Zinc in PDB 4kw9: Crystal Structure of Green Fluorescent Protein

The structure of Crystal Structure of Green Fluorescent Protein, PDB code: 4kw9 was solved by T.J.Barnard, X.Yu, N.Noinaj, J.W.Taraska, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.33 / 1.80
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	72.798, 72.798, 114.942, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 21

The structure of Crystal Structure of Green Fluorescent Protein also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Green Fluorescent Protein (pdb code 4kw9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Green Fluorescent Protein, PDB code: 4kw9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of Green Fluorescent Protein


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 Green Fluorescent Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:15.4 occ:0.91 NE2 A:HIS204 2.0 13.3 1.0 ND1 A:HIS202 2.0 12.2 1.0 CL A:CL306 2.2 14.2 1.0 HB3 A:HIS202 2.8 15.6 1.0 CE1 A:HIS204 2.9 14.0 1.0 CG A:HIS202 3.0 12.4 1.0 CE1 A:HIS202 3.0 12.9 1.0 CD2 A:HIS204 3.1 13.8 1.0 HE1 A:HIS204 3.1 16.8 1.0 HE1 A:HIS202 3.2 15.5 1.0 HD2 A:HIS204 3.3 16.6 1.0 CB A:HIS202 3.3 13.0 1.0 HA A:HIS202 3.5 14.0 1.0 HB2 A:HIS147 3.7 17.5 1.0 CA A:HIS202 4.0 11.7 1.0 ND1 A:HIS204 4.1 14.8 1.0 NE2 A:HIS202 4.1 14.4 1.0 CD2 A:HIS202 4.1 14.4 1.0 O A:HOH499 4.1 27.2 1.0 HB2 A:HIS202 4.1 15.6 1.0 CG A:HIS204 4.2 13.9 1.0 H A:THR203 4.5 14.3 1.0 HG2 A:LYS149 4.5 16.3 1.0 CB A:HIS147 4.6 14.6 1.0 HG3 A:LYS149 4.6 16.3 1.0 HD1 A:HIS147 4.7 20.8 1.0 C A:HIS202 4.7 11.7 1.0 HE2 A:LYS149 4.8 35.6 1.0 N A:THR203 4.8 11.9 1.0 HB3 A:HIS147 4.8 17.5 1.0 HD1 A:HIS204 4.8 17.7 1.0 HE2 A:TYR200 4.9 15.0 1.0 HE2 A:HIS202 4.9 17.3 1.0 HD2 A:HIS202 5.0 17.3 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Green Fluorescent Protein


