Zinc in PDB 6eyv: Crystal Structure of the Pyoverdine Maturation Protein Pvdp in Complex with the Mock Substrates L-Tyrosine and Zinc.

The structure of Crystal Structure of the Pyoverdine Maturation Protein Pvdp in Complex with the Mock Substrates L-Tyrosine and Zinc., PDB code: 6eyv was solved by J.Poppe, W.Blankenfeldt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.09 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.332, 109.143, 82.510, 90.00, 95.66, 90.00
R / Rfree (%)	20.5 / 26.2

The binding sites of Zinc atom in the Crystal Structure of the Pyoverdine Maturation Protein Pvdp in Complex with the Mock Substrates L-Tyrosine and Zinc. (pdb code 6eyv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Pyoverdine Maturation Protein Pvdp in Complex with the Mock Substrates L-Tyrosine and Zinc., PDB code: 6eyv:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Pyoverdine Maturation Protein Pvdp in Complex with the Mock Substrates L-Tyrosine and Zinc.


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 the Pyoverdine Maturation Protein Pvdp in Complex with the Mock Substrates L-Tyrosine and Zinc. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn900 b:33.7 occ:1.00 O B:HOH1009 1.9 31.8 1.0 NE2 B:HIS220 2.0 25.5 1.0 NE2 B:HIS216 2.1 33.1 1.0 NE2 B:HIS271 2.3 22.4 1.0 HH B:TYR902 2.8 51.7 1.0 CE1 B:HIS216 2.8 30.5 1.0 CD2 B:HIS220 2.9 24.3 1.0 HE1 B:HIS216 2.9 36.8 1.0 HD2 B:HIS220 3.0 29.4 1.0 CE1 B:HIS220 3.1 29.3 1.0 CD2 B:HIS216 3.2 30.4 1.0 CD2 B:HIS271 3.2 23.1 1.0 HD2 B:HIS271 3.3 27.9 1.0 CE1 B:HIS271 3.3 27.8 1.0 HE1 B:HIS220 3.4 35.4 1.0 HD2 B:HIS216 3.5 36.8 1.0 OH B:TYR902 3.5 42.9 1.0 HE1 B:MET270 3.5 36.3 1.0 HE1 B:HIS271 3.6 33.6 1.0 ZN B:ZN901 3.8 53.2 1.0 HE2 B:PHE428 3.9 44.0 1.0 HZ B:PHE428 3.9 38.3 1.0 ND1 B:HIS216 3.9 25.8 1.0 HE2 B:TYR902 4.1 39.3 1.0 CG B:HIS220 4.1 27.3 1.0 ND1 B:HIS220 4.1 28.2 1.0 CG B:HIS216 4.1 33.4 1.0 HE3 B:MET270 4.2 36.3 1.0 CE B:MET270 4.3 30.1 1.0 CG B:HIS271 4.4 23.2 1.0 HE1 B:MET274 4.4 40.2 1.0 ND1 B:HIS271 4.4 26.7 1.0 CZ B:TYR902 4.4 26.5 1.0 HB3 B:PRO419 4.5 31.2 1.0 HE1 B:HIS375 4.5 35.9 1.0 HE1 B:HIS432 4.6 32.2 1.0 CE2 B:PHE428 4.6 36.5 1.0 CE2 B:TYR902 4.6 32.6 1.0 CZ B:PHE428 4.6 31.8 1.0 NE2 B:HIS375 4.6 25.3 1.0 HE2 B:MET270 4.6 36.3 1.0 HD1 B:HIS216 4.7 31.1 1.0 HE3 B:TRP219 4.7 36.1 1.0 HZ3 B:TRP219 4.7 31.6 1.0 HG B:SER422 4.8 37.3 1.0 NE2 B:HIS432 4.8 21.2 1.0 CE1 B:HIS375 4.9 29.7 1.0 CE1 B:HIS432 4.9 26.7 1.0 HE1 B:PHE267 4.9 27.6 1.0 HD1 B:HIS220 4.9 34.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Pyoverdine Maturation Protein Pvdp in Complex with the Mock Substrates L-Tyrosine and Zinc.


