68.8 occ:0.50 OD2 A:ASP342 3.1 59.5 1.0 O A:HOH698 3.1 50.2 1.0 OD1 A:ASP342 3.4 58.6 1.0 CG A:ASP342 3.6 57.5 1.0 NH2 A:ARG340 3.6 57.9 1.0 O A:HOH585 4.5 40.9 1.0 O A:HOH545 4.6 50.1 1.0 CZ A:ARG340 4.7 57.1 1.0 NH1 A:ARG340 4.8 58.1 1.0 CB A:ASP342 5.0 54.3 1.0

Cadmium binding site 8 out of 15 in the Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd451 b:77.0 occ:1.00 OE2 A:GLU80 2.7 43.9 1.0 OE1 A:GLU80 2.7 45.2 1.0 O A:HOH644 2.7 51.6 1.0 CD A:GLU80 3.0 43.8 1.0 O A:HOH578 3.0 37.0 1.0 O A:HOH592 3.5 50.1 1.0 O A:HOH627 4.0 52.8 1.0 O A:HIS75 4.2 36.1 1.0 ND1 A:HIS75 4.3 40.4 1.0 N A:SER77 4.4 34.4 1.0 CG A:GLU80 4.4 42.5 1.0 CE1 A:HIS75 4.5 39.4 1.0 O A:HOH635 4.5 49.0 1.0 OG A:SER77 4.6 36.7 1.0 CA A:LYS76 4.7 33.2 1.0 CB A:SER77 4.8 36.4 1.0 C A:HIS75 5.0 35.3 1.0

Cadmium binding site 9 out of 15 in the Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd452 b:92.1 occ:0.75 O A:HOH695 2.3 58.3 1.0 OD2 A:ASP66 2.5 67.1 1.0 O A:HOH561 2.5 51.1 1.0 OD1 A:ASP66 2.5 65.7 1.0 O A:HOH640 2.6 56.1 1.0 CG A:ASP66 2.8 65.5 1.0 O A:HOH573 3.8 57.1 1.0 NH1 A:ARG107 4.1 55.1 1.0 CB A:ASP66 4.3 64.4 1.0 N A:ALA67 4.5 66.3 1.0 N A:HIS68 4.6 68.4 1.0 O A:HIS68 4.7 68.0 1.0 CB A:ALA67 4.9 67.4 1.0 CZ A:ARG107 5.0 53.3 1.0

Cadmium binding site 10 out of 15 in the Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd453 b:97.5 occ:1.00 O A:HOH687 2.7 55.2 1.0 NE2 A:HIS75 2.8 38.8 1.0 O A:HOH536 2.9 58.4 1.0 O A:HOH588 3.3 37.7 1.0 CE1 A:HIS75 3.5 39.4 1.0 CD2 A:HIS75 3.9 38.0 1.0 O A:HOH697 4.5 53.5 1.0 O A:HOH511 4.6 40.9 1.0 ND1 A:HIS75 4.7 40.4 1.0 CG A:HIS75 4.9 37.9 1.0

S.C.Peck, H.A.Cooke, R.M.Cicchillo, P.Malova, F.Hammerschmidt, S.K.Nair, W.A.Van Der Donk. Mechanism and Substrate Recognition of 2-Hydroxyethylphosphonate Dioxygenase. Biochemistry V. 50 6598 2011.
ISSN: ISSN 0006-2960
PubMed: 21711001
DOI: 10.1021/BI200804R