Iron in PDB 8cyf: WHIB3 Bound to SIGMAAR4-Rnap Beta Flap Tip Chimera and Dna

All present enzymatic activity of WHIB3 Bound to SIGMAAR4-Rnap Beta Flap Tip Chimera and Dna:
2.7.7.6;

The structure of WHIB3 Bound to SIGMAAR4-Rnap Beta Flap Tip Chimera and Dna, PDB code: 8cyf was solved by T.Wan, L.M.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.15 / 2.44
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.697, 72.934, 95.38, 90, 90, 90
R / Rfree (%)	22.2 / 25.1

The structure of WHIB3 Bound to SIGMAAR4-Rnap Beta Flap Tip Chimera and Dna also contains other interesting chemical elements:

Arsenic

(As)

1 atom

The binding sites of Iron atom in the WHIB3 Bound to SIGMAAR4-Rnap Beta Flap Tip Chimera and Dna (pdb code 8cyf). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the WHIB3 Bound to SIGMAAR4-Rnap Beta Flap Tip Chimera and Dna, PDB code: 8cyf:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the WHIB3 Bound to SIGMAAR4-Rnap Beta Flap Tip Chimera and Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of WHIB3 Bound to SIGMAAR4-Rnap Beta Flap Tip Chimera and Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:54.1 occ:1.00 FE1 A:SF4200 0.0 54.1 1.0 S2 A:SF4200 2.1 50.3 1.0 S4 A:SF4200 2.1 55.4 1.0 S3 A:SF4200 2.2 54.0 1.0 SG A:CYS53 2.3 59.6 1.0 FE2 A:SF4200 2.7 58.2 1.0 FE3 A:SF4200 2.7 53.2 1.0 FE4 A:SF4200 2.7 52.5 1.0 CB A:CYS53 3.4 62.0 1.0 S1 A:SF4200 3.5 50.4 1.0 CA A:CYS53 3.7 63.9 1.0 N A:GLY77 4.2 52.8 1.0 CE1 A:PHE31 4.2 60.6 1.0 N A:CYS53 4.3 63.2 1.0 N A:GLY78 4.5 52.3 1.0 CA A:GLY77 4.7 51.3 1.0 SG A:CYS62 4.7 53.8 1.0 CB A:CYS56 4.7 61.2 1.0 SG A:CYS23 4.8 60.5 1.0 SG A:CYS56 4.8 62.1 1.0 CZ A:PHE31 4.8 62.7 1.0 C A:CYS53 5.0 66.2 1.0 CD1 A:PHE31 5.0 60.9 1.0

Iron binding site 2 out of 4 in the WHIB3 Bound to SIGMAAR4-Rnap Beta Flap Tip Chimera and Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of WHIB3 Bound to SIGMAAR4-Rnap Beta Flap Tip Chimera and Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:58.2 occ:1.00 FE2 A:SF4200 0.0 58.2 1.0 S1 A:SF4200 2.1 50.4 1.0 S3 A:SF4200 2.1 54.0 1.0 S4 A:SF4200 2.2 55.4 1.0 SG A:CYS56 2.4 62.1 1.0 FE4 A:SF4200 2.7 52.5 1.0 FE1 A:SF4200 2.7 54.1 1.0 FE3 A:SF4200 2.8 53.2 1.0 CB A:CYS56 3.1 61.2 1.0 S2 A:SF4200 3.6 50.3 1.0 N A:LEU22 4.1 65.2 1.0 CA A:GLY21 4.3 60.1 1.0 CG2 A:VAL58 4.5 56.3 1.0 CA A:CYS56 4.6 64.3 1.0 CA A:CYS53 4.7 63.9 1.0 SG A:CYS23 4.7 60.5 1.0 SG A:CYS53 4.7 59.6 1.0 C A:GLY21 4.7 62.0 1.0 N A:ILE59 4.7 57.5 1.0 CB A:CYS62 4.7 58.0 1.0 CB A:LEU22 4.8 66.2 1.0 CA A:ILE59 4.8 56.5 1.0 SG A:CYS62 4.8 53.8 1.0 C A:VAL58 4.9 56.4 1.0 CB A:CYS53 5.0 62.0 1.0

Iron binding site 3 out of 4 in the WHIB3 Bound to SIGMAAR4-Rnap Beta Flap Tip Chimera and Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of WHIB3 Bound to SIGMAAR4-Rnap Beta Flap Tip Chimera and Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:53.2 occ:1.00 FE3 A:SF4200 0.0 53.2 1.0 S4 A:SF4200 2.1 55.4 1.0 S2 A:SF4200 2.1 50.3 1.0 S1 A:SF4200 2.2 50.4 1.0 SG A:CYS62 2.2 53.8 1.0 FE1 A:SF4200 2.7 54.1 1.0 FE2 A:SF4200 2.8 58.2 1.0 FE4 A:SF4200 2.8 52.5 1.0 CB A:CYS62 3.0 58.0 1.0 N A:GLY77 3.6 52.8 1.0 S3 A:SF4200 3.8 54.0 1.0 CA A:GLY77 4.2 51.3 1.0 CG B:PRO517 4.4 61.9 1.0 CA A:CYS62 4.4 58.4 1.0 SG A:CYS53 4.6 59.6 1.0 C A:TRP76 4.6 55.5 1.0 CZ3 A:TRP17 4.7 60.7 1.0 CA A:TRP76 4.7 52.3 1.0 CH2 A:TRP17 4.9 56.6 1.0 SG A:CYS23 4.9 60.5 1.0 CD B:PRO517 5.0 59.5 1.0

Iron binding site 4 out of 4 in the WHIB3 Bound to SIGMAAR4-Rnap Beta Flap Tip Chimera and Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of WHIB3 Bound to SIGMAAR4-Rnap Beta Flap Tip Chimera and Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:52.5 occ:1.00 FE4 A:SF4200 0.0 52.5 1.0 S1 A:SF4200 2.1 50.4 1.0 S3 A:SF4200 2.2 54.0 1.0 S2 A:SF4200 2.2 50.3 1.0 SG A:CYS23 2.3 60.5 1.0 FE2 A:SF4200 2.7 58.2 1.0 FE1 A:SF4200 2.7 54.1 1.0 FE3 A:SF4200 2.8 53.2 1.0 CB A:CYS23 3.5 61.2 1.0 S4 A:SF4200 3.6 55.4 1.0 N A:CYS23 4.0 65.2 1.0 CA A:CYS23 4.4 63.7 1.0 CG B:PRO517 4.4 61.9 1.0 N A:LEU22 4.5 65.2 1.0 CE1 A:PHE31 4.5 60.6 1.0 CB B:PRO517 4.5 63.0 1.0 CZ A:PHE31 4.6 62.7 1.0 CE1 B:HIS516 4.6 58.9 1.0 CA A:GLY21 4.6 60.1 1.0 SG A:CYS56 4.7 62.1 1.0 C A:GLY21 4.8 62.0 1.0 SG A:CYS53 4.9 59.6 1.0 CD B:PRO517 4.9 59.5 1.0 SG A:CYS62 4.9 53.8 1.0

T.Wan, M.Horova, V.Khetrapal, S.Li, C.Jones, A.Schacht, X.Sun, L.Zhang. Structural Basis of Dna Binding By the Whib-Like Transcription Factor WHIB3 in Mycobacterium Tuberculosis. J.Biol.Chem. 04777 2023.
ISSN: ESSN 1083-351X
PubMed: 37142222
DOI: 10.1016/J.JBC.2023.104777