Atomistry » Zinc » PDB 5c4a-5cds » 5cbx
Atomistry »
  Zinc »
    PDB 5c4a-5cds »
      5cbx »

Zinc in PDB 5cbx: Ancgr Dna Binding Domain - (+)Gre Complex

Protein crystallography data

The structure of Ancgr Dna Binding Domain - (+)Gre Complex, PDB code: 5cbx was solved by W.H.Hudson, E.A.Ortlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.33 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.820, 81.575, 116.520, 90.00, 97.19, 90.00
R / Rfree (%) 21.1 / 22.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Ancgr Dna Binding Domain - (+)Gre Complex (pdb code 5cbx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Ancgr Dna Binding Domain - (+)Gre Complex, PDB code: 5cbx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5cbx

Go back to Zinc Binding Sites List in 5cbx
Zinc binding site 1 out of 8 in the Ancgr Dna Binding Domain - (+)Gre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ancgr Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:41.9
occ:1.00
 SG A:CYS424 2.3 44.2 1.0
SG A:CYS421 2.3 41.8 1.0
SG A:CYS438 2.3 42.8 1.0
SG A:CYS441 2.4 38.3 1.0
CB A:CYS421 3.2 46.9 1.0
CB A:CYS441 3.2 36.0 1.0
CB A:CYS424 3.4 43.3 1.0
CB A:CYS438 3.4 45.7 1.0
N A:CYS424 3.6 43.8 1.0
N A:CYS438 3.8 44.2 1.0
CA A:CYS424 4.0 41.7 1.0
CA A:CYS438 4.2 43.9 1.0
OG A:SER440 4.3 45.2 1.0
NH1 A:ARG470 4.3 41.4 1.0
CB A:VAL423 4.3 40.3 1.0
N A:CYS441 4.3 36.1 1.0
CA A:CYS441 4.4 37.6 1.0
CB A:ASP426 4.6 50.5 1.0
C A:VAL423 4.7 45.4 1.0
CA A:CYS421 4.7 46.0 1.0
C A:CYS424 4.7 45.3 1.0
N A:GLY425 4.8 46.6 1.0
O A:CYS438 4.8 43.0 1.0
CG1 A:VAL423 4.8 40.6 1.0
C A:CYS438 4.8 46.2 1.0
N A:ASP426 4.8 52.3 1.0
CA A:VAL423 4.9 41.7 1.0
NH2 A:ARG477 5.0 35.3 1.0
C A:THR437 5.0 47.9 1.0
N A:VAL423 5.0 41.7 1.0

Zinc binding site 2 out of 8 in 5cbx

Go back to Zinc Binding Sites List in 5cbx
Zinc binding site 2 out of 8 in the Ancgr Dna Binding Domain - (+)Gre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ancgr Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:38.4
occ:1.00
 SG A:CYS476 2.2 39.2 1.0
SG A:CYS457 2.3 39.0 1.0
SG A:CYS473 2.3 35.3 1.0
SG A:CYS463 2.4 39.7 1.0
CB A:CYS463 3.1 43.3 1.0
CB A:CYS457 3.3 38.8 1.0
CB A:CYS476 3.4 32.1 1.0
CB A:CYS473 3.4 36.4 1.0
O A:HOH604 3.9 35.5 1.0
CA A:CYS457 4.0 36.6 1.0
N A:CYS463 4.2 42.7 1.0
CA A:ASN461 4.2 46.5 1.0
CA A:CYS463 4.2 40.4 1.0
O A:HOH602 4.3 46.6 1.0
N A:CYS476 4.3 31.6 1.0
CA A:CYS476 4.4 32.0 1.0
N A:ASN461 4.5 49.4 1.0
N A:GLY459 4.6 39.7 1.0
N A:ALA458 4.6 38.6 1.0
C A:CYS457 4.7 38.1 1.0
C A:ASN461 4.8 47.8 1.0
CA A:CYS473 4.8 38.0 1.0
O A:HOH625 4.8 42.0 1.0
CA A:GLY459 5.0 42.7 1.0
N A:ASP462 5.0 47.0 1.0

Zinc binding site 3 out of 8 in 5cbx

Go back to Zinc Binding Sites List in 5cbx
Zinc binding site 3 out of 8 in the Ancgr Dna Binding Domain - (+)Gre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ancgr Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:39.2
occ:1.00
 SG B:CYS424 2.3 42.4 1.0
SG B:CYS421 2.3 37.9 1.0
SG B:CYS441 2.3 36.1 1.0
SG B:CYS438 2.4 40.4 1.0
CB B:CYS441 3.2 34.2 1.0
CB B:CYS421 3.3 42.0 1.0
CB B:CYS424 3.4 39.3 1.0
N B:CYS424 3.6 39.5 1.0
CB B:CYS438 3.6 42.5 1.0
N B:CYS438 4.0 41.2 1.0
CA B:CYS424 4.0 36.1 1.0
CB B:VAL423 4.3 39.9 1.0
N B:CYS441 4.3 38.5 1.0
CA B:CYS438 4.3 43.8 1.0
CA B:CYS441 4.4 36.8 1.0
OG B:SER440 4.4 43.6 1.0
NH1 B:ARG470 4.4 41.4 1.0
CB B:ASP426 4.5 49.1 1.0
C B:CYS424 4.6 45.6 1.0
N B:GLY425 4.7 44.0 1.0
C B:VAL423 4.7 45.6 1.0
N B:ASP426 4.7 46.7 1.0
CA B:CYS421 4.7 40.9 1.0
O B:CYS438 4.8 41.1 1.0
NH2 B:ARG477 4.9 35.2 1.0
CA B:VAL423 4.9 41.2 1.0
CG1 B:VAL423 4.9 35.3 1.0
C B:CYS438 4.9 42.5 1.0
N B:VAL423 5.0 38.6 1.0

Zinc binding site 4 out of 8 in 5cbx

Go back to Zinc Binding Sites List in 5cbx
Zinc binding site 4 out of 8 in the Ancgr Dna Binding Domain - (+)Gre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ancgr Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:36.0
occ:1.00
 SG B:CYS457 2.3 37.0 1.0
SG B:CYS473 2.3 32.2 1.0
SG B:CYS476 2.3 34.8 1.0
SG B:CYS463 2.4 39.4 1.0
CB B:CYS463 3.0 34.7 1.0
CB B:CYS473 3.4 33.1 1.0
CB B:CYS457 3.4 33.0 1.0
CB B:CYS476 3.4 27.6 1.0
O B:HOH611 3.8 37.3 1.0
CA B:CYS457 4.1 37.2 1.0
N B:CYS463 4.1 40.8 1.0
CA B:CYS463 4.2 40.0 1.0
N B:CYS476 4.2 29.4 1.0
CA B:ASN461 4.2 38.5 1.0
O B:HOH601 4.3 40.4 1.0
CA B:CYS476 4.3 27.9 1.0
N B:ASN461 4.5 36.0 1.0
O A:HOH625 4.6 42.0 1.0
N B:GLY459 4.7 35.4 1.0
C B:ASN461 4.7 40.2 1.0
N B:ALA458 4.8 34.7 1.0
O B:HOH607 4.8 35.9 1.0
CA B:CYS473 4.8 33.9 1.0
C B:CYS457 4.9 38.7 1.0
N B:ASP462 5.0 40.7 1.0

Zinc binding site 5 out of 8 in 5cbx

Go back to Zinc Binding Sites List in 5cbx
Zinc binding site 5 out of 8 in the Ancgr Dna Binding Domain - (+)Gre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Ancgr Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn501

b:36.8
occ:1.00
 SG E:CYS424 2.2 35.2 1.0
SG E:CYS438 2.3 39.2 1.0
SG E:CYS441 2.3 37.3 1.0
SG E:CYS421 2.4 37.3 1.0
CB E:CYS441 3.3 34.6 1.0
CB E:CYS424 3.3 35.8 1.0
CB E:CYS421 3.3 39.1 1.0
N E:CYS424 3.6 39.9 1.0
CB E:CYS438 3.6 40.9 1.0
N E:CYS438 3.9 40.0 1.0
CA E:CYS424 4.0 36.7 1.0
CA E:CYS438 4.3 39.2 1.0
N E:CYS441 4.3 33.6 1.0
OG E:SER440 4.4 39.8 1.0
CA E:CYS441 4.4 37.4 1.0
CB E:VAL423 4.4 37.2 1.0
NH1 E:ARG470 4.5 37.8 1.0
CB E:ASP426 4.6 40.8 1.0
C E:CYS424 4.6 40.0 1.0
N E:GLY425 4.7 37.8 1.0
C E:VAL423 4.7 40.1 1.0
N E:ASP426 4.7 39.8 1.0
CA E:CYS421 4.8 40.2 1.0
O E:CYS438 4.9 42.6 1.0
NH2 E:ARG477 4.9 36.0 1.0
C E:CYS438 4.9 41.6 1.0
CA E:VAL423 4.9 38.8 1.0

Zinc binding site 6 out of 8 in 5cbx

Go back to Zinc Binding Sites List in 5cbx
Zinc binding site 6 out of 8 in the Ancgr Dna Binding Domain - (+)Gre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Ancgr Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn502

b:33.4
occ:1.00
 SG E:CYS473 2.3 31.1 1.0
SG E:CYS457 2.3 34.2 1.0
SG E:CYS463 2.3 34.1 1.0
SG E:CYS476 2.4 33.7 1.0
CB E:CYS463 3.1 34.2 1.0
CB E:CYS457 3.3 31.8 1.0
CB E:CYS473 3.3 28.9 1.0
CB E:CYS476 3.5 31.7 1.0
O E:HOH616 3.8 34.7 1.0
N E:CYS463 4.0 33.4 1.0
CA E:CYS457 4.0 34.9 1.0
CA E:CYS463 4.2 33.1 1.0
N E:CYS476 4.2 31.2 1.0
O E:HOH613 4.3 34.0 1.0
CA E:ASN461 4.3 34.7 1.0
CA E:CYS476 4.5 30.6 1.0
N E:ASN461 4.6 32.2 1.0
C E:ASN461 4.7 36.4 1.0
N E:ALA458 4.7 32.9 1.0
CA E:CYS473 4.7 29.6 1.0
O F:HOH631 4.8 38.5 1.0
N E:ASP462 4.8 37.5 1.0
C E:CYS457 4.8 32.7 1.0
N E:GLY459 4.9 34.1 1.0
OD1 E:ASN461 4.9 34.5 1.0
O E:HOH615 4.9 41.6 1.0
CB E:ALA475 5.0 32.0 1.0

Zinc binding site 7 out of 8 in 5cbx

Go back to Zinc Binding Sites List in 5cbx
Zinc binding site 7 out of 8 in the Ancgr Dna Binding Domain - (+)Gre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Ancgr Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn501

b:35.6
occ:1.00
 SG F:CYS438 2.2 34.4 1.0
SG F:CYS424 2.3 37.2 1.0
SG F:CYS441 2.4 33.6 1.0
SG F:CYS421 2.4 35.6 1.0
CB F:CYS441 3.2 33.5 1.0
CB F:CYS421 3.2 38.5 1.0
CB F:CYS424 3.4 36.6 1.0
CB F:CYS438 3.6 35.5 1.0
N F:CYS424 3.6 40.4 1.0
N F:CYS438 4.0 34.3 1.0
CA F:CYS424 4.0 39.8 1.0
N F:CYS441 4.3 31.1 1.0
CA F:CYS438 4.3 35.1 1.0
CA F:CYS441 4.3 33.8 1.0
NH1 F:ARG470 4.4 35.0 1.0
CB F:VAL423 4.4 36.1 1.0
OG F:SER440 4.4 40.7 1.0
CB F:ASP426 4.6 44.9 1.0
C F:CYS424 4.7 39.7 1.0
CA F:CYS421 4.7 35.6 1.0
C F:VAL423 4.7 40.6 1.0
N F:GLY425 4.8 42.1 1.0
N F:ASP426 4.8 39.8 1.0
O F:CYS438 4.9 33.5 1.0
NH2 F:ARG477 4.9 34.8 1.0
C F:CYS438 4.9 39.1 1.0
CG1 F:VAL423 4.9 31.4 1.0
CA F:VAL423 5.0 37.3 1.0

Zinc binding site 8 out of 8 in 5cbx

Go back to Zinc Binding Sites List in 5cbx
Zinc binding site 8 out of 8 in the Ancgr Dna Binding Domain - (+)Gre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Ancgr Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn502

b:33.2
occ:1.00
 SG F:CYS473 2.3 32.1 1.0
SG F:CYS457 2.3 34.6 1.0
SG F:CYS476 2.3 33.3 1.0
SG F:CYS463 2.4 33.3 1.0
CB F:CYS463 3.1 38.5 1.0
CB F:CYS457 3.2 36.3 1.0
CB F:CYS473 3.3 33.8 1.0
CB F:CYS476 3.4 28.6 1.0
O F:HOH611 3.7 31.6 1.0
CA F:CYS457 3.9 36.7 1.0
N F:CYS463 4.1 35.3 1.0
O F:HOH601 4.2 40.3 1.0
N F:CYS476 4.2 29.2 1.0
CA F:CYS463 4.3 35.8 1.0
CA F:ASN461 4.3 38.1 1.0
CA F:CYS476 4.4 26.5 1.0
N F:ASN461 4.6 37.9 1.0
O F:HOH631 4.6 38.5 1.0
N F:ALA458 4.7 34.2 1.0
N F:GLY459 4.7 35.9 1.0
C F:CYS457 4.7 33.9 1.0
O F:HOH614 4.7 35.6 1.0
CA F:CYS473 4.7 33.6 1.0
C F:ASN461 4.8 40.2 1.0
N F:ASP462 5.0 41.1 1.0

Reference:

W.H.Hudson, B.R.Kossmann, I.M.De Vera, S.W.Chuo, E.R.Weikum, G.N.Eick, J.W.Thornton, I.N.Ivanov, D.J.Kojetin, E.A.Ortlund. Distal Substitutions Drive Divergent Dna Specificity Among Paralogous Transcription Factors Through Subdivision of Conformational Space. Proc.Natl.Acad.Sci.Usa V. 113 326 2016.
ISSN: ESSN 1091-6490
PubMed: 26715749
DOI: 10.1073/PNAS.1518960113
Page generated: Sun Oct 27 14:01:46 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy