Zinc in PDB 4x9j: Egr-1 with Doubly Methylated Dna

The structure of Egr-1 with Doubly Methylated Dna, PDB code: 4x9j was solved by M.A.White, L.Zandarashvili, J.Iwahara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.36 / 1.41
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	44.009, 55.989, 128.952, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 20

The binding sites of Zinc atom in the Egr-1 with Doubly Methylated Dna (pdb code 4x9j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Egr-1 with Doubly Methylated Dna, PDB code: 4x9j:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Egr-1 with Doubly Methylated Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Egr-1 with Doubly Methylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:19.2 occ:0.84 NE2 A:HIS129 1.9 22.4 1.0 NE2 A:HIS125 2.0 15.6 1.0 SG A:CYS107 2.3 20.3 1.0 SG A:CYS112 2.3 34.5 1.0 CE1 A:HIS129 2.9 23.8 1.0 CD2 A:HIS129 2.9 21.4 1.0 CD2 A:HIS125 3.0 22.6 1.0 CE1 A:HIS125 3.1 23.6 1.0 HE1 A:HIS129 3.1 28.5 1.0 CB A:CYS107 3.1 19.6 1.0 HB3 A:CYS112 3.1 46.4 1.0 HB3 A:CYS107 3.1 23.5 1.0 HD2 A:HIS125 3.1 27.1 1.0 CB A:CYS112 3.1 38.6 1.0 HB2 A:CYS107 3.1 23.5 1.0 HD2 A:HIS129 3.2 25.7 1.0 HB2 A:CYS112 3.2 46.4 1.0 HE1 A:HIS125 3.3 28.3 1.0 HB A:VAL109 3.6 27.4 1.0 HB2 A:ARG114 3.9 31.5 1.0 ND1 A:HIS129 4.0 24.4 1.0 CG A:HIS129 4.1 20.5 1.0 CG A:HIS125 4.1 16.1 1.0 ND1 A:HIS125 4.2 19.3 1.0 HG3 A:ARG114 4.3 44.9 1.0 HG2 A:ARG114 4.4 44.9 1.0 H A:VAL109 4.5 25.0 1.0 CB A:VAL109 4.5 22.8 1.0 HG23 A:VAL109 4.5 29.1 1.0 CA A:CYS107 4.5 16.6 1.0 HG21 A:VAL109 4.5 29.1 1.0 CA A:CYS112 4.6 42.0 1.0 HD13 A:ILE126 4.6 36.0 1.0 H A:ARG114 4.6 36.4 1.0 CG A:ARG114 4.7 37.4 1.0 CB A:ARG114 4.7 26.2 1.0 CG2 A:VAL109 4.8 24.3 1.0 HD1 A:HIS129 4.8 29.3 1.0 HA A:CYS107 4.8 19.9 1.0 HA A:CYS112 4.9 50.3 1.0 HE2 A:PHE116 4.9 26.8 1.0 HA A:ILE126 4.9 21.4 1.0 HD1 A:HIS125 4.9 23.1 1.0

Zinc binding site 2 out of 3 in the Egr-1 with Doubly Methylated Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Egr-1 with Doubly Methylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:13.3 occ:0.91 NE2 A:HIS157 2.0 11.8 1.0 NE2 A:HIS153 2.1 12.8 1.0 SG A:CYS140 2.3 17.4 1.0 SG A:CYS137 2.3 14.7 1.0 CD2 A:HIS157 2.9 14.8 1.0 HD2 A:HIS157 3.0 17.8 1.0 H A:CYS140 3.0 20.5 1.0 CD2 A:HIS153 3.0 13.3 1.0 CE1 A:HIS153 3.1 9.9 1.0 HB3 A:CYS137 3.1 15.1 1.0 CE1 A:HIS157 3.1 17.1 1.0 HB3 A:CYS140 3.2 19.1 1.0 CB A:CYS137 3.2 12.6 1.0 HD2 A:HIS153 3.2 16.0 1.0 HE1 A:HIS153 3.3 11.9 1.0 HB2 A:CYS137 3.3 15.1 1.0 CB A:CYS140 3.3 15.9 1.0 HE1 A:HIS157 3.4 20.6 1.0 N A:CYS140 3.6 17.1 1.0 HB A:ILE139 3.7 21.2 1.0 O A:HOH694 3.9 29.4 1.0 CA A:CYS140 4.0 19.3 1.0 CG A:HIS157 4.1 12.3 1.0 HB2 A:CYS140 4.1 19.1 1.0 HB3 A:ARG142 4.1 21.3 1.0 ND1 A:HIS153 4.2 10.4 1.0 ND1 A:HIS157 4.2 13.8 1.0 CG A:HIS153 4.2 9.4 1.0 H A:ARG142 4.3 21.9 1.0 H A:ILE139 4.4 23.1 1.0 HE1 A:PHE144 4.5 17.1 1.0 H A:MET141 4.5 17.1 1.0 CB A:ILE139 4.5 17.7 1.0 HA A:ILE154 4.6 12.2 1.0 CA A:CYS137 4.6 14.9 1.0 HZ A:PHE144 4.6 19.6 1.0 C A:ILE139 4.7 15.8 1.0 HG22 A:ILE139 4.7 21.3 1.0 C A:CYS140 4.7 20.2 1.0 HB2 A:ARG142 4.8 21.3 1.0 HA A:CYS140 4.8 23.2 1.0 N A:MET141 4.9 14.2 1.0 CB A:ARG142 4.9 17.7 1.0 HA A:CYS137 4.9 17.9 1.0 HD1 A:HIS153 4.9 12.5 1.0 CA A:ILE139 5.0 16.6 1.0 N A:ILE139 5.0 19.2 1.0 HD1 A:HIS157 5.0 16.6 1.0 HG1 A:THR156 5.0 18.9 1.0