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 the Pyoverdine Maturation Protein Pvdp in Complex with the Mock Substrates L-Tyrosine and Zinc. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:53.2 occ:1.00 O B:HOH1009 2.0 31.8 1.0 NE2 B:HIS432 2.1 21.2 1.0 NE2 B:HIS375 2.1 25.3 1.0 NE2 B:HIS379 2.1 35.4 1.0 HE2 B:PHE428 2.8 44.0 1.0 HE1 B:HIS379 2.8 37.8 1.0 CE1 B:HIS379 2.8 31.3 1.0 CE1 B:HIS375 2.9 29.7 1.0 CE1 B:HIS432 3.0 26.7 1.0 HE1 B:HIS432 3.1 32.2 1.0 HE1 B:HIS375 3.1 35.9 1.0 CD2 B:HIS375 3.1 23.1 1.0 CD2 B:HIS432 3.2 25.1 1.0 CD2 B:HIS379 3.3 28.4 1.0 CE2 B:PHE428 3.4 36.5 1.0 HD2 B:HIS375 3.4 27.9 1.0 HD2 B:HIS432 3.5 30.4 1.0 HD2 B:HIS379 3.7 34.3 1.0 HE1 B:PHE431 3.7 36.3 1.0 OH B:TYR902 3.8 42.9 1.0 ZN B:ZN900 3.8 33.7 1.0 ND1 B:HIS379 4.0 28.3 1.0 HZ B:PHE428 4.0 38.3 1.0 ND1 B:HIS375 4.0 28.5 1.0 CZ B:PHE428 4.1 31.8 1.0 HD2 B:PHE428 4.1 41.0 1.0 HH B:TYR902 4.1 51.7 1.0 CD2 B:PHE428 4.1 34.0 1.0 ND1 B:HIS432 4.1 21.1 1.0 CZ B:TYR902 4.2 26.5 1.0 CG B:HIS375 4.2 24.9 1.0 HD2 B:HIS271 4.2 27.9 1.0 CG B:HIS379 4.3 28.4 1.0 CG B:HIS432 4.3 24.8 1.0 NE2 B:HIS271 4.3 22.4 1.0 HE1 B:HIS216 4.3 36.8 1.0 HE1 B:TYR902 4.4 37.3 1.0 CE1 B:TYR902 4.4 30.9 1.0 HG B:SER422 4.4 37.3 1.0 HE1 B:PHE267 4.4 27.6 1.0 CD2 B:HIS271 4.5 23.1 1.0 CE1 B:PHE431 4.5 30.0 1.0 HZ B:PHE431 4.5 31.0 1.0 HD1 B:HIS379 4.7 34.2 1.0 HD1 B:HIS375 4.8 34.5 1.0 CE2 B:TYR902 4.8 32.6 1.0 HD1 B:HIS432 4.9 25.6 1.0 CZ B:PHE431 5.0 25.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Pyoverdine Maturation Protein Pvdp in Complex with the Mock Substrates L-Tyrosine and Zinc.


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 the Pyoverdine Maturation Protein Pvdp in Complex with the Mock Substrates L-Tyrosine and Zinc. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:37.3 occ:1.00 O A:HOH701 2.0 43.8 1.0 NE2 A:HIS220 2.0 28.5 1.0 NE2 A:HIS271 2.3 22.6 1.0 NE2 A:HIS216 2.3 42.4 1.0 HH A:TYR603 2.5 55.0 1.0 CE1 A:HIS216 2.9 41.7 1.0 HE1 A:HIS216 3.0 50.2 1.0 CD2 A:HIS220 3.0 27.7 1.0 CE1 A:HIS220 3.0 32.8 1.0 HD2 A:HIS220 3.1 33.5 1.0 CD2 A:HIS271 3.1 27.9 1.0 OH A:TYR603 3.2 45.6 1.0 HD2 A:HIS271 3.2 33.7 1.0 HE1 A:HIS220 3.3 39.6 1.0 CE1 A:HIS271 3.4 26.3 1.0 CD2 A:HIS216 3.4 39.3 1.0 ZN A:ZN602 3.5 55.6 1.0 HE1 A:HIS271 3.6 31.8 1.0 HE1 A:MET270 3.7 35.3 1.0 HE2 A:PHE428 3.7 46.1 1.0 HD2 A:HIS216 3.7 47.4 1.0 HZ A:PHE428 3.7 43.9 1.0 HE1 A:MET274 3.9 45.3 1.0 ND1 A:HIS216 4.0 33.4 1.0 HE2 A:TYR603 4.1 37.7 1.0 CG A:HIS220 4.1 28.0 1.0 ND1 A:HIS220 4.1 29.4 1.0 CZ A:TYR603 4.2 27.7 1.0 CG A:HIS216 4.3 36.6 1.0 HE1 A:HIS432 4.3 37.3 1.0 HE3 A:MET270 4.3 35.3 1.0 CG A:HIS271 4.4 25.7 1.0 HE1 A:HIS375 4.4 36.4 1.0 NE2 A:HIS375 4.4 27.2 1.0 CE2 A:PHE428 4.4 38.2 1.0 HB3 A:PRO419 4.4 34.5 1.0 CZ A:PHE428 4.4 36.4 1.0 ND1 A:HIS271 4.4 28.0 1.0 CE A:MET270 4.4 29.2 1.0 HG A:SER422 4.5 41.0 1.0 CE2 A:TYR603 4.6 31.2 1.0 NE2 A:HIS432 4.6 23.0 1.0 CE1 A:HIS432 4.7 30.9 1.0 CE1 A:HIS375 4.7 30.2 1.0 HD1 A:HIS216 4.7 40.4 1.0 CE A:MET274 4.8 37.6 1.0 HE2 A:MET270 4.8 35.3 1.0 HE1 A:PHE267 4.9 36.9 1.0 HE1 A:HIS379 4.9 35.1 1.0 HD1 A:HIS220 4.9 35.5 1.0 HZ3 A:TRP219 4.9 31.3 1.0 HE2 A:MET274 4.9 45.3 1.0 HE3 A:TRP219 4.9 32.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Pyoverdine Maturation Protein Pvdp in Complex with the Mock Substrates L-Tyrosine and Zinc.


