Copper in PDB 9cst: Streptavidin-E101Q-K121A Bound to Cu(II)-Biotin-Ethyl-Dipicolylamine Cofactor

The structure of Streptavidin-E101Q-K121A Bound to Cu(II)-Biotin-Ethyl-Dipicolylamine Cofactor, PDB code: 9cst was solved by K.S.Uyeda, A.H.Follmer, A.S.Borovik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.09 / 1.13
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	57.82, 57.82, 184.139, 90, 90, 90
R / Rfree (%)	14.2 / 16

The binding sites of Copper atom in the Streptavidin-E101Q-K121A Bound to Cu(II)-Biotin-Ethyl-Dipicolylamine Cofactor (pdb code 9cst). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Streptavidin-E101Q-K121A Bound to Cu(II)-Biotin-Ethyl-Dipicolylamine Cofactor, PDB code: 9cst:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Streptavidin-E101Q-K121A Bound to Cu(II)-Biotin-Ethyl-Dipicolylamine Cofactor


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Streptavidin-E101Q-K121A Bound to Cu(II)-Biotin-Ethyl-Dipicolylamine Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu202 b:30.0 occ:0.67 N5 A:QG7201 1.8 36.0 1.0 N3 A:QG7201 2.0 33.4 0.9 N4 A:QG7201 2.0 39.0 0.9 C11 A:QG7201 2.4 36.9 1.0 H5 A:QG7201 2.5 44.2 1.0 C12 A:QG7201 2.5 37.1 1.0 C18 A:QG7201 2.7 36.0 0.9 CU A:CU203 2.8 31.9 0.3 C17 A:QG7201 2.9 36.2 1.0 C22 A:QG7201 2.9 37.7 0.9 H22 A:QG7201 3.1 26.9 1.0 C16 A:QG7201 3.1 36.9 0.5 H30 A:QG7201 3.2 45.2 1.0 C23 A:QG7201 3.2 25.8 0.6 H28 A:QG7201 3.4 44.3 1.0 H6 A:QG7201 3.5 44.2 1.0 H3 A:QG7201 3.5 43.5 1.0 H25 A:QG7201 3.5 31.0 0.8 C24 A:QG7201 3.6 22.4 1.0 H4 A:QG7201 3.7 43.5 1.0 C13 A:QG7201 3.9 35.6 0.9 H23 A:QG7201 4.0 26.9 1.0 H26 A:QG7201 4.0 31.0 0.7 C19 A:QG7201 4.1 36.7 0.9 C21 A:QG7201 4.2 39.9 0.6 C15 A:QG7201 4.3 34.9 0.8 O A:HOH410 4.4 45.6 1.0 C14 A:QG7201 4.6 34.8 1.0 HB2 A:ASN49 4.6 19.8 1.0 H29 A:QG7201 4.7 42.8 1.0 C20 A:QG7201 4.8 39.8 0.9 O1 A:QG7201 4.8 14.6 0.9 H33 A:QG7201 4.9 44.0 1.0 N6 A:QG7201 5.0 15.4 0.9

Copper binding site 2 out of 4 in the Streptavidin-E101Q-K121A Bound to Cu(II)-Biotin-Ethyl-Dipicolylamine Cofactor


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Streptavidin-E101Q-K121A Bound to Cu(II)-Biotin-Ethyl-Dipicolylamine Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu203 b:31.9 occ:0.30 H5 A:QG7201 1.2 44.2 1.0 H3 A:QG7201 1.2 43.5 1.0 C11 A:QG7201 1.4 36.9 1.0 C17 A:QG7201 1.6 36.2 1.0 N3 A:QG7201 1.7 33.4 0.9 H6 A:QG7201 1.7 44.2 1.0 C18 A:QG7201 2.5 36.0 0.9 H4 A:QG7201 2.6 43.5 1.0 C23 A:QG7201 2.8 25.8 0.6 CU A:CU202 2.8 30.0 0.7 H26 A:QG7201 2.9 31.0 0.7 C12 A:QG7201 2.9 37.1 1.0 N5 A:QG7201 3.1 36.0 1.0 HD11 A:LEU124 3.3 20.6 1.0 H25 A:QG7201 3.3 31.0 0.8 O A:HOH422 3.3 34.4 1.0 O A:HOH410 3.4 45.6 1.0 C19 A:QG7201 3.5 36.7 0.9 H33 A:QG7201 3.6 44.0 1.0 N4 A:QG7201 3.7 39.0 0.9 C13 A:QG7201 3.8 35.6 0.9 H29 A:QG7201 3.8 42.8 1.0 C24 A:QG7201 4.1 22.4 1.0 HD12 A:LEU124 4.1 20.6 1.0 CD1 A:LEU124 4.1 17.1 1.0 H23 A:QG7201 4.2 26.9 1.0 C22 A:QG7201 4.2 37.7 0.9 H22 A:QG7201 4.3 26.9 1.0 O A:HOH342 4.4 22.0 1.0 O A:HOH333 4.6 16.1 1.0 C20 A:QG7201 4.6 39.8 0.9 HD13 A:LEU124 4.6 20.6 1.0 HG A:SER112 4.9 19.2 1.0 C21 A:QG7201 4.9 39.9 0.6 C16 A:QG7201 5.0 36.9 0.5 HG A:LEU124 5.0 16.2 1.0 H30 A:QG7201 5.0 45.2 1.0 HD21 A:LEU124 5.0 17.8 1.0

Copper binding site 3 out of 4 in the Streptavidin-E101Q-K121A Bound to Cu(II)-Biotin-Ethyl-Dipicolylamine Cofactor


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Streptavidin-E101Q-K121A Bound to Cu(II)-Biotin-Ethyl-Dipicolylamine Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu204 b:14.8 occ:0.18 O A:HOH382 1.5 32.1 1.0 NE2 A:HIS127 1.9 18.9 1.0 O A:HOH391 2.5 32.4 1.0 CE1 A:HIS127 2.8 17.7 1.0 HE1 A:HIS127 3.0 21.3 1.0 CD2 A:HIS127 3.0 13.3 1.0 HD2 A:HIS127 3.2 16.0 1.0 ND1 A:HIS127 3.9 16.9 1.0 O A:HOH397 4.0 34.1 1.0 CG A:HIS127 4.0 12.9 1.0 O A:HOH361 4.4 17.7 1.0

Copper binding site 4 out of 4 in the Streptavidin-E101Q-K121A Bound to Cu(II)-Biotin-Ethyl-Dipicolylamine Cofactor


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Streptavidin-E101Q-K121A Bound to Cu(II)-Biotin-Ethyl-Dipicolylamine Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu205 b:85.6 occ:0.90 NE2 A:HIS87 2.6 16.8 1.0 O A:HOH412 3.2 42.7 1.0 CD2 A:HIS87 3.5 16.2 1.0 HD2 A:HIS87 3.5 19.5 1.0 CE1 A:HIS87 3.7 15.9 1.0 HE1 A:HIS87 3.9 19.0 1.0 O A:HOH326 4.1 32.9 1.0 CG A:HIS87 4.7 15.3 1.0 ND1 A:HIS87 4.8 15.6 1.0 HB3 A:ASN85 4.8 17.8 1.0 O A:ASN85 4.9 16.6 1.0

K.S.Uyeda, A.H.Follmer, A.S.Borovik. Selective Oxidation of Active Site Aromatic Residues in Engineered Cu Proteins Chem Sci 2024.
ISSN: ESSN 2041-6539
DOI: 10.1039/D4SC06667G