Zinc in PDB 2dfy: Crystal Structure of A Cyclized Protein Fusion of LMO4 Lim Domains 1 and 2 with the Lim Interacting Domain of LDB1

The structure of Crystal Structure of A Cyclized Protein Fusion of LMO4 Lim Domains 1 and 2 with the Lim Interacting Domain of LDB1, PDB code: 2dfy was solved by C.M.J.Jeffries, S.C.Graham, C.A.Collyer, 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)	10.00 / 1.65
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	61.333, 61.333, 93.019, 90.00, 90.00, 120.00
R / Rfree (%)	16.7 / 19.4

The binding sites of Zinc atom in the Crystal Structure of A Cyclized Protein Fusion of LMO4 Lim Domains 1 and 2 with the Lim Interacting Domain of LDB1 (pdb code 2dfy). 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 A Cyclized Protein Fusion of LMO4 Lim Domains 1 and 2 with the Lim Interacting Domain of LDB1, PDB code: 2dfy:
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 A Cyclized Protein Fusion of LMO4 Lim Domains 1 and 2 with the Lim Interacting Domain of LDB1


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 A Cyclized Protein Fusion of LMO4 Lim Domains 1 and 2 with the Lim Interacting Domain of LDB1 within 5.0Å range: probe atom residue distance (Å) B Occ X:Zn601 b:34.1 occ:1.00 ND1 X:HIS44 2.1 33.9 1.0 SG X:CYS47 2.3 33.4 1.0 SG X:CYS26 2.3 35.4 1.0 SG X:CYS23 2.3 32.0 1.0 CB X:CYS23 3.0 33.1 1.0 CE1 X:HIS44 3.1 32.9 1.0 CG X:HIS44 3.1 31.0 1.0 CB X:CYS47 3.2 31.7 1.0 CB X:CYS26 3.2 36.6 1.0 CB X:HIS44 3.4 30.2 1.0 N X:CYS26 3.7 36.3 1.0 CA X:CYS26 4.1 35.8 1.0 N X:HIS44 4.1 29.5 1.0 NE2 X:HIS44 4.2 30.1 1.0 CD2 X:HIS44 4.3 32.4 1.0 CA X:HIS44 4.4 29.1 1.0 CA X:CYS23 4.5 33.6 1.0 NH1 X:ARG46 4.6 39.5 1.0 O C:HOH654 4.6 46.3 1.0 NH2 X:ARG46 4.6 39.1 1.0 C X:GLY25 4.6 35.0 1.0 CA X:CYS47 4.6 31.9 1.0 CZ X:ARG46 4.7 37.5 1.0 C X:CYS26 4.8 36.7 1.0 CA X:GLY25 4.9 34.6 1.0 N X:GLY25 4.9 33.5 1.0 O X:HIS44 4.9 29.6 1.0 C X:CYS23 5.0 33.2 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of A Cyclized Protein Fusion of LMO4 Lim Domains 1 and 2 with the Lim Interacting Domain of LDB1


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 A Cyclized Protein Fusion of LMO4 Lim Domains 1 and 2 with the Lim Interacting Domain of LDB1 within 5.0Å range: probe atom residue distance (Å) B Occ X:Zn602 b:34.8 occ:1.00 OD2 X:ASP76 2.1 35.8 1.0 SG X:CYS53 2.3 35.1 1.0 SG X:CYS73 2.3 34.0 1.0 SG X:CYS50 2.3 32.1 1.0 CG X:ASP76 3.1 35.5 1.0 CB X:CYS50 3.1 30.4 1.0 CB X:CYS53 3.2 34.4 1.0 CB X:CYS73 3.4 34.0 1.0 CB X:ASP76 3.5 35.0 1.0 N X:CYS53 3.7 35.0 1.0 N X:CYS73 4.0 31.6 1.0 CA X:CYS53 4.0 33.9 1.0 OD1 X:ASP76 4.2 38.4 1.0 CA X:CYS73 4.3 33.0 1.0 N X:ASP76 4.4 35.6 1.0 O X:HOH663 4.5 49.9 1.0 CB X:SER52 4.6 34.4 1.0 CA X:ASP76 4.6 35.5 1.0 CA X:CYS50 4.6 30.2 1.0 C X:SER52 4.8 35.2 1.0 C X:CYS53 4.8 33.5 1.0 CB X:ALA55 4.9 32.8 1.0 C X:CYS73 4.9 33.8 1.0 N X:SER52 5.0 33.2 1.0 N X:GLN54 5.0 33.1 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of A Cyclized Protein Fusion of LMO4 Lim Domains 1 and 2 with the Lim Interacting Domain of LDB1


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 A Cyclized Protein Fusion of LMO4 Lim Domains 1 and 2 with the Lim Interacting Domain of LDB1 within 5.0Å range: probe atom residue distance (Å) B Occ X:Zn603 b:52.9 occ:0.70 OD2 X:ASP140 2.0 65.1 1.0 SG X:CYS137 2.3 60.5 1.0 SG X:CYS115 2.3 57.5 1.0 SG X:CYS118 2.3 59.0 1.0 CG X:ASP140 3.0 66.2 1.0 CB X:CYS115 3.1 58.5 1.0 CB X:CYS118 3.2 61.2 1.0 CB X:CYS137 3.3 60.3 1.0 CB X:ASP140 3.4 66.1 1.0 N X:CYS118 3.7 61.5 1.0 N X:CYS137 3.8 59.3 1.0 CA X:CYS118 4.0 61.4 1.0 CA X:CYS137 4.1 60.2 1.0 OD1 X:ASP140 4.1 66.9 1.0 N X:ASP140 4.5 65.7 1.0 CA X:CYS115 4.5 58.2 1.0 CA X:ASP140 4.6 65.9 1.0 CB X:THR117 4.7 61.1 1.0 C X:CYS137 4.7 61.1 1.0 C X:CYS118 4.8 61.6 1.0 O X:CYS137 4.8 60.8 1.0 N X:ARG119 4.9 61.7 1.0 C X:THR117 4.9 61.6 1.0 C X:PHE136 5.0 58.5 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of A Cyclized Protein Fusion of LMO4 Lim Domains 1 and 2 with the Lim Interacting Domain of LDB1


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 A Cyclized Protein Fusion of LMO4 Lim Domains 1 and 2 with the Lim Interacting Domain of LDB1 within 5.0Å range: probe atom residue distance (Å) B Occ X:Zn604 b:58.5 occ:1.00 ND1 X:HIS109 2.1 57.3 1.0 SG X:CYS90 2.3 57.4 1.0 SG X:CYS112 2.3 56.2 1.0 SG X:CYS87 2.5 53.3 1.0 CE1 X:HIS109 3.0 57.9 1.0 CB X:CYS87 3.1 52.3 1.0 CG X:HIS109 3.2 55.9 1.0 CB X:CYS112 3.2 56.9 1.0 CB X:CYS90 3.2 58.2 1.0 CB X:HIS109 3.5 55.7 1.0 N X:CYS90 3.8 58.1 1.0 CA X:CYS90 4.1 58.2 1.0 N X:HIS109 4.2 55.1 1.0 NE2 X:HIS109 4.2 57.1 1.0 CD2 X:HIS109 4.3 56.2 1.0 CA X:HIS109 4.5 55.6 1.0 CA X:CYS87 4.6 53.1 1.0 CB X:ALA89 4.6 56.3 1.0 CA X:CYS112 4.6 56.9 1.0 C X:ALA89 4.9 57.7 1.0 C X:CYS90 4.9 58.5 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of A Cyclized Protein Fusion of LMO4 Lim Domains 1 and 2 with the Lim Interacting Domain of LDB1


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 A Cyclized Protein Fusion of LMO4 Lim Domains 1 and 2 with the Lim Interacting Domain of LDB1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:34.0 occ:1.00 ND1 C:HIS44 2.2 34.5 1.0 SG C:CYS47 2.3 33.3 1.0 SG C:CYS26 2.3 35.1 1.0 SG C:CYS23 2.3 31.6 1.0 CB C:CYS23 3.0 32.4 1.0 CE1 C:HIS44 3.1 33.2 1.0 CG C:HIS44 3.2 31.4 1.0 CB C:CYS47 3.2 31.1 1.0 CB C:CYS26 3.2 35.9 1.0 CB C:HIS44 3.5 31.1 1.0 N C:CYS26 3.7 36.1 1.0 CA C:CYS26 4.1 35.8 1.0 N C:HIS44 4.1 29.7 1.0 NE2 C:HIS44 4.2 31.9 1.0 CD2 C:HIS44 4.3 33.4 1.0 CA C:HIS44 4.4 29.1 1.0 CA C:CYS23 4.5 33.2 1.0 C C:GLY25 4.6 35.0 1.0 O X:HOH638 4.6 44.8 1.0 NH1 C:ARG46 4.6 39.4 1.0 CA C:CYS47 4.6 31.7 1.0 NH2 C:ARG46 4.7 39.0 1.0 CZ C:ARG46 4.7 37.6 1.0 CA C:GLY25 4.8 34.4 1.0 C C:CYS26 4.8 36.8 1.0 N C:GLY25 4.9 33.6 1.0 O C:HIS44 4.9 30.0 1.0 C C:CYS23 5.0 33.3 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of A Cyclized Protein Fusion of LMO4 Lim Domains 1 and 2 with the Lim Interacting Domain of LDB1


