Zinc in PDB 3mmk: The Structural Basis For Partial Redundancy in A Class of Transcription Factors, the Lim-Homeodomain Proteins, in Neural Cell Type Specification

The structure of The Structural Basis For Partial Redundancy in A Class of Transcription Factors, the Lim-Homeodomain Proteins, in Neural Cell Type Specification, PDB code: 3mmk was solved by M.S.Gadd, D.B.Langley, J.M.Guss, J.M.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.14 / 2.16
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.823, 88.734, 49.851, 90.00, 111.85, 90.00
R / Rfree (%)	23.5 / 26.5

The structure of The Structural Basis For Partial Redundancy in A Class of Transcription Factors, the Lim-Homeodomain Proteins, in Neural Cell Type Specification also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Zinc atom in the The Structural Basis For Partial Redundancy in A Class of Transcription Factors, the Lim-Homeodomain Proteins, in Neural Cell Type Specification (pdb code 3mmk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the The Structural Basis For Partial Redundancy in A Class of Transcription Factors, the Lim-Homeodomain Proteins, in Neural Cell Type Specification, PDB code: 3mmk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the The Structural Basis For Partial Redundancy in A Class of Transcription Factors, the Lim-Homeodomain Proteins, in Neural Cell Type Specification


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structural Basis For Partial Redundancy in A Class of Transcription Factors, the Lim-Homeodomain Proteins, in Neural Cell Type Specification within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn864 b:50.1 occ:0.80 OD2 A:ASP143 2.2 45.4 1.0 SG A:CYS140 2.4 38.9 1.0 SG A:CYS120 2.4 45.9 1.0 SG A:CYS117 2.4 43.3 1.0 CG A:ASP143 3.0 45.0 1.0 CB A:CYS140 3.2 42.2 1.0 CB A:CYS120 3.2 48.5 1.0 CB A:CYS117 3.2 34.5 1.0 CB A:ASP143 3.5 38.5 1.0 N A:CYS120 3.7 43.1 1.0 N A:CYS140 4.0 39.2 1.0 OD1 A:ASP143 4.0 47.1 1.0 CA A:CYS120 4.0 45.5 1.0 CA A:CYS140 4.2 42.0 1.0 CB A:ILE119 4.6 40.8 1.0 N A:ASP143 4.6 39.5 1.0 CA A:CYS117 4.7 38.7 1.0 CA A:ASP143 4.7 40.2 1.0 C A:ILE119 4.8 48.0 1.0 C A:CYS140 4.8 39.0 1.0 O A:CYS140 4.9 39.3 1.0 CG2 A:ILE119 4.9 41.9 1.0 C A:CYS120 4.9 46.1 1.0

Zinc binding site 2 out of 8 in the The Structural Basis For Partial Redundancy in A Class of Transcription Factors, the Lim-Homeodomain Proteins, in Neural Cell Type Specification


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structural Basis For Partial Redundancy in A Class of Transcription Factors, the Lim-Homeodomain Proteins, in Neural Cell Type Specification within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn867 b:57.4 occ:0.80 ND1 A:HIS111 2.2 57.5 1.0 SG A:CYS114 2.4 54.0 1.0 SG A:CYS89 2.4 51.5 1.0 SG A:CYS92 2.4 63.3 1.0 CB A:CYS89 2.9 62.5 1.0 CE1 A:HIS111 3.2 61.1 1.0 CB A:CYS114 3.2 43.2 1.0 CG A:HIS111 3.2 58.8 1.0 CB A:CYS92 3.3 61.8 1.0 CB A:HIS111 3.6 52.1 1.0 N A:CYS92 3.8 62.2 1.0 N A:HIS111 4.1 44.8 1.0 CA A:CYS92 4.1 64.7 1.0 NE2 A:HIS111 4.3 65.3 1.0 CD2 A:HIS111 4.3 63.0 1.0 CA A:CYS89 4.4 66.2 1.0 CA A:HIS111 4.5 48.4 1.0 CE1 A:HIS113 4.6 49.1 1.0 CA A:CYS114 4.7 45.5 1.0 CB A:ALA91 4.8 51.6 1.0 C A:CYS89 4.8 65.2 1.0 C A:CYS92 4.8 67.8 1.0 C A:ALA91 4.9 59.0 1.0 N A:GLN93 5.0 71.7 1.0

Zinc binding site 3 out of 8 in the The Structural Basis For Partial Redundancy in A Class of Transcription Factors, the Lim-Homeodomain Proteins, in Neural Cell Type Specification


