Zinc in PDB 4jcj: Crystal Structure of ISL1 Lim Domains with LDB1 Lim-Interaction Domain

The structure of Crystal Structure of ISL1 Lim Domains with LDB1 Lim-Interaction Domain, PDB code: 4jcj was solved by M.S.Gadd, D.A.Jacques, 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)	48.29 / 3.00
Space group	P 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	57.310, 56.639, 179.342, 90.00, 90.00, 90.00
R / Rfree (%)	25.4 / 29.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of ISL1 Lim Domains with LDB1 Lim-Interaction Domain (pdb code 4jcj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of ISL1 Lim Domains with LDB1 Lim-Interaction Domain, PDB code: 4jcj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Crystal Structure of ISL1 Lim Domains with LDB1 Lim-Interaction Domain


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 ISL1 Lim Domains with LDB1 Lim-Interaction Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:43.0 occ:1.00 ND1 A:HIS39 2.1 42.9 1.0 SG A:CYS17 2.3 30.1 1.0 SG A:CYS20 2.3 42.7 1.0 SG A:CYS42 2.3 56.1 1.0 CG A:HIS39 3.0 35.1 1.0 CE1 A:HIS39 3.2 47.9 1.0 CB A:HIS39 3.2 36.0 1.0 CB A:CYS17 3.3 32.9 1.0 CB A:CYS42 3.3 44.8 1.0 CB A:CYS20 3.4 38.9 1.0 N A:CYS20 3.9 37.1 1.0 CD2 A:HIS39 4.2 41.9 1.0 NE2 A:HIS39 4.2 47.0 1.0 CA A:CYS20 4.2 38.5 1.0 N A:HIS39 4.4 32.6 1.0 CA A:HIS39 4.4 34.2 1.0 CA A:CYS17 4.7 33.8 1.0 CA A:CYS42 4.7 40.7 1.0 C A:GLY19 4.8 36.0 1.0 O A:CYS17 4.8 34.7 1.0 CA A:GLY19 4.9 33.4 1.0 C A:CYS17 4.9 33.4 1.0 N A:GLY19 4.9 33.6 1.0 N A:CYS42 4.9 38.3 1.0 C A:CYS20 5.0 39.1 1.0

Zinc binding site 2 out of 12 in the Crystal Structure of ISL1 Lim Domains with LDB1 Lim-Interaction Domain


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 ISL1 Lim Domains with LDB1 Lim-Interaction Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:35.0 occ:1.00 OD2 A:ASP70 2.0 51.6 1.0 SG A:CYS45 2.3 36.5 1.0 SG A:CYS48 2.3 30.5 1.0 SG A:CYS67 2.3 36.4 1.0 CG A:ASP70 2.5 48.1 1.0 OD1 A:ASP70 3.1 50.0 1.0 CB A:ASP70 3.3 43.9 1.0 CB A:CYS45 3.3 35.2 1.0 CB A:CYS48 3.3 36.2 1.0 CB A:CYS67 3.4 34.8 1.0 N A:CYS48 3.9 39.0 1.0 N A:CYS67 3.9 35.2 1.0 CA A:CYS67 4.1 36.2 1.0 CA A:CYS48 4.2 37.2 1.0 N A:ASP70 4.2 43.0 1.0 CA A:ASP70 4.4 44.4 1.0 O A:CYS67 4.4 43.7 1.0 C A:CYS67 4.6 39.5 1.0 CA A:CYS45 4.7 33.0 1.0 C A:CYS48 5.0 34.7 1.0 CB A:GLU47 5.0 45.6 1.0 C A:GLU47 5.0 40.4 1.0

Zinc binding site 3 out of 12 in the Crystal Structure of ISL1 Lim Domains with LDB1 Lim-Interaction Domain