Zinc binding site 3 out of 3 in the Egr-1 with Doubly Methylated Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Egr-1 with Doubly Methylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:8.1 occ:0.91 NE2 A:HIS185 2.0 12.0 1.0 NE2 A:HIS181 2.0 6.7 1.0 SG A:CYS168 2.3 10.3 1.0 SG A:CYS165 2.4 8.7 1.0 CD2 A:HIS181 3.0 10.7 1.0 CE1 A:HIS185 3.0 11.5 1.0 CD2 A:HIS185 3.0 10.7 1.0 HB3 A:CYS165 3.0 12.1 1.0 CE1 A:HIS181 3.1 6.5 1.0 CB A:CYS165 3.1 10.1 1.0 HD2 A:HIS181 3.1 12.8 1.0 HB3 A:CYS168 3.1 10.7 1.0 HB2 A:CYS165 3.1 12.1 1.0 HE1 A:HIS185 3.2 13.8 1.0 H A:CYS168 3.2 10.4 1.0 HD2 A:HIS185 3.2 12.8 1.0 HE1 A:HIS181 3.3 7.7 1.0 CB A:CYS168 3.3 8.9 1.0 HB A:ILE167 3.5 11.8 1.0 N A:CYS168 3.8 8.7 1.0 HB3 A:ARG170 4.0 12.6 1.0 CA A:CYS168 4.1 9.7 1.0 HA A:THR182 4.1 10.3 1.0 HB2 A:CYS168 4.1 10.7 1.0 ND1 A:HIS185 4.1 14.3 1.0 CG A:HIS181 4.1 5.8 1.0 ND1 A:HIS181 4.1 7.6 1.0 CG A:HIS185 4.2 9.7 1.0 H A:ARG170 4.2 11.9 1.0 H A:ILE167 4.4 9.8 1.0 H A:GLY169 4.5 10.7 1.0 CB A:ILE167 4.5 9.9 1.0 CA A:CYS165 4.6 9.0 1.0 HB2 A:ARG170 4.7 12.6 1.0 C A:ILE167 4.7 11.1 1.0 C A:CYS168 4.7 10.2 1.0 CB A:ARG170 4.8 10.5 1.0 HG22 A:ILE167 4.8 13.1 1.0 N A:GLY169 4.8 8.9 1.0 HD11 A:ILE184 4.9 15.0 1.0 HE2 A:PHE172 4.9 12.2 1.0 HG12 A:ILE184 4.9 12.4 1.0 HD1 A:HIS185 4.9 17.2 1.0 HA A:CYS165 4.9 10.8 1.0 HA A:CYS168 4.9 11.7 1.0 HD1 A:HIS181 4.9 9.2 1.0 N A:ARG170 5.0 9.9 1.0 N A:ILE167 5.0 8.2 1.0 CA A:ILE167 5.0 7.4 1.0

M.A.White, L.Zandarashvili, J.Iwahara. Structural Impact of Complete Cpg Methylation Within Target Dna on Specific Complex Formation of the Inducible Transcription Factor Egr-1 To Be Published.