Zinc in PDB 1rut: Complex of LMO4 Lim Domains 1 and 2 with the LDB1 Lid Domain

The structure of Complex of LMO4 Lim Domains 1 and 2 with the LDB1 Lid Domain, PDB code: 1rut was solved by J.E.Deane, D.P.Ryan, M.J.Maher, A.H.Y.Kwan, M.Bacca, J.P.Mackay, J.M.Guss, J.E.Visvader, J.M.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.13 / 1.30
Space group	P 3 1 2
Cell size a, b, c (Å), α, β, γ (°)	61.344, 61.344, 93.159, 90.00, 90.00, 120.00
R / Rfree (%)	15.5 / 19.3

The binding sites of Zinc atom in the Complex of LMO4 Lim Domains 1 and 2 with the LDB1 Lid Domain (pdb code 1rut). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Complex of LMO4 Lim Domains 1 and 2 with the LDB1 Lid Domain, PDB code: 1rut:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Complex of LMO4 Lim Domains 1 and 2 with the LDB1 Lid Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complex of LMO4 Lim Domains 1 and 2 with the LDB1 Lid Domain within 5.0Å range: probe atom residue distance (Å) B Occ X:Zn601 b:15.5 occ:1.00 ND1 X:HIS44 2.1 14.0 1.0 SG X:CYS47 2.3 15.4 1.0 SG X:CYS26 2.3 17.1 1.0 SG X:CYS23 2.3 14.4 1.0 CE1 X:HIS44 3.0 13.8 1.0 CB X:CYS23 3.0 14.4 1.0 CG X:HIS44 3.1 13.5 1.0 CB X:CYS47 3.2 14.7 1.0 CB X:CYS26 3.3 18.5 1.0 CB X:HIS44 3.5 13.0 1.0 N X:CYS26 3.7 17.4 1.0 CA X:CYS26 4.1 18.0 1.0 N X:HIS44 4.1 12.8 1.0 O X:HOH740 4.1 33.7 1.0 NE2 X:HIS44 4.2 15.0 1.0 CD2 X:HIS44 4.2 14.6 1.0 CA X:HIS44 4.4 12.8 1.0 CA X:CYS23 4.5 14.8 1.0 C X:GLY25 4.6 18.4 1.0 NH1 X:ARG46 4.6 22.6 1.0 CA X:CYS47 4.6 13.4 1.0 O X:HOH686 4.6 29.6 1.0 NH2 X:ARG46 4.6 20.8 1.0 CZ X:ARG46 4.7 19.6 1.0 CA X:GLY25 4.8 16.4 1.0 C X:CYS26 4.8 18.6 1.0 N X:GLY25 4.9 15.7 1.0 O X:HIS44 4.9 13.5 1.0 N X:CYS47 5.0 13.3 1.0 C X:CYS23 5.0 16.0 1.0

Zinc binding site 2 out of 4 in the Complex of LMO4 Lim Domains 1 and 2 with the LDB1 Lid Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complex of LMO4 Lim Domains 1 and 2 with the LDB1 Lid Domain within 5.0Å range: probe atom residue distance (Å) B Occ X:Zn602 b:14.7 occ:1.00 OD2 X:ASP76 2.0 15.7 1.0 SG X:CYS53 2.3 15.2 1.0 SG X:CYS73 2.3 14.3 1.0 SG X:CYS50 2.3 13.6 1.0 CG X:ASP76 3.0 16.0 1.0 CB X:CYS50 3.1 13.4 1.0 CB X:CYS53 3.3 16.3 1.0 CB X:CYS73 3.4 13.7 1.0 CB X:ASP76 3.4 14.7 1.0 N X:CYS53 3.7 15.8 1.0 N X:CYS73 4.0 12.8 1.0 CA X:CYS53 4.0 16.0 1.0 OD1 X:ASP76 4.1 18.9 1.0 CA X:CYS73 4.3 13.9 1.0 N X:ASP76 4.4 15.2 1.0 O X:HOH677 4.4 28.2 1.0 CA X:ASP76 4.5 15.3 1.0 CB X:SER52 4.6 17.4 1.0 CA X:CYS50 4.6 13.0 1.0 C X:CYS53 4.8 15.2 1.0 C X:SER52 4.8 16.5 1.0 CB X:ALA55 4.8 15.3 1.0 C X:CYS73 4.9 13.9 1.0 O X:CYS73 4.9 14.0 1.0 N X:GLN54 4.9 14.9 1.0

Zinc binding site 3 out of 4 in the Complex of LMO4 Lim Domains 1 and 2 with the LDB1 Lid Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Complex of LMO4 Lim Domains 1 and 2 with the LDB1 Lid Domain within 5.0Å range: probe atom residue distance (Å) B Occ X:Zn603 b:21.6 occ:1.00 OD2 X:ASP140 2.0 23.1 1.0 SG X:CYS137 2.3 21.4 1.0 SG X:CYS118 2.3 22.1 1.0 SG X:CYS115 2.3 20.0 1.0 CG X:ASP140 3.0 24.9 1.0 CB X:CYS115 3.1 19.7 1.0 CB X:CYS118 3.3 23.1 1.0 CB X:CYS137 3.3 20.6 1.0 CB X:ASP140 3.4 24.0 1.0 N X:CYS118 3.8 23.4 1.0 N X:CYS137 4.0 20.7 1.0 OD1 X:ASP140 4.1 28.6 1.0 CA X:CYS118 4.1 24.5 1.0 CA X:CYS137 4.2 21.4 1.0 O X:HOH699 4.3 26.0 1.0 O X:HOH717 4.4 25.8 1.0 N X:ASP140 4.5 25.2 1.0 CA X:ASP140 4.6 24.6 1.0 CB X:THR117 4.6 23.7 1.0 CA X:CYS115 4.6 19.9 1.0 C X:CYS137 4.8 22.6 1.0 C X:CYS118 4.9 22.8 1.0 C X:THR117 4.9 24.5 1.0 O X:CYS137 4.9 22.2 1.0 N X:ARG119 5.0 21.8 1.0

Zinc binding site 4 out of 4 in the Complex of LMO4 Lim Domains 1 and 2 with the LDB1 Lid Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Complex of LMO4 Lim Domains 1 and 2 with the LDB1 Lid Domain within 5.0Å range: probe atom residue distance (Å) B Occ X:Zn604 b:24.2 occ:1.00 ND1 X:HIS109 2.1 23.1 1.0 SG X:CYS112 2.3 24.5 1.0 SG X:CYS90 2.3 24.6 1.0 SG X:CYS87 2.3 21.9 1.0 CB X:CYS87 3.0 20.8 1.0 CE1 X:HIS109 3.0 26.0 1.0 CG X:HIS109 3.2 22.2 1.0 CB X:CYS112 3.2 21.5 1.0 CB X:CYS90 3.3 24.9 1.0 CB X:HIS109 3.5 21.2 1.0 N X:CYS90 3.8 23.7 1.0 CA X:CYS90 4.1 24.5 1.0 N X:HIS109 4.1 20.9 1.0 NE2 X:HIS109 4.2 26.3 1.0 CD2 X:HIS109 4.3 25.6 1.0 CA X:HIS109 4.4 20.3 1.0 CA X:CYS87 4.5 21.1 1.0 CA X:CYS112 4.6 21.6 1.0 CB X:ALA89 4.7 23.4 1.0 C X:ALA89 4.9 25.5 1.0 C X:CYS90 4.9 25.1 1.0

J.E.Deane, D.P.Ryan, M.Sunde, M.J.Maher, J.M.Guss, J.E.Visvader, J.M.Matthews. Tandem Lim Domains Provide Synergistic Binding in the LMO4:LDB1 Complex Embo J. V. 23 3589 2004.
ISSN: ISSN 0261-4189
PubMed: 15343268
DOI: 10.1038/SJ.EMBOJ.7600376