Zinc in PDB 5l0m: Hlrh-1 Dna Binding Domain - 12BP OCT4 Promoter Complex

The structure of Hlrh-1 Dna Binding Domain - 12BP OCT4 Promoter Complex, PDB code: 5l0m was solved by M.L.Tuntland, E.A.Ortlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.94 / 2.20
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	40.931, 40.931, 105.055, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 19.7

The binding sites of Zinc atom in the Hlrh-1 Dna Binding Domain - 12BP OCT4 Promoter Complex (pdb code 5l0m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Hlrh-1 Dna Binding Domain - 12BP OCT4 Promoter Complex, PDB code: 5l0m:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Hlrh-1 Dna Binding Domain - 12BP OCT4 Promoter Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Hlrh-1 Dna Binding Domain - 12BP OCT4 Promoter Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:54.6 occ:1.00 SG A:CYS141 2.3 51.1 1.0 SG A:CYS138 2.3 49.8 1.0 SG A:CYS128 2.4 61.1 1.0 SG A:CYS122 2.4 56.7 1.0 HB2 A:CYS122 2.9 65.8 1.0 HB2 A:CYS141 3.1 65.5 1.0 HB2 A:CYS128 3.2 70.8 1.0 CB A:CYS122 3.2 54.8 1.0 CB A:CYS138 3.3 45.0 1.0 H A:CYS128 3.3 73.1 1.0 HB3 A:CYS138 3.3 54.0 1.0 CB A:CYS141 3.3 54.5 1.0 HB2 A:CYS138 3.3 54.0 1.0 H A:CYS141 3.4 54.1 1.0 CB A:CYS128 3.4 59.0 1.0 HA A:CYS122 3.6 77.9 1.0 HA A:GLN126 3.6 76.9 1.0 HB3 A:TYR140 3.8 63.5 1.0 HD2 A:TYR140 3.8 63.4 1.0 H A:GLN126 3.9 80.3 1.0 HB3 A:CYS122 4.0 65.8 1.0 CA A:CYS122 4.0 64.9 1.0 HB3 A:CYS141 4.0 65.5 1.0 N A:CYS141 4.0 45.1 1.0 N A:CYS128 4.1 60.9 1.0 O A:HOH305 4.1 64.2 1.0 HB3 A:CYS128 4.1 70.8 1.0 CA A:CYS141 4.3 43.2 1.0 H A:ILE123 4.3 89.2 1.0 CA A:GLN126 4.4 64.1 1.0 CA A:CYS128 4.4 65.3 1.0 H A:GLU124 4.4 96.6 1.0 N A:GLN126 4.5 66.9 1.0 H A:ASN127 4.5 81.1 1.0 CD2 A:TYR140 4.7 52.8 1.0 HA A:CYS141 4.7 51.9 1.0 N A:ASN127 4.7 67.6 1.0 HB3 A:GLU124 4.7 0.3 1.0 CA A:CYS138 4.7 50.4 1.0 CB A:TYR140 4.7 52.9 1.0 C A:GLN126 4.8 64.1 1.0 N A:ILE123 4.9 74.3 1.0 C A:CYS122 4.9 70.8 1.0 HA A:CYS138 4.9 60.4 1.0 HA A:CYS128 4.9 78.4 1.0

Zinc binding site 2 out of 2 in the Hlrh-1 Dna Binding Domain - 12BP OCT4 Promoter Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Hlrh-1 Dna Binding Domain - 12BP OCT4 Promoter Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:42.9 occ:1.00 SG A:CYS103 2.3 42.7 1.0 SG A:CYS86 2.3 41.0 1.0 SG A:CYS89 2.4 45.3 1.0 SG A:CYS106 2.4 46.4 1.0 HB2 A:CYS106 2.8 51.5 1.0 HB3 A:CYS86 3.2 53.8 1.0 CB A:CYS86 3.2 44.8 1.0 CB A:CYS106 3.2 42.9 1.0 H A:CYS89 3.2 59.6 1.0 HB2 A:CYS86 3.3 53.8 1.0 HB A:VAL88 3.3 58.5 1.0 HB3 A:CYS89 3.4 54.2 1.0 H A:CYS103 3.4 55.3 1.0 HB3 A:CYS103 3.5 54.0 1.0 CB A:CYS89 3.5 45.2 1.0 CB A:CYS103 3.6 45.0 1.0 H A:CYS106 3.8 47.6 1.0 N A:CYS89 3.8 49.7 1.0 HB3 A:ASP91 3.8 57.1 1.0 HG A:SER105 3.8 53.7 1.0 HB3 A:CYS106 3.8 51.5 1.0 H A:ASP91 3.9 56.7 1.0 HH11 A:ARG135 4.0 48.6 1.0 HH21 A:ARG142 4.2 56.6 1.0 CA A:CYS89 4.2 46.8 1.0 N A:CYS103 4.2 46.1 1.0 OG A:SER105 4.2 44.8 1.0 HB2 A:CYS89 4.3 54.2 1.0 HB2 A:CYS103 4.3 54.0 1.0 CB A:VAL88 4.3 48.8 1.0 N A:CYS106 4.3 39.7 1.0 H A:VAL88 4.3 53.0 1.0 HB2 A:ASP91 4.3 57.1 1.0 CA A:CYS106 4.3 43.1 1.0 CA A:CYS103 4.4 47.1 1.0 H A:GLY90 4.5 54.9 1.0 CB A:ASP91 4.5 47.6 1.0 HB A:THR102 4.5 52.0 1.0 NH1 A:ARG135 4.6 40.5 1.0 HG12 A:VAL88 4.6 60.2 1.0 HD2 A:ARG135 4.6 60.0 1.0 CA A:CYS86 4.7 47.4 1.0 HA A:CYS106 4.7 51.7 1.0 C A:VAL88 4.7 45.2 1.0 N A:ASP91 4.7 47.2 1.0 HH12 A:ARG135 4.7 48.6 1.0 C A:CYS89 4.8 49.8 1.0 N A:GLY90 4.8 45.7 1.0 CA A:VAL88 4.9 48.3 1.0 HG11 A:VAL88 4.9 60.2 1.0 CG1 A:VAL88 4.9 50.2 1.0 N A:VAL88 4.9 44.2 1.0 HA A:CYS86 4.9 56.9 1.0 HD3 A:ARG135 4.9 60.0 1.0 NH2 A:ARG142 5.0 47.1 1.0

E.R.Weikum, M.L.Tuntland, M.N.Murphy, E.A.Ortlund. A Structural Investigation Into OCT4 Regulation By Orphan Nuclear Receptors, Germ Cell Nuclear Factor (Gcnf), and Liver Receptor Homolog-1 (Lrh-1). J. Mol. Biol. V. 428 4981 2016.
ISSN: ESSN 1089-8638
PubMed: 27984042
DOI: 10.1016/J.JMB.2016.10.025