Zinc in PDB 4h54: Crystal Structure of the Diguanylate Cyclase Dgcz

All present enzymatic activity of Crystal Structure of the Diguanylate Cyclase Dgcz:
2.7.7.65;

The structure of Crystal Structure of the Diguanylate Cyclase Dgcz, PDB code: 4h54 was solved by F.Zaehringer, T.Schirmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	73.20 / 3.90
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	102.593, 102.593, 129.156, 90.00, 90.00, 120.00
R / Rfree (%)	24.2 / 24.1

The structure of Crystal Structure of the Diguanylate Cyclase Dgcz also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Diguanylate Cyclase Dgcz (pdb code 4h54). 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 the Diguanylate Cyclase Dgcz, PDB code: 4h54:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Diguanylate Cyclase Dgcz


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 Diguanylate Cyclase Dgcz within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:28.7 occ:1.00 NE2 A:HIS83 2.1 36.7 1.0 NE2 A:HIS22 2.2 23.6 1.0 NE2 A:HIS79 2.3 33.4 1.0 CE1 A:HIS83 2.6 36.6 1.0 CE1 A:HIS22 3.0 24.7 1.0 CE1 A:HIS79 3.0 38.2 1.0 CD2 A:HIS22 3.2 21.2 1.0 CD2 A:HIS83 3.3 43.2 1.0 CD2 A:HIS79 3.4 34.5 1.0 ND1 A:HIS83 3.8 42.9 1.0 ND1 A:HIS22 4.1 23.9 1.0 CG A:HIS83 4.2 47.4 1.0 ND1 A:HIS79 4.3 43.3 1.0 CG A:HIS22 4.3 21.1 1.0 CG A:HIS79 4.5 42.8 1.0 CE A:MET82 4.6 21.4 1.0 CB A:PHE54 4.9 32.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Diguanylate Cyclase Dgcz


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 Diguanylate Cyclase Dgcz within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:29.3 occ:1.00 NE2 B:HIS83 2.0 45.2 1.0 NE2 B:HIS79 2.1 33.0 1.0 NE2 B:HIS22 2.2 21.1 1.0 CE1 B:HIS83 2.6 50.0 1.0 CE1 B:HIS79 2.9 43.5 1.0 CE1 B:HIS22 3.0 18.8 1.0 CD2 B:HIS83 3.2 56.7 1.0 CD2 B:HIS79 3.2 34.1 1.0 CD2 B:HIS22 3.3 20.0 1.0 ND1 B:HIS83 3.8 63.0 1.0 ND1 B:HIS79 4.1 52.3 1.0 CG B:HIS83 4.1 67.8 1.0 ND1 B:HIS22 4.2 16.6 1.0 CG B:HIS79 4.3 45.8 1.0 CG B:HIS22 4.3 17.1 1.0 CE B:MET82 4.4 33.8 1.0

F.Zahringer, E.Lacanna, U.Jenal, T.Schirmer, A.Boehm. Structure and Signaling Mechanism of A Zinc-Sensory Diguanylate Cyclase. Structure V. 21 1149 2013.
ISSN: ISSN 0969-2126
PubMed: 23769666
DOI: 10.1016/J.STR.2013.04.026