Zinc in PDB 5emp: Transcription Factor Grdbd and Mmgre Complex

The structure of Transcription Factor Grdbd and Mmgre Complex, PDB code: 5emp was solved by T.Lian, J.Jin, X.Su, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.01 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.279, 100.492, 112.043, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23.8

The binding sites of Zinc atom in the Transcription Factor Grdbd and Mmgre Complex (pdb code 5emp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Transcription Factor Grdbd and Mmgre Complex, PDB code: 5emp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Transcription Factor Grdbd and Mmgre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Transcription Factor Grdbd and Mmgre Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:41.7 occ:1.00 SG A:CYS440 2.3 43.9 1.0 SG A:CYS457 2.3 46.1 1.0 SG A:CYS460 2.3 43.2 1.0 SG A:CYS443 2.3 40.9 1.0 CB A:CYS460 3.2 33.5 1.0 CB A:CYS440 3.2 44.7 1.0 CB A:CYS443 3.2 30.2 1.0 CB A:CYS457 3.5 34.7 1.0 N A:CYS443 3.6 38.1 1.0 N A:CYS457 3.9 41.2 1.0 CA A:CYS443 4.0 41.5 1.0 N A:CYS460 4.3 31.3 1.0 CA A:CYS460 4.3 34.3 1.0 CA A:CYS457 4.3 40.9 1.0 CB A:VAL442 4.4 44.0 1.0 OG A:SER459 4.4 40.7 1.0 NH2 A:ARG489 4.4 36.4 1.0 C A:VAL442 4.6 42.9 1.0 C A:CYS443 4.7 47.6 1.0 CA A:CYS440 4.7 46.3 1.0 N A:SER444 4.8 45.6 1.0 CB A:ASP445 4.8 44.4 1.0 CA A:VAL442 4.8 43.8 1.0 N A:VAL442 4.9 39.4 1.0 CG1 A:VAL442 4.9 39.2 1.0 C A:CYS457 5.0 42.0 1.0 NH2 A:ARG496 5.0 32.3 1.0 N A:ASP445 5.0 49.9 1.0

Zinc binding site 2 out of 4 in the Transcription Factor Grdbd and Mmgre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Transcription Factor Grdbd and Mmgre Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:28.5 occ:1.00 SG A:CYS482 2.3 25.0 1.0 SG A:CYS476 2.3 26.6 1.0 SG A:CYS492 2.3 26.8 1.0 SG A:CYS495 2.3 31.4 1.0 CB A:CYS482 3.2 24.3 1.0 CB A:CYS495 3.3 27.2 1.0 CB A:CYS492 3.3 21.9 1.0 CB A:CYS476 3.3 22.0 1.0 N A:CYS482 3.8 26.4 1.0 O A:HOH706 3.8 20.4 1.0 CA A:CYS476 4.0 25.5 1.0 O A:HOH703 4.1 30.7 1.0 CA A:CYS482 4.1 25.4 1.0 N A:CYS495 4.2 30.5 1.0 CA A:CYS495 4.3 25.8 1.0 CA A:ASN480 4.5 29.1 1.0 N A:ASP481 4.5 34.0 1.0 N A:ASN480 4.6 34.4 1.0 N A:ALA477 4.6 24.1 1.0 O B:HOH727 4.6 34.4 1.0 NH2 A:ARG498 4.7 49.4 1.0 CA A:CYS492 4.7 28.8 1.0 C A:CYS476 4.8 27.5 1.0 C A:ASN480 4.8 35.3 1.0 N A:GLY478 4.8 27.9 1.0 C A:ASP481 5.0 30.4 1.0

Zinc binding site 3 out of 4 in the Transcription Factor Grdbd and Mmgre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Transcription Factor Grdbd and Mmgre Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:34.7 occ:1.00 SG B:CYS440 2.3 30.7 1.0 SG B:CYS460 2.3 34.8 1.0 SG B:CYS457 2.4 33.3 1.0 SG B:CYS443 2.4 35.9 1.0 CB B:CYS440 3.3 25.5 1.0 CB B:CYS460 3.3 32.9 1.0 CB B:CYS443 3.4 25.6 1.0 CB B:CYS457 3.6 33.1 1.0 N B:CYS443 3.7 35.3 1.0 N B:CYS457 3.9 34.3 1.0 CA B:CYS443 4.1 31.4 1.0 NH1 B:ARG489 4.2 40.0 1.0 N B:CYS460 4.2 34.6 1.0 CA B:CYS457 4.3 31.6 1.0 CB B:VAL442 4.3 35.0 1.0 CA B:CYS460 4.4 33.7 1.0 C B:VAL442 4.6 40.5 1.0 CA B:CYS440 4.7 37.8 1.0 O B:CYS457 4.7 33.7 1.0 CB B:ASP445 4.7 41.5 1.0 C B:CYS443 4.8 38.7 1.0 C B:CYS457 4.8 34.7 1.0 NH2 B:ARG496 4.8 33.9 1.0 CA B:VAL442 4.9 33.2 1.0 CG1 B:VAL442 4.9 24.2 1.0 N B:VAL442 4.9 38.4 1.0 N B:SER444 5.0 33.5 1.0 CB B:THR456 5.0 38.2 1.0

Zinc binding site 4 out of 4 in the Transcription Factor Grdbd and Mmgre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Transcription Factor Grdbd and Mmgre Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:26.8 occ:1.00 SG B:CYS482 2.3 24.3 1.0 SG B:CYS492 2.3 26.7 1.0 SG B:CYS476 2.3 29.9 1.0 SG B:CYS495 2.4 30.4 1.0 CB B:CYS482 3.2 24.7 1.0 CB B:CYS492 3.3 22.1 1.0 CB B:CYS476 3.3 18.0 1.0 CB B:CYS495 3.3 22.8 1.0 O B:HOH708 3.7 23.3 1.0 N B:CYS482 4.0 24.3 1.0 CA B:CYS476 4.0 32.5 1.0 CA B:CYS482 4.2 28.9 1.0 N B:CYS495 4.2 23.0 1.0 CA B:CYS495 4.3 26.2 1.0 CA B:ASN480 4.5 38.4 1.0 N B:ASN480 4.6 35.4 1.0 N B:ASP481 4.6 30.7 1.0 O B:HOH711 4.6 28.4 1.0 O B:HOH727 4.6 34.4 1.0 N B:ALA477 4.7 28.0 1.0 CA B:CYS492 4.7 31.9 1.0 C B:CYS476 4.7 30.8 1.0 C B:ASN480 4.8 30.1 1.0 N B:GLY478 4.8 28.2 1.0 O B:HOH721 4.8 44.6 1.0

T.Lian, J.Jin, X.Su. The Effects of Cytosine Methylation on General Transcription Factors To Be Published.