Atomistry » Gold » PDB 1a52-3k3g » 1io4
Atomistry »
  Gold »
    PDB 1a52-3k3g »
      1io4 »

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

Protein crystallography data

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

Gold Binding Sites:

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 1io4

Go back to Gold Binding Sites List in 1io4
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 1io4

Go back to Gold Binding Sites List in 1io4
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 1io4

Go back to Gold Binding Sites List in 1io4
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

Reference:

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
Page generated: Sat Dec 12 01:53:02 2020

Last articles

Zn in 7L0B
Zn in 7KZZ
Zn in 7KZL
Zn in 7L3O
Zn in 7L52
Zn in 7L6T
Zn in 7KZ7
Zn in 7L6R
Zn in 7KKM
Zn in 7KKQ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy