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Zinc in PDB 5cbz: Ancmr Dna Binding Domain - (+)Gre Complex

Protein crystallography data

The structure of Ancmr Dna Binding Domain - (+)Gre Complex, PDB code: 5cbz 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) 25.00 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.532, 81.150, 116.416, 90.00, 96.80, 90.00
R / Rfree (%) 19.6 / 23

Zinc Binding Sites:

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

Zinc binding site 1 out of 8 in 5cbz

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Zinc binding site 1 out of 8 in the Ancmr 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 Ancmr Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:45.8
occ:1.00
 SG A:CYS421 2.2 43.4 1.0
SG A:CYS424 2.3 45.1 1.0
SG A:CYS438 2.3 46.0 1.0
SG A:CYS441 2.4 42.1 1.0
CB A:CYS441 3.2 34.4 1.0
CB A:CYS421 3.3 48.5 1.0
CB A:CYS424 3.4 45.1 1.0
CB A:CYS438 3.4 43.2 1.0
N A:CYS424 3.5 45.7 1.0
N A:CYS438 3.9 45.8 1.0
CA A:CYS424 4.0 43.1 1.0
NH1 A:ARG470 4.2 42.3 1.0
CA A:CYS438 4.2 45.7 1.0
CB A:VAL423 4.3 40.1 1.0
N A:CYS441 4.3 37.7 1.0
CA A:CYS441 4.3 39.6 1.0
OG A:SER440 4.4 41.8 1.0
C A:VAL423 4.6 46.2 1.0
C A:CYS424 4.6 51.1 1.0
CB A:ASP426 4.7 48.5 1.0
N A:GLY425 4.7 53.1 1.0
CA A:CYS421 4.7 52.2 1.0
CG1 A:VAL423 4.7 41.2 1.0
CA A:VAL423 4.8 47.5 1.0
N A:ASP426 4.8 53.4 1.0
C A:CYS438 4.9 47.3 1.0
N A:VAL423 4.9 44.9 1.0
O A:CYS438 5.0 43.5 1.0

Zinc binding site 2 out of 8 in 5cbz

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Zinc binding site 2 out of 8 in the Ancmr 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 Ancmr Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:34.6
occ:1.00
 SG A:CYS476 2.3 32.8 1.0
SG A:CYS457 2.3 36.0 1.0
SG A:CYS473 2.3 31.8 1.0
SG A:CYS463 2.4 36.9 1.0
CB A:CYS463 3.2 36.6 1.0
CB A:CYS457 3.3 33.2 1.0
CB A:CYS473 3.4 31.9 1.0
CB A:CYS476 3.4 29.7 1.0
O A:HOH604 3.9 29.4 1.0
NH2 A:ARG479 4.0 54.9 1.0
CA A:CYS457 4.0 33.4 1.0
N A:CYS463 4.0 39.5 1.0
CA A:CYS463 4.2 39.0 1.0
CA A:ASN461 4.3 47.0 1.0
N A:CYS476 4.3 32.5 1.0
CA A:CYS476 4.4 30.7 1.0
O A:HOH601 4.5 43.8 1.0
N A:ASN461 4.6 44.2 1.0
O A:HOH621 4.7 42.5 1.0
N A:ALA458 4.7 34.9 1.0
N A:GLY459 4.7 38.8 1.0
C A:ASN461 4.7 46.5 1.0
CA A:CYS473 4.7 36.4 1.0
C A:CYS457 4.8 35.0 1.0
N A:ASP462 4.9 45.3 1.0
O A:CYS473 5.0 31.3 1.0

