Zinc in PDB 2ypa: Structure of the Scl:E47:LMO2:LDB1 Complex Bound to Dna

The structure of Structure of the Scl:E47:LMO2:LDB1 Complex Bound to Dna, PDB code: 2ypa was solved by K.El Omari, S.J.Hoosdally, K.Tuladhar, D.Karia, E.Ponsele, O.Platonova, P.Vyas, R.Patient, C.Porcher, E.J.Mancini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.15 / 2.80
Space group	F 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	102.966, 141.044, 148.793, 90.00, 90.00, 90.00
R / Rfree (%)	22.401 / 26.945

The binding sites of Zinc atom in the Structure of the Scl:E47:LMO2:LDB1 Complex Bound to Dna (pdb code 2ypa). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of the Scl:E47:LMO2:LDB1 Complex Bound to Dna, PDB code: 2ypa:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of the Scl:E47:LMO2:LDB1 Complex Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Scl:E47:LMO2:LDB1 Complex Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1156 b:91.1 occ:1.00 SG C:CYS125 2.1 0.2 1.0 OD2 C:ASP147 2.1 0.4 1.0 SG C:CYS122 2.4 91.8 1.0 SG C:CYS144 2.4 93.4 1.0 CB C:CYS122 3.1 90.6 1.0 CG C:ASP147 3.2 0.5 1.0 CB C:CYS144 3.3 91.5 1.0 CB C:CYS125 3.3 0.3 1.0 CB C:ASP147 3.6 99.3 1.0 N C:CYS125 3.6 0.7 1.0 N C:CYS144 4.0 89.3 1.0 CA C:CYS125 4.1 0.3 1.0 CA C:CYS144 4.2 90.6 1.0 OD1 C:ASP147 4.3 0.5 1.0 CB C:ALA124 4.3 0.2 1.0 N C:ASP147 4.5 0.1 1.0 CA C:CYS122 4.6 88.2 1.0 C C:ALA124 4.7 0.6 1.0 CA C:ASP147 4.7 98.8 1.0 CA C:ALA124 4.9 0.1 1.0 C C:CYS144 4.9 90.5 1.0 C C:CYS125 4.9 0.8 1.0 N C:ALA124 5.0 99.6 1.0 N C:GLN126 5.0 0.7 1.0 O C:CYS144 5.0 85.6 1.0

Zinc binding site 2 out of 4 in the Structure of the Scl:E47:LMO2:LDB1 Complex Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Scl:E47:LMO2:LDB1 Complex Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1157 b:79.1 occ:1.00 SG C:CYS97 1.9 83.2 1.0 SG C:CYS119 2.4 83.5 1.0 SG C:CYS94 2.5 75.5 1.0 ND1 C:HIS116 2.5 70.9 1.0 CB C:CYS94 3.0 73.7 1.0 CB C:CYS97 3.0 83.3 1.0 CE1 C:HIS116 3.2 71.5 1.0 CB C:CYS119 3.5 81.8 1.0 N C:CYS97 3.6 80.7 1.0 CG C:HIS116 3.7 71.9 1.0 CA C:CYS97 3.9 83.0 1.0 CB C:HIS116 4.2 72.9 1.0 NE2 C:HIS116 4.4 70.1 1.0 CA C:CYS94 4.5 72.3 1.0 CB C:SER96 4.6 81.8 1.0 N C:HIS116 4.6 72.9 1.0 CD2 C:HIS116 4.7 70.5 1.0 C C:SER96 4.7 80.6 1.0 C C:CYS97 4.7 84.5 1.0 CA C:CYS119 4.9 81.8 1.0 N C:ASP98 4.9 84.9 1.0 C C:CYS94 5.0 74.4 1.0

Zinc binding site 3 out of 4 in the Structure of the Scl:E47:LMO2:LDB1 Complex Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Scl:E47:LMO2:LDB1 Complex Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1158 b:78.5 occ:1.00 OD2 C:ASP83 1.7 76.7 1.0 SG C:CYS60 2.1 85.9 1.0 SG C:CYS57 2.4 96.4 1.0 SG C:CYS80 2.4 77.7 1.0 CG C:ASP83 2.9 76.0 1.0 CB C:CYS57 3.1 95.3 1.0 CB C:CYS60 3.2 87.5 1.0 CB C:CYS80 3.5 78.5 1.0 N C:CYS60 3.6 90.6 1.0 CB C:ASP83 3.7 75.2 1.0 OD1 C:ASP83 3.8 74.7 1.0 SG C:CYS62 3.8 0.8 1.0 CA C:CYS60 3.9 88.6 1.0 N C:CYS80 4.1 80.3 1.0 CA C:CYS80 4.4 78.7 1.0 CB C:LEU59 4.5 84.2 1.0 CA C:CYS57 4.5 93.1 1.0 C C:CYS60 4.6 92.1 1.0 C C:LEU59 4.7 90.2 1.0 N C:GLY61 4.7 92.6 1.0 N C:ASP83 4.8 74.8 1.0 N C:LEU59 4.8 85.2 1.0 CA C:ASP83 4.9 74.3 1.0 CA C:LEU59 4.9 85.9 1.0 C C:CYS57 4.9 89.1 1.0

Zinc binding site 4 out of 4 in the Structure of the Scl:E47:LMO2:LDB1 Complex Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Scl:E47:LMO2:LDB1 Complex Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1159 b:0.9 occ:1.00 SG C:CYS33 2.1 0.2 1.0 SG C:CYS54 2.4 0.3 1.0 SG C:CYS30 2.4 0.6 1.0 ND1 C:HIS51 2.9 0.1 1.0 CB C:CYS54 3.0 0.8 1.0 CB C:CYS30 3.0 0.6 1.0 CB C:HIS51 3.3 0.2 1.0 N C:CYS33 3.3 0.9 1.0 CB C:CYS33 3.3 0.2 1.0 CG C:HIS51 3.5 0.8 1.0 CA C:CYS33 3.9 0.4 1.0 N C:HIS51 3.9 0.6 1.0 CE1 C:HIS51 4.1 0.5 1.0 CA C:HIS51 4.2 0.0 1.0 C C:GLY32 4.3 1.0 1.0 N C:GLY32 4.3 0.9 1.0 CA C:GLY32 4.4 0.6 1.0 CA C:CYS30 4.4 0.2 1.0 CA C:CYS54 4.5 0.4 1.0 C C:CYS30 4.7 0.8 1.0 C C:CYS33 4.7 0.7 1.0 N C:GLN34 4.8 0.2 1.0 CD2 C:HIS51 4.8 0.8 1.0 N C:CYS54 4.9 0.2 1.0 O C:CYS30 5.0 0.5 1.0

K.El Omari, S.J.Hoosdally, K.Tuladhar, D.Karia, E.Hall-Ponsele, O.Platonova, P.Vyas, R.Patient, C.Porcher, E.J.Mancini. Structural Basis For LMO2-Driven Recruitment of the Scl:E47BHLH Heterodimer to Hematopoietic-Specific Transcriptional Targets. Cell Rep. V. 4 135 2013.
ISSN: ISSN 2211-1247
PubMed: 23831025
DOI: 10.1016/J.CELREP.2013.06.008