Gold in PDB 1io4: Crystal Structure of Runx-1/AML1/Cbfalpha Runt Domain- Cbfbeta Core Domain Heterodimer and C/Ebpbeta Bzip Homodimer Bound to A Dna Fragment From the Csf-1R Promoter

The structure of Crystal Structure of Runx-1/AML1/Cbfalpha Runt Domain- Cbfbeta Core Domain Heterodimer and C/Ebpbeta Bzip Homodimer Bound to A Dna Fragment From the Csf-1R Promoter, PDB code: 1io4 was solved by T.H.Tahirov, K.Ogata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.95 / 3.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	121.108, 163.600, 109.326, 90.00, 90.00, 90.00
R / Rfree (%)	24.7 / 29.9

The binding sites of Gold atom in the Crystal Structure of Runx-1/AML1/Cbfalpha Runt Domain- Cbfbeta Core Domain Heterodimer and C/Ebpbeta Bzip Homodimer Bound to A Dna Fragment From the Csf-1R Promoter (pdb code 1io4). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 3 binding sites of Gold where determined in the Crystal Structure of Runx-1/AML1/Cbfalpha Runt Domain- Cbfbeta Core Domain Heterodimer and C/Ebpbeta Bzip Homodimer Bound to A Dna Fragment From the Csf-1R Promoter, PDB code: 1io4:
Jump to Gold binding site number: 1; 2; 3;

Gold binding site 1 out of 3 in the Crystal Structure of Runx-1/AML1/Cbfalpha Runt Domain- Cbfbeta Core Domain Heterodimer and C/Ebpbeta Bzip Homodimer Bound to A Dna Fragment From the Csf-1R Promoter


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 1 of Crystal Structure of Runx-1/AML1/Cbfalpha Runt Domain- Cbfbeta Core Domain Heterodimer and C/Ebpbeta Bzip Homodimer Bound to A Dna Fragment From the Csf-1R Promoter within 5.0Å range: probe atom residue distance (Å) B Occ C:Au200 b:89.8 occ:1.00 SG C:CYS81 2.4 0.5 1.0 CB C:CYS81 2.7 33.2 1.0 C C:CYS81 3.7 39.7 1.0 CA C:CYS81 3.9 39.1 1.0 O C:CYS81 3.9 29.2 1.0 CB C:ASN82 4.0 12.7 1.0 N C:ASN82 4.1 56.3 1.0 O C:VAL137 4.2 12.1 1.0 NH2 C:ARG139 4.4 46.2 1.0 CA C:ASN82 4.7 34.7 1.0 CG1 C:VAL137 4.7 43.9 1.0 CZ C:ARG139 4.8 81.1 1.0 N C:CYS81 4.9 10.6 1.0 CG2 C:VAL170 4.9 20.1 1.0 CA C:VAL137 5.0 19.0 1.0 C C:VAL137 5.0 18.8 1.0

Gold binding site 2 out of 3 in the Crystal Structure of Runx-1/AML1/Cbfalpha Runt Domain- Cbfbeta Core Domain Heterodimer and C/Ebpbeta Bzip Homodimer Bound to A Dna Fragment From the Csf-1R Promoter


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 2 of Crystal Structure of Runx-1/AML1/Cbfalpha Runt Domain- Cbfbeta Core Domain Heterodimer and C/Ebpbeta Bzip Homodimer Bound to A Dna Fragment From the Csf-1R Promoter within 5.0Å range: probe atom residue distance (Å) B Occ D:Au200 b:0.4 occ:0.40 OE2 D:GLU24 2.5 0.3 1.0 SG D:CYS124 2.6 72.7 1.0 CD D:GLU24 3.1 0.9 1.0 CG D:GLU24 3.5 0.0 1.0 OE1 D:GLU24 4.1 0.7 1.0 O D:LYS111 4.2 91.6 1.0 N D:CYS124 4.3 69.7 1.0 CB D:CYS124 4.3 86.7 1.0 O D:MET122 4.4 0.8 1.0 CA D:GLY112 4.5 94.4 1.0 C D:LYS111 4.5 0.3 1.0 OE2 D:GLU126 4.5 0.5 1.0 CA D:GLY123 4.6 77.1 1.0 C D:GLY123 4.6 67.0 1.0 N D:GLY112 4.6 93.7 1.0 CB D:LYS111 4.7 0.6 1.0 CB D:GLU24 4.9 0.7 1.0 CA D:CYS124 4.9 82.0 1.0

Gold binding site 3 out of 3 in the Crystal Structure of Runx-1/AML1/Cbfalpha Runt Domain- Cbfbeta Core Domain Heterodimer and C/Ebpbeta Bzip Homodimer Bound to A Dna Fragment From the Csf-1R Promoter


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 3 of Crystal Structure of Runx-1/AML1/Cbfalpha Runt Domain- Cbfbeta Core Domain Heterodimer and C/Ebpbeta Bzip Homodimer Bound to A Dna Fragment From the Csf-1R Promoter within 5.0Å range: probe atom residue distance (Å) B Occ D:Au201 b:1.0 occ:0.25 SG D:CYS48 3.0 0.9 1.0 CG D:GLN45 3.3 0.7 1.0 CB D:CYS48 3.4 0.7 1.0 CA D:GLN45 3.7 0.2 1.0 O D:GLN45 3.8 94.3 1.0 CB D:GLN45 3.9 0.0 1.0 CD1 D:LEU116 4.0 0.4 1.0 CG2 D:VAL95 4.1 76.4 1.0 C D:GLN45 4.2 0.0 1.0 CD D:GLN45 4.5 0.2 1.0 CA D:CYS48 4.8 0.1 1.0 N D:GLN45 5.0 1.0 1.0 CD1 D:LEU88 5.0 0.1 1.0 CG D:LEU116 5.0 90.0 1.0

T.H.Tahirov, T.Inoue-Bungo, H.Morii, A.Fujikawa, M.Sasaki, K.Kimura, M.Shiina, K.Sato, T.Kumasaka, M.Yamamoto, S.Ishii, K.Ogata. Structural Analyses of Dna Recognition By the AML1/Runx-1 Runt Domain and Its Allosteric Control By Cbfbeta. Cell(Cambridge,Mass.) V. 104 755 2001.
ISSN: ISSN 0092-8674
PubMed: 11257229
DOI: 10.1016/S0092-8674(01)00271-9