Zinc in PDB 5krb: Gcnf Dna Binding Domain - OCT4 DR0 Complex

The structure of Gcnf Dna Binding Domain - OCT4 DR0 Complex, PDB code: 5krb was solved by E.R.Weikum, E.A.Ortlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.94 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.649, 69.469, 84.536, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 26.8

The binding sites of Zinc atom in the Gcnf Dna Binding Domain - OCT4 DR0 Complex (pdb code 5krb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Gcnf Dna Binding Domain - OCT4 DR0 Complex, PDB code: 5krb:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Gcnf Dna Binding Domain - OCT4 DR0 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Gcnf Dna Binding Domain - OCT4 DR0 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:41.5 occ:1.00 SG B:CYS92 2.3 43.2 1.0 SG B:CYS78 2.3 43.4 1.0 SG B:CYS75 2.4 42.6 1.0 SG B:CYS95 2.4 45.0 1.0 HB2 B:CYS95 3.0 56.0 1.0 HB B:ILE77 3.1 57.1 1.0 H B:CYS78 3.1 57.9 1.0 H B:CYS92 3.2 55.2 1.0 CB B:CYS95 3.3 46.6 1.0 HB3 B:CYS75 3.3 61.5 1.0 CB B:CYS75 3.3 51.2 1.0 HB2 B:CYS75 3.5 61.5 1.0 HB3 B:CYS78 3.5 55.8 1.0 H B:CYS95 3.5 45.6 1.0 HH11 B:ARG124 3.5 55.5 1.0 CB B:CYS78 3.5 46.5 1.0 HB3 B:CYS92 3.6 56.1 1.0 CB B:CYS92 3.6 46.7 1.0 N B:CYS78 3.8 48.3 1.0 HB3 B:CYS95 3.9 56.0 1.0 HB3 B:ASP80 3.9 61.3 1.0 N B:CYS92 4.0 46.0 1.0 CB B:ILE77 4.1 47.6 1.0 NH1 B:ARG124 4.1 46.3 1.0 HH21 B:ARG131 4.1 50.3 1.0 HH12 B:ARG124 4.1 55.5 1.0 N B:CYS95 4.2 38.0 1.0 H B:ILE77 4.2 53.3 1.0 CA B:CYS78 4.2 46.2 1.0 H B:ASP80 4.3 57.9 1.0 HB2 B:CYS78 4.3 55.8 1.0 CA B:CYS95 4.3 44.4 1.0 HD2 B:ARG124 4.3 54.7 1.0 HB2 B:CYS92 4.4 56.1 1.0 CA B:CYS92 4.4 45.1 1.0 HG12 B:ILE77 4.5 57.0 1.0 HB2 B:SER91 4.5 61.5 1.0 HB2 B:ASP80 4.6 61.3 1.0 HG13 B:ILE77 4.6 57.0 1.0 CG1 B:ILE77 4.7 47.5 1.0 CB B:ASP80 4.7 51.1 1.0 C B:ILE77 4.7 48.6 1.0 HA B:SER91 4.7 60.1 1.0 H B:GLY79 4.7 55.4 1.0 HG21 B:ILE77 4.7 59.1 1.0 HA B:CYS95 4.8 53.2 1.0 HG22 B:ILE77 4.8 59.1 1.0 CA B:CYS75 4.8 42.0 1.0 CA B:ILE77 4.8 45.4 1.0 HD3 B:ARG124 4.8 54.7 1.0 CG2 B:ILE77 4.8 49.2 1.0 N B:ILE77 4.9 44.5 1.0 HE B:ARG131 4.9 51.4 1.0 C B:CYS78 4.9 48.4 1.0 NH2 B:ARG131 4.9 41.9 1.0 N B:ASP80 5.0 48.2 1.0

