Zinc in PDB 4kfz: Crystal Structure of LMO2 and Anti-LMO2 Vh Complex

The structure of Crystal Structure of LMO2 and Anti-LMO2 Vh Complex, PDB code: 4kfz was solved by H.Sewell, T.Tanaka, K.El Omari, A.Cruz-Migoni, E.J.Mancini, N.Fuentes-Fernandez, J.Chambers, T.H.Rabbitts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.80
Space group	P 6
Cell size a, b, c (Å), α, β, γ (°)	124.260, 124.260, 81.440, 90.00, 90.00, 120.00
R / Rfree (%)	23.9 / 25.8

The binding sites of Zinc atom in the Crystal Structure of LMO2 and Anti-LMO2 Vh Complex (pdb code 4kfz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of LMO2 and Anti-LMO2 Vh Complex, PDB code: 4kfz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of LMO2 and Anti-LMO2 Vh Complex


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 LMO2 and Anti-LMO2 Vh Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:46.0 occ:1.00 ND1 A:HIS51 2.2 44.9 1.0 SG A:CYS54 2.2 46.2 1.0 SG A:CYS33 2.2 46.8 1.0 SG A:CYS30 2.3 46.2 1.0 CB A:CYS30 2.9 48.1 1.0 CE1 A:HIS51 3.1 45.4 1.0 CB A:CYS54 3.2 45.8 1.0 CG A:HIS51 3.2 44.6 1.0 CB A:CYS33 3.2 48.1 1.0 CB A:HIS51 3.5 44.5 1.0 N A:CYS33 3.7 48.2 1.0 N A:HIS51 4.0 43.6 1.0 CA A:CYS33 4.0 48.8 1.0 NE2 A:HIS51 4.2 45.5 1.0 CD2 A:HIS51 4.3 44.9 1.0 CA A:HIS51 4.4 44.2 1.0 CA A:CYS30 4.4 49.0 1.0 C A:GLY32 4.4 48.1 1.0 CA A:CYS54 4.6 45.6 1.0 N A:GLY32 4.8 47.2 1.0 CA A:GLY32 4.8 47.4 1.0 C A:CYS33 4.9 49.8 1.0 C A:CYS30 4.9 48.9 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of LMO2 and Anti-LMO2 Vh Complex


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 LMO2 and Anti-LMO2 Vh Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:42.1 occ:1.00 OD2 A:ASP83 2.0 46.6 1.0 SG A:CYS80 2.1 45.6 1.0 SG A:CYS60 2.2 45.3 1.0 SG A:CYS57 2.4 43.7 1.0 CG A:ASP83 3.0 47.2 1.0 CB A:CYS57 3.2 43.6 1.0 CB A:CYS60 3.3 45.7 1.0 CB A:CYS80 3.3 45.9 1.0 CB A:ASP83 3.5 47.9 1.0 SG A:CYS62 3.8 44.9 1.0 N A:CYS60 3.8 46.0 1.0 N A:CYS80 4.0 46.6 1.0 N C:SER103 4.0 47.5 1.0 CA C:SER103 4.0 48.0 1.0 CB C:SER103 4.0 49.3 1.0 OD1 A:ASP83 4.0 47.5 1.0 CA A:CYS60 4.1 45.9 1.0 CA A:CYS80 4.2 46.1 1.0 CA A:CYS57 4.7 44.0 1.0 N A:ASP83 4.7 48.5 1.0 CA A:ASP83 4.7 48.6 1.0 N A:GLY61 4.7 46.0 1.0 CB A:LEU59 4.8 46.7 1.0 OG C:SER103 4.8 49.9 1.0 C A:CYS60 4.8 45.9 1.0 CG C:GLU102 4.9 49.4 1.0 C A:LEU59 4.9 46.5 1.0 C A:CYS80 5.0 46.5 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of LMO2 and Anti-LMO2 Vh Complex


