Zinc in PDB 8ifo: Crystal Structure of Estrogen Related Receptor-Gamma Dna Binding Domain Complexed with PLA2G12B Promoter

The structure of Crystal Structure of Estrogen Related Receptor-Gamma Dna Binding Domain Complexed with PLA2G12B Promoter, PDB code: 8ifo was solved by T.Xu, X.Zhen, J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.29 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	77.403, 74.434, 111.02, 90, 104.98, 90
R / Rfree (%)	21.9 / 26

The binding sites of Zinc atom in the Crystal Structure of Estrogen Related Receptor-Gamma Dna Binding Domain Complexed with PLA2G12B Promoter (pdb code 8ifo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of Estrogen Related Receptor-Gamma Dna Binding Domain Complexed with PLA2G12B Promoter, PDB code: 8ifo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Crystal Structure of Estrogen Related Receptor-Gamma Dna Binding Domain Complexed with PLA2G12B Promoter


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 Estrogen Related Receptor-Gamma Dna Binding Domain Complexed with PLA2G12B Promoter within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:60.2 occ:1.00 SG A:CYS148 2.2 57.0 1.0 SG A:CYS128 2.3 63.6 1.0 SG A:CYS131 2.4 68.9 1.0 SG A:CYS145 2.4 55.0 1.0 CB A:CYS148 3.1 55.2 1.0 CB A:CYS128 3.3 68.8 1.0 CB A:CYS131 3.3 72.0 1.0 CB A:CYS145 3.7 57.2 1.0 N A:CYS131 3.9 76.5 1.0 N A:CYS145 4.0 56.5 1.0 N A:CYS148 4.0 51.7 1.0 CA A:CYS131 4.2 77.3 1.0 CA A:CYS148 4.2 53.4 1.0 NH1 A:ARG177 4.2 61.9 1.0 CA A:CYS145 4.4 56.1 1.0 CB A:VAL130 4.4 75.5 1.0 CB A:ASP133 4.6 72.7 1.0 CA A:CYS128 4.7 74.2 1.0 CG1 A:VAL130 4.7 75.2 1.0 C A:CYS131 4.8 81.4 1.0 C A:VAL130 4.8 79.2 1.0 NH2 A:ARG184 4.8 58.4 1.0 O A:CYS145 4.9 51.0 1.0 CD A:ARG177 4.9 62.1 1.0 C A:CYS145 4.9 53.0 1.0 N A:ASP133 4.9 78.9 1.0 N A:GLY132 5.0 83.9 1.0

Zinc binding site 2 out of 7 in the Crystal Structure of Estrogen Related Receptor-Gamma Dna Binding Domain Complexed with PLA2G12B Promoter


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 Estrogen Related Receptor-Gamma Dna Binding Domain Complexed with PLA2G12B Promoter within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:97.9 occ:1.00 SG A:CYS164 2.1 119.8 1.0 SG A:CYS180 2.4 87.7 1.0 SG A:CYS183 2.5 95.6 1.0 SG A:CYS170 2.5 92.9 1.0 CB A:CYS164 2.8 113.7 1.0 CB A:CYS180 3.3 85.0 1.0 CA A:CYS164 3.5 110.1 1.0 CB A:CYS183 3.6 87.7 1.0 CB A:CYS170 3.7 91.9 1.0 N A:CYS183 4.1 83.9 1.0 CD A:PRO165 4.3 104.8 1.0 CA A:ASN168 4.3 113.5 1.0 N A:CYS170 4.4 102.7 1.0 CA A:CYS183 4.4 85.0 1.0 C A:CYS164 4.4 113.9 1.0 N A:ASN168 4.5 118.0 1.0 CB A:ALA182 4.6 88.7 1.0 N A:PRO165 4.6 111.2 1.0 CA A:CYS170 4.6 98.4 1.0 N A:CYS164 4.6 109.8 1.0 CA A:CYS180 4.8 80.8 1.0 N A:GLU169 4.8 113.8 1.0 N A:ALA166 4.8 116.5 1.0 C A:ASN168 4.8 113.5 1.0 CB A:ALA166 4.9 117.3 1.0

Zinc binding site 3 out of 7 in the Crystal Structure of Estrogen Related Receptor-Gamma Dna Binding Domain Complexed with PLA2G12B Promoter


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 Estrogen Related Receptor-Gamma Dna Binding Domain Complexed with PLA2G12B Promoter within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:121.6 occ:1.00 N3 G:DA14 3.1 53.1 1.0 CG A:LYS125 3.3 119.5 1.0 O4' G:DA15 3.6 52.9 1.0 C2 G:DA14 3.7 52.2 1.0 CD A:LYS125 3.8 119.5 1.0 C4' G:DA15 3.9 57.3 1.0 N A:LYS125 4.0 120.8 1.0 C5' G:DA15 4.2 62.7 1.0 C4 G:DA14 4.2 50.6 1.0 C1' G:DA14 4.2 57.9 1.0 O4' G:DA14 4.2 61.4 1.0 N2 G:DG13 4.3 48.6 1.0 CB A:LYS125 4.6 111.3 1.0 N9 G:DA14 4.6 55.2 1.0 C1' G:DA15 4.7 52.5 1.0 CA A:LYS125 4.8 112.9 1.0

Zinc binding site 4 out of 7 in the Crystal Structure of Estrogen Related Receptor-Gamma Dna Binding Domain Complexed with PLA2G12B Promoter


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 Estrogen Related Receptor-Gamma Dna Binding Domain Complexed with PLA2G12B Promoter within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:58.6 occ:1.00 SG B:CYS170 2.2 59.5 1.0 SG B:CYS180 2.3 57.5 1.0 SG B:CYS183 2.4 52.9 1.0 SG B:CYS164 2.4 65.5 1.0 CB B:CYS170 3.2 58.7 1.0 CB B:CYS180 3.2 54.7 1.0 CB B:CYS164 3.2 64.6 1.0 CB B:CYS183 3.5 50.9 1.0 CA B:CYS164 3.9 65.2 1.0 N B:CYS170 4.1 63.2 1.0 N B:CYS183 4.2 49.5 1.0 CA B:CYS170 4.3 61.8 1.0 CA B:ASN168 4.5 66.2 1.0 CD B:PRO165 4.5 65.9 1.0 CA B:CYS183 4.5 49.7 1.0 N B:ASN168 4.6 68.4 1.0 CA B:CYS180 4.6 53.9 1.0 N B:GLU169 4.7 67.5 1.0 C B:CYS164 4.8 68.5 1.0 CB B:ALA166 4.8 69.9 1.0 C B:ASN168 4.8 66.1 1.0 N B:PRO165 4.9 68.6 1.0 CB B:ALA182 4.9 54.3 1.0 N B:ALA166 5.0 70.3 1.0 N B:CYS164 5.0 65.5 1.0

Zinc binding site 5 out of 7 in the Crystal Structure of Estrogen Related Receptor-Gamma Dna Binding Domain Complexed with PLA2G12B Promoter


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 Estrogen Related Receptor-Gamma Dna Binding Domain Complexed with PLA2G12B Promoter within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:45.0 occ:1.00 SG B:CYS148 2.3 45.3 1.0 SG B:CYS131 2.3 44.7 1.0 SG B:CYS145 2.3 48.5 1.0 SG B:CYS128 2.3 41.8 1.0 CB B:CYS148 3.1 41.7 1.0 CB B:CYS128 3.3 44.2 1.0 CB B:CYS131 3.4 46.7 1.0 CB B:CYS145 3.7 46.6 1.0 N B:CYS131 3.9 47.3 1.0 N B:CYS148 4.0 40.3 1.0 N B:CYS145 4.0 42.8 1.0 CA B:CYS148 4.2 41.2 1.0 CA B:CYS131 4.2 48.1 1.0 NH1 B:ARG177 4.3 51.2 1.0 CA B:CYS145 4.4 44.1 1.0 CB B:VAL130 4.4 47.4 1.0 CB B:ASP133 4.6 49.4 1.0 CA B:CYS128 4.7 45.9 1.0 NH2 B:ARG184 4.8 50.0 1.0 CG1 B:VAL130 4.8 49.0 1.0 C B:CYS131 4.8 50.4 1.0 C B:VAL130 4.8 48.5 1.0 CD B:ARG177 4.9 51.3 1.0 O B:CYS145 4.9 40.9 1.0 N B:ASP133 4.9 51.3 1.0 N B:GLY132 5.0 51.0 1.0 C B:CYS145 5.0 41.7 1.0

