Atomistry » Zinc » PDB 3ujz-3v2j » 3us2
Atomistry »
  Zinc »
    PDB 3ujz-3v2j »
      3us2 »

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

Go back to Zinc Binding Sites List in 3us2
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

Go back to Zinc Binding Sites List in 3us2
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

Go back to Zinc Binding Sites List in 3us2
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

Go back to Zinc Binding Sites List in 3us2
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

Go back to Zinc Binding Sites List in 3us2
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

Go back to Zinc Binding Sites List in 3us2
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

Go back to Zinc Binding Sites List in 3us2
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy