Zinc in PDB 2rh6: Structure of Xac Npp For Evaluation of Refinement Methodology

All present enzymatic activity of Structure of Xac Npp For Evaluation of Refinement Methodology:
3.6.1.9;

The structure of Structure of Xac Npp For Evaluation of Refinement Methodology, PDB code: 2rh6 was solved by J.G.Zalatan, T.D.Fenn, A.T.Brunger, D.Hershlag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.90 / 1.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.049, 78.620, 129.953, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 21.1

The binding sites of Zinc atom in the Structure of Xac Npp For Evaluation of Refinement Methodology (pdb code 2rh6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Xac Npp For Evaluation of Refinement Methodology, PDB code: 2rh6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Xac Npp For Evaluation of Refinement Methodology


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Xac Npp For Evaluation of Refinement Methodology within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:14.6 occ:1.00 OD2 A:ASP257 2.0 13.5 1.0 OD1 A:ASP54 2.0 14.8 1.0 OG1 A:THR90 2.1 13.9 1.0 NE2 A:HIS258 2.2 13.9 1.0 O1P A:AMP433 2.5 36.5 1.0 CG A:ASP54 2.7 12.9 1.0 CG A:ASP257 2.8 13.6 1.0 OD2 A:ASP54 2.9 14.1 1.0 OD1 A:ASP257 3.0 12.7 1.0 CD2 A:HIS258 3.0 12.2 1.0 CB A:THR90 3.1 12.6 1.0 CE1 A:HIS258 3.1 12.1 1.0 CG2 A:THR90 3.3 12.4 1.0 CA A:THR90 3.5 12.4 1.0 P A:AMP433 3.9 35.9 1.0 OD1 A:ASP210 4.0 16.5 1.0 N A:THR90 4.0 12.2 1.0 CE1 A:HIS363 4.1 12.8 1.0 CB A:ASP54 4.1 11.7 1.0 CG A:HIS258 4.1 11.5 1.0 ND1 A:HIS258 4.2 12.0 1.0 CG A:ASP210 4.2 13.6 1.0 CB A:ASP257 4.2 11.3 1.0 O2P A:AMP433 4.2 29.4 1.0 NE2 A:HIS363 4.3 11.9 1.0 N A:GLY55 4.3 12.4 1.0 ZN A:ZN2 4.3 14.9 1.0 CE1 A:HIS94 4.4 12.6 1.0 OD2 A:ASP210 4.5 16.2 1.0 C5' A:AMP433 4.5 37.5 1.0 CA A:ASP54 4.5 11.9 1.0 O5' A:AMP433 4.5 37.0 1.0 C A:LEU89 4.7 12.6 1.0 C A:ASP54 4.7 12.0 1.0 ND1 A:HIS363 4.8 12.0 1.0 ND1 A:HIS94 4.8 12.5 1.0 CB A:ASP210 4.8 13.4 1.0 C A:THR90 4.8 12.3 1.0 CA A:GLY55 4.9 12.8 1.0 O3P A:AMP433 5.0 35.5 1.0

Zinc binding site 2 out of 4 in the Structure of Xac Npp For Evaluation of Refinement Methodology


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Xac Npp For Evaluation of Refinement Methodology within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:14.9 occ:1.00 O3P A:AMP433 1.9 35.5 1.0 NE2 A:HIS214 2.0 16.5 1.0 NE2 A:HIS363 2.1 11.9 1.0 OD2 A:ASP210 2.2 16.2 1.0 O1P A:AMP433 2.3 36.5 1.0 OD1 A:ASP210 2.4 16.5 1.0 P A:AMP433 2.5 35.9 1.0 CG A:ASP210 2.6 13.6 1.0 CE1 A:HIS214 2.9 13.6 1.0 CD2 A:HIS363 3.0 13.3 1.0 CD2 A:HIS214 3.1 16.2 1.0 CE1 A:HIS363 3.1 12.8 1.0 O5' A:AMP433 3.7 37.0 1.0 O2P A:AMP433 3.7 29.4 1.0 O A:HOH534 4.1 24.8 1.0 ND1 A:HIS214 4.1 16.9 1.0 C5' A:AMP433 4.1 37.5 1.0 CB A:ASP210 4.1 13.4 1.0 CG A:HIS363 4.2 11.7 1.0 CG A:HIS214 4.2 14.6 1.0 OG1 A:THR90 4.2 13.9 1.0 ND1 A:HIS363 4.2 12.0 1.0 CE1 A:HIS258 4.2 12.1 1.0 NE2 A:HIS258 4.3 13.9 1.0 ZN A:ZN1 4.3 14.6 1.0 OD1 A:ASP54 4.6 14.8 1.0 CE A:MET260 4.7 16.2 1.0 O A:ASP210 4.7 14.5 1.0 O A:HOH441 4.8 15.6 1.0 CA A:ASP210 5.0 14.0 1.0

