Bismuth in PDB 9pq4: Bi-Bound Structure of the H77C Variant of TRICYT2

The structure of Bi-Bound Structure of the H77C Variant of TRICYT2, PDB code: 9pq4 was solved by V.H.Eng, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.02 / 1.48
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.84, 71.75, 76.12, 90, 90, 90
R / Rfree (%)	15.7 / 21.8

The structure of Bi-Bound Structure of the H77C Variant of TRICYT2 also contains other interesting chemical elements:

Sodium	(Na)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Bismuth atom in the Bi-Bound Structure of the H77C Variant of TRICYT2 (pdb code 9pq4). This binding sites where shown within 5.0 Angstroms radius around Bismuth atom.
In total 4 binding sites of Bismuth where determined in the Bi-Bound Structure of the H77C Variant of TRICYT2, PDB code: 9pq4:
Jump to Bismuth binding site number: 1; 2; 3; 4;

Bismuth binding site 1 out of 4 in the Bi-Bound Structure of the H77C Variant of TRICYT2


Mono view


Stereo pair view

A full contact list of Bismuth with other atoms in the Bi binding site number 1 of Bi-Bound Structure of the H77C Variant of TRICYT2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Bi201 b:23.9 occ:0.66 BI B:BS3201 0.0 23.9 0.7 BI B:BS3201 1.6 20.5 0.1 BI B:BS3201 2.3 65.3 0.2 SG A:CYS77 2.7 27.8 1.0 SG B:CYS77 2.8 39.1 1.0 SG C:CYS77 2.8 40.0 1.0 BI B:BS3201 3.1 34.5 0.1 O A:HOH389 3.2 27.8 1.0 O C:HOH397 3.4 57.0 1.0 O B:HOH348 3.5 64.7 1.0 O B:HOH394 3.6 60.0 1.0 CB B:CYS77 3.6 34.9 1.0 CB A:CYS77 3.6 23.4 1.0 O C:HOH311 3.8 83.9 1.0 CB C:CYS77 3.8 35.7 1.0 O B:HOH371 4.0 44.4 1.0 CA B:CYS77 4.4 31.7 1.0 O B:HOH357 4.5 46.9 1.0 O B:HOH316 4.6 74.0 1.0 NE2 A:HIS73 4.6 37.6 1.0 CA A:CYS77 4.6 23.1 1.0 CA C:CYS77 4.8 34.3 1.0

Bismuth binding site 2 out of 4 in the Bi-Bound Structure of the H77C Variant of TRICYT2


Mono view


Stereo pair view

A full contact list of Bismuth with other atoms in the Bi binding site number 2 of Bi-Bound Structure of the H77C Variant of TRICYT2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Bi201 b:65.3 occ:0.16 BI B:BS3201 0.0 65.3 0.2 BI B:BS3201 2.3 23.9 0.7 O C:HOH397 2.6 57.0 1.0 O B:HOH348 2.6 64.7 1.0 CB C:CYS77 2.9 35.7 1.0 SG C:CYS77 3.0 40.0 1.0 BI B:BS3201 3.1 20.5 0.1 O B:HOH357 3.1 46.9 1.0 O C:HOH408 3.3 58.4 1.0 SG B:CYS77 3.5 39.1 1.0 BI B:BS3201 3.8 34.5 0.1 O A:HOH389 4.0 27.8 1.0 CB B:CYS77 4.0 34.9 1.0 CA B:CYS77 4.1 31.7 1.0 CA C:CYS77 4.2 34.3 1.0 O C:HOH335 4.5 49.1 1.0 ND2 B:ASN80 4.5 36.5 1.0 CB B:ASN80 4.5 35.6 1.0 OE2 C:GLU81 4.6 67.2 1.0 O B:HOH394 4.6 60.0 1.0 O B:CYS77 4.7 37.8 1.0 C C:CYS77 4.8 36.2 1.0 C B:CYS77 4.9 33.8 1.0 CD C:GLU81 4.9 65.0 1.0 O C:CYS77 4.9 40.9 1.0 SG A:CYS77 5.0 27.8 1.0

Bismuth binding site 3 out of 4 in the Bi-Bound Structure of the H77C Variant of TRICYT2


Mono view


Stereo pair view

A full contact list of Bismuth with other atoms in the Bi binding site number 3 of Bi-Bound Structure of the H77C Variant of TRICYT2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Bi201 b:20.5 occ:0.12 BI B:BS3201 0.0 20.5 0.1 BI B:BS3201 1.6 23.9 0.7 O B:HOH371 2.4 44.4 1.0 O B:HOH394 2.7 60.0 1.0 SG B:CYS77 2.8 39.1 1.0 SG A:CYS77 2.9 27.8 1.0 CB B:CYS77 2.9 34.9 1.0 O B:HOH348 3.0 64.7 1.0 BI B:BS3201 3.1 65.3 0.2 CB A:CYS77 3.5 23.4 1.0 CA B:CYS77 3.9 31.7 1.0 O A:HOH389 3.9 27.8 1.0 O B:HOH316 3.9 74.0 1.0 CA A:CYS77 4.0 23.1 1.0 O C:HOH397 4.1 57.0 1.0 BI B:BS3201 4.2 34.5 0.1 SG C:CYS77 4.4 40.0 1.0 C B:CYS77 4.4 33.8 1.0 O B:CYS77 4.5 37.8 1.0 ND2 A:ASN80 4.5 38.2 1.0 OE2 B:GLU81 4.8 66.9 1.0 O C:HOH311 4.9 83.9 1.0 O A:CYS77 5.0 27.7 1.0 C A:CYS77 5.0 24.8 1.0

Bismuth binding site 4 out of 4 in the Bi-Bound Structure of the H77C Variant of TRICYT2


Mono view


Stereo pair view

A full contact list of Bismuth with other atoms in the Bi binding site number 4 of Bi-Bound Structure of the H77C Variant of TRICYT2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Bi201 b:34.5 occ:0.06 BI B:BS3201 0.0 34.5 0.1 O C:HOH421 2.3 37.3 1.0 SG B:CYS77 2.5 39.1 1.0 SG C:CYS77 2.6 40.0 1.0 NE2 A:HIS73 2.7 37.6 1.0 BI B:BS3201 3.1 23.9 0.7 CD2 A:HIS73 3.5 37.2 1.0 O B:HOH347 3.6 25.3 1.0 O B:HOH357 3.7 46.9 1.0 O B:HOH402 3.7 62.7 1.0 SG A:CYS77 3.8 27.8 1.0 BI B:BS3201 3.8 65.3 0.2 CE1 A:HIS73 3.8 39.1 1.0 BI B:BS3201 4.2 20.5 0.1 CB C:CYS77 4.2 35.7 1.0 CB B:CYS77 4.3 34.9 1.0 O C:HOH388 4.5 22.9 1.0 O C:HIS73 4.5 28.1 1.0 CG A:HIS73 4.8 34.0 1.0 O B:HOH316 4.8 74.0 1.0 O B:HIS73 4.9 26.7 1.0 ND1 A:HIS73 4.9 36.5 1.0 O C:HOH311 5.0 83.9 1.0 CA B:CYS77 5.0 31.7 1.0

V.H.Eng, M.Gascon, A.Kakkis, F.A.Tezcan. Design of A Protein Scaffold with A Selective, Bi-Containing Heterodinuclear Metal Coordination Motif. J.Inorg.Biochem. V. 274 13104 2025.
ISSN: ISSN 0162-0134
PubMed: 41072111
DOI: 10.1016/J.JINORGBIO.2025.113104