Zinc in PDB 3w20: Crystal Structure of A Novel N-Substituted L-Amino Acid Dioxygenase From Burkholderia Ambifaria Ammd

The structure of Crystal Structure of A Novel N-Substituted L-Amino Acid Dioxygenase From Burkholderia Ambifaria Ammd, PDB code: 3w20 was solved by H.M.Qin, T.Miyakawa, M.Z.Jia, A.Nakamura, J.Ohtsuka, Y.L.Xue, T.Kawashima, T.Kasahara, M.Hibi, J.Ogawa, M.Tanokura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.77
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.999, 70.956, 147.893, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 24.1

The binding sites of Zinc atom in the Crystal Structure of A Novel N-Substituted L-Amino Acid Dioxygenase From Burkholderia Ambifaria Ammd (pdb code 3w20). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of A Novel N-Substituted L-Amino Acid Dioxygenase From Burkholderia Ambifaria Ammd, PDB code: 3w20:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of A Novel N-Substituted L-Amino Acid Dioxygenase From Burkholderia Ambifaria Ammd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Novel N-Substituted L-Amino Acid Dioxygenase From Burkholderia Ambifaria Ammd within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:18.2 occ:0.50 OD2 A:ASP157 1.9 22.1 1.0 NE2 A:HIS246 2.1 19.4 1.0 NE2 A:HIS155 2.3 33.0 1.0 CG A:ASP157 2.8 18.8 1.0 CE1 A:HIS246 3.0 18.0 1.0 OD1 A:ASP157 3.0 18.4 1.0 CE1 A:HIS155 3.0 34.1 1.0 CD2 A:HIS246 3.2 19.4 1.0 CD2 A:HIS155 3.4 28.6 1.0 ND1 A:HIS246 4.2 18.2 1.0 ND1 A:HIS155 4.2 33.6 1.0 CZ A:PHE261 4.2 17.2 1.0 CB A:ASP157 4.3 15.6 1.0 CG A:HIS246 4.3 16.8 1.0 CZ A:PHE240 4.4 15.9 1.0 CG A:HIS155 4.4 27.8 1.0 CE1 A:PHE261 4.5 16.1 1.0 CE1 A:PHE240 4.6 15.8 1.0 N A:ASP157 4.8 15.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of A Novel N-Substituted L-Amino Acid Dioxygenase From Burkholderia Ambifaria Ammd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Novel N-Substituted L-Amino Acid Dioxygenase From Burkholderia Ambifaria Ammd within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:50.9 occ:0.50 NE2 B:HIS246 2.6 17.8 1.0 OD2 B:ASP157 2.7 21.8 1.0 CE1 B:HIS155 3.3 43.0 1.0 CE1 B:HIS246 3.3 17.7 1.0 CZ B:PHE261 3.7 16.9 1.0 CD2 B:HIS246 3.7 19.2 1.0 CG B:ASP157 3.8 23.9 1.0 CE1 B:PHE261 3.8 14.6 1.0 CZ B:PHE240 3.8 15.9 1.0 NE2 B:HIS155 3.9 46.4 1.0 CE1 B:PHE240 4.3 16.8 1.0 CB B:ASP157 4.3 17.9 1.0 ND1 B:HIS155 4.4 38.4 1.0 ND1 B:HIS246 4.6 18.6 1.0 OD1 B:ASP157 4.7 27.8 1.0 CG B:HIS246 4.8 18.4 1.0 CB B:SER242 4.8 13.7 1.0 CE2 B:PHE240 4.9 14.4 1.0 CE2 B:PHE261 5.0 15.8 1.0

H.M.Qin, T.Miyakawa, M.Z.Jia, A.Nakamura, J.Ohtsuka, Y.L.Xue, T.Kawashima, T.Kasahara, M.Hibi, J.Ogawa, M.Tanokura. Crystal Structure of A Novel N-Substituted L-Amino Acid Dioxygenase From Burkholderia Ambifaria Ammd Plos One V. 8 63996 2013.
ISSN: ESSN 1932-6203
PubMed: 23724013
DOI: 10.1371/JOURNAL.PONE.0063996