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 A Cyclized Protein Fusion of LMO4 Lim Domains 1 and 2 with the Lim Interacting Domain of LDB1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn602 b:34.9 occ:1.00 OD2 C:ASP76 2.1 35.4 1.0 SG C:CYS53 2.3 34.4 1.0 SG C:CYS73 2.3 34.2 1.0 SG C:CYS50 2.3 32.0 1.0 CG C:ASP76 3.1 35.6 1.0 CB C:CYS50 3.1 30.5 1.0 CB C:CYS53 3.3 34.8 1.0 CB C:CYS73 3.4 33.5 1.0 CB C:ASP76 3.4 34.9 1.0 N C:CYS53 3.7 35.0 1.0 N C:CYS73 4.0 31.4 1.0 CA C:CYS53 4.1 34.0 1.0 OD1 C:ASP76 4.2 37.5 1.0 CA C:CYS73 4.3 32.9 1.0 N C:ASP76 4.4 35.4 1.0 CB C:SER52 4.5 34.0 1.0 CA C:ASP76 4.5 35.5 1.0 O C:HOH663 4.6 49.1 1.0 CA C:CYS50 4.6 30.5 1.0 C C:SER52 4.8 35.1 1.0 C C:CYS53 4.8 33.4 1.0 C C:CYS73 4.9 33.7 1.0 CB C:ALA55 4.9 32.4 1.0 N C:GLN54 5.0 32.9 1.0 N C:SER52 5.0 33.2 1.0 O C:CYS73 5.0 33.3 1.0 CA C:SER52 5.0 34.4 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of A Cyclized Protein Fusion of LMO4 Lim Domains 1 and 2 with the Lim Interacting Domain of LDB1


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 A Cyclized Protein Fusion of LMO4 Lim Domains 1 and 2 with the Lim Interacting Domain of LDB1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn603 b:53.3 occ:0.70 OD2 C:ASP140 2.0 64.3 1.0 SG C:CYS118 2.3 59.9 1.0 SG C:CYS137 2.3 60.6 1.0 SG C:CYS115 2.3 57.5 1.0 CG C:ASP140 2.9 66.0 1.0 CB C:CYS115 3.1 58.4 1.0 CB C:CYS118 3.2 61.5 1.0 CB C:CYS137 3.3 60.1 1.0 CB C:ASP140 3.3 66.0 1.0 N C:CYS118 3.7 61.5 1.0 N C:CYS137 3.8 59.2 1.0 OD1 C:ASP140 4.0 68.0 1.0 CA C:CYS118 4.0 61.4 1.0 CA C:CYS137 4.1 60.1 1.0 N C:ASP140 4.5 65.7 1.0 CA C:ASP140 4.5 65.9 1.0 CA C:CYS115 4.6 58.2 1.0 CB C:THR117 4.7 61.2 1.0 C C:CYS137 4.8 61.1 1.0 C C:CYS118 4.8 61.6 1.0 O C:CYS137 4.8 60.8 1.0 N C:ARG119 4.9 61.6 1.0 C C:THR117 4.9 61.6 1.0 C C:PHE136 5.0 58.5 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of A Cyclized Protein Fusion of LMO4 Lim Domains 1 and 2 with the Lim Interacting Domain of LDB1


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 A Cyclized Protein Fusion of LMO4 Lim Domains 1 and 2 with the Lim Interacting Domain of LDB1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn604 b:58.5 occ:1.00 ND1 C:HIS109 2.2 57.7 1.0 SG C:CYS90 2.3 57.8 1.0 SG C:CYS112 2.3 56.2 1.0 SG C:CYS87 2.4 52.7 1.0 CB C:CYS87 3.0 52.3 1.0 CE1 C:HIS109 3.1 58.4 1.0 CG C:HIS109 3.2 56.3 1.0 CB C:CYS112 3.2 56.8 1.0 CB C:CYS90 3.3 58.5 1.0 CB C:HIS109 3.5 55.9 1.0 N C:CYS90 3.8 58.1 1.0 N C:HIS109 4.1 55.1 1.0 CA C:CYS90 4.1 58.2 1.0 NE2 C:HIS109 4.2 58.2 1.0 CD2 C:HIS109 4.3 57.2 1.0 CA C:HIS109 4.4 55.6 1.0 CA C:CYS87 4.5 53.0 1.0 CB C:ALA89 4.6 56.5 1.0 CA C:CYS112 4.6 56.8 1.0 C C:ALA89 4.8 57.7 1.0 C C:CYS90 4.9 58.4 1.0

C.M.J.Jeffries, S.C.Graham, P.H.Stokes, C.A.Collyer, J.M.Guss, J.M.Matthews. Stabilization of A Binary Protein Complex By Intein-Mediated Cyclization Protein Sci. V. 15 2612 2006.
ISSN: ISSN 0961-8368
PubMed: 17001033
DOI: 10.1110/PS.062377006