Zinc binding site 6 out of 7 in the Crystal Structure of Estrogen Related Receptor-Gamma Dna Binding Domain Complexed with PLA2G12B Promoter


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 Estrogen Related Receptor-Gamma Dna Binding Domain Complexed with PLA2G12B Promoter within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:52.5 occ:1.00 SG F:CYS180 2.2 46.9 1.0 SG F:CYS183 2.3 49.9 1.0 SG F:CYS170 2.3 58.0 1.0 SG F:CYS164 2.5 58.4 1.0 CB F:CYS170 3.1 55.8 1.0 CB F:CYS180 3.2 45.8 1.0 CB F:CYS164 3.2 57.3 1.0 CB F:CYS183 3.3 46.8 1.0 CA F:CYS164 4.0 57.5 1.0 N F:CYS170 4.1 60.0 1.0 N F:CYS183 4.1 44.7 1.0 CA F:CYS170 4.2 58.7 1.0 CA F:CYS183 4.3 45.3 1.0 O F:HOH413 4.4 54.8 1.0 CA F:ASN168 4.5 61.0 1.0 CA F:CYS180 4.6 44.5 1.0 N F:ASN168 4.7 63.3 1.0 CD F:PRO165 4.7 59.4 1.0 N F:GLU169 4.8 64.0 1.0 C F:ASN168 4.8 62.0 1.0 C F:CYS164 4.9 61.5 1.0 CB F:ALA182 4.9 46.8 1.0 CB F:ALA166 4.9 65.4 1.0

Zinc binding site 7 out of 7 in the Crystal Structure of Estrogen Related Receptor-Gamma Dna Binding Domain Complexed with PLA2G12B Promoter


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 Estrogen Related Receptor-Gamma Dna Binding Domain Complexed with PLA2G12B Promoter within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn302 b:41.5 occ:1.00 SG F:CYS148 2.2 39.0 1.0 SG F:CYS128 2.3 41.9 1.0 SG F:CYS145 2.3 41.3 1.0 SG F:CYS131 2.3 39.5 1.0 CB F:CYS148 3.1 35.7 1.0 CB F:CYS128 3.2 43.0 1.0 CB F:CYS131 3.4 40.6 1.0 CB F:CYS145 3.6 40.6 1.0 N F:CYS131 3.9 41.6 1.0 N F:CYS145 4.0 37.9 1.0 N F:CYS148 4.1 35.7 1.0 CA F:CYS131 4.2 42.3 1.0 CA F:CYS148 4.2 35.7 1.0 NH1 F:ARG177 4.3 44.3 1.0 CA F:CYS145 4.3 39.7 1.0 CB F:VAL130 4.4 40.9 1.0 CB F:ASP133 4.6 45.2 1.0 CA F:CYS128 4.7 43.1 1.0 CG1 F:VAL130 4.8 41.5 1.0 NH2 F:ARG184 4.8 37.7 1.0 C F:VAL130 4.8 42.3 1.0 C F:CYS131 4.8 44.4 1.0 N F:ASP133 4.9 44.8 1.0 O F:CYS145 4.9 38.5 1.0 C F:CYS145 4.9 39.1 1.0 N F:GLY132 4.9 44.7 1.0 CD F:ARG177 5.0 45.1 1.0 CA F:VAL130 5.0 41.4 1.0

X.Zhen, Q.Gan, L.Qu, Y.Dong, C.Pan, J.Liu, N.Wang, T.Xu. Err Gamma-Dbd Undergoes Dimerization and Conformational Rearrangement Upon Binding to the Downstream Site of the DR1 Element Biochem.Biophys.Res.Commun. V. 656 16 2023.
ISSN: ESSN 1090-2104
DOI: 10.1016/J.BBRC.2023.03.038