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 ISL1 Lim Domains with LDB1 Lim-Interaction Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:46.5 occ:1.00 ND1 A:HIS101 2.2 60.5 1.0 SG A:CYS82 2.3 72.1 1.0 SG A:CYS104 2.3 67.6 1.0 SG A:CYS79 2.3 48.5 1.0 CE1 A:HIS101 3.1 63.3 1.0 CG A:HIS101 3.1 55.0 1.0 CB A:CYS104 3.1 61.7 1.0 CB A:CYS79 3.2 54.2 1.0 CB A:CYS82 3.3 73.4 1.0 CB A:HIS101 3.4 50.2 1.0 N A:CYS82 3.5 66.6 1.0 CA A:CYS82 4.0 73.0 1.0 NE2 A:HIS101 4.1 66.3 1.0 N A:HIS101 4.1 44.8 1.0 CD2 A:HIS101 4.2 59.0 1.0 CB A:LYS81 4.2 57.4 1.0 CA A:HIS101 4.4 46.3 1.0 C A:LYS81 4.5 66.3 1.0 CA A:CYS104 4.6 59.4 1.0 CA A:CYS79 4.6 54.3 1.0 C A:CYS82 4.8 76.3 1.0 CA A:LYS81 4.8 59.8 1.0 N A:LYS81 4.8 56.8 1.0 C A:CYS79 4.9 56.1 1.0 N A:SER83 4.9 73.0 1.0

Zinc binding site 4 out of 12 in the Crystal Structure of ISL1 Lim Domains with LDB1 Lim-Interaction Domain


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 ISL1 Lim Domains with LDB1 Lim-Interaction Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:45.4 occ:1.00 OD2 A:ASP132 2.0 63.3 1.0 SG A:CYS110 2.3 55.1 1.0 SG A:CYS107 2.3 53.9 1.0 SG A:CYS129 2.3 58.8 1.0 CG A:ASP132 2.6 64.3 1.0 CB A:ASP132 3.2 65.1 1.0 CB A:CYS110 3.3 61.6 1.0 CB A:CYS107 3.4 52.1 1.0 CB A:CYS129 3.4 51.7 1.0 OD1 A:ASP132 3.5 68.8 1.0 N A:CYS110 3.5 59.5 1.0 N A:CYS129 3.7 49.0 1.0 CA A:CYS110 4.0 64.0 1.0 CA A:CYS129 4.1 50.2 1.0 CB A:ALA109 4.2 59.5 1.0 N A:ASP132 4.2 60.8 1.0 CA A:ASP132 4.4 64.3 1.0 C A:ALA109 4.5 62.0 1.0 O A:CYS129 4.6 58.0 1.0 NE A:ARG112 4.7 72.8 1.0 C A:CYS129 4.7 53.9 1.0 C A:PHE128 4.8 48.0 1.0 CA A:CYS107 4.8 52.9 1.0 CA A:ALA109 4.8 60.8 1.0 NH2 A:ARG112 4.9 68.6 1.0 N A:ALA109 4.9 57.6 1.0 C A:CYS110 4.9 67.0 1.0 CA A:PHE128 4.9 49.7 1.0

Zinc binding site 5 out of 12 in the Crystal Structure of ISL1 Lim Domains with LDB1 Lim-Interaction Domain


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 ISL1 Lim Domains with LDB1 Lim-Interaction Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:43.6 occ:1.00 OD2 B:ASP132 2.0 66.5 1.0 SG B:CYS129 2.3 60.5 1.0 SG B:CYS107 2.3 52.2 1.0 SG B:CYS110 2.3 54.2 1.0 CG B:ASP132 2.4 65.0 1.0 OD1 B:ASP132 2.8 66.1 1.0 CB B:CYS129 3.2 59.9 1.0 CB B:CYS110 3.3 58.7 1.0 CB B:ASP132 3.4 64.4 1.0 CB B:CYS107 3.4 49.8 1.0 N B:CYS129 3.7 58.1 1.0 N B:CYS110 3.8 57.3 1.0 CA B:CYS129 4.0 58.7 1.0 CA B:CYS110 4.2 59.6 1.0 N B:ASP132 4.4 65.0 1.0 CB B:ALA109 4.4 59.1 1.0 NE B:ARG112 4.4 60.9 1.0 O B:CYS129 4.5 62.3 1.0 CA B:ASP132 4.5 65.7 1.0 C B:CYS129 4.6 60.6 1.0 CA B:CYS107 4.8 49.5 1.0 C B:ALA109 4.9 60.6 1.0 NH2 B:ARG112 4.9 59.0 1.0 C B:PHE128 4.9 58.3 1.0

