Atomistry » Zinc » PDB 3qla-3qym » 3qym
Atomistry »
  Zinc »
    PDB 3qla-3qym »
      3qym »

Zinc in PDB 3qym: Structure of P63 Dna Binding Domain in Complex with A 10 Base Pair A/T Rich Response Element Half Site

Protein crystallography data

The structure of Structure of P63 Dna Binding Domain in Complex with A 10 Base Pair A/T Rich Response Element Half Site, PDB code: 3qym was solved by O.Herzberg, C.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.72 / 3.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 123.872, 180.198, 104.379, 90.00, 92.62, 90.00
R / Rfree (%) 24.5 / 27.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of P63 Dna Binding Domain in Complex with A 10 Base Pair A/T Rich Response Element Half Site (pdb code 3qym). 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 10 Base Pair A/T Rich Response Element Half Site, PDB code: 3qym:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3qym

Go back to Zinc Binding Sites List in 3qym
Zinc binding site 1 out of 8 in the Structure of P63 Dna Binding Domain in Complex with A 10 Base Pair A/T Rich Response Element Half Site


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 10 Base Pair A/T Rich Response Element Half Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:0.6
occ:1.00
ND1 A:HIS208 2.1 0.6 1.0
SG A:CYS269 2.3 0.7 1.0
SG A:CYS205 2.3 0.8 1.0
SG A:CYS273 2.3 0.2 1.0
CE1 A:HIS208 3.0 0.8 1.0
CG A:HIS208 3.2 0.0 1.0
CB A:CYS273 3.3 0.3 1.0
CB A:CYS269 3.5 0.7 1.0
CB A:CYS205 3.6 0.1 1.0
CB A:HIS208 3.6 0.2 1.0
CA A:CYS269 4.0 0.2 1.0
N A:CYS205 4.1 0.2 1.0
NE2 A:HIS208 4.2 0.7 1.0
CD2 A:HIS208 4.3 0.4 1.0
CA A:CYS205 4.4 0.3 1.0
N A:HIS208 4.5 0.4 1.0
N A:ASN270 4.6 0.2 1.0
O A:MET268 4.6 0.5 1.0
C A:CYS269 4.6 0.2 1.0
CA A:HIS208 4.7 0.5 1.0
CA A:CYS273 4.7 0.4 1.0
O A:CYS205 5.0 0.3 1.0
C A:CYS205 5.0 0.6 1.0

Zinc binding site 2 out of 8 in 3qym

Go back to Zinc Binding Sites List in 3qym
Zinc binding site 2 out of 8 in the Structure of P63 Dna Binding Domain in Complex with A 10 Base Pair A/T Rich Response Element Half Site


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 10 Base Pair A/T Rich Response Element Half Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn901

b:0.8
occ:1.00
ND1 B:HIS208 2.1 0.0 1.0
SG B:CYS269 2.3 0.7 1.0
SG B:CYS273 2.3 0.1 1.0
SG B:CYS205 2.3 90.7 1.0
CE1 B:HIS208 3.0 0.4 1.0
CG B:HIS208 3.2 0.2 1.0
CB B:CYS273 3.3 0.0 1.0
CB B:CYS269 3.5 0.8 1.0
CB B:HIS208 3.6 0.2 1.0
CB B:CYS205 3.6 0.1 1.0
CA B:CYS269 3.9 0.0 1.0
N B:CYS205 4.1 96.1 1.0
NE2 B:HIS208 4.1 0.1 1.0
CD2 B:HIS208 4.2 0.0 1.0
CA B:CYS205 4.4 0.0 1.0
N B:HIS208 4.5 0.1 1.0
N B:ASN270 4.5 0.1 1.0
O B:MET268 4.6 0.8 1.0
C B:CYS269 4.6 0.6 1.0
CA B:HIS208 4.7 0.0 1.0
CA B:CYS273 4.7 0.6 1.0

Zinc binding site 3 out of 8 in 3qym

Go back to Zinc Binding Sites List in 3qym
Zinc binding site 3 out of 8 in the Structure of P63 Dna Binding Domain in Complex with A 10 Base Pair A/T Rich Response Element Half Site


