Zinc in PDB 3mvi: Crystal Structure of Holo Mada at 1.6 A Resolution

All present enzymatic activity of Crystal Structure of Holo Mada at 1.6 A Resolution:
3.5.4.4;

The structure of Crystal Structure of Holo Mada at 1.6 A Resolution, PDB code: 3mvi was solved by W.Niu, Q.Shu, Z.Chen, S.Mathews, E.Di Cera, C.Frieden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.66 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.670, 93.804, 88.048, 90.00, 105.27, 90.00
R / Rfree (%)	16.8 / 20.5

The binding sites of Zinc atom in the Crystal Structure of Holo Mada at 1.6 A Resolution (pdb code 3mvi). 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 Holo Mada at 1.6 A Resolution, PDB code: 3mvi:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Holo Mada at 1.6 A Resolution


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 Holo Mada at 1.6 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:14.3 occ:1.00 O A:HOH616 2.1 12.5 1.0 NE2 A:HIS15 2.1 12.4 1.0 NE2 A:HIS17 2.1 8.9 1.0 NE2 A:HIS214 2.1 12.3 1.0 OD1 A:ASP295 2.4 12.0 1.0 CD2 A:HIS17 3.0 11.3 1.0 CE1 A:HIS15 3.0 11.1 1.0 CE1 A:HIS214 3.1 11.9 1.0 CE1 A:HIS17 3.1 11.7 1.0 CD2 A:HIS15 3.1 10.0 1.0 CD2 A:HIS214 3.2 11.2 1.0 O A:HOH672 3.2 29.8 1.0 CG A:ASP295 3.4 13.0 1.0 OD2 A:ASP295 3.7 15.7 1.0 NE2 A:HIS238 4.0 13.3 1.0 O A:HOH445 4.1 22.6 1.0 ND1 A:HIS17 4.2 11.2 1.0 ND1 A:HIS15 4.2 9.6 1.0 CG A:HIS17 4.2 11.4 1.0 ND1 A:HIS214 4.2 10.7 1.0 CG A:HIS15 4.2 10.1 1.0 CG A:HIS214 4.3 10.2 1.0 O A:HOH506 4.5 29.4 1.0 CB A:ASP295 4.7 12.6 1.0 OD2 A:ASP296 4.7 19.5 1.0 O A:HOH647 4.7 35.8 1.0 CE1 A:HIS238 4.8 13.4 1.0 CD2 A:HIS238 4.8 13.1 1.0 O A:HOH629 4.9 25.7 1.0 CD A:ARG101 4.9 11.6 1.0 NH1 A:ARG101 5.0 11.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Holo Mada at 1.6 A Resolution


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 Holo Mada at 1.6 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:16.7 occ:1.00 NE2 B:HIS15 2.1 11.2 1.0 NE2 B:HIS17 2.1 10.9 1.0 O B:HOH619 2.1 16.0 1.0 NE2 B:HIS214 2.1 11.9 1.0 OD1 B:ASP295 2.5 17.9 1.0 CD2 B:HIS17 3.0 10.2 1.0 CD2 B:HIS15 3.0 10.7 1.0 CE1 B:HIS214 3.1 13.1 1.0 CE1 B:HIS15 3.1 11.8 1.0 CD2 B:HIS214 3.1 12.5 1.0 CE1 B:HIS17 3.2 13.4 1.0 O B:HOH549 3.4 21.6 1.0 CG B:ASP295 3.5 15.7 1.0 NE2 B:HIS238 3.8 15.2 1.0 OD2 B:ASP295 3.8 15.5 1.0 O B:HOH501 4.1 24.7 1.0 ND1 B:HIS15 4.2 11.5 1.0 CG B:HIS15 4.2 10.3 1.0 ND1 B:HIS214 4.2 12.9 1.0 CG B:HIS17 4.2 10.5 1.0 ND1 B:HIS17 4.2 10.7 1.0 CG B:HIS214 4.3 12.3 1.0 O B:HOH583 4.6 30.6 1.0 CD2 B:HIS238 4.6 13.5 1.0 O B:HOH554 4.7 26.0 1.0 CE1 B:HIS238 4.7 14.7 1.0 CB B:ASP295 4.8 11.9 1.0 CD B:ARG101 4.9 10.6 1.0 OD2 B:ASP296 4.9 17.6 1.0 O B:HOH509 5.0 28.1 1.0 NH1 B:ARG101 5.0 13.4 1.0

W.Niu, Q.Shu, Z.Chen, S.Mathews, E.Di Cera, C.Frieden. The Role of ZN2+ on the Structure and Stability of Murine Adenosine Deaminase. J.Phys.Chem.B V. 114 16156 2010.
ISSN: ISSN 1089-5647
PubMed: 20815357
DOI: 10.1021/JP106041V