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structural Basis For Partial Redundancy in A Class of Transcription Factors, the Lim-Homeodomain Proteins, in Neural Cell Type Specification within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn869 b:51.7 occ:0.80 SG A:CYS54 2.4 68.6 1.0 SG A:CYS30 2.4 45.9 1.0 ND1 A:HIS51 2.4 44.0 1.0 SG A:CYS33 2.4 56.6 1.0 CB A:CYS30 2.9 47.1 1.0 CB A:CYS54 3.2 52.9 1.0 CB A:CYS33 3.2 44.2 1.0 CG A:HIS51 3.3 47.4 1.0 CB A:HIS51 3.4 43.0 1.0 CE1 A:HIS51 3.5 41.9 1.0 N A:CYS33 3.7 52.2 1.0 CA A:CYS33 4.1 48.8 1.0 N A:HIS51 4.1 47.6 1.0 CA A:HIS51 4.4 43.7 1.0 CA A:CYS30 4.4 48.5 1.0 CD2 A:HIS51 4.5 45.3 1.0 NE2 A:HIS51 4.5 44.5 1.0 CA A:CYS54 4.7 55.0 1.0 C A:GLY32 4.8 55.9 1.0 C A:CYS33 4.8 52.0 1.0 CA A:GLY32 5.0 52.8 1.0

Zinc binding site 4 out of 8 in the The Structural Basis For Partial Redundancy in A Class of Transcription Factors, the Lim-Homeodomain Proteins, in Neural Cell Type Specification


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structural Basis For Partial Redundancy in A Class of Transcription Factors, the Lim-Homeodomain Proteins, in Neural Cell Type Specification within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn870 b:74.7 occ:0.90 SG A:CYS77 2.4 64.3 1.0 OD2 A:ASP80 2.5 79.9 1.0 SG A:CYS57 2.5 58.0 1.0 SG A:CYS60 2.5 66.1 1.0 CB A:CYS57 3.1 61.0 1.0 CG A:ASP80 3.2 77.9 1.0 CB A:ASP80 3.3 75.7 1.0 CB A:CYS77 3.3 57.1 1.0 CB A:CYS60 3.5 82.5 1.0 N A:CYS60 3.9 83.2 1.0 N A:CYS77 4.0 49.7 1.0 CA A:CYS77 4.2 55.1 1.0 CA A:CYS60 4.3 82.5 1.0 OD1 A:ASP80 4.3 78.0 1.0 N A:ASP80 4.5 76.3 1.0 CA A:ASP80 4.5 76.1 1.0 CB A:ASP59 4.6 89.4 1.0 CA A:CYS57 4.6 63.0 1.0 C A:CYS77 4.9 60.8 1.0 C A:CYS60 4.9 83.0 1.0 C A:ASP59 5.0 85.6 1.0

Zinc binding site 5 out of 8 in the The Structural Basis For Partial Redundancy in A Class of Transcription Factors, the Lim-Homeodomain Proteins, in Neural Cell Type Specification


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Structural Basis For Partial Redundancy in A Class of Transcription Factors, the Lim-Homeodomain Proteins, in Neural Cell Type Specification within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn865 b:45.7 occ:0.80 ND1 B:HIS111 2.3 44.0 1.0 SG B:CYS114 2.4 41.1 1.0 SG B:CYS89 2.4 42.8 1.0 SG B:CYS92 2.4 50.5 1.0 CB B:CYS89 2.9 50.6 1.0 CB B:CYS114 3.2 35.3 1.0 CE1 B:HIS111 3.3 44.1 1.0 CG B:HIS111 3.3 47.0 1.0 CB B:CYS92 3.3 44.5 1.0 CB B:HIS111 3.5 43.6 1.0 N B:CYS92 3.8 46.9 1.0 N B:HIS111 4.1 36.7 1.0 CA B:CYS92 4.1 46.5 1.0 NE2 B:HIS111 4.4 45.6 1.0 CD2 B:HIS111 4.4 46.2 1.0 CA B:CYS89 4.4 49.9 1.0 CA B:HIS111 4.5 40.4 1.0 NE2 B:HIS113 4.6 52.7 1.0 CA B:CYS114 4.7 38.1 1.0 CB B:ALA91 4.8 41.4 1.0 C B:CYS92 4.9 49.8 1.0 C B:ALA91 4.9 46.4 1.0 C B:CYS89 4.9 49.3 1.0 N B:GLN93 4.9 48.1 1.0

Zinc binding site 6 out of 8 in the The Structural Basis For Partial Redundancy in A Class of Transcription Factors, the Lim-Homeodomain Proteins, in Neural Cell Type Specification


