Zinc in PDB 2xjy: Crystal Structure of the LMO2:LDB1-Lid Complex, P21 Crystal Form

The structure of Crystal Structure of the LMO2:LDB1-Lid Complex, P21 Crystal Form, PDB code: 2xjy was solved by K.El Omari, D.Karia, C.Porcher, E.J.Mancini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.74 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	25.140, 54.360, 61.800, 90.00, 95.45, 90.00
R / Rfree (%)	20.12 / 22.89

The binding sites of Zinc atom in the Crystal Structure of the LMO2:LDB1-Lid Complex, P21 Crystal Form (pdb code 2xjy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the LMO2:LDB1-Lid Complex, P21 Crystal Form, PDB code: 2xjy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the LMO2:LDB1-Lid Complex, P21 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the LMO2:LDB1-Lid Complex, P21 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:84.9 occ:1.00 SG A:CYS33 2.2 83.2 1.0 SG A:CYS54 2.2 72.6 1.0 ND1 A:HIS51 2.3 73.9 1.0 SG A:CYS30 2.5 77.5 1.0 CB A:CYS33 3.1 78.9 1.0 CG A:HIS51 3.2 72.7 1.0 CB A:CYS54 3.3 66.0 1.0 CB A:CYS30 3.3 74.6 1.0 CB A:HIS51 3.3 67.7 1.0 CE1 A:HIS51 3.4 74.9 1.0 N A:CYS33 3.9 75.2 1.0 CA A:CYS33 4.1 77.2 1.0 N A:HIS51 4.2 62.6 1.0 CA A:HIS51 4.4 65.5 1.0 CD2 A:HIS51 4.4 76.9 1.0 NE2 A:HIS51 4.5 77.1 1.0 CA A:CYS54 4.6 65.0 1.0 C A:GLY32 4.7 76.8 1.0 CA A:CYS30 4.7 73.1 1.0 C A:CYS33 4.9 82.4 1.0 N A:CYS54 4.9 67.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the LMO2:LDB1-Lid Complex, P21 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the LMO2:LDB1-Lid Complex, P21 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:56.4 occ:1.00 OD2 A:ASP83 2.1 65.1 1.0 SG A:CYS80 2.3 44.7 1.0 SG A:CYS60 2.4 54.3 1.0 SG A:CYS57 2.4 48.9 1.0 CG A:ASP83 3.1 56.1 1.0 CB A:CYS57 3.1 46.0 1.0 CB A:CYS60 3.4 51.7 1.0 CB A:ASP83 3.5 43.0 1.0 CB A:CYS80 3.6 41.1 1.0 N A:CYS60 3.9 51.2 1.0 N A:CYS80 4.2 40.9 1.0 CA A:CYS60 4.2 52.7 1.0 OD1 A:ASP83 4.2 55.9 1.0 SG A:CYS62 4.3 64.0 1.0 NH2 A:ARG82 4.4 94.4 1.0 N A:ASP83 4.4 40.3 1.0 CA A:CYS80 4.5 40.7 1.0 CA A:ASP83 4.6 40.1 1.0 CA A:CYS57 4.6 46.8 1.0 CB A:LEU59 4.9 47.6 1.0 C A:LEU59 4.9 53.8 1.0 N A:GLY61 4.9 58.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the LMO2:LDB1-Lid Complex, P21 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the LMO2:LDB1-Lid Complex, P21 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:53.8 occ:1.00 SG A:CYS97 2.2 57.4 1.0 ND1 A:HIS116 2.2 52.5 1.0 SG A:CYS119 2.3 48.8 1.0 SG A:CYS94 2.5 49.4 1.0 CG A:HIS116 3.2 49.7 1.0 CE1 A:HIS116 3.2 52.3 1.0 CB A:CYS94 3.2 46.4 1.0 CB A:CYS119 3.3 43.8 1.0 CB A:CYS97 3.3 54.5 1.0 CB A:HIS116 3.4 45.8 1.0 N A:CYS97 3.8 52.5 1.0 N A:HIS116 4.1 44.4 1.0 CA A:CYS97 4.1 54.5 1.0 NE2 A:HIS116 4.3 52.0 1.0 CD2 A:HIS116 4.3 51.2 1.0 CA A:HIS116 4.4 44.2 1.0 CA A:CYS119 4.7 43.8 1.0 CA A:CYS94 4.7 46.5 1.0 CB A:SER96 4.8 49.2 1.0 C A:SER96 4.9 54.8 1.0 C A:CYS97 4.9 60.5 1.0 N A:CYS119 5.0 45.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the LMO2:LDB1-Lid Complex, P21 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the LMO2:LDB1-Lid Complex, P21 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:44.4 occ:1.00 OD2 A:ASP147 2.1 51.1 1.0 SG A:CYS125 2.2 42.2 1.0 SG A:CYS122 2.3 41.2 1.0 SG A:CYS144 2.3 47.0 1.0 CG A:ASP147 3.0 47.5 1.0 CB A:CYS122 3.1 37.5 1.0 CB A:CYS125 3.2 40.3 1.0 CB A:CYS144 3.6 41.8 1.0 N A:CYS125 3.6 40.3 1.0 CB A:ASP147 3.7 41.8 1.0 OD1 A:ASP147 3.9 47.1 1.0 CA A:CYS125 4.0 41.0 1.0 N A:CYS144 4.3 41.2 1.0 CB A:ALA124 4.4 38.8 1.0 CA A:CYS144 4.5 41.0 1.0 CA A:CYS122 4.5 37.4 1.0 C A:ALA124 4.8 43.8 1.0 C A:CYS125 4.8 49.1 1.0 CB A:LYS127 4.9 52.3 1.0 N A:ASP147 4.9 41.6 1.0 N A:GLN126 4.9 46.9 1.0 CA A:ASP147 5.0 40.7 1.0 CA A:ALA124 5.0 39.0 1.0

K.El Omari, S.J.Hoosdally, K.Tuladhar, D.Karia, P.Vyas, R.Patient, C.Porcher, E.J.Mancini. Structure of the Leukemia Oncogene LMO2: Implications For the Assembly of A Hematopoietic Transcription Factor Complex. Blood V. 117 2146 2011.
ISSN: ISSN 0006-4971
PubMed: 21076045
DOI: 10.1182/BLOOD-2010-07-293357