Zinc in PDB 2gbx: Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl

The structure of Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl, PDB code: 2gbx was solved by D.J.Ferraro, E.N.Brown, C.Yu, R.E.Parales, D.T.Gibson, S.Ramaswamy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.48 / 2.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	133.940, 133.940, 219.708, 90.00, 90.00, 120.00
R / Rfree (%)	23.7 / 26.8

The structure of Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl also contains other interesting chemical elements:

Iron

(Fe)

9 atoms

The binding sites of Zinc atom in the Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl (pdb code 2gbx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl, PDB code: 2gbx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl


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 Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn460 b:60.2 occ:1.00 O B:HOH491 2.0 23.4 1.0 ND1 B:HIS19 2.4 29.4 1.0 SD B:MET39 3.2 33.1 0.5 CE1 B:HIS19 3.3 29.4 1.0 CG B:HIS19 3.5 29.4 1.0 CE B:MET39 3.7 33.1 0.5 CB B:HIS19 3.8 29.4 1.0 CA B:HIS19 4.0 29.4 1.0 N B:PHE151 4.1 33.5 1.0 CG B:MET39 4.3 33.1 0.5 NE2 B:HIS19 4.4 29.4 1.0 CD2 B:HIS19 4.5 29.4 1.0 O B:PHE151 4.6 33.5 1.0 SD B:MET39 4.6 33.1 0.5 O B:HIS19 4.6 29.4 1.0 CA B:GLY150 4.7 33.6 1.0 C B:HIS19 4.8 29.4 1.0 CB B:PHE151 4.9 33.5 1.0 C B:GLY150 4.9 33.6 1.0 CG B:MET39 4.9 33.1 0.5 CA B:PHE151 5.0 33.5 1.0

Zinc binding site 2 out of 9 in the Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl


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 Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn464 b:51.8 occ:1.00 O B:HOH470 2.5 9.6 1.0 ND1 B:HIS136 2.5 31.7 1.0 O B:HOH469 2.5 10.2 1.0 O B:HOH476 2.8 13.5 1.0 CE1 B:HIS136 3.4 31.7 1.0 CG B:HIS136 3.6 31.7 1.0 CB B:ALA162 3.7 32.7 1.0 CB B:HIS136 3.9 31.7 1.0 CA B:HIS136 4.1 31.7 1.0 CG2 B:THR165 4.2 32.6 1.0 O B:VAL135 4.3 31.6 1.0 CA B:THR165 4.5 32.6 1.0 NE2 B:HIS136 4.6 31.7 1.0 CD2 B:HIS136 4.7 31.7 1.0 CD2 B:LEU170 4.7 32.8 1.0 N B:ALA162 4.8 32.7 1.0 OG1 B:THR165 4.8 32.6 1.0 CB B:THR165 4.8 32.6 1.0 CA B:ALA162 4.8 32.7 1.0 N B:THR137 4.9 31.9 1.0 N B:GLN166 4.9 32.7 1.0

Zinc binding site 3 out of 9 in the Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn468 b:83.9 occ:1.00 ND1 B:HIS45 2.6 34.4 1.0 O B:HOH495 3.0 46.5 1.0 CE1 B:HIS45 3.1 34.4 1.0 CG B:HIS45 3.3 34.4 1.0 CD B:ARG155 3.5 33.3 1.0 NE B:ARG155 3.5 33.3 1.0 CB B:HIS45 3.9 34.4 1.0 NE2 B:HIS45 4.0 34.4 1.0 CD2 B:HIS45 4.1 34.4 1.0 CZ B:ARG155 4.4 33.3 1.0 CG B:PRO65 4.5 37.7 1.0 CG B:ARG155 4.9 33.2 1.0 NH2 B:ARG155 5.0 33.3 1.0

Zinc binding site 4 out of 9 in the Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn462 b:54.5 occ:1.00 ND1 D:HIS136 2.4 34.8 1.0 O D:HOH471 2.5 13.0 1.0 O D:HOH489 2.5 33.9 1.0 O D:HOH470 2.7 2.4 1.0 CE1 D:HIS136 3.2 34.8 1.0 CG D:HIS136 3.5 34.8 1.0 CB D:HIS136 3.9 34.8 1.0 CB D:ALA162 4.1 36.0 1.0 CA D:HIS136 4.2 34.8 1.0 NE2 D:HIS136 4.4 34.8 1.0 O D:VAL135 4.4 34.6 1.0 CG2 D:THR165 4.5 35.9 1.0 CD2 D:LEU170 4.5 35.9 1.0 CD2 D:HIS136 4.6 34.8 1.0 CD2 D:LEU160 4.7 36.2 1.0 CA D:THR165 4.7 35.9 1.0 N D:ALA162 4.8 36.1 1.0 N D:THR137 4.9 34.9 1.0 OG1 D:THR165 4.9 35.9 1.0 CB D:THR165 5.0 35.9 1.0 CA D:ALA162 5.0 36.0 1.0

Zinc binding site 5 out of 9 in the Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn465 b:54.5 occ:1.00 O D:HOH488 2.1 33.7 1.0 ND1 D:HIS19 2.2 34.1 1.0 CE1 D:HIS19 3.1 34.1 1.0 CG D:HIS19 3.3 34.1 1.0 CB D:HIS19 3.7 34.1 1.0 SD D:MET39 3.8 36.9 0.5 CA D:HIS19 4.0 34.1 1.0 N D:PHE151 4.2 36.9 1.0 NE2 D:HIS19 4.3 34.1 1.0 CE D:MET39 4.3 36.9 0.5 CD2 D:HIS19 4.4 34.1 1.0 CE D:MET39 4.6 36.9 0.5 O D:PHE151 4.6 36.9 1.0 CA D:GLY150 4.6 36.9 1.0 O D:HIS19 4.7 34.1 1.0 CD2 D:PHE151 4.8 36.9 1.0 C D:HIS19 4.9 34.1 1.0 C D:GLY150 4.9 36.9 1.0 CG D:MET39 4.9 36.9 0.5 CB D:PHE151 4.9 36.9 1.0

Zinc binding site 6 out of 9 in the Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn469 b:98.8 occ:1.00 ND1 D:HIS45 2.3 38.8 1.0 CE1 D:HIS45 3.1 38.8 1.0 NE D:ARG155 3.2 36.6 1.0 CG D:HIS45 3.2 38.8 1.0 CD D:ARG155 3.3 36.6 1.0 CB D:HIS45 3.6 38.9 1.0 NE2 D:HIS45 4.1 38.8 1.0 CZ D:ARG155 4.2 36.6 1.0 CD2 D:HIS45 4.2 38.8 1.0 CG D:ARG155 4.6 36.6 1.0 NH2 D:ARG155 4.7 36.6 1.0 CG D:PRO65 4.8 44.0 1.0 O D:HIS45 4.9 39.0 1.0

Zinc binding site 7 out of 9 in the Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn463 b:54.9 occ:1.00 ND1 F:HIS136 2.4 33.6 1.0 O F:HOH468 2.5 10.3 1.0 O F:HOH469 2.8 2.4 1.0 CE1 F:HIS136 3.1 33.6 1.0 CG F:HIS136 3.5 33.6 1.0 CB F:HIS136 4.0 33.6 1.0 CB F:ALA162 4.1 34.5 1.0 CA F:HIS136 4.1 33.6 1.0 O F:VAL135 4.2 33.4 1.0 CG2 F:THR165 4.3 34.3 1.0 NE2 F:HIS136 4.3 33.6 1.0 CA F:THR165 4.5 34.3 1.0 CD2 F:HIS136 4.5 33.6 1.0 CD2 F:LEU170 4.6 34.2 1.0 N F:GLN166 4.7 34.2 1.0 CB F:THR165 4.8 34.2 1.0 OG1 F:THR165 4.9 34.3 1.0 N F:ALA162 5.0 34.6 1.0

Zinc binding site 8 out of 9 in the Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn466 b:84.9 occ:1.00 ND1 F:HIS45 2.3 34.0 1.0 O F:HOH470 2.6 52.8 1.0 CE1 F:HIS45 3.1 34.0 1.0 CG F:HIS45 3.3 34.0 1.0 CB F:HIS45 3.6 34.0 1.0 CD F:ARG155 4.0 35.6 1.0 CG F:ARG155 4.2 35.6 1.0 NE2 F:HIS45 4.2 34.0 1.0 CD2 F:HIS45 4.3 34.0 1.0 NE F:ARG155 4.4 35.6 1.0 O F:HIS45 4.7 34.1 1.0 CB F:ARG155 4.8 35.6 1.0 CE3 F:TRP47 4.8 34.4 1.0 CG F:PRO65 5.0 37.5 1.0

Zinc binding site 9 out of 9 in the Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn467 b:56.1 occ:1.00 ND1 F:HIS19 2.3 29.8 1.0 CE1 F:HIS19 3.1 29.8 1.0 CG F:HIS19 3.4 29.8 1.0 CB F:HIS19 3.8 29.8 1.0 N F:PHE151 3.8 36.0 1.0 CA F:HIS19 4.1 29.8 1.0 NE2 F:HIS19 4.3 29.8 1.0 CA F:GLY150 4.3 36.0 1.0 O F:PHE151 4.4 36.0 1.0 CD2 F:HIS19 4.4 29.8 1.0 CE F:MET39 4.5 32.8 1.0 C F:GLY150 4.5 36.0 1.0 CD2 F:PHE151 4.7 36.0 1.0 CA F:PHE151 4.7 36.0 1.0 CB F:PHE151 4.8 36.0 1.0 CG F:MET39 4.9 32.8 1.0 O F:HIS19 5.0 29.8 1.0 O F:HOH473 5.0 30.6 1.0

D.J.Ferraro, E.N.Brown, C.L.Yu, R.E.Parales, D.T.Gibson, S.Ramaswamy. Structural Investigations of the Ferredoxin and Terminal Oxygenase Components of the Biphenyl 2,3-Dioxygenase From Sphingobium Yanoikuyae B1. Bmc Struct.Biol. V. 7 10 2007.
ISSN: ESSN 1472-6807
PubMed: 17349044
DOI: 10.1186/1472-6807-7-10