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

Protein crystallography data

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

Zinc Binding Sites:

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 3w20

Go back to Zinc Binding Sites List in 3w20
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 3w20

Go back to Zinc Binding Sites List in 3w20
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

Reference:

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
Page generated: Wed Dec 16 04:56:51 2020

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