Atomistry » Zinc » PDB 5eh2-5ety » 5emc
Atomistry »
  Zinc »
    PDB 5eh2-5ety »
      5emc »

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

Protein crystallography data

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

Zinc Binding Sites:

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 5emc

Go back to Zinc Binding Sites List in 5emc
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 5emc

Go back to Zinc Binding Sites List in 5emc
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 5emc

Go back to Zinc Binding Sites List in 5emc
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 5emc

Go back to Zinc Binding Sites List in 5emc
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

Reference:

J.Jin, T.Lian, X.D.Su. The Effects of Cytosine Methylation on General Transcription Factors To Be Published.
Page generated: Wed Dec 16 06:10:09 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy