Cadmium in PDB 4zxa: Crystal Structure of Hydroquinone 1,2-Dioxygenase Pnpcd in Complex with CD2+ and 4-Hydroxybenzonitrile

The structure of Crystal Structure of Hydroquinone 1,2-Dioxygenase Pnpcd in Complex with CD2+ and 4-Hydroxybenzonitrile, PDB code: 4zxa was solved by S.Liu, T.Su, C.Zhang, L.Gu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.73 / 2.49
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.023, 181.048, 186.813, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 23.7

The binding sites of Cadmium atom in the Crystal Structure of Hydroquinone 1,2-Dioxygenase Pnpcd in Complex with CD2+ and 4-Hydroxybenzonitrile (pdb code 4zxa). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Crystal Structure of Hydroquinone 1,2-Dioxygenase Pnpcd in Complex with CD2+ and 4-Hydroxybenzonitrile, PDB code: 4zxa:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Crystal Structure of Hydroquinone 1,2-Dioxygenase Pnpcd in Complex with CD2+ and 4-Hydroxybenzonitrile


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Hydroquinone 1,2-Dioxygenase Pnpcd in Complex with CD2+ and 4-Hydroxybenzonitrile within 5.0Å range: probe atom residue distance (Å) B Occ W:Cd401 b:28.2 occ:1.00 ND1 W:HIS256 2.2 24.9 1.0 NE2 W:HIS303 2.2 21.4 1.0 OD1 W:ASN258 2.3 25.4 1.0 NAA W:H8N402 2.3 25.6 1.0 OE1 W:GLU262 2.4 27.7 1.0 OE2 W:GLU262 2.5 21.9 1.0 CD W:GLU262 2.8 26.5 1.0 CE1 W:HIS303 2.9 20.9 1.0 CE1 W:HIS256 3.0 22.7 1.0 CG W:HIS256 3.2 24.3 1.0 CD2 W:HIS303 3.4 23.7 1.0 CG W:ASN258 3.4 26.7 1.0 CAC W:H8N402 3.5 26.1 1.0 CB W:HIS256 3.6 18.8 1.0 ND2 W:ASN258 3.7 21.3 1.0 ND1 W:HIS303 4.1 27.7 1.0 NE2 W:HIS256 4.2 30.0 1.0 CG W:GLU262 4.3 24.1 1.0 CD2 W:HIS256 4.3 25.2 1.0 CG W:HIS303 4.3 25.1 1.0 O W:HIS256 4.7 24.3 1.0 CB W:ASN258 4.7 22.8 1.0 CE2 W:PHE79 4.8 30.2 1.0 C W:HIS256 4.9 21.2 1.0 CA W:HIS256 4.9 22.8 1.0 CZ W:PHE264 4.9 19.5 1.0 CAI W:H8N402 4.9 22.3 1.0 CA W:ASN258 5.0 24.0 1.0

Cadmium binding site 2 out of 4 in the Crystal Structure of Hydroquinone 1,2-Dioxygenase Pnpcd in Complex with CD2+ and 4-Hydroxybenzonitrile


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Hydroquinone 1,2-Dioxygenase Pnpcd in Complex with CD2+ and 4-Hydroxybenzonitrile within 5.0Å range: probe atom residue distance (Å) B Occ X:Cd401 b:49.7 occ:1.00 NAA X:H8N402 2.1 17.8 1.0 NE2 X:HIS303 2.3 33.3 1.0 OD1 X:ASN258 2.5 48.6 1.0 OE1 X:GLU262 2.6 40.5 1.0 ND1 X:HIS256 2.7 36.6 1.0 CE1 X:HIS303 2.7 42.4 1.0 OE2 X:GLU262 2.9 41.4 1.0 CD X:GLU262 2.9 41.4 1.0 CAC X:H8N402 3.2 29.5 1.0 CG X:HIS256 3.3 38.0 1.0 CE1 X:HIS256 3.3 40.0 1.0 CG X:ASN258 3.3 44.8 1.0 CD2 X:HIS303 3.6 40.4 1.0 ND2 X:ASN258 3.6 40.3 1.0 CB X:HIS256 3.7 34.0 1.0 ND1 X:HIS303 3.9 41.8 1.0 CD2 X:HIS256 4.0 43.3 1.0 NE2 X:HIS256 4.0 41.6 1.0 CG X:GLU262 4.2 37.3 1.0 O X:HIS256 4.3 46.3 1.0 CG X:HIS303 4.4 36.6 1.0 C X:HIS256 4.5 39.4 1.0 CB X:ASN258 4.6 44.7 1.0 CAI X:H8N402 4.7 31.4 1.0 CA X:HIS256 4.7 32.0 1.0 CA X:ASN258 4.8 44.8 1.0 N X:ASN258 4.9 48.0 1.0 CZ X:PHE264 4.9 31.4 1.0