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 10 Base Pair A/T Rich Response Element Half Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn901

b:99.8
occ:1.00
ND1 C:HIS208 2.1 1.0 1.0
SG C:CYS269 2.3 91.9 1.0
SG C:CYS273 2.3 94.6 1.0
SG C:CYS205 2.3 85.0 1.0
CE1 C:HIS208 3.0 0.4 1.0
CG C:HIS208 3.2 0.7 1.0
CB C:CYS273 3.3 0.9 1.0
CB C:CYS269 3.5 0.1 1.0
CB C:HIS208 3.6 75.8 1.0
CB C:CYS205 3.6 0.3 1.0
CA C:CYS269 3.9 77.9 1.0
N C:CYS205 4.1 79.8 1.0
NE2 C:HIS208 4.1 0.3 1.0
CD2 C:HIS208 4.3 90.9 1.0
CA C:CYS205 4.4 82.1 1.0
N C:HIS208 4.5 0.8 1.0
N C:ASN270 4.5 0.1 1.0
O C:MET268 4.6 0.9 1.0
C C:CYS269 4.6 91.6 1.0
CA C:HIS208 4.7 0.3 1.0
CA C:CYS273 4.7 0.2 1.0

Zinc binding site 4 out of 8 in 3qym

Go back to Zinc Binding Sites List in 3qym
Zinc binding site 4 out of 8 in the Structure of P63 Dna Binding Domain in Complex with A 10 Base Pair A/T Rich Response Element Half Site


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 10 Base Pair A/T Rich Response Element Half Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn901

b:0.0
occ:1.00
ND1 D:HIS208 2.1 0.2 1.0
SG D:CYS269 2.3 99.7 1.0
SG D:CYS273 2.3 0.7 1.0
SG D:CYS205 2.3 95.9 1.0
CE1 D:HIS208 3.0 0.0 1.0
CG D:HIS208 3.2 0.9 1.0
CB D:CYS273 3.3 0.1 1.0
CB D:CYS269 3.5 0.5 1.0
CB D:HIS208 3.6 85.8 1.0
CB D:CYS205 3.6 0.8 1.0
CA D:CYS269 3.9 94.0 1.0
N D:CYS205 4.1 75.8 1.0
NE2 D:HIS208 4.1 1.0 1.0
CD2 D:HIS208 4.3 97.5 1.0
CA D:CYS205 4.4 82.7 1.0
N D:HIS208 4.5 0.1 1.0
N D:ASN270 4.5 0.6 1.0
O D:MET268 4.6 0.8 1.0
C D:CYS269 4.6 0.2 1.0
CA D:HIS208 4.7 0.8 1.0
CA D:CYS273 4.7 0.8 1.0

Zinc binding site 5 out of 8 in 3qym

Go back to Zinc Binding Sites List in 3qym
Zinc binding site 5 out of 8 in the Structure of P63 Dna Binding Domain in Complex with A 10 Base Pair A/T Rich Response Element Half Site


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 10 Base Pair A/T Rich Response Element Half Site within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn901

b:0.6
occ:1.00
ND1 E:HIS208 2.1 0.8 1.0
SG E:CYS269 2.3 81.8 1.0
SG E:CYS205 2.3 84.8 1.0
SG E:CYS273 2.4 87.1 1.0
CE1 E:HIS208 3.0 0.8 1.0
CG E:HIS208 3.2 0.8 1.0
CB E:CYS273 3.3 0.5 1.0
CB E:CYS269 3.5 1.0 1.0
CB E:CYS205 3.5 0.6 1.0
CB E:HIS208 3.5 81.7 1.0
CA E:CYS269 4.0 86.7 1.0
N E:CYS205 4.0 63.4 1.0
NE2 E:HIS208 4.2 0.2 1.0
CD2 E:HIS208 4.3 89.8 1.0
CA E:CYS205 4.4 72.0 1.0
N E:HIS208 4.4 99.9 1.0
O E:MET268 4.6 1.0 1.0
N E:ASN270 4.6 0.1 1.0
CA E:HIS208 4.6 0.5 1.0
C E:CYS269 4.6 94.2 1.0
CA E:CYS273 4.7 0.0 1.0
O E:CYS205 5.0 93.2 1.0
C E:CYS205 5.0 80.9 1.0

Zinc binding site 6 out of 8 in 3qym

Go back to Zinc Binding Sites List in 3qym
Zinc binding site 6 out of 8 in the Structure of P63 Dna Binding Domain in Complex with A 10 Base Pair A/T Rich Response Element Half Site