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 Green Fluorescent Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:40.9 occ:0.70 NE2 A:HIS147 2.1 17.9 1.0 O A:HOH586 2.1 35.4 1.0 O A:HOH525 2.1 31.1 1.0 O A:HOH415 2.1 17.0 0.9 CE1 A:HIS147 2.9 16.8 1.0 HE1 A:HIS147 3.0 20.2 1.0 CD2 A:HIS147 3.2 17.1 1.0 HD2 A:HIS147 3.4 20.6 1.0 ND1 A:HIS147 4.1 17.3 1.0 CG A:HIS147 4.2 15.7 1.0 HD1 A:HIS147 4.9 20.8 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Green Fluorescent Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Green Fluorescent Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:32.4 occ:0.64 ND1 A:HIS169 2.0 36.2 1.0 O A:HOH439 2.2 11.6 0.6 O A:HOH410 2.2 20.3 1.0 O A:HOH404 2.3 12.4 1.0 CE1 A:HIS169 2.8 36.4 1.0 HE1 A:HIS169 2.8 43.7 1.0 CG A:HIS169 3.2 33.7 1.0 HB2 A:HIS169 3.2 40.4 1.0 HE2 A:PHE100 3.3 22.4 1.0 HG1 A:THR167 3.4 38.5 1.0 HG22 A:THR59 3.7 21.9 1.0 CB A:HIS169 3.8 33.6 1.0 OG1 A:THR167 3.8 32.1 1.0 NE2 A:HIS169 4.0 34.4 1.0 HB A:THR167 4.0 33.1 1.0 HA A:THR59 4.0 23.4 1.0 HD11 A:LEU141 4.1 48.3 1.0 H A:HIS169 4.1 42.5 1.0 HB2 A:ALA179 4.2 22.2 1.0 CE2 A:PHE100 4.2 18.7 1.0 CD2 A:HIS169 4.2 36.2 1.0 HG3 A:GLN177 4.3 33.4 1.0 N A:HIS169 4.3 35.5 1.0 HD13 A:LEU141 4.3 48.3 1.0 HB3 A:ALA179 4.3 22.2 1.0 HG2 A:GLN177 4.4 33.4 1.0 HB3 A:GLN177 4.5 38.6 1.0 CB A:THR167 4.5 27.6 1.0 HB3 A:HIS169 4.5 40.4 1.0 HD2 A:PHE100 4.5 24.3 1.0 CD1 A:LEU141 4.5 40.2 1.0 HD12 A:LEU141 4.5 48.3 1.0 O A:GLN177 4.5 29.6 1.0 CG2 A:THR59 4.6 18.3 1.0 CA A:HIS169 4.7 35.7 1.0 CB A:ALA179 4.7 18.5 1.0 HE2 A:HIS169 4.7 41.2 1.0 C A:ARG168 4.8 34.9 1.0 CG A:GLN177 4.8 27.9 1.0 HA A:ARG168 4.8 45.8 1.0 CD2 A:PHE100 4.8 20.2 1.0 CA A:THR59 4.9 19.5 1.0 HE2 A:HIS181 4.9 25.1 1.0 HG23 A:THR59 5.0 21.9 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Green Fluorescent Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Green Fluorescent Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:46.8 occ:0.58 ND1 A:HIS139 2.0 45.7 1.0 O A:HOH562 2.1 16.8 0.8 O A:HOH605 2.1 28.8 0.8 O A:HOH405 2.2 14.6 1.0 HE1 A:HIS139 2.7 59.6 1.0 CE1 A:HIS139 2.7 49.7 1.0 HA A:PRO56 3.1 26.1 1.0 HB3 A:PRO56 3.2 28.8 1.0 CG A:HIS139 3.3 46.8 1.0 HB3 A:HIS139 3.6 56.2 1.0 CA A:PRO56 3.9 21.8 1.0 HG3 A:PRO56 3.9 31.6 1.0 CB A:HIS139 3.9 46.8 1.0 CB A:PRO56 3.9 24.0 1.0 NE2 A:HIS139 3.9 47.7 1.0 HA A:HIS139 4.0 52.3 1.0 H A:TRP57 4.0 23.5 1.0 CD2 A:HIS139 4.2 45.1 1.0 O A:HOH571 4.4 43.1 1.0 CA A:HIS139 4.4 43.6 1.0 CG A:PRO56 4.4 26.3 1.0 H A:LEU141 4.5 56.1 1.0 HE2 A:HIS139 4.6 57.2 1.0 HD2 A:PRO58 4.7 22.4 1.0 N A:TRP57 4.7 19.6 1.0 C A:HIS139 4.7 49.6 1.0 HB2 A:LEU141 4.7 48.2 1.0 HB2 A:PRO56 4.8 28.8 1.0 N A:PRO56 4.8 25.1 1.0 HB2 A:HIS139 4.8 56.2 1.0 O A:HIS139 4.8 54.0 1.0 C A:PRO56 4.8 21.7 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Green Fluorescent Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Green Fluorescent Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:25.2 occ:0.24 OE2 A:GLU124 2.0 34.4 0.9 O A:HOH448 2.2 37.5 1.0 OE1 A:GLU124 2.2 28.4 0.9 O A:HOH513 2.2 25.0 0.8 O A:HOH429 2.2 15.9 0.9 CD A:GLU124 2.4 29.7 0.9 CG A:GLU124 3.9 14.6 0.9 O A:HOH426 3.9 20.9 1.0 HG2 A:GLU124 4.2 17.5 0.9 HG3 A:GLU124 4.4 17.5 0.9 HB3 A:GLU124 4.5 16.6 0.9 O A:HOH589 4.7 44.9 1.0 CB A:GLU124 4.7 13.9 0.9 HB2 A:GLU124 4.8 16.6 0.9

T.J.Barnard, X.Yu, N.Noinaj, J.W.Taraska. Crystal Structure of Green Fluorescent Protein To Be Published.