Cadmium binding site 3 out of 4 in the Crystal Structure of Hydroquinone 1,2-Dioxygenase Pnpcd in Complex with CD2+ and 4-Hydroxybenzonitrile


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Hydroquinone 1,2-Dioxygenase Pnpcd in Complex with CD2+ and 4-Hydroxybenzonitrile within 5.0Å range: probe atom residue distance (Å) B Occ Y:Cd401 b:55.3 occ:1.00 NAA Y:H8N402 2.0 13.6 1.0 ND1 Y:HIS256 2.3 34.3 1.0 NE2 Y:HIS303 2.4 31.5 1.0 OD1 Y:ASN258 2.7 41.4 1.0 OE2 Y:GLU262 2.7 36.7 1.0 CE1 Y:HIS303 2.8 30.2 1.0 OE1 Y:GLU262 2.9 47.0 1.0 CE1 Y:HIS256 3.0 31.2 1.0 CAC Y:H8N402 3.1 24.2 1.0 CD Y:GLU262 3.1 41.1 1.0 CG Y:HIS256 3.2 28.4 1.0 CD2 Y:HIS303 3.6 34.3 1.0 CB Y:HIS256 3.7 22.8 1.0 CG Y:ASN258 3.8 37.4 1.0 NE2 Y:HIS256 4.0 30.1 1.0 ND1 Y:HIS303 4.0 37.1 1.0 CD2 Y:HIS256 4.1 29.8 1.0 O Y:HIS256 4.2 32.6 1.0 ND2 Y:ASN258 4.2 37.8 1.0 CG Y:HIS303 4.4 27.9 1.0 CZ Y:PHE264 4.5 35.4 1.0 CG Y:GLU262 4.5 42.6 1.0 CAI Y:H8N402 4.6 22.3 1.0 C Y:HIS256 4.7 29.9 1.0 CA Y:HIS256 4.9 23.7 1.0 O Y:HOH565 5.0 33.4 1.0 CE1 Y:PHE264 5.0 32.6 1.0

Cadmium binding site 4 out of 4 in the Crystal Structure of Hydroquinone 1,2-Dioxygenase Pnpcd in Complex with CD2+ and 4-Hydroxybenzonitrile


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Hydroquinone 1,2-Dioxygenase Pnpcd in Complex with CD2+ and 4-Hydroxybenzonitrile within 5.0Å range: probe atom residue distance (Å) B Occ Z:Cd401 b:31.1 occ:1.00 ND1 Z:HIS256 2.2 23.6 1.0 NE2 Z:HIS303 2.3 24.6 1.0 NAA Z:H8N402 2.3 28.2 1.0 OE1 Z:GLU262 2.3 27.3 1.0 OD1 Z:ASN258 2.5 28.5 1.0 OE2 Z:GLU262 2.7 24.6 1.0 CD Z:GLU262 2.8 29.1 1.0 CE1 Z:HIS256 2.9 26.9 1.0 CE1 Z:HIS303 3.1 33.0 1.0 CD2 Z:HIS303 3.4 26.1 1.0 CG Z:HIS256 3.4 26.9 1.0 CAC Z:H8N402 3.5 33.5 1.0 CG Z:ASN258 3.5 23.6 1.0 ND2 Z:ASN258 3.8 20.8 1.0 CB Z:HIS256 3.9 21.7 1.0 NE2 Z:HIS256 4.2 23.5 1.0 ND1 Z:HIS303 4.3 30.5 1.0 CG Z:GLU262 4.3 25.2 1.0 CD2 Z:HIS256 4.4 24.6 1.0 CG Z:HIS303 4.4 22.7 1.0 O Z:HIS256 4.6 25.2 1.0 CE2 Z:PHE79 4.8 28.0 1.0 CB Z:ASN258 4.8 29.2 1.0 O Z:HOH512 4.8 35.5 1.0 CZ Z:PHE264 4.9 23.6 1.0 C Z:HIS256 4.9 26.8 1.0 CAI Z:H8N402 4.9 32.2 1.0

S.Liu, T.Su, C.Zhang, W.M.Zhang, D.Zhu, J.Su, T.Wei, K.Wang, Y.Huang, L.Guo, S.Xu, N.Y.Zhou, L.Gu. Crystal Structure of Pnpcd, A Two-Subunit Hydroquinone 1,2-Dioxygenase, Reveals A Novel Structural Class of FE2+-Dependent Dioxygenases. J.Biol.Chem. V. 290 24547 2015.
ISSN: ESSN 1083-351X
PubMed: 26304122
DOI: 10.1074/JBC.M115.673558