Zinc in PDB 3w21: Crystal Structure of A Novel N-Substituted L-Amino Acid Dioxygenase in Complex with Alpha-Kg From Burkholderia Ambifaria Ammd

The structure of Crystal Structure of A Novel N-Substituted L-Amino Acid Dioxygenase in Complex with Alpha-Kg From Burkholderia Ambifaria Ammd, PDB code: 3w21 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)	32.80 / 1.98
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.593, 71.143, 147.876, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 27.8

The binding sites of Zinc atom in the Crystal Structure of A Novel N-Substituted L-Amino Acid Dioxygenase in Complex with Alpha-Kg From Burkholderia Ambifaria Ammd (pdb code 3w21). 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 in Complex with Alpha-Kg From Burkholderia Ambifaria Ammd, PDB code: 3w21:
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 in Complex with Alpha-Kg 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 in Complex with Alpha-Kg From Burkholderia Ambifaria Ammd within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:33.0 occ:0.50 O1 A:AKG302 1.9 61.1 1.0 OD2 A:ASP157 2.1 35.9 1.0 NE2 A:HIS246 2.1 30.0 1.0 NE2 A:HIS155 2.2 50.7 1.0 O5 A:AKG302 2.6 61.7 1.0 C1 A:AKG302 2.8 59.9 1.0 CE1 A:HIS246 3.0 29.7 1.0 CG A:ASP157 3.0 32.7 1.0 CE1 A:HIS155 3.1 51.4 1.0 C2 A:AKG302 3.1 65.4 1.0 OD1 A:ASP157 3.2 27.6 1.0 CD2 A:HIS246 3.2 28.0 1.0 CD2 A:HIS155 3.3 48.3 1.0 O2 A:AKG302 3.9 47.2 1.0 ND1 A:HIS246 4.2 26.9 1.0 ND1 A:HIS155 4.2 52.3 1.0 CZ A:PHE261 4.2 27.6 1.0 CZ A:PHE240 4.3 27.6 1.0 CG A:HIS246 4.3 26.9 1.0 CG A:HIS155 4.4 44.9 1.0 O A:HOH471 4.4 52.1 1.0 CB A:ASP157 4.5 27.9 1.0 CE1 A:PHE261 4.5 26.6 1.0 C3 A:AKG302 4.6 64.1 1.0 CE2 A:PHE240 4.7 27.8 1.0 N A:ASP157 5.0 27.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of A Novel N-Substituted L-Amino Acid Dioxygenase in Complex with Alpha-Kg 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 in Complex with Alpha-Kg From Burkholderia Ambifaria Ammd within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:53.8 occ:0.50 NE2 B:HIS246 2.2 29.4 1.0 NE2 B:HIS155 2.5 67.7 1.0 OD2 B:ASP157 2.8 35.0 1.0 CE1 B:HIS246 3.0 29.8 1.0 CD2 B:HIS246 3.3 26.6 1.0 CE1 B:HIS155 3.4 60.0 1.0 CD2 B:HIS155 3.4 56.5 1.0 O B:HOH435 3.6 49.8 1.0 CG B:ASP157 3.9 36.3 1.0 CZ B:PHE261 4.1 31.8 1.0 CZ B:PHE240 4.1 30.7 1.0 ND1 B:HIS246 4.2 30.3 1.0 CE1 B:PHE261 4.3 30.4 1.0 CG B:HIS246 4.4 29.9 1.0 ND1 B:HIS155 4.4 63.4 1.0 CB B:ASP157 4.4 34.8 1.0 CG B:HIS155 4.5 57.9 1.0 CE2 B:PHE240 4.5 30.1 1.0 OD1 B:ASP157 4.9 38.7 1.0 N B:ASP157 4.9 30.5 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