Cadmium in PDB 2b3p: Crystal Structure of A Superfolder Green Fluorescent Protein

The structure of Crystal Structure of A Superfolder Green Fluorescent Protein, PDB code: 2b3p was solved by J.D.Pedelacq, S.Cabantous, T.H.Tran, T.C.Terwilliger, G.S.Waldo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	7.99 / 1.40
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	88.456, 88.456, 69.346, 90.00, 90.00, 120.00
R / Rfree (%)	20.6 / 21.8

The binding sites of Cadmium atom in the Crystal Structure of A Superfolder Green Fluorescent Protein (pdb code 2b3p). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Crystal Structure of A Superfolder Green Fluorescent Protein, PDB code: 2b3p:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in the Crystal Structure of A Superfolder Green Fluorescent Protein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of A Superfolder Green Fluorescent Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd801 b:12.2 occ:1.00 OD2 A:ASP102 2.4 12.4 1.0 OD1 A:ASP102 2.4 13.0 1.0 OXT A:ACY707 2.7 38.4 1.0 CG A:ASP102 2.7 13.2 1.0 O A:ACY707 2.9 39.1 1.0 C A:ACY707 3.2 39.6 1.0 NZ A:LYS131 4.0 13.3 1.0 O A:HOH1030 4.1 25.6 1.0 CB A:ASP102 4.2 11.8 1.0 O A:HOH904 4.3 34.2 1.0 CH3 A:ACY707 4.6 39.8 1.0 O A:ASP102 4.7 10.7 1.0

Cadmium binding site 2 out of 9 in the Crystal Structure of A Superfolder Green Fluorescent Protein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of A Superfolder Green Fluorescent Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd802 b:13.1 occ:1.00 OD2 A:ASP76 2.4 15.6 1.0 O A:HOH930 2.4 15.7 1.0 OXT A:ACY703 2.5 14.8 1.0 CD2 A:HIS77 2.5 11.9 1.0 O A:ACY703 2.5 14.9 1.0 CD2 A:HIS231 2.6 19.1 1.0 C A:ACY703 2.8 17.0 1.0 CG A:ASP76 3.3 17.0 1.0 CG A:HIS231 3.4 18.9 1.0 CG A:HIS77 3.4 13.5 1.0 NE2 A:HIS77 3.5 15.2 1.0 OD1 A:ASP76 3.6 20.8 1.0 CB A:HIS231 3.7 20.8 1.0 NE2 A:HIS231 3.7 21.0 1.0 CB A:HIS77 3.9 12.8 1.0 N A:HIS77 4.1 12.8 1.0 CH3 A:ACY703 4.3 17.1 1.0 O A:HOH830 4.3 13.1 1.0 O A:HOH883 4.5 21.6 1.0 CE1 A:HIS77 4.6 13.1 1.0 ND1 A:HIS77 4.6 14.5 1.0 ND1 A:HIS231 4.6 21.6 1.0 CA A:HIS77 4.7 13.7 1.0 N A:ASP76 4.7 12.3 1.0 CB A:ASP76 4.7 13.8 1.0 CE1 A:HIS231 4.7 20.8 1.0 CA A:HIS231 4.8 20.3 1.0 CB A:PRO75 4.8 12.4 1.0 C A:ASP76 5.0 14.3 1.0

Cadmium binding site 3 out of 9 in the Crystal Structure of A Superfolder Green Fluorescent Protein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of A Superfolder Green Fluorescent Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd803 b:14.2 occ:1.00 OE2 A:GLU111 2.3 10.8 1.0 OE1 A:GLU111 2.5 15.2 1.0 CD A:GLU111 2.7 14.3 1.0 CG A:GLU111 4.2 11.3 1.0 NZ A:LYS113 4.2 22.1 1.0 O A:HOH914 4.5 29.0 1.0 O A:HOH1119 4.6 37.7 1.0 NH1 A:ARG109 4.9 15.4 1.0 NH2 A:ARG109 5.0 14.1 1.0

Cadmium binding site 4 out of 9 in the Crystal Structure of A Superfolder Green Fluorescent Protein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of A Superfolder Green Fluorescent Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd804 b:27.3 occ:1.00 OE2 A:GLU17 2.6 25.6 1.0 OE1 A:GLU17 2.6 26.0 1.0 OXT A:ACY705 2.6 24.3 1.0 O A:HOH962 2.6 32.8 1.0 O A:ACY701 2.8 42.2 1.0 OXT A:ACY701 2.8 42.4 1.0 CD A:GLU17 2.9 23.1 1.0 O A:ACY705 2.9 27.9 1.0 C A:ACY705 3.2 24.9 1.0 C A:ACY701 3.2 41.9 1.0 O A:HOH1033 3.4 31.1 1.0 CG A:GLU17 4.4 18.9 1.0 O A:HOH951 4.4 35.6 1.0 NH2 A:ARG30 4.4 31.7 1.0 CH3 A:ACY705 4.6 25.1 1.0 NH1 A:ARG122 4.6 25.5 1.0 CH3 A:ACY701 4.6 41.2 1.0 O A:HOH1009 4.7 34.7 1.0

Cadmium binding site 5 out of 9 in the Crystal Structure of A Superfolder Green Fluorescent Protein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of A Superfolder Green Fluorescent Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd805 b:34.6 occ:1.00 OE1 A:GLU142 2.4 19.3 1.0 OE2 A:GLU142 2.5 23.8 1.0 O A:HOH1137 2.5 23.9 1.0 CD A:GLU142 2.7 21.0 1.0 CG A:GLU142 4.2 18.2 1.0 ND2 A:ASN170 4.4 17.5 1.0 O A:VAL171 4.6 16.9 1.0 O A:HOH1104 4.6 24.2 1.0 CB A:ASN170 4.8 13.8 1.0 ND2 A:ASN144 5.0 15.3 1.0

Cadmium binding site 6 out of 9 in the Crystal Structure of A Superfolder Green Fluorescent Protein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of A Superfolder Green Fluorescent Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd806 b:38.3 occ:1.00 OE2 A:GLU132 2.4 28.2 1.0 O A:HOH955 2.7 37.8 1.0 CD A:GLU132 3.3 24.5 1.0 OE1 A:GLU132 3.6 25.2 1.0 CG A:GLU132 4.6 20.9 1.0 O A:HOH1003 4.7 25.1 1.0

Cadmium binding site 7 out of 9 in the Crystal Structure of A Superfolder Green Fluorescent Protein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of A Superfolder Green Fluorescent Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd807 b:45.1 occ:1.00 OD2 A:ASP36 2.6 15.3 1.0 O A:HOH928 3.4 39.1 1.0 CG A:ASP36 3.5 11.5 1.0 CB A:ASP36 3.6 10.4 1.0 CD A:LYS41 4.3 19.9 1.0 ND2 A:ASN39 4.5 11.8 1.0 NZ A:LYS41 4.6 23.7 1.0 OD1 A:ASP36 4.6 13.5 1.0 O A:HOH964 4.7 26.5 1.0 CG2 A:VAL11 4.7 17.4 1.0 CE A:LYS41 4.9 22.7 1.0

Cadmium binding site 8 out of 9 in the Crystal Structure of A Superfolder Green Fluorescent Protein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of A Superfolder Green Fluorescent Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd808 b:66.8 occ:1.00 OE2 A:GLU32 2.6 23.7 1.0 OE1 A:GLU32 2.6 26.3 1.0 CD A:GLU32 3.0 23.7 1.0 CG A:GLU32 4.5 21.0 1.0 NH1 A:ARG30 4.5 31.7 1.0 NE A:ARG30 5.0 28.4 1.0

Cadmium binding site 9 out of 9 in the Crystal Structure of A Superfolder Green Fluorescent Protein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of A Superfolder Green Fluorescent Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd809 b:84.6 occ:1.00 O A:HOH907 2.7 31.1 1.0 O A:ACY706 2.9 28.5 1.0 O A:ASN149 2.9 9.9 1.0 N A:LYS166 3.0 11.8 1.0 CB A:PHE165 3.3 9.8 1.0 CA A:PHE165 3.4 9.9 1.0 C A:ACY706 3.6 30.1 1.0 C A:PHE165 3.7 9.7 1.0 O A:LYS166 3.8 14.5 1.0 O A:HOH862 3.8 24.9 1.0 CE2 A:TYR151 3.8 12.1 1.0 OXT A:ACY706 3.9 31.6 1.0 CA A:LYS166 4.1 11.9 1.0 C A:ASN149 4.1 9.4 1.0 O A:HOH1073 4.2 40.7 1.0 N A:ASN149 4.3 8.7 1.0 C A:LYS166 4.3 12.5 1.0 CD2 A:TYR151 4.3 11.2 1.0 CB A:LYS166 4.4 15.6 1.0 O A:HOH925 4.6 34.8 1.0 CH3 A:ACY706 4.6 31.8 1.0 CA A:ASN149 4.6 8.7 1.0 CG A:PHE165 4.6 8.7 1.0 CB A:ASN149 4.8 10.0 1.0 N A:PHE165 4.8 10.2 1.0 O A:ASN164 4.9 12.5 1.0 CB A:HIS148 4.9 8.4 1.0 CZ A:TYR151 5.0 13.1 1.0 O A:PHE165 5.0 10.2 1.0

J.D.Pedelacq, S.Cabantous, T.Tran, T.C.Terwilliger, G.S.Waldo. Engineering and Characterization of A Superfolder Green Fluorescent Protein. Nat.Biotechnol. V. 24 79 2006.
ISSN: ISSN 1087-0156
PubMed: 16369541
DOI: 10.1038/NBT1172