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

Protein crystallography data

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

Other elements in 2vad:

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

Chlorine (Cl) 3 atoms

Zinc Binding Sites:

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 2vad

Go back to Zinc Binding Sites List in 2vad
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 2vad

Go back to Zinc Binding Sites List in 2vad
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 2vad

Go back to Zinc Binding Sites List in 2vad
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

Reference:

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
Page generated: Wed Dec 16 03:54:56 2020

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