Zinc binding site 6 out of 12 in the Crystal Structure of ISL1 Lim Domains with LDB1 Lim-Interaction Domain


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 ISL1 Lim Domains with LDB1 Lim-Interaction Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:41.2 occ:1.00 ND1 B:HIS39 2.1 47.3 1.0 SG B:CYS17 2.3 30.4 1.0 SG B:CYS42 2.3 53.9 1.0 SG B:CYS20 2.3 53.2 1.0 CE1 B:HIS39 2.9 54.5 1.0 CB B:CYS17 3.0 38.7 1.0 CG B:HIS39 3.1 49.8 1.0 CB B:CYS42 3.2 49.0 1.0 CB B:CYS20 3.4 42.5 1.0 CB B:HIS39 3.6 49.6 1.0 N B:CYS20 3.7 38.7 1.0 NE2 B:HIS39 4.1 57.6 1.0 CA B:CYS20 4.2 41.7 1.0 CD2 B:HIS39 4.2 53.2 1.0 N B:HIS39 4.3 42.7 1.0 CA B:CYS17 4.4 39.3 1.0 CA B:HIS39 4.6 46.3 1.0 CA B:CYS42 4.7 47.7 1.0 C B:GLY19 4.7 40.1 1.0 N B:GLY21 4.7 40.7 1.0 C B:CYS17 4.7 39.5 1.0 O B:CYS17 4.8 41.5 1.0 N B:GLY19 4.8 39.4 1.0 CA B:GLY19 4.9 39.2 1.0 O B:ASN22 4.9 43.7 1.0 C B:CYS20 4.9 41.9 1.0

Zinc binding site 7 out of 12 in the Crystal Structure of ISL1 Lim Domains with LDB1 Lim-Interaction Domain


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 ISL1 Lim Domains with LDB1 Lim-Interaction Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:41.1 occ:1.00 OD2 B:ASP70 2.0 51.5 1.0 SG B:CYS45 2.3 45.6 1.0 SG B:CYS67 2.3 32.6 1.0 SG B:CYS48 2.3 35.7 1.0 CG B:ASP70 2.5 46.5 1.0 CB B:CYS45 3.2 45.1 1.0 CB B:ASP70 3.2 40.8 1.0 OD1 B:ASP70 3.3 43.5 1.0 CB B:CYS48 3.3 41.5 1.0 CB B:CYS67 3.4 28.6 1.0 N B:CYS48 3.8 41.8 1.0 N B:CYS67 4.1 30.2 1.0 CA B:CYS48 4.2 42.3 1.0 NH2 B:ARG69 4.2 56.7 1.0 CA B:CYS67 4.3 29.6 1.0 N B:ASP70 4.4 40.1 1.0 CA B:ASP70 4.4 41.7 1.0 O B:CYS67 4.5 36.6 1.0 CA B:CYS45 4.6 42.6 1.0 CB B:GLU47 4.7 49.5 1.0 C B:CYS67 4.7 32.7 1.0 CZ B:ARG69 4.8 55.6 1.0 C B:GLU47 4.9 45.0 1.0 C B:CYS48 5.0 42.2 1.0

Zinc binding site 8 out of 12 in the Crystal Structure of ISL1 Lim Domains with LDB1 Lim-Interaction Domain