Zinc binding site 2 out of 4 in the Gcnf Dna Binding Domain - OCT4 DR0 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Gcnf Dna Binding Domain - OCT4 DR0 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:51.6 occ:1.00 SG B:CYS127 2.2 48.0 1.0 SG B:CYS117 2.3 47.7 1.0 SG B:CYS130 2.4 49.0 1.0 SG B:CYS111 2.5 53.5 1.0 HB2 B:CYS117 2.8 67.9 1.0 HB2 B:CYS130 3.1 53.8 1.0 CB B:CYS117 3.1 56.6 1.0 H B:CYS117 3.2 69.8 1.0 HB2 B:CYS111 3.3 67.1 1.0 CB B:CYS127 3.3 47.2 1.0 CB B:CYS130 3.4 44.9 1.0 HB2 B:CYS127 3.4 56.6 1.0 HB3 B:CYS127 3.4 56.6 1.0 CB B:CYS111 3.5 55.9 1.0 HA B:LYS115 3.6 74.3 1.0 H B:CYS130 3.6 46.1 1.0 H B:LYS115 3.8 79.7 1.0 HB3 B:CYS117 3.8 67.9 1.0 N B:CYS117 3.9 58.1 1.0 HA B:CYS111 3.9 66.5 1.0 HB3 B:CYS130 4.1 53.8 1.0 HD2 B:TYR129 4.1 62.0 1.0 CA B:CYS117 4.1 56.5 1.0 HB2 B:ARG113 4.2 80.0 1.0 H B:ASN116 4.2 70.9 1.0 N B:CYS130 4.2 38.4 1.0 CA B:LYS115 4.3 61.9 1.0 HB3 B:CYS111 4.3 67.1 1.0 HB3 B:TYR129 4.3 56.2 1.0 CA B:CYS111 4.3 55.5 1.0 N B:LYS115 4.3 66.4 1.0 CA B:CYS130 4.4 41.7 1.0 N B:ASN116 4.5 59.1 1.0 C B:LYS115 4.6 60.1 1.0 HA B:CYS117 4.6 67.8 1.0 H B:ARG113 4.6 79.2 1.0 HD3 B:ARG113 4.7 91.3 1.0 CA B:CYS127 4.7 47.1 1.0 HA B:CYS130 4.7 50.0 1.0 H B:ASP114 4.7 79.1 1.0 H B:SER112 4.9 76.2 1.0 HA B:CYS127 4.9 56.6 1.0 CD2 B:TYR129 5.0 51.7 1.0 O B:HOH308 5.0 61.0 1.0

Zinc binding site 3 out of 4 in the Gcnf Dna Binding Domain - OCT4 DR0 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Gcnf Dna Binding Domain - OCT4 DR0 Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn201 b:50.8 occ:1.00 SG G:CYS78 2.4 58.2 1.0 SG G:CYS75 2.4 53.2 1.0 SG G:CYS92 2.4 51.1 1.0 SG G:CYS95 2.5 46.2 1.0 HB2 G:CYS95 3.0 55.5 1.0 H G:CYS92 3.2 56.6 1.0 HB G:ILE77 3.3 61.6 1.0 CB G:CYS95 3.3 46.2 1.0 H G:CYS78 3.4 64.7 1.0 HB3 G:CYS75 3.4 69.0 1.0 CB G:CYS75 3.4 57.5 1.0 H G:CYS95 3.5 54.8 1.0 HB2 G:CYS75 3.5 69.0 1.0 HB3 G:CYS78 3.6 72.8 1.0 CB G:CYS78 3.6 60.7 1.0 HH11 G:ARG124 3.7 74.4 1.0 HB3 G:CYS92 3.8 65.5 1.0 CB G:CYS92 3.8 54.6 1.0 N G:CYS78 3.9 54.0 1.0 HB3 G:ASP80 3.9 76.4 1.0 HB3 G:CYS95 4.0 55.5 1.0 HH21 G:ARG131 4.0 58.9 1.0 N G:CYS92 4.1 47.2 1.0 NH1 G:ARG124 4.1 62.0 1.0 HD2 G:ARG124 4.1 71.0 1.0 N G:CYS95 4.1 45.6 1.0 HD12 G:ILE77 4.2 66.0 1.0 HH12 G:ARG124 4.2 74.4 1.0 CB G:ILE77 4.3 51.3 1.0 H G:ILE77 4.3 63.5 1.0 CA G:CYS78 4.3 60.2 1.0 CA G:CYS95 4.4 43.9 1.0 HB2 G:CYS78 4.4 72.8 1.0 HB2 G:SER91 4.4 62.4 1.0 H G:ASP80 4.5 76.9 1.0 CA G:CYS92 4.5 50.8 1.0 HB2 G:CYS92 4.5 65.5 1.0 HB2 G:ASP80 4.6 76.4 1.0 HG22 G:ILE77 4.6 61.1 1.0 HA G:SER91 4.7 63.9 1.0 CB G:ASP80 4.7 63.7 1.0 HG21 G:ILE77 4.8 61.1 1.0 HA G:CYS95 4.8 52.7 1.0 C G:ILE77 4.8 53.7 1.0 H G:GLY79 4.8 66.8 1.0 CG2 G:ILE77 4.8 51.0 1.0 HD3 G:ARG124 4.9 71.0 1.0 NH2 G:ARG131 4.9 49.0 1.0 CA G:CYS75 4.9 56.0 1.0 CD G:ARG124 4.9 59.2 1.0 CA G:ILE77 4.9 53.0 1.0 CD1 G:ILE77 4.9 55.0 1.0 HE G:ARG131 4.9 52.8 1.0 N G:ILE77 5.0 52.9 1.0 CZ G:ARG124 5.0 61.2 1.0