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 the Pyoverdine Maturation Protein Pvdp in Complex with the Mock Substrates L-Tyrosine and Zinc. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:55.6 occ:1.00 O A:HOH701 1.9 43.8 1.0 NE2 A:HIS375 2.1 27.2 1.0 NE2 A:HIS379 2.1 33.0 1.0 NE2 A:HIS432 2.1 23.0 1.0 HE2 A:PHE428 2.7 46.1 1.0 HE1 A:HIS379 2.7 35.1 1.0 CE1 A:HIS379 2.8 29.1 1.0 CE1 A:HIS375 2.9 30.2 1.0 CE1 A:HIS432 3.0 30.9 1.0 HE1 A:HIS432 3.0 37.3 1.0 HE1 A:HIS375 3.1 36.4 1.0 CD2 A:HIS375 3.1 28.9 1.0 CD2 A:HIS432 3.3 24.4 1.0 CD2 A:HIS379 3.3 24.1 1.0 HD2 A:HIS375 3.3 34.9 1.0 CE2 A:PHE428 3.4 38.2 1.0 ZN A:ZN601 3.5 37.3 1.0 HD2 A:HIS432 3.5 29.6 1.0 HE1 A:PHE431 3.7 36.2 1.0 HD2 A:HIS379 3.7 29.1 1.0 OH A:TYR603 3.9 45.6 1.0 HH A:TYR603 3.9 55.0 1.0 HZ A:PHE428 4.0 43.9 1.0 ND1 A:HIS379 4.0 25.0 1.0 ND1 A:HIS375 4.0 29.4 1.0 CZ A:PHE428 4.0 36.4 1.0 CZ A:TYR603 4.1 27.7 1.0 CG A:HIS375 4.1 27.8 1.0 HD2 A:PHE428 4.1 45.1 1.0 CD2 A:PHE428 4.1 37.4 1.0 ND1 A:HIS432 4.1 27.6 1.0 HD2 A:HIS271 4.2 33.7 1.0 CG A:HIS379 4.3 22.8 1.0 NE2 A:HIS271 4.3 22.6 1.0 CG A:HIS432 4.3 25.7 1.0 HG A:SER422 4.3 41.0 1.0 HE1 A:HIS216 4.4 50.2 1.0 CE2 A:TYR603 4.4 31.2 1.0 HE1 A:PHE267 4.4 36.9 1.0 CD2 A:HIS271 4.5 27.9 1.0 HZ A:PHE431 4.5 32.9 1.0 CE1 A:PHE431 4.5 30.0 1.0 HE2 A:TYR603 4.5 37.7 1.0 CE1 A:TYR603 4.6 31.2 1.0 HD1 A:HIS379 4.7 30.3 1.0 HD1 A:HIS375 4.8 35.5 1.0 HE1 A:HIS220 4.8 39.6 1.0 NE2 A:HIS220 4.9 28.5 1.0 HD1 A:HIS432 4.9 33.3 1.0 HE1 A:TYR603 4.9 37.6 1.0 CZ A:PHE431 4.9 27.2 1.0 OG A:SER422 4.9 34.0 1.0 HB2 A:SER422 5.0 34.5 1.0

J.Poppe, J.Reichelt, W.Blankenfeldt. Pseudomonas Aeruginosapyoverdine Maturation Enzyme Pvdp Has A Noncanonical Domain Architecture and Affords Insight Into A New Subclass of Tyrosinases. J. Biol. Chem. V. 293 14926 2018.
ISSN: ESSN 1083-351X
PubMed: 30030378
DOI: 10.1074/JBC.RA118.002560