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 ISL1 Lim Domains with LDB1 Lim-Interaction Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:49.4 occ:1.00 ND1 B:HIS101 2.1 63.4 1.0 SG B:CYS104 2.3 71.7 1.0 SG B:CYS82 2.3 76.1 1.0 SG B:CYS79 2.4 59.2 1.0 CG B:HIS101 3.0 61.1 1.0 CE1 B:HIS101 3.1 62.1 1.0 CB B:CYS104 3.2 63.8 1.0 CB B:CYS82 3.3 77.8 1.0 CB B:CYS79 3.3 62.6 1.0 CB B:HIS101 3.3 57.0 1.0 N B:CYS82 3.8 70.5 1.0 CD2 B:HIS101 4.1 64.8 1.0 NE2 B:HIS101 4.1 69.6 1.0 CA B:CYS82 4.1 77.3 1.0 N B:HIS101 4.2 50.7 1.0 CA B:HIS101 4.4 53.1 1.0 CA B:CYS104 4.5 60.9 1.0 CB B:LYS81 4.6 61.3 1.0 CA B:CYS79 4.7 61.4 1.0 N B:CYS104 4.7 60.0 1.0 O B:CYS79 4.8 69.9 1.0 C B:LYS81 4.9 69.8 1.0

Zinc binding site 9 out of 12 in the Crystal Structure of ISL1 Lim Domains with LDB1 Lim-Interaction Domain


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 ISL1 Lim Domains with LDB1 Lim-Interaction Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:31.7 occ:1.00 ND1 C:HIS39 2.1 48.7 1.0 SG C:CYS42 2.3 48.3 1.0 SG C:CYS17 2.3 42.2 1.0 SG C:CYS20 2.3 41.1 1.0 CE1 C:HIS39 3.1 54.5 1.0 CG C:HIS39 3.1 45.4 1.0 CB C:CYS42 3.3 46.1 1.0 CB C:CYS17 3.3 44.6 1.0 CB C:CYS20 3.4 42.1 1.0 CB C:HIS39 3.5 37.4 1.0 N C:CYS20 3.8 40.3 1.0 CA C:CYS20 4.2 42.4 1.0 N C:HIS39 4.2 31.0 1.0 NE2 C:HIS39 4.2 56.8 1.0 CD2 C:HIS39 4.3 53.1 1.0 CA C:HIS39 4.4 33.3 1.0 CA C:CYS42 4.7 44.2 1.0 CA C:CYS17 4.7 44.7 1.0 C C:GLY19 4.8 40.0 1.0 C C:CYS20 4.9 43.9 1.0 CA C:GLY19 5.0 39.1 1.0

Zinc binding site 10 out of 12 in the Crystal Structure of ISL1 Lim Domains with LDB1 Lim-Interaction Domain


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 ISL1 Lim Domains with LDB1 Lim-Interaction Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:33.5 occ:1.00 OD2 C:ASP70 2.0 47.1 1.0 SG C:CYS45 2.3 32.0 1.0 SG C:CYS48 2.3 20.6 1.0 SG C:CYS67 2.3 32.3 1.0 CG C:ASP70 2.4 44.0 1.0 CB C:ASP70 3.0 40.8 1.0 OD1 C:ASP70 3.2 48.8 1.0 CB C:CYS48 3.2 33.6 1.0 CB C:CYS45 3.4 38.1 1.0 CB C:CYS67 3.5 27.2 1.0 N C:CYS48 3.7 33.7 1.0 N C:CYS67 4.0 31.9 1.0 NH1 C:ARG69 4.0 54.5 1.0 CA C:CYS48 4.0 35.0 1.0 N C:ASP70 4.2 39.3 1.0 CA C:ASP70 4.2 41.3 1.0 CA C:CYS67 4.2 28.5 1.0 O C:CYS67 4.3 32.4 1.0 CZ C:ARG69 4.6 55.5 1.0 CB C:GLU47 4.6 36.3 1.0 C C:CYS67 4.6 31.4 1.0 C C:GLU47 4.8 35.6 1.0 CA C:CYS45 4.8 36.1 1.0 NE C:ARG69 4.9 51.6 1.0 C C:CYS48 4.9 36.5 1.0

M.S.Gadd, D.A.Jacques, I.Nisevic, V.J.Craig, A.H.Kwan, J.M.Guss, J.M.Matthews. A Structural Basis For the Regulation of the Lim-Homeodomain Protein Islet 1 (ISL1) By Intra- and Intermolecular Interactions. J.Biol.Chem. V. 288 21924 2013.
ISSN: ISSN 0021-9258
PubMed: 23750000
DOI: 10.1074/JBC.M113.478586