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 10 Base Pair A/T Rich Response Element Half Site within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn901

b:0.7
occ:1.00
ND1 F:HIS208 2.1 0.3 1.0
SG F:CYS269 2.3 94.1 1.0
SG F:CYS205 2.3 88.4 1.0
SG F:CYS273 2.3 0.4 1.0
CE1 F:HIS208 3.0 0.1 1.0
CG F:HIS208 3.2 0.7 1.0
CB F:CYS273 3.3 0.5 1.0
CB F:CYS269 3.5 0.9 1.0
CB F:CYS205 3.5 0.3 1.0
CB F:HIS208 3.6 89.9 1.0
CA F:CYS269 4.0 93.8 1.0
N F:CYS205 4.1 80.4 1.0
NE2 F:HIS208 4.2 0.5 1.0
CD2 F:HIS208 4.3 98.2 1.0
CA F:CYS205 4.4 91.8 1.0
N F:HIS208 4.5 1.0 1.0
N F:ASN270 4.6 0.8 1.0
O F:MET268 4.6 0.8 1.0
C F:CYS269 4.6 0.4 1.0
CA F:HIS208 4.7 0.0 1.0
CA F:CYS273 4.7 0.9 1.0
O F:CYS205 5.0 0.8 1.0
C F:CYS205 5.0 0.8 1.0

Zinc binding site 7 out of 8 in 3qym

Go back to Zinc Binding Sites List in 3qym
Zinc binding site 7 out of 8 in the Structure of P63 Dna Binding Domain in Complex with A 10 Base Pair A/T Rich Response Element Half Site


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 10 Base Pair A/T Rich Response Element Half Site within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn901

b:0.9
occ:1.00
ND1 G:HIS208 2.1 0.2 1.0
SG G:CYS205 2.3 96.3 1.0
SG G:CYS269 2.3 0.7 1.0
SG G:CYS273 2.3 0.6 1.0
CE1 G:HIS208 3.0 0.1 1.0
CG G:HIS208 3.2 1.0 1.0
CB G:CYS273 3.3 0.2 1.0
CB G:CYS205 3.5 0.9 1.0
CB G:HIS208 3.5 0.0 1.0
CB G:CYS269 3.6 0.3 1.0
CA G:CYS269 4.0 1.0 1.0
N G:CYS205 4.1 86.4 1.0
NE2 G:HIS208 4.2 0.5 1.0
CD2 G:HIS208 4.3 0.5 1.0
CA G:CYS205 4.4 97.9 1.0
N G:HIS208 4.4 0.0 1.0
N G:ASN270 4.6 0.5 1.0
O G:MET268 4.6 0.1 1.0
CA G:HIS208 4.6 0.7 1.0
C G:CYS269 4.7 0.9 1.0
CA G:CYS273 4.7 0.3 1.0
O G:CYS205 5.0 98.7 1.0
C G:CYS205 5.0 0.1 1.0

Zinc binding site 8 out of 8 in 3qym

Go back to Zinc Binding Sites List in 3qym
Zinc binding site 8 out of 8 in the Structure of P63 Dna Binding Domain in Complex with A 10 Base Pair A/T Rich Response Element Half Site


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 10 Base Pair A/T Rich Response Element Half Site within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn901

b:0.1
occ:1.00
ND1 H:HIS208 2.1 0.3 1.0
SG H:CYS273 2.3 0.4 1.0
SG H:CYS269 2.3 0.7 1.0
SG H:CYS205 2.3 97.7 1.0
CE1 H:HIS208 3.0 0.4 1.0
CG H:HIS208 3.2 0.8 1.0
CB H:CYS273 3.3 0.2 1.0
CB H:CYS269 3.5 0.3 1.0
CB H:HIS208 3.6 92.8 1.0
CB H:CYS205 3.6 0.5 1.0
CA H:CYS269 3.9 100.0 1.0
N H:CYS205 4.1 94.2 1.0
NE2 H:HIS208 4.1 0.4 1.0
CD2 H:HIS208 4.2 0.6 1.0
CA H:CYS205 4.4 98.5 1.0
N H:HIS208 4.5 0.5 1.0
N H:ASN270 4.5 0.6 1.0
O H:MET268 4.6 0.6 1.0
C H:CYS269 4.6 1.0 1.0
CA H:HIS208 4.7 0.5 1.0
CA H:CYS273 4.7 0.0 1.0

Reference:

C.Chen, N.Gorlatova, Z.Kelman, O.Herzberg. Structures of P63 Dna Binding Domain in Complexes with Half-Site and with Spacer-Containing Full Response Elements. Proc.Natl.Acad.Sci.Usa V. 108 6456 2011.
ISSN: ISSN 0027-8424
PubMed: 21464285
DOI: 10.1073/PNAS.1013657108
Page generated: Wed Dec 16 04:46:25 2020

Last articles

Zn in 7NN0
Zn in 7NIO
Zn in 7LUP
Zn in 7M1Y
Zn in 7LO4
Zn in 7KWO
Zn in 7KJY
Zn in 7KCQ
Zn in 7KC2
Zn in 7KCB
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy