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Zinc in PDB 3us2: Structure of P63 Dna Binding Domain in Complex with A 19 Base Pair A/T Rich Response Element Containing Two Half Sites with A Single Base Pair Overlap

Protein crystallography data

The structure of Structure of P63 Dna Binding Domain in Complex with A 19 Base Pair A/T Rich Response Element Containing Two Half Sites with A Single Base Pair Overlap, PDB code: 3us2 was solved by C.Chen, O.Herzberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.87 / 4.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 119.739, 180.544, 98.174, 90.00, 90.05, 90.00
R / Rfree (%) 32.6 / 33.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of P63 Dna Binding Domain in Complex with A 19 Base Pair A/T Rich Response Element Containing Two Half Sites with A Single Base Pair Overlap (pdb code 3us2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of P63 Dna Binding Domain in Complex with A 19 Base Pair A/T Rich Response Element Containing Two Half Sites with A Single Base Pair Overlap, PDB code: 3us2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3us2

Go back to Zinc Binding Sites List in 3us2
Zinc binding site 1 out of 8 in the Structure of P63 Dna Binding Domain in Complex with A 19 Base Pair A/T Rich Response Element Containing Two Half Sites with A Single Base Pair Overlap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of P63 Dna Binding Domain in Complex with A 19 Base Pair A/T Rich Response Element Containing Two Half Sites with A Single Base Pair Overlap within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:0.7
occ:1.00
 ND1 A:HIS208 2.0 0.8 1.0
SG A:CYS205 2.2 0.7 1.0
SG A:CYS273 2.3 0.3 1.0
SG A:CYS269 2.4 0.5 1.0
CE1 A:HIS208 2.8 0.8 1.0
CB A:CYS273 3.1 0.3 1.0
CG A:HIS208 3.1 0.6 1.0
CB A:CYS205 3.4 0.9 1.0
CB A:HIS208 3.6 0.8 1.0
CB A:CYS269 3.7 1.0 1.0
N A:CYS205 3.8 0.7 1.0
NE2 A:HIS208 4.0 0.2 1.0
CA A:CYS269 4.1 1.0 1.0
CA A:CYS205 4.1 0.9 1.0
CD2 A:HIS208 4.2 0.1 1.0
N A:HIS208 4.3 0.9 1.0
CA A:CYS273 4.5 0.7 1.0
O A:CYS205 4.5 1.0 1.0
CA A:HIS208 4.6 0.4 1.0
N A:ASN270 4.6 1.0 1.0
C A:CYS205 4.7 0.6 1.0
O A:MET268 4.7 0.4 1.0
C A:CYS269 4.8 0.6 1.0
C A:ARG204 4.9 0.8 1.0

Zinc binding site 2 out of 8 in 3us2

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Zinc binding site 2 out of 8 in the Structure of P63 Dna Binding Domain in Complex with A 19 Base Pair A/T Rich Response Element Containing Two Half Sites with A Single Base Pair Overlap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of P63 Dna Binding Domain in Complex with A 19 Base Pair A/T Rich Response Element Containing Two Half Sites with A Single Base Pair Overlap within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn901

b:0.0
occ:1.00
 ND1 B:HIS208 1.9 0.5 1.0
SG B:CYS205 2.3 0.2 1.0
SG B:CYS269 2.3 0.7 1.0
SG B:CYS273 2.4 0.6 1.0
CE1 B:HIS208 2.7 0.9 1.0
CG B:HIS208 3.0 0.9 1.0
CB B:CYS273 3.1 0.9 1.0
CB B:CYS205 3.4 0.9 1.0
CB B:HIS208 3.6 0.4 1.0
CB B:CYS269 3.6 0.7 1.0
CA B:CYS269 3.7 0.8 1.0
NE2 B:HIS208 3.9 0.8 1.0
N B:CYS205 3.9 0.8 1.0
CD2 B:HIS208 4.1 0.8 1.0
CA B:CYS205 4.2 0.0 1.0
N B:ASN270 4.3 0.3 1.0
N B:HIS208 4.4 0.4 1.0
O B:CYS205 4.5 0.2 1.0
C B:CYS269 4.5 0.7 1.0
CA B:CYS273 4.6 0.9 1.0
CA B:HIS208 4.6 0.5 1.0
O B:MET268 4.7 0.5 1.0
C B:CYS205 4.7 0.4 1.0
CG B:ARG204 4.9 0.1 1.0
N B:CYS269 5.0 0.0 1.0

Zinc binding site 3 out of 8 in 3us2

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Zinc binding site 3 out of 8 in the Structure of P63 Dna Binding Domain in Complex with A 19 Base Pair A/T Rich Response Element Containing Two Half Sites with A Single Base Pair Overlap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of P63 Dna Binding Domain in Complex with A 19 Base Pair A/T Rich Response Element Containing Two Half Sites with A Single Base Pair Overlap within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn901

b:0.1
occ:1.00
 ND1 C:HIS208 2.1 0.9 1.0
SG C:CYS273 2.2 0.7 1.0
SG C:CYS205 2.3 0.9 1.0
SG C:CYS269 2.4 0.8 1.0
CE1 C:HIS208 2.8 0.8 1.0
CB C:CYS273 3.0 0.6 1.0
CG C:HIS208 3.2 0.9 1.0
CB C:CYS205 3.5 0.6 1.0
CB C:CYS269 3.6 0.3 1.0
CB C:HIS208 3.8 0.5 1.0
CA C:CYS269 3.9 0.7 1.0
N C:CYS205 3.9 0.8 1.0
NE2 C:HIS208 4.0 0.1 1.0
CA C:CYS205 4.2 0.9 1.0
CD2 C:HIS208 4.2 0.0 1.0
CA C:CYS273 4.3 0.4 1.0
N C:HIS208 4.4 0.1 1.0
N C:ASN270 4.5 0.0 1.0
O C:CYS205 4.6 0.2 1.0
C C:CYS269 4.6 0.3 1.0
O C:MET268 4.7 0.4 1.0
CA C:HIS208 4.8 0.0 1.0
C C:CYS205 4.8 0.6 1.0

Zinc binding site 4 out of 8 in 3us2

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Zinc binding site 4 out of 8 in the Structure of P63 Dna Binding Domain in Complex with A 19 Base Pair A/T Rich Response Element Containing Two Half Sites with A Single Base Pair Overlap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of P63 Dna Binding Domain in Complex with A 19 Base Pair A/T Rich Response Element Containing Two Half Sites with A Single Base Pair Overlap within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn901

b:0.4
occ:1.00
 ND1 D:HIS208 2.1 0.7 1.0
SG D:CYS205 2.2 1.0 1.0
SG D:CYS269 2.3 0.0 1.0
SG D:CYS273 2.3 0.3 1.0
CB D:CYS273 2.9 0.2 1.0
CE1 D:HIS208 2.9 0.5 1.0
CB D:CYS205 3.1 0.5 1.0
CG D:HIS208 3.3 0.8 1.0
CB D:CYS269 3.6 0.6 1.0
CB D:HIS208 3.8 0.3 1.0
N D:CYS205 3.8 0.7 1.0
CA D:CYS269 3.8 0.7 1.0
CA D:CYS205 4.0 0.4 1.0
NE2 D:HIS208 4.1 0.1 1.0
CD2 D:HIS208 4.3 0.1 1.0
CA D:CYS273 4.4 0.4 1.0
N D:ASN270 4.4 0.9 1.0
O D:CYS205 4.5 0.1 1.0
N D:HIS208 4.5 0.9 1.0
C D:CYS269 4.6 0.2 1.0
C D:CYS205 4.6 0.7 1.0
CA D:HIS208 4.8 0.2 1.0
O D:MET268 4.8 0.1 1.0
C D:ARG204 4.9 0.3 1.0

Zinc binding site 5 out of 8 in 3us2

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Zinc binding site 5 out of 8 in the Structure of P63 Dna Binding Domain in Complex with A 19 Base Pair A/T Rich Response Element Containing Two Half Sites with A Single Base Pair Overlap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of P63 Dna Binding Domain in Complex with A 19 Base Pair A/T Rich Response Element Containing Two Half Sites with A Single Base Pair Overlap within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn901

b:1.0
occ:1.00
 ND1 G:HIS208 2.0 0.9 1.0
SG G:CYS205 2.2 0.2 1.0
SG G:CYS269 2.4 0.8 1.0
SG G:CYS273 2.4 0.6 1.0
CE1 G:HIS208 2.9 0.7 1.0
CB G:CYS273 3.1 0.0 1.0
CG G:HIS208 3.2 0.4 1.0
CB G:CYS205 3.4 0.1 1.0
CB G:HIS208 3.6 0.5 1.0
CB G:CYS269 3.7 1.0 1.0
N G:CYS205 3.8 0.3 1.0
CA G:CYS269 4.0 0.7 1.0
NE2 G:HIS208 4.1 0.0 1.0
CA G:CYS205 4.1 0.5 1.0
CD2 G:HIS208 4.2 0.8 1.0
N G:HIS208 4.3 0.2 1.0
O G:CYS205 4.5 0.1 1.0
CA G:CYS273 4.5 1.0 1.0
CA G:HIS208 4.6 0.4 1.0
N G:ASN270 4.6 0.6 1.0
C G:CYS205 4.7 0.4 1.0
O G:MET268 4.7 0.7 1.0
C G:CYS269 4.8 0.3 1.0
C G:ARG204 4.9 0.7 1.0
CG G:ARG204 5.0 0.0 1.0

Zinc binding site 6 out of 8 in 3us2

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Zinc binding site 6 out of 8 in the Structure of P63 Dna Binding Domain in Complex with A 19 Base Pair A/T Rich Response Element Containing Two Half Sites with A Single Base Pair Overlap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of P63 Dna Binding Domain in Complex with A 19 Base Pair A/T Rich Response Element Containing Two Half Sites with A Single Base Pair Overlap within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn901

b:0.6
occ:1.00
 ND1 H:HIS208 1.9 0.4 1.0
SG H:CYS205 2.2 1.0 1.0
SG H:CYS269 2.4 0.0 1.0
SG H:CYS273 2.5 0.7 1.0
CE1 H:HIS208 2.7 0.9 1.0
CG H:HIS208 3.1 0.7 1.0
CB H:CYS273 3.1 0.3 1.0
CB H:CYS205 3.3 0.0 1.0
CB H:HIS208 3.6 0.3 1.0
CB H:CYS269 3.7 0.6 1.0
CA H:CYS269 3.8 0.2 1.0
NE2 H:HIS208 3.9 0.5 1.0
N H:CYS205 3.9 0.8 1.0
CD2 H:HIS208 4.1 0.4 1.0
CA H:CYS205 4.2 0.4 1.0
N H:HIS208 4.3 0.3 1.0
N H:ASN270 4.4 0.7 1.0
O H:CYS205 4.4 0.2 1.0
CA H:CYS273 4.6 0.5 1.0
C H:CYS269 4.6 0.1 1.0
CA H:HIS208 4.6 0.1 1.0
C H:CYS205 4.7 1.0 1.0
O H:MET268 4.7 0.3 1.0
CG H:ARG204 5.0 0.5 1.0

Zinc binding site 7 out of 8 in 3us2

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Zinc binding site 7 out of 8 in the Structure of P63 Dna Binding Domain in Complex with A 19 Base Pair A/T Rich Response Element Containing Two Half Sites with A Single Base Pair Overlap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of P63 Dna Binding Domain in Complex with A 19 Base Pair A/T Rich Response Element Containing Two Half Sites with A Single Base Pair Overlap within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn901

b:0.6
occ:1.00
 ND1 I:HIS208 2.0 0.3 1.0
SG I:CYS205 2.1 0.9 1.0
SG I:CYS273 2.2 0.3 1.0
SG I:CYS269 2.4 0.4 1.0
CE1 I:HIS208 2.8 0.1 1.0
CB I:CYS273 3.0 0.4 1.0
CG I:HIS208 3.1 0.6 1.0
CB I:CYS205 3.4 0.1 1.0
CB I:HIS208 3.6 0.6 1.0
CB I:CYS269 3.7 0.7 1.0
N I:CYS205 3.9 0.1 1.0
NE2 I:HIS208 4.0 0.2 1.0
CA I:CYS269 4.0 0.0 1.0
CD2 I:HIS208 4.2 0.9 1.0
CA I:CYS205 4.2 0.2 1.0
N I:HIS208 4.4 0.8 1.0
CA I:CYS273 4.4 0.8 1.0
O I:CYS205 4.6 0.7 1.0
N I:ASN270 4.6 0.4 1.0
CA I:HIS208 4.7 0.2 1.0
O I:MET268 4.7 0.4 1.0
C I:CYS269 4.8 0.6 1.0
C I:CYS205 4.8 0.4 1.0

Zinc binding site 8 out of 8 in 3us2

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Zinc binding site 8 out of 8 in the Structure of P63 Dna Binding Domain in Complex with A 19 Base Pair A/T Rich Response Element Containing Two Half Sites with A Single Base Pair Overlap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of P63 Dna Binding Domain in Complex with A 19 Base Pair A/T Rich Response Element Containing Two Half Sites with A Single Base Pair Overlap within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn901

b:0.1
occ:1.00
 ND1 J:HIS208 2.1 0.3 1.0
SG J:CYS205 2.2 0.8 1.0
SG J:CYS273 2.3 0.0 1.0
SG J:CYS269 2.3 0.5 1.0
CB J:CYS273 2.8 0.1 1.0
CE1 J:HIS208 2.9 0.8 1.0
CB J:CYS205 3.2 0.7 1.0
CG J:HIS208 3.3 0.9 1.0
CB J:CYS269 3.6 0.8 1.0
CA J:CYS269 3.8 0.5 1.0
CB J:HIS208 3.8 0.6 1.0
N J:CYS205 3.8 0.7 1.0
CA J:CYS205 4.1 0.5 1.0
NE2 J:HIS208 4.1 0.5 1.0
CA J:CYS273 4.3 0.8 1.0
N J:ASN270 4.3 0.4 1.0
CD2 J:HIS208 4.3 0.6 1.0
O J:CYS205 4.5 0.6 1.0
N J:HIS208 4.6 0.5 1.0
C J:CYS269 4.6 0.4 1.0
C J:CYS205 4.7 0.9 1.0
CA J:HIS208 4.9 0.9 1.0
O J:MET268 4.9 0.2 1.0
C J:ARG204 5.0 0.6 1.0

Reference:

C.Chen, N.Gorlatova, O.Herzberg. Pliable Dna Conformation of Response Elements Bound to Transcription Factor P63. J.Biol.Chem. V. 287 7477 2012.
ISSN: ISSN 0021-9258
PubMed: 22247550
DOI: 10.1074/JBC.M111.315820
Page generated: Sat Oct 26 17:26:15 2024

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