Zinc binding site 3 out of 4 in the Structure of Xac Npp For Evaluation of Refinement Methodology


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Xac Npp For Evaluation of Refinement Methodology within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1 b:14.8 occ:1.00 OD2 B:ASP257 2.0 13.5 1.0 OD1 B:ASP54 2.1 13.7 1.0 NE2 B:HIS258 2.1 13.5 1.0 OG1 B:THR90 2.1 15.7 1.0 O1P B:AMP433 2.5 34.8 1.0 CG B:ASP54 2.8 13.2 1.0 CG B:ASP257 2.9 13.4 1.0 OD2 B:ASP54 2.9 15.2 1.0 CD2 B:HIS258 3.0 12.1 1.0 CE1 B:HIS258 3.0 12.3 1.0 OD1 B:ASP257 3.1 11.8 1.0 CB B:THR90 3.1 13.8 1.0 CG2 B:THR90 3.5 14.2 1.0 CA B:THR90 3.5 13.6 1.0 OD1 B:ASP210 3.8 16.9 1.0 P B:AMP433 3.9 34.6 1.0 N B:THR90 4.0 13.5 1.0 CG B:HIS258 4.1 12.2 1.0 ND1 B:HIS258 4.1 12.2 1.0 CB B:ASP54 4.1 12.0 1.0 CG B:ASP210 4.2 14.9 1.0 O2P B:AMP433 4.2 24.7 1.0 N B:GLY55 4.2 12.4 1.0 CE1 B:HIS363 4.2 14.1 1.0 CB B:ASP257 4.3 11.5 1.0 ZN B:ZN2 4.4 14.8 1.0 NE2 B:HIS363 4.4 11.5 1.0 C5' B:AMP433 4.4 34.0 1.0 CA B:ASP54 4.5 11.8 1.0 O5' B:AMP433 4.5 32.8 1.0 OD2 B:ASP210 4.5 17.6 1.0 CE1 B:HIS94 4.6 13.9 1.0 C B:ASP54 4.7 11.8 1.0 C B:LEU89 4.7 13.8 1.0 CB B:ASP210 4.8 12.8 1.0 C B:THR90 4.9 13.8 1.0 ND1 B:HIS363 4.9 13.3 1.0 CA B:GLY55 4.9 12.6 1.0 ND1 B:HIS94 5.0 14.4 1.0

Zinc binding site 4 out of 4 in the Structure of Xac Npp For Evaluation of Refinement Methodology


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Xac Npp For Evaluation of Refinement Methodology within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2 b:14.8 occ:1.00 NE2 B:HIS214 2.0 16.3 1.0 NE2 B:HIS363 2.1 11.5 1.0 O3P B:AMP433 2.1 31.5 1.0 OD1 B:ASP210 2.3 16.9 1.0 O1P B:AMP433 2.3 34.8 1.0 OD2 B:ASP210 2.4 17.6 1.0 CG B:ASP210 2.7 14.9 1.0 P B:AMP433 2.7 34.6 1.0 CE1 B:HIS214 2.9 13.6 1.0 CD2 B:HIS363 3.0 13.8 1.0 CD2 B:HIS214 3.1 14.7 1.0 CE1 B:HIS363 3.1 14.1 1.0 O2P B:AMP433 3.8 24.7 1.0 O B:HOH588 3.9 28.4 1.0 O5' B:AMP433 3.9 32.8 1.0 ND1 B:HIS214 4.1 16.7 1.0 CB B:ASP210 4.2 12.8 1.0 CG B:HIS214 4.2 14.6 1.0 C5' B:AMP433 4.2 34.0 1.0 CE1 B:HIS258 4.2 12.3 1.0 CG B:HIS363 4.2 11.7 1.0 ND1 B:HIS363 4.2 13.3 1.0 NE2 B:HIS258 4.3 13.5 1.0 OG1 B:THR90 4.3 15.7 1.0 ZN B:ZN1 4.4 14.8 1.0 CE B:MET260 4.6 17.3 1.0 OD1 B:ASP54 4.6 13.7 1.0 O B:ASP210 4.7 13.1 1.0 O B:HOH455 4.7 17.3 1.0 CA B:ASP210 4.9 13.6 1.0 C B:ASP210 5.0 13.9 1.0

T.D.Fenn, E.Pozharski, M.A.Wilson. Crystallographic Goodness of Fit: A New Treatment of Model Complexity To Be Published.