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Structural Basis For Partial Redundancy in A Class of Transcription Factors, the Lim-Homeodomain Proteins, in Neural Cell Type Specification within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn866 b:47.4 occ:0.80 OD2 B:ASP143 2.2 48.0 1.0 SG B:CYS120 2.4 48.7 1.0 SG B:CYS117 2.4 37.7 1.0 SG B:CYS140 2.4 41.7 1.0 CG B:ASP143 3.1 49.3 1.0 CB B:CYS117 3.1 36.4 1.0 CB B:CYS120 3.2 43.2 1.0 CB B:CYS140 3.3 39.4 1.0 CB B:ASP143 3.6 44.4 1.0 N B:CYS120 3.6 43.3 1.0 CA B:CYS120 4.0 43.7 1.0 OD1 B:ASP143 4.0 55.2 1.0 N B:CYS140 4.1 33.0 1.0 CA B:CYS140 4.2 34.8 1.0 CB B:ILE119 4.4 44.3 1.0 CA B:CYS117 4.6 36.4 1.0 C B:ILE119 4.7 47.2 1.0 N B:ASP143 4.8 42.4 1.0 CG2 B:ILE119 4.8 46.1 1.0 CA B:ASP143 4.8 42.0 1.0 C B:CYS120 4.8 42.5 1.0 O B:CYS140 4.8 36.8 1.0 C B:CYS140 4.9 35.5 1.0 CA B:ILE119 4.9 44.3 1.0 N B:ILE119 4.9 43.7 1.0 N B:ASN121 5.0 39.6 1.0

Zinc binding site 7 out of 8 in the The Structural Basis For Partial Redundancy in A Class of Transcription Factors, the Lim-Homeodomain Proteins, in Neural Cell Type Specification


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Structural Basis For Partial Redundancy in A Class of Transcription Factors, the Lim-Homeodomain Proteins, in Neural Cell Type Specification within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn868 b:54.1 occ:0.80 SG B:CYS54 2.3 53.1 1.0 SG B:CYS33 2.4 50.4 1.0 ND1 B:HIS51 2.4 46.9 1.0 SG B:CYS30 2.5 51.3 1.0 CB B:CYS30 3.0 45.8 1.0 CB B:CYS33 3.2 48.3 1.0 CB B:CYS54 3.2 43.6 1.0 CG B:HIS51 3.2 46.5 1.0 CB B:HIS51 3.4 42.2 1.0 CE1 B:HIS51 3.4 46.3 1.0 N B:CYS33 3.7 50.1 1.0 CA B:CYS33 4.0 49.9 1.0 N B:HIS51 4.2 46.0 1.0 CA B:HIS51 4.4 43.8 1.0 CD2 B:HIS51 4.4 44.9 1.0 NE2 B:HIS51 4.5 43.6 1.0 CA B:CYS30 4.5 46.6 1.0 CA B:CYS54 4.6 48.6 1.0 C B:CYS33 4.8 49.4 1.0 C B:GLY32 4.8 55.1 1.0 N B:ASN34 4.9 51.5 1.0 N B:CYS54 5.0 51.1 1.0

Zinc binding site 8 out of 8 in the The Structural Basis For Partial Redundancy in A Class of Transcription Factors, the Lim-Homeodomain Proteins, in Neural Cell Type Specification


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Structural Basis For Partial Redundancy in A Class of Transcription Factors, the Lim-Homeodomain Proteins, in Neural Cell Type Specification within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn871 b:80.4 occ:0.90 OD1 B:ASP80 2.4 86.6 1.0 SG B:CYS77 2.5 68.4 1.0 SG B:CYS57 2.6 65.2 1.0 SG B:CYS60 2.7 73.2 1.0 CG B:ASP80 3.1 85.3 1.0 CB B:CYS57 3.2 59.1 1.0 CB B:ASP80 3.3 82.1 1.0 CB B:CYS60 3.5 68.3 1.0 CB B:CYS77 3.6 57.1 1.0 N B:CYS60 3.7 71.4 1.0 CA B:CYS60 4.2 69.6 1.0 N B:CYS77 4.2 47.5 1.0 OD2 B:ASP80 4.2 86.6 1.0 CB B:ASP59 4.4 69.2 1.0 N B:ASP80 4.4 80.8 1.0 CA B:ASP80 4.5 79.8 1.0 CA B:CYS77 4.5 54.1 1.0 CA B:CYS57 4.7 59.7 1.0 C B:ASP59 4.8 72.8 1.0 C B:CYS60 4.9 69.9 1.0 O B:CYS77 4.9 60.3 1.0 CA B:ASP59 5.0 68.7 1.0

M.S.Gadd, M.Bhati, C.M.Jeffries, D.B.Langley, J.Trewhella, J.M.Guss, J.M.Matthews. The Structural Basis For Partial Redundancy in A Class of Transcription Factors, the Lim-Homeodomain Proteins, in Neural Cell Type Specification. J.Biol.Chem. 2011.
ISSN: ESSN 1083-351X
PubMed: 22025611
DOI: 10.1074/JBC.M111.248559