Zinc binding site 4 out of 4 in the Gcnf Dna Binding Domain - OCT4 DR0 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Gcnf Dna Binding Domain - OCT4 DR0 Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn202 b:63.2 occ:1.00 SG G:CYS127 2.2 49.3 1.0 SG G:CYS111 2.4 62.2 1.0 SG G:CYS130 2.5 53.5 1.0 SG G:CYS117 2.6 64.0 1.0 HB2 G:CYS117 3.1 76.5 1.0 CB G:CYS127 3.2 55.1 1.0 HB2 G:CYS127 3.3 66.1 1.0 H G:CYS117 3.3 74.8 1.0 HB2 G:CYS130 3.3 64.6 1.0 HB2 G:CYS111 3.3 63.1 1.0 HB3 G:CYS127 3.3 66.1 1.0 CB G:CYS117 3.5 63.7 1.0 CB G:CYS111 3.5 52.6 1.0 H G:CYS130 3.5 53.7 1.0 CB G:CYS130 3.5 53.9 1.0 HA G:LYS115 3.6 76.4 1.0 HH11 G:ARG113 3.8 89.1 1.0 HA G:CYS111 3.9 73.9 1.0 HB3 G:TYR129 4.0 60.6 1.0 HD2 G:TYR129 4.0 66.7 1.0 H G:ASN116 4.1 73.7 1.0 N G:CYS117 4.1 62.4 1.0 H G:LYS115 4.1 78.6 1.0 N G:CYS130 4.2 44.8 1.0 HB3 G:CYS117 4.2 76.5 1.0 HB2 G:ARG113 4.2 86.6 1.0 HB3 G:CYS130 4.3 64.6 1.0 HB3 G:CYS111 4.3 63.1 1.0 CA G:CYS111 4.3 61.6 1.0 HH12 G:ARG113 4.4 89.1 1.0 NH1 G:ARG113 4.4 74.3 1.0 CA G:LYS115 4.4 63.7 1.0 CA G:CYS117 4.4 62.9 1.0 CA G:CYS130 4.5 49.7 1.0 H G:SER112 4.5 79.3 1.0 N G:ASN116 4.5 61.4 1.0 H G:ARG113 4.6 85.1 1.0 N G:LYS115 4.6 65.5 1.0 HD2 G:ARG113 4.6 88.5 1.0 CA G:CYS127 4.7 58.0 1.0 HA G:CYS130 4.8 59.7 1.0 C G:LYS115 4.8 62.1 1.0 CD2 G:TYR129 4.8 55.6 1.0 HA G:CYS127 4.9 69.5 1.0 CB G:TYR129 4.9 50.5 1.0 HA G:CYS117 5.0 75.4 1.0 N G:SER112 5.0 66.1 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