Zinc in PDB 5emc: Transcription Factor Grdbd and Smgre Complex

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

Resolution Low / High (Å)	37.26 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.942, 99.643, 112.229, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 26.1

The binding sites of Zinc atom in the Transcription Factor Grdbd and Smgre Complex (pdb code 5emc). 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 Smgre Complex, PDB code: 5emc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Transcription Factor Grdbd and Smgre 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 Smgre Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:37.1 occ:1.00 SG A:CYS440 2.3 42.1 1.0 SG A:CYS443 2.3 36.5 1.0 SG A:CYS460 2.4 37.0 1.0 SG A:CYS457 2.4 36.7 1.0 CB A:CYS460 3.2 37.8 1.0 CB A:CYS440 3.3 34.5 1.0 CB A:CYS443 3.4 27.0 1.0 CB A:CYS457 3.6 39.6 1.0 N A:CYS443 3.7 30.7 1.0 N A:CYS457 3.9 43.2 1.0 CA A:CYS443 4.1 36.4 1.0 CA A:CYS457 4.3 40.3 1.0 CA A:CYS460 4.3 36.7 1.0 N A:CYS460 4.3 28.1 1.0 CB A:VAL442 4.4 37.1 1.0 NH2 A:ARG489 4.4 37.3 1.0 OG A:SER459 4.5 39.4 1.0 C A:VAL442 4.7 37.1 1.0 CB A:ASP445 4.7 29.5 1.0 CA A:CYS440 4.7 40.9 1.0 C A:CYS443 4.7 36.4 1.0 N A:SER444 4.9 36.8 1.0 CA A:VAL442 4.9 36.4 1.0 N A:ASP445 4.9 46.7 1.0 CD A:ARG489 5.0 24.4 1.0 C A:CYS457 5.0 35.8 1.0 CG1 A:VAL442 5.0 30.6 1.0

Zinc binding site 2 out of 4 in the Transcription Factor Grdbd and Smgre 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 Smgre Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:22.4 occ:1.00 SG A:CYS492 2.3 23.1 1.0 SG A:CYS482 2.3 20.6 1.0 SG A:CYS476 2.4 25.2 1.0 SG A:CYS495 2.4 27.8 1.0 CB A:CYS482 3.2 20.1 1.0 CB A:CYS476 3.3 20.5 1.0 CB A:CYS495 3.3 21.5 1.0 CB A:CYS492 3.4 20.4 1.0 O A:HOH713 3.8 19.4 1.0 N A:CYS482 3.9 23.5 1.0 CA A:CYS476 4.0 20.4 1.0 O A:HOH742 4.0 25.6 1.0 CA A:CYS482 4.1 26.9 1.0 O A:HOH702 4.3 22.1 1.0 N A:CYS495 4.3 22.2 1.0 CA A:ASN480 4.3 21.1 1.0 CA A:CYS495 4.4 22.2 1.0 N A:ASP481 4.5 30.7 1.0 N A:ASN480 4.5 29.9 1.0 C A:ASN480 4.7 21.3 1.0 N A:ALA477 4.7 22.1 1.0 NH1 A:ARG498 4.7 35.4 1.0 N A:GLY478 4.8 18.9 1.0 CA A:CYS492 4.8 34.9 1.0 C A:CYS476 4.8 19.9 1.0 OD1 A:ASN480 4.9 21.7 1.0

Zinc binding site 3 out of 4 in the Transcription Factor Grdbd and Smgre 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 Smgre Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:29.1 occ:1.00 SG B:CYS443 2.3 32.6 1.0 SG B:CYS460 2.3 30.4 1.0 SG B:CYS440 2.4 23.6 1.0 SG B:CYS457 2.5 28.5 1.0 CB B:CYS460 3.1 26.2 1.0 CB B:CYS440 3.2 22.1 1.0 CB B:CYS443 3.2 22.4 1.0 CB B:CYS457 3.5 23.1 1.0 N B:CYS443 3.8 34.3 1.0 N B:CYS457 3.9 31.0 1.0 CA B:CYS443 4.0 29.4 1.0 CA B:CYS457 4.2 23.3 1.0 NH1 B:ARG489 4.2 30.7 1.0 N B:CYS460 4.3 23.3 1.0 CA B:CYS460 4.3 28.5 1.0 OG B:SER459 4.4 33.2 1.0 CB B:VAL442 4.5 39.4 1.0 C B:CYS443 4.6 33.9 1.0 CB B:ASP445 4.6 41.0 1.0 CA B:CYS440 4.6 34.8 1.0 O B:CYS457 4.7 22.9 1.0 N B:SER444 4.7 25.8 1.0 C B:VAL442 4.7 38.3 1.0 N B:ASP445 4.8 28.4 1.0 C B:CYS457 4.8 25.9 1.0

Zinc binding site 4 out of 4 in the Transcription Factor Grdbd and Smgre 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 Smgre Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:24.2 occ:1.00 SG B:CYS492 2.2 25.0 1.0 SG B:CYS482 2.3 26.6 1.0 SG B:CYS476 2.3 24.9 1.0 SG B:CYS495 2.5 22.5 1.0 CB B:CYS482 3.1 17.5 1.0 CB B:CYS476 3.2 17.9 1.0 CB B:CYS492 3.3 21.3 1.0 CB B:CYS495 3.3 17.1 1.0 O B:HOH723 3.6 20.2 1.0 CA B:CYS476 3.9 26.5 1.0 N B:CYS482 4.0 17.2 1.0 CA B:CYS482 4.1 20.1 1.0 N B:CYS495 4.3 25.6 1.0 CA B:CYS495 4.4 23.0 1.0 CA B:ASN480 4.5 36.2 1.0 N B:ASP481 4.6 24.5 1.0 N B:ALA477 4.6 28.2 1.0 N B:ASN480 4.6 29.1 1.0 C B:CYS476 4.7 30.0 1.0 O B:HOH711 4.7 20.4 1.0 CA B:CYS492 4.7 38.4 1.0 N B:GLY478 4.8 21.0 1.0 C B:ASN480 4.8 29.0 1.0 O B:HOH718 4.9 41.2 1.0

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