Zinc in PDB 2vad: Monomeric Red Fluorescent Protein, Dsred.M1

The structure of Monomeric Red Fluorescent Protein, Dsred.M1, PDB code: 2vad was solved by D.E.Strongin, B.Bevis, N.Khuong, M.E.Downing, R.L.Strack, K.Sundaram, B.S.Glick, R.J.Keenan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.34 / 1.59
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.892, 62.151, 81.882, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 19.7

The structure of Monomeric Red Fluorescent Protein, Dsred.M1 also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Zinc atom in the Monomeric Red Fluorescent Protein, Dsred.M1 (pdb code 2vad). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Monomeric Red Fluorescent Protein, Dsred.M1, PDB code: 2vad:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Monomeric Red Fluorescent Protein, Dsred.M1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Monomeric Red Fluorescent Protein, Dsred.M1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1224 b:14.9 occ:0.75 NE2 A:HIS75 2.1 16.6 1.0 NE2 A:HIS193 2.1 19.4 1.0 CL A:CL1227 2.3 15.7 0.8 CL A:CL1228 2.3 18.1 0.8 CE1 A:HIS75 3.0 15.2 1.0 CE1 A:HIS193 3.0 17.9 1.0 CD2 A:HIS75 3.2 13.9 1.0 CD2 A:HIS193 3.2 15.7 1.0 O A:HOH2058 3.6 20.7 1.0 ND1 A:HIS75 4.2 13.8 1.0 ND1 A:HIS193 4.2 16.3 1.0 CG A:HIS75 4.3 12.6 1.0 CG A:HIS193 4.3 15.8 1.0 CG2 A:VAL195 4.4 15.1 1.0 CB A:ALA219 4.6 14.1 1.0 O A:PRO80 4.6 15.7 1.0 CD1 A:LEU150 4.7 20.6 1.0 CD2 A:LEU157 4.8 17.5 1.0 CG2 A:ILE79 4.8 15.9 1.0 CE A:MET83 4.9 23.5 1.0

Zinc binding site 2 out of 3 in the Monomeric Red Fluorescent Protein, Dsred.M1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Monomeric Red Fluorescent Protein, Dsred.M1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1225 b:16.5 occ:1.00 OD2 A:ASP78 2.0 16.8 1.0 NE2 A:HIS221 2.0 16.4 1.0 CL A:CL1229 2.2 21.0 1.0 CG A:ASP78 2.7 17.7 1.0 OD1 A:ASP78 2.8 16.9 1.0 CD2 A:HIS221 3.0 14.9 1.0 CE1 A:HIS221 3.0 14.6 1.0 O A:HOH2055 4.1 29.4 1.0 O A:HOH2056 4.1 24.8 1.0 ND1 A:HIS221 4.2 16.2 1.0 CB A:ASP78 4.2 15.2 1.0 CG A:HIS221 4.2 15.5 1.0

Zinc binding site 3 out of 3 in the Monomeric Red Fluorescent Protein, Dsred.M1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Monomeric Red Fluorescent Protein, Dsred.M1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1226 b:17.6 occ:0.50 NE2 A:HIS172 1.9 13.6 0.5 OE2 A:GLU144 2.0 19.5 0.5 CE1 A:HIS172 2.8 16.3 0.5 CD A:GLU144 2.9 21.7 0.5 CD2 A:HIS172 3.0 15.8 0.5 OE1 A:GLU144 3.3 22.8 0.5 ND1 A:HIS172 4.0 16.4 0.5 CG A:HIS172 4.1 16.8 0.5 CG A:GLU144 4.2 21.8 1.0

D.E.Strongin, B.Bevis, N.Khuong, M.E.Downing, R.L.Strack, K.Sundaram, B.S.Glick, R.J.Keenan. Structural Rearrangements Near the Chromophore Influence the Maturation Speed and Brightness of Dsred Variants. Protein Eng.Des.Sel. V. 20 525 2007.
ISSN: ISSN 1741-0126
PubMed: 17962222
DOI: 10.1093/PROTEIN/GZM046