Zinc binding site 3 out of 8 in 5cbz

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Zinc binding site 3 out of 8 in the Ancmr 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 Ancmr Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:40.6
occ:1.00
 SG B:CYS441 2.2 35.4 1.0
SG B:CYS424 2.3 40.6 1.0
SG B:CYS421 2.3 41.0 1.0
SG B:CYS438 2.4 41.2 1.0
CB B:CYS441 3.2 35.2 1.0
CB B:CYS421 3.3 43.5 1.0
CB B:CYS424 3.3 37.4 1.0
CB B:CYS438 3.5 41.3 1.0
N B:CYS424 3.6 39.6 1.0
N B:CYS438 3.9 41.8 1.0
CA B:CYS424 4.0 35.9 1.0
CA B:CYS438 4.3 45.6 1.0
N B:CYS441 4.3 36.9 1.0
CA B:CYS441 4.3 41.2 1.0
CB B:VAL423 4.3 41.3 1.0
OG B:SER440 4.6 42.0 1.0
C B:CYS424 4.6 43.7 1.0
CB B:ASP426 4.6 47.7 1.0
NH1 B:ARG470 4.6 41.0 1.0
C B:VAL423 4.7 43.9 1.0
N B:GLY425 4.7 41.2 1.0
CA B:CYS421 4.8 43.4 1.0
N B:ASP426 4.9 46.4 1.0
CG1 B:VAL423 4.9 36.8 1.0
C B:CYS438 4.9 42.6 1.0
O B:CYS438 4.9 44.6 1.0
NH2 B:ARG477 4.9 36.7 1.0
CA B:VAL423 4.9 38.8 1.0

Zinc binding site 4 out of 8 in 5cbz

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Zinc binding site 4 out of 8 in the Ancmr 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 Ancmr Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:32.2
occ:1.00
 SG B:CYS473 2.2 32.9 1.0
SG B:CYS457 2.3 31.4 1.0
SG B:CYS476 2.3 33.1 1.0
SG B:CYS463 2.5 33.9 1.0
CB B:CYS463 3.1 28.3 1.0
CB B:CYS457 3.3 31.5 1.0
CB B:CYS473 3.3 32.8 1.0
CB B:CYS476 3.4 30.5 1.0
O A:HOH606 3.8 30.8 1.0
CA B:CYS457 3.9 36.3 1.0
N B:CYS463 4.1 34.5 1.0
N B:CYS476 4.1 31.7 1.0
CA B:CYS463 4.2 35.7 1.0
CA B:CYS476 4.3 26.6 1.0
CA B:ASN461 4.4 35.6 1.0
O B:HOH615 4.5 40.0 1.0
N B:ASN461 4.6 32.6 1.0
N B:ALA458 4.7 30.8 1.0
CA B:CYS473 4.7 31.4 1.0
O A:HOH621 4.7 42.5 1.0
N B:GLY459 4.8 33.4 1.0
C B:CYS457 4.8 35.6 1.0
O B:HOH607 4.8 32.4 1.0
C B:ASN461 4.8 37.2 1.0
N B:ASP462 4.9 37.8 1.0

Zinc binding site 5 out of 8 in 5cbz

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Zinc binding site 5 out of 8 in the Ancmr 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 Ancmr Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn501

b:34.2
occ:1.00
 SG E:CYS438 2.3 33.4 1.0
SG E:CYS424 2.3 35.7 1.0
SG E:CYS421 2.4 32.6 1.0
SG E:CYS441 2.4 34.3 1.0
CB E:CYS441 3.2 32.5 1.0
CB E:CYS421 3.2 32.8 1.0
CB E:CYS424 3.3 32.3 1.0
CB E:CYS438 3.6 33.7 1.0
N E:CYS424 3.6 34.4 1.0
N E:CYS438 4.0 29.0 1.0
CA E:CYS424 4.0 33.8 1.0
N E:CYS441 4.3 31.4 1.0
CA E:CYS438 4.3 34.3 1.0
CB E:VAL423 4.3 36.3 1.0
CA E:CYS441 4.3 35.3 1.0
NH1 E:ARG470 4.4 32.3 1.0
OG E:SER440 4.5 37.3 1.0
CB E:ASP426 4.6 42.6 1.0
C E:CYS424 4.6 34.2 1.0
CA E:CYS421 4.7 34.2 1.0
C E:VAL423 4.7 37.6 1.0
N E:GLY425 4.7 34.3 1.0
N E:ASP426 4.7 38.4 1.0
NH2 E:ARG477 4.9 33.8 1.0
CG1 E:VAL423 4.9 32.5 1.0
CA E:VAL423 4.9 35.0 1.0
C E:CYS438 5.0 35.4 1.0
O E:CYS438 5.0 35.3 1.0

Zinc binding site 6 out of 8 in 5cbz

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Zinc binding site 6 out of 8 in the Ancmr 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 Ancmr Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn502

b:29.7
occ:1.00
 SG E:CYS457 2.2 31.4 1.0
SG E:CYS476 2.2 29.2 1.0
SG E:CYS473 2.3 30.9 1.0
SG E:CYS463 2.3 33.7 1.0
CB E:CYS457 3.2 30.9 1.0
CB E:CYS463 3.3 36.7 1.0
CB E:CYS473 3.3 30.3 1.0
CB E:CYS476 3.3 26.3 1.0
CA E:CYS457 3.9 33.6 1.0
O E:HOH603 3.9 26.7 1.0
N E:CYS463 4.0 33.6 1.0
N E:CYS476 4.2 31.7 1.0
CA E:CYS463 4.3 33.1 1.0
CA E:CYS476 4.3 28.8 1.0
CA E:ASN461 4.4 34.4 1.0
O E:HOH615 4.5 37.2 1.0
N E:ASN461 4.5 32.9 1.0
O E:HOH621 4.7 31.5 1.0
N E:ALA458 4.7 31.9 1.0
O E:HOH632 4.7 31.8 1.0
C E:ASN461 4.7 33.9 1.0
CA E:CYS473 4.7 33.5 1.0
C E:CYS457 4.7 30.4 1.0
N E:GLY459 4.7 31.2 1.0
N E:ASP462 4.7 39.4 1.0

Zinc binding site 7 out of 8 in 5cbz

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Zinc binding site 7 out of 8 in the Ancmr 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 Ancmr Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn501

b:38.0
occ:1.00
 SG F:CYS438 2.2 38.1 1.0
SG F:CYS424 2.2 37.3 1.0
SG F:CYS421 2.4 38.6 1.0
SG F:CYS441 2.4 40.3 1.0
CB F:CYS441 3.3 39.0 1.0
CB F:CYS424 3.3 39.7 1.0
CB F:CYS421 3.3 42.2 1.0
N F:CYS424 3.4 41.1 1.0
CB F:CYS438 3.5 41.8 1.0
CA F:CYS424 3.9 37.2 1.0
N F:CYS438 3.9 43.8 1.0
CA F:CYS438 4.3 42.1 1.0
CB F:VAL423 4.3 39.9 1.0
N F:CYS441 4.4 36.6 1.0
OG F:SER440 4.4 37.7 1.0
CA F:CYS441 4.4 39.2 1.0
NH1 F:ARG470 4.4 35.7 1.0
CB F:ASP426 4.4 44.7 1.0
C F:VAL423 4.5 42.2 1.0
C F:CYS424 4.6 42.6 1.0
N F:GLY425 4.7 44.3 1.0
N F:ASP426 4.7 45.7 1.0
CA F:CYS421 4.8 45.7 1.0
NH2 F:ARG477 4.8 34.1 1.0
CA F:VAL423 4.8 40.9 1.0
N F:VAL423 4.9 40.3 1.0
C F:CYS438 4.9 41.4 1.0
CG1 F:VAL423 4.9 40.2 1.0
O F:CYS438 5.0 43.9 1.0

Zinc binding site 8 out of 8 in 5cbz

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Zinc binding site 8 out of 8 in the Ancmr 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 Ancmr Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn502

b:33.6
occ:1.00
 SG F:CYS473 2.3 29.6 1.0
SG F:CYS457 2.3 31.9 1.0
SG F:CYS463 2.3 31.6 1.0
SG F:CYS476 2.4 31.9 1.0
CB F:CYS463 3.1 31.8 1.0
CB F:CYS457 3.3 29.5 1.0
CB F:CYS473 3.3 29.3 1.0
CB F:CYS476 3.5 32.4 1.0
N F:CYS463 3.9 33.6 1.0
O E:HOH616 3.9 31.8 1.0
CA F:CYS457 4.0 30.6 1.0
CA F:CYS463 4.1 30.6 1.0
N F:CYS476 4.3 31.8 1.0
O F:HOH603 4.4 32.9 1.0
CA F:ASN461 4.4 33.6 1.0
CA F:CYS476 4.4 30.1 1.0
O F:HOH608 4.5 38.4 1.0
N F:ASN461 4.6 34.7 1.0
O E:HOH632 4.7 31.8 1.0
CA F:CYS473 4.7 27.8 1.0
N F:ALA458 4.7 28.6 1.0
C F:ASN461 4.7 37.0 1.0
N F:ASP462 4.8 31.6 1.0
C F:CYS457 4.8 32.4 1.0
N F:GLY459 4.9 30.7 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 14:06:11 2024

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