Zinc in PDB 2xjz: Crystal Structure of the LMO2:LDB1-Lid Complex, C2 Crystal Form

The structure of Crystal Structure of the LMO2:LDB1-Lid Complex, C2 Crystal Form, PDB code: 2xjz 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)	48.32 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	179.920, 55.530, 114.710, 90.00, 90.11, 90.00
R / Rfree (%)	22.8 / 24.4

The structure of Crystal Structure of the LMO2:LDB1-Lid Complex, C2 Crystal Form also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the LMO2:LDB1-Lid Complex, C2 Crystal Form (pdb code 2xjz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 20 binding sites of Zinc where determined in the Crystal Structure of the LMO2:LDB1-Lid Complex, C2 Crystal Form, PDB code: 2xjz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 20 in the Crystal Structure of the LMO2:LDB1-Lid Complex, C2 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, C2 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:87.7 occ:1.00 OD2 A:ASP140 2.0 69.1 1.0 SG A:CYS118 2.4 60.8 1.0 SG A:CYS115 2.4 59.3 1.0 SG A:CYS137 2.6 58.5 1.0 CG A:ASP140 2.9 62.3 1.0 CB A:CYS115 3.2 52.6 1.0 CB A:CYS137 3.4 53.4 1.0 CB A:ASP140 3.4 59.0 1.0 CB A:CYS118 3.5 58.9 1.0 N A:CYS118 3.7 59.2 1.0 OD1 A:ASP140 3.9 60.0 1.0 N A:CYS137 4.1 56.5 1.0 CA A:CYS118 4.2 59.1 1.0 CA A:CYS137 4.2 54.8 1.0 CB A:ALA117 4.3 60.3 1.0 CA A:CYS115 4.6 52.0 1.0 CA A:ASP140 4.7 59.1 1.0 O A:CYS137 4.7 63.6 1.0 C A:ALA117 4.8 63.8 1.0 N A:ASP140 4.8 58.8 1.0 C A:CYS137 4.8 61.7 1.0 CA A:ALA117 4.8 59.6 1.0 N A:ALA117 4.8 59.3 1.0

Zinc binding site 2 out of 20 in the Crystal Structure of the LMO2:LDB1-Lid Complex, C2 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, C2 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:78.9 occ:1.00 ND1 A:HIS109 2.3 54.5 1.0 SG A:CYS112 2.3 56.2 1.0 SG A:CYS87 2.4 59.5 1.0 SG A:CYS90 2.4 69.2 1.0 CB A:CYS87 3.1 56.3 1.0 CB A:CYS112 3.2 51.1 1.0 CG A:HIS109 3.3 50.8 1.0 CE1 A:HIS109 3.3 54.2 1.0 CB A:CYS90 3.4 67.1 1.0 CB A:HIS109 3.5 46.0 1.0 N A:CYS90 3.8 67.5 1.0 N A:HIS109 4.0 45.6 1.0 CA A:CYS90 4.2 68.4 1.0 CA A:HIS109 4.4 44.2 1.0 CD2 A:HIS109 4.4 51.9 1.0 NE2 A:HIS109 4.4 53.2 1.0 CA A:CYS87 4.5 57.8 1.0 CA A:CYS112 4.6 49.5 1.0 CB A:SER89 4.7 65.6 1.0 C A:SER89 4.9 71.8 1.0 C A:CYS90 5.0 74.1 1.0 C A:CYS87 5.0 64.2 1.0

Zinc binding site 3 out of 20 in the Crystal Structure of the LMO2:LDB1-Lid Complex, C2 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, C2 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:91.0 occ:1.00 OD2 A:ASP76 1.9 86.2 1.0 SG A:CYS50 2.3 80.7 1.0 SG A:CYS53 2.4 80.8 1.0 SG A:CYS73 2.4 60.4 1.0 CG A:ASP76 2.9 75.5 1.0 CB A:CYS50 3.2 78.4 1.0 CB A:ASP76 3.3 55.5 1.0 CB A:CYS73 3.5 56.0 1.0 CB A:CYS53 3.6 78.9 1.0 N A:CYS53 3.9 79.5 1.0 OD1 A:ASP76 4.1 76.9 1.0 N A:CYS73 4.1 56.0 1.0 SG A:CYS55 4.2 86.3 1.0 CA A:CYS53 4.3 80.6 1.0 CA A:CYS73 4.4 54.4 1.0 CB A:LEU52 4.4 73.7 1.0 N A:ASP76 4.5 50.8 1.0 CA A:ASP76 4.5 51.5 1.0 CA A:CYS50 4.6 79.9 1.0 C A:LEU52 4.8 82.6 1.0 CA A:LEU52 4.9 75.9 1.0 N A:LEU52 4.9 75.6 1.0 O A:CYS73 5.0 56.5 1.0

Zinc binding site 4 out of 20 in the Crystal Structure of the LMO2:LDB1-Lid Complex, C2 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, C2 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:0.0 occ:1.00 SG A:CYS47 2.2 0.4 1.0 SG A:CYS26 2.2 0.8 1.0 ND1 A:HIS44 2.2 0.8 1.0 CE1 A:HIS44 2.4 0.2 1.0 CB A:CYS47 3.3 0.3 1.0 CG A:HIS44 3.4 0.6 1.0 CB A:CYS26 3.4 0.5 1.0 NE2 A:HIS44 3.5 0.8 1.0 N A:CYS26 3.6 0.7 1.0 CD2 A:HIS44 4.0 1.0 1.0 CA A:CYS26 4.0 0.8 1.0 O A:GLN28 4.2 0.4 1.0 CB A:HIS44 4.2 0.4 1.0 CA A:CYS47 4.7 0.9 1.0 N A:HIS44 4.7 0.2 1.0 C A:CYS26 4.7 0.6 1.0 C A:GLY25 4.7 1.0 1.0 N A:GLN27 4.8 0.5 1.0 CA A:GLY25 4.9 0.8 1.0 N A:GLN28 4.9 0.1 1.0

Zinc binding site 5 out of 20 in the Crystal Structure of the LMO2:LDB1-Lid Complex, C2 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the LMO2:LDB1-Lid Complex, C2 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:83.8 occ:1.00 SG B:CYS118 2.2 70.4 1.0 SG B:CYS137 2.3 69.8 1.0 SG B:CYS115 2.4 56.4 1.0 OD2 B:ASP140 2.6 93.7 1.0 CG B:ASP140 3.0 84.5 1.0 CB B:CYS115 3.2 50.3 1.0 CB B:CYS118 3.4 68.3 1.0 CB B:ASP140 3.5 69.5 1.0 CB B:CYS137 3.6 62.9 1.0 N B:CYS118 3.7 63.7 1.0 OD1 B:ASP140 3.7 87.7 1.0 CA B:CYS118 4.1 65.6 1.0 CD B:LYS120 4.2 67.9 1.0 N B:CYS137 4.4 59.1 1.0 CB B:ALA117 4.4 61.1 1.0 CA B:CYS137 4.5 60.8 1.0 CA B:CYS115 4.7 47.6 1.0 CA B:ASP140 4.7 69.5 1.0 N B:ASP140 4.7 70.2 1.0 CB B:LYS120 4.7 57.8 1.0 C B:ALA117 4.7 66.8 1.0 O B:CYS137 4.8 67.0 1.0 CA B:ALA117 4.9 59.3 1.0 C B:CYS118 4.9 67.1 1.0 N B:ALA117 4.9 56.2 1.0

Zinc binding site 6 out of 20 in the Crystal Structure of the LMO2:LDB1-Lid Complex, C2 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the LMO2:LDB1-Lid Complex, C2 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:61.8 occ:1.00 SG B:CYS87 2.3 40.0 1.0 ND1 B:HIS109 2.3 33.7 1.0 SG B:CYS90 2.4 37.8 1.0 SG B:CYS112 2.4 41.9 1.0 CB B:CYS87 3.0 34.0 1.0 CB B:CYS112 3.2 37.0 1.0 CE1 B:HIS109 3.3 33.1 1.0 CG B:HIS109 3.3 31.7 1.0 CB B:CYS90 3.4 35.4 1.0 CB B:HIS109 3.6 29.6 1.0 N B:CYS90 3.7 36.4 1.0 N B:HIS109 4.0 29.6 1.0 CA B:CYS90 4.1 35.6 1.0 CA B:HIS109 4.4 28.9 1.0 CA B:CYS87 4.4 32.1 1.0 NE2 B:HIS109 4.4 33.4 1.0 CD2 B:HIS109 4.5 33.1 1.0 CB B:SER89 4.6 40.4 1.0 CA B:CYS112 4.6 37.4 1.0 C B:SER89 4.8 42.4 1.0 N B:SER89 4.9 33.5 1.0 C B:CYS90 4.9 42.3 1.0 CA B:SER89 4.9 35.6 1.0 C B:CYS87 5.0 38.6 1.0

Zinc binding site 7 out of 20 in the Crystal Structure of the LMO2:LDB1-Lid Complex, C2 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the LMO2:LDB1-Lid Complex, C2 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:90.0 occ:1.00 OD2 B:ASP76 1.9 57.7 1.0 SG B:CYS73 2.3 55.5 1.0 SG B:CYS53 2.3 73.8 1.0 SG B:CYS50 2.5 70.8 1.0 CG B:ASP76 3.0 62.9 1.0 CB B:CYS50 3.3 68.7 1.0 CB B:CYS73 3.4 52.0 1.0 CB B:ASP76 3.4 49.6 1.0 CB B:CYS53 3.6 70.5 1.0 SG B:CYS55 4.0 79.4 1.0 N B:CYS53 4.0 69.3 1.0 OD1 B:ASP76 4.1 67.7 1.0 N B:CYS73 4.1 51.1 1.0 CA B:CYS73 4.4 50.4 1.0 N B:ASP76 4.4 46.5 1.0 CA B:CYS53 4.4 71.5 1.0 CA B:ASP76 4.5 45.6 1.0 NH2 B:ARG75 4.7 87.0 1.0 CB B:LEU52 4.7 59.2 1.0 CA B:CYS50 4.8 70.1 1.0 O B:CYS73 4.9 52.4 1.0 C B:LEU52 4.9 70.8 1.0 C B:CYS73 4.9 53.0 1.0

Zinc binding site 8 out of 20 in the Crystal Structure of the LMO2:LDB1-Lid Complex, C2 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the LMO2:LDB1-Lid Complex, C2 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn204 b:0.3 occ:1.00 SG B:CYS23 2.2 0.8 1.0 SG B:CYS26 2.4 0.2 1.0 SG B:CYS47 2.4 0.2 1.0 ND1 B:HIS44 2.4 0.9 1.0 CB B:CYS23 2.8 0.9 1.0 CE1 B:HIS44 3.1 0.8 1.0 CB B:CYS47 3.2 0.2 1.0 N B:CYS26 3.3 0.0 1.0 CB B:CYS26 3.3 0.9 1.0 CG B:HIS44 3.6 0.5 1.0 CA B:CYS26 3.8 0.3 1.0 CB B:HIS44 4.1 1.0 1.0 CA B:CYS23 4.2 0.2 1.0 N B:HIS44 4.3 0.2 1.0 C B:GLY25 4.3 0.2 1.0 NE2 B:HIS44 4.4 0.1 1.0 N B:GLY25 4.4 0.1 1.0 N B:GLN27 4.5 0.7 1.0 C B:CYS26 4.5 0.4 1.0 CA B:GLY25 4.5 0.6 1.0 O B:GLN28 4.6 0.4 1.0 CD2 B:HIS44 4.6 0.9 1.0 CA B:CYS47 4.6 0.5 1.0 C B:CYS23 4.7 0.8 1.0 CA B:HIS44 4.9 0.9 1.0 N B:GLN28 5.0 1.0 1.0 N B:GLY24 5.0 0.5 1.0

Zinc binding site 9 out of 20 in the Crystal Structure of the LMO2:LDB1-Lid Complex, C2 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the LMO2:LDB1-Lid Complex, C2 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:94.6 occ:1.00 SG C:CYS118 2.3 69.5 1.0 OD2 C:ASP140 2.4 0.6 1.0 SG C:CYS115 2.5 67.2 1.0 SG C:CYS137 2.7 81.0 1.0 CG C:ASP140 2.9 0.5 1.0 CB C:ASP140 3.3 99.0 1.0 CB C:CYS115 3.4 59.4 1.0 CB C:CYS118 3.4 69.3 1.0 CB C:CYS137 3.6 73.6 1.0 OD1 C:ASP140 3.7 0.2 1.0 N C:CYS118 3.7 71.5 1.0 CA C:CYS118 4.1 69.6 1.0 CB C:ALA117 4.2 76.5 1.0 N C:CYS137 4.3 73.7 1.0 N C:ASP140 4.4 97.1 1.0 CA C:CYS137 4.5 74.2 1.0 CA C:ASP140 4.5 99.4 1.0 CD C:LYS120 4.5 89.6 1.0 C C:ALA117 4.7 77.3 1.0 CA C:CYS115 4.8 58.2 1.0 CA C:ALA117 4.8 73.5 1.0 N C:ALA117 4.9 69.7 1.0 O C:CYS137 4.9 85.1 1.0 CB C:LYS120 4.9 62.0 1.0 C C:CYS137 5.0 83.6 1.0 C C:CYS118 5.0 72.5 1.0

Zinc binding site 10 out of 20 in the Crystal Structure of the LMO2:LDB1-Lid Complex, C2 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the LMO2:LDB1-Lid Complex, C2 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:62.6 occ:1.00 ND1 C:HIS109 2.1 38.8 1.0 SG C:CYS112 2.3 41.9 1.0 SG C:CYS90 2.4 51.6 1.0 SG C:CYS87 2.5 44.4 1.0 CG C:HIS109 3.1 37.3 1.0 CB C:CYS87 3.1 37.0 1.0 CE1 C:HIS109 3.1 36.6 1.0 CB C:CYS112 3.3 39.0 1.0 CB C:HIS109 3.3 36.1 1.0 CB C:CYS90 3.5 49.5 1.0 N C:HIS109 3.9 38.2 1.0 N C:CYS90 4.0 50.2 1.0 CA C:HIS109 4.2 36.6 1.0 CD2 C:HIS109 4.2 36.8 1.0 NE2 C:HIS109 4.3 35.7 1.0 CA C:CYS90 4.3 49.8 1.0 CA C:CYS87 4.6 35.3 1.0 CA C:CYS112 4.6 39.6 1.0 CB C:SER89 4.9 48.5 1.0 O C:HIS109 4.9 40.6 1.0 N C:CYS112 4.9 40.2 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