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 LMO2 and Anti-LMO2 Vh Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:61.8 occ:1.00 SG A:CYS119 2.1 61.3 1.0 SG A:CYS97 2.2 79.8 1.0 ND1 A:HIS116 2.2 61.2 1.0 SG A:CYS94 2.5 75.4 1.0 CB A:CYS119 3.1 61.4 1.0 CE1 A:HIS116 3.1 61.9 1.0 CB A:CYS97 3.3 81.4 1.0 CG A:HIS116 3.3 60.9 1.0 CB A:CYS94 3.3 77.8 1.0 N A:CYS97 3.6 81.4 1.0 CB A:HIS116 3.6 60.4 1.0 CA A:CYS97 4.0 82.3 1.0 N A:HIS116 4.1 59.4 1.0 NE2 A:HIS116 4.3 61.3 1.0 CB A:SER96 4.3 78.2 1.0 CD2 A:HIS116 4.4 61.0 1.0 CA A:HIS116 4.5 59.5 1.0 CA A:CYS119 4.5 61.4 1.0 C A:SER96 4.6 80.8 1.0 CA A:SER96 4.8 79.0 1.0 CA A:CYS94 4.8 79.2 1.0 N A:SER96 4.8 78.0 1.0 C A:CYS97 4.8 83.7 1.0 OG A:SER96 5.0 78.6 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of LMO2 and Anti-LMO2 Vh Complex


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 LMO2 and Anti-LMO2 Vh Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:66.2 occ:1.00 SG A:CYS125 2.1 68.0 1.0 OD2 A:ASP147 2.1 84.3 1.0 SG A:CYS122 2.2 65.1 1.0 SG A:CYS144 2.3 71.7 1.0 CB A:CYS122 3.1 64.5 1.0 CG A:ASP147 3.1 86.2 1.0 CB A:CYS125 3.3 68.9 1.0 CB A:CYS144 3.4 72.2 1.0 N A:CYS125 3.5 68.5 1.0 NE2 A:GLN146 3.7 89.7 1.0 CB A:ASP147 3.9 86.5 1.0 CA A:CYS125 3.9 68.8 1.0 N A:CYS144 4.0 71.3 1.0 OD1 A:ASP147 4.0 87.0 1.0 CA A:CYS144 4.2 73.0 1.0 CB A:ALA124 4.5 68.7 1.0 CG A:LYS127 4.5 67.2 1.0 CA A:CYS122 4.5 63.9 1.0 C A:CYS125 4.6 68.7 1.0 C A:ALA124 4.7 69.0 1.0 N A:GLN126 4.7 68.3 1.0 CD A:GLN146 4.8 90.1 1.0 N A:ALA124 4.8 67.5 1.0 CA A:ALA124 4.9 68.5 1.0 CD A:LYS127 4.9 68.4 1.0 N A:ASP147 4.9 87.4 1.0 C A:CYS144 4.9 75.5 1.0 CE A:LYS127 4.9 68.4 1.0 O A:CYS144 5.0 76.8 1.0 CA A:ASP147 5.0 88.4 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of LMO2 and Anti-LMO2 Vh Complex


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 LMO2 and Anti-LMO2 Vh Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:60.9 occ:1.00 ND1 B:HIS51 2.1 58.4 1.0 SG B:CYS54 2.2 63.1 1.0 SG B:CYS33 2.2 63.1 1.0 SG B:CYS30 2.3 61.6 1.0 CB B:CYS30 3.0 61.0 1.0 CE1 B:HIS51 3.0 58.2 1.0 CG B:HIS51 3.2 57.8 1.0 CB B:CYS54 3.2 63.9 1.0 CB B:CYS33 3.3 65.5 1.0 CB B:HIS51 3.6 58.4 1.0 N B:CYS33 3.6 65.9 1.0 CA B:CYS33 4.0 66.8 1.0 N B:HIS51 4.2 58.7 1.0 NE2 B:HIS51 4.2 57.4 1.0 CD2 B:HIS51 4.3 57.0 1.0 C B:GLY32 4.5 66.6 1.0 CA B:HIS51 4.5 58.7 1.0 CA B:CYS30 4.5 61.3 1.0 CA B:CYS54 4.6 64.8 1.0 CA B:GLY32 4.7 65.7 1.0 N B:GLY32 4.8 64.8 1.0 C B:CYS33 4.8 67.6 1.0 N B:GLN34 5.0 67.2 1.0 C B:CYS30 5.0 62.6 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of LMO2 and Anti-LMO2 Vh Complex


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 LMO2 and Anti-LMO2 Vh Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:64.6 occ:1.00 OD2 B:ASP83 2.0 75.8 1.0 SG B:CYS60 2.1 71.2 1.0 SG B:CYS80 2.2 71.7 1.0 SG B:CYS57 2.4 68.3 1.0 CG B:ASP83 3.1 76.9 1.0 CB B:CYS57 3.1 67.6 1.0 CB B:CYS60 3.4 72.6 1.0 CB B:CYS80 3.5 70.7 1.0 CB B:ASP83 3.6 77.3 1.0 SG B:CYS62 3.7 66.5 1.0 N B:CYS60 3.8 73.2 1.0 N B:CYS80 4.0 71.8 1.0 N D:SER103 4.1 77.2 1.0 CA D:SER103 4.1 79.1 1.0 OD1 B:ASP83 4.1 78.3 1.0 CA B:CYS60 4.1 72.9 1.0 CB D:SER103 4.2 80.9 1.0 CA B:CYS80 4.4 71.3 1.0 CA B:CYS57 4.6 68.0 1.0 CB B:LEU59 4.7 76.1 1.0 N B:GLY61 4.8 71.2 1.0 C B:CYS60 4.8 71.8 1.0 CA B:ASP83 4.8 78.7 1.0 N B:ASP83 4.9 77.6 1.0 C B:LEU59 4.9 74.6 1.0 OG D:SER103 4.9 82.5 1.0 CB B:CYS62 5.0 67.5 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of LMO2 and Anti-LMO2 Vh Complex


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 LMO2 and Anti-LMO2 Vh Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:0.5 occ:1.00 SG B:CYS119 2.1 0.4 1.0 ND1 B:HIS116 2.2 0.2 1.0 SG B:CYS97 2.3 0.0 1.0 SG B:CYS94 2.6 0.0 1.0 CG B:HIS116 3.1 0.6 1.0 CE1 B:HIS116 3.1 0.5 1.0 CB B:CYS119 3.2 0.4 1.0 CB B:CYS97 3.2 0.3 1.0 CB B:CYS94 3.3 0.8 1.0 CB B:HIS116 3.4 0.6 1.0 N B:CYS97 3.7 0.3 1.0 N B:HIS116 3.9 0.5 1.0 CA B:CYS97 4.0 0.8 1.0 NE2 B:HIS116 4.2 0.4 1.0 CD2 B:HIS116 4.3 0.1 1.0 CA B:HIS116 4.3 0.3 1.0 CA B:CYS119 4.6 0.3 1.0 CB B:SER96 4.6 0.9 1.0 C B:SER96 4.8 0.1 1.0 CA B:CYS94 4.8 0.6 1.0 C B:CYS97 4.9 0.6 1.0 N B:SER96 4.9 0.6 1.0 N B:ASP98 5.0 0.1 1.0 N B:CYS119 5.0 0.2 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of LMO2 and Anti-LMO2 Vh Complex


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 LMO2 and Anti-LMO2 Vh Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn204 b:0.3 occ:1.00 SG B:CYS125 2.0 0.9 1.0 SG B:CYS144 2.0 0.6 1.0 OD2 B:ASP147 2.1 0.5 1.0 SG B:CYS122 2.7 0.5 1.0 CG B:ASP147 3.1 0.8 1.0 NE2 B:GLN146 3.2 0.5 1.0 CB B:CYS125 3.3 0.0 1.0 CB B:CYS122 3.4 0.5 1.0 CB B:CYS144 3.5 0.5 1.0 N B:CYS125 3.8 0.1 1.0 CB B:ASP147 3.8 0.9 1.0 OD1 B:ASP147 4.0 1.0 1.0 CA B:CYS125 4.1 0.1 1.0 CD B:GLN146 4.2 0.8 1.0 N B:CYS144 4.3 0.3 1.0 CA B:CYS144 4.5 0.0 1.0 N B:ASP147 4.7 0.2 1.0 CB B:ALA124 4.8 0.8 1.0 C B:CYS125 4.8 0.1 1.0 CG B:GLN146 4.9 0.8 1.0 CA B:ASP147 4.9 0.0 1.0 CA B:CYS122 4.9 0.2 1.0 OE1 B:GLN146 4.9 0.6 1.0 C B:ALA124 4.9 0.8 1.0 O B:CYS144 5.0 0.9 1.0

H.Sewell, T.Tanaka, K.E.Omari, E.J.Mancini, A.Cruz, N.Fernandez-Fuentes, J.Chambers, T.H.Rabbitts. Conformational Flexibility of the Oncogenic Protein LMO2 Primes the Formation of the Multi-Protein Transcription Complex. Sci Rep V. 4 3643 2014.
ISSN: ESSN 2045-2322
PubMed: 24407558
DOI: 10.1038/SREP03643