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Zinc in PDB 5emq: Transcription Factor Grdbd and Gre Complex

Protein crystallography data

The structure of Transcription Factor Grdbd and Gre Complex, PDB code: 5emq 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) 37.36 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.032, 100.384, 111.897, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 22.4

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 5emq

Go back to Zinc Binding Sites List in 5emq
Zinc binding site 1 out of 4 in the Transcription Factor Grdbd and Gre 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 Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:42.7
occ:1.00
SG A:CYS443 2.3 41.8 1.0
SG A:CYS440 2.3 43.2 1.0
SG A:CYS460 2.4 41.5 1.0
SG A:CYS457 2.4 46.2 1.0
CB A:CYS460 3.2 37.9 1.0
CB A:CYS440 3.2 48.1 1.0
CB A:CYS443 3.2 33.9 1.0
CB A:CYS457 3.6 39.8 1.0
N A:CYS443 3.7 33.2 1.0
N A:CYS457 3.9 40.9 1.0
CA A:CYS443 4.0 36.0 1.0
CA A:CYS460 4.3 35.5 1.0
N A:CYS460 4.3 30.4 1.0
CA A:CYS457 4.3 47.3 1.0
NH2 A:ARG489 4.4 36.5 1.0
CB A:VAL442 4.4 39.4 1.0
OG A:SER459 4.6 39.7 1.0
C A:VAL442 4.6 42.2 1.0
C A:CYS443 4.7 42.6 1.0
CA A:CYS440 4.7 51.8 1.0
N A:SER444 4.7 41.9 1.0
CB A:ASP445 4.7 40.0 1.0
CG1 A:VAL442 4.9 37.6 1.0
CA A:VAL442 4.9 42.6 1.0
N A:VAL442 4.9 47.7 1.0
N A:ASP445 4.9 45.4 1.0
C A:CYS457 5.0 45.0 1.0
O A:CYS457 5.0 51.2 1.0

Zinc binding site 2 out of 4 in 5emq

Go back to Zinc Binding Sites List in 5emq
Zinc binding site 2 out of 4 in the Transcription Factor Grdbd and Gre 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 Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:32.4
occ:1.00
SG A:CYS492 2.3 24.8 1.0
SG A:CYS476 2.4 28.2 1.0
SG A:CYS495 2.4 30.4 1.0
SG A:CYS482 2.4 25.4 1.0
CB A:CYS482 3.2 28.3 1.0
CB A:CYS492 3.3 21.5 1.0
CB A:CYS476 3.4 25.5 1.0
CB A:CYS495 3.4 22.0 1.0
O A:HOH702 3.8 23.6 1.0
N A:CYS482 3.9 30.9 1.0
CA A:CYS476 4.0 27.7 1.0
O A:HOH701 4.1 31.2 1.0
CA A:CYS482 4.2 26.1 1.0
N A:CYS495 4.3 29.9 1.0
CA A:CYS495 4.4 29.0 1.0
CA A:ASN480 4.5 34.4 1.0
N A:ASP481 4.5 35.3 1.0
N A:ASN480 4.6 39.6 1.0
N A:ALA477 4.6 30.3 1.0
O A:HOH706 4.7 35.0 1.0
CA A:CYS492 4.7 27.9 1.0
N A:GLY478 4.7 35.6 1.0
C A:CYS476 4.8 25.9 1.0
C A:ASN480 4.8 34.2 1.0

Zinc binding site 3 out of 4 in 5emq

Go back to Zinc Binding Sites List in 5emq
Zinc binding site 3 out of 4 in the Transcription Factor Grdbd and Gre 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 Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:33.2
occ:1.00
SG B:CYS460 2.3 32.2 1.0
SG B:CYS443 2.3 31.5 1.0
SG B:CYS440 2.4 27.3 1.0
SG B:CYS457 2.4 32.5 1.0
CB B:CYS440 3.2 23.7 1.0
CB B:CYS460 3.3 29.2 1.0
O B:HOH701 3.3 89.6 1.0
CB B:CYS443 3.4 27.8 1.0
CB B:CYS457 3.6 40.0 1.0
N B:CYS443 3.8 35.0 1.0
N B:CYS457 3.9 40.7 1.0
CA B:CYS443 4.1 26.1 1.0
CA B:CYS457 4.3 40.5 1.0
CB B:VAL442 4.3 38.5 1.0
N B:CYS460 4.4 31.7 1.0
CA B:CYS460 4.4 26.8 1.0
NH1 B:ARG489 4.5 34.6 1.0
OG B:SER459 4.6 34.9 1.0
CB B:ASP445 4.6 42.3 1.0
CA B:CYS440 4.7 33.5 1.0
C B:VAL442 4.7 38.7 1.0
C B:CYS443 4.7 35.5 1.0
O B:CYS457 4.8 29.9 1.0
CG1 B:VAL442 4.9 29.9 1.0
N B:SER444 4.9 25.9 1.0
C B:CYS457 4.9 34.0 1.0
CA B:VAL442 4.9 32.8 1.0
N B:ASP445 4.9 34.6 1.0
NH1 B:ARG496 4.9 30.6 1.0

Zinc binding site 4 out of 4 in 5emq

Go back to Zinc Binding Sites List in 5emq
Zinc binding site 4 out of 4 in the Transcription Factor Grdbd and Gre 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 Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:30.2
occ:1.00
SG B:CYS492 2.3 27.7 1.0
SG B:CYS482 2.3 28.7 1.0
SG B:CYS476 2.4 29.7 1.0
SG B:CYS495 2.5 30.3 1.0
CB B:CYS482 3.3 21.3 1.0
CB B:CYS476 3.3 21.5 1.0
CB B:CYS492 3.3 25.9 1.0
CB B:CYS495 3.4 17.4 1.0
O B:HOH707 3.7 26.8 1.0
CA B:CYS476 4.0 28.2 1.0
N B:CYS482 4.0 24.2 1.0
CA B:CYS482 4.3 31.4 1.0
N B:CYS495 4.3 23.8 1.0
CA B:CYS495 4.4 22.3 1.0
CA B:ASN480 4.5 39.1 1.0
O B:HOH705 4.5 31.2 1.0
N B:ASP481 4.5 30.6 1.0
N B:ASN480 4.6 35.8 1.0
N B:ALA477 4.6 27.7 1.0
CA B:CYS492 4.8 30.9 1.0
N B:GLY478 4.8 33.6 1.0
C B:ASN480 4.8 35.4 1.0
C B:CYS476 4.8 34.8 1.0
O B:HOH720 4.9 40.4 1.0

Reference:

T.Lian, J.Jin, X.Su. The Effects of Cytosine Methylation on General Transcription Factors To Be Published.
Page generated: Wed Dec 16 06:10:11 2020

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