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Zinc in PDB 3vd2: Structure of P73 Dna Binding Domain Tetramer Modulates P73 Transactivation

Protein crystallography data

The structure of Structure of P73 Dna Binding Domain Tetramer Modulates P73 Transactivation, PDB code: 3vd2 was solved by A.S.Ethayathulla, P.W.Tse, S.Nguyen, H.Viadiu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.69 / 4.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.400, 91.127, 137.475, 90.00, 90.20, 90.00
R / Rfree (%) 24.8 / 28.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of P73 Dna Binding Domain Tetramer Modulates P73 Transactivation (pdb code 3vd2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of P73 Dna Binding Domain Tetramer Modulates P73 Transactivation, PDB code: 3vd2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3vd2

Go back to Zinc Binding Sites List in 3vd2
Zinc binding site 1 out of 6 in the Structure of P73 Dna Binding Domain Tetramer Modulates P73 Transactivation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of P73 Dna Binding Domain Tetramer Modulates P73 Transactivation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:73.6
occ:1.00
 ND1 A:HIS197 2.0 68.7 1.0
SG A:CYS194 2.3 77.6 1.0
SG A:CYS262 2.3 75.7 1.0
SG A:CYS258 2.3 62.5 1.0
CE1 A:HIS197 2.6 69.6 1.0
CB A:CYS262 3.0 73.9 1.0
CB A:CYS194 3.1 76.8 1.0
CG A:HIS197 3.3 68.5 1.0
CB A:CYS258 3.5 65.0 1.0
NE2 A:HIS197 3.9 70.0 1.0
CB A:HIS197 3.9 68.5 1.0
CA A:CYS258 4.1 66.9 1.0
N A:CYS194 4.1 76.8 1.0
CA A:CYS194 4.1 76.9 1.0
CD2 A:HIS197 4.2 69.5 1.0
O A:CYS194 4.3 77.3 1.0
CA A:CYS262 4.3 73.6 1.0
O A:MET257 4.5 68.6 1.0
N A:HIS197 4.5 71.5 1.0
C A:CYS194 4.6 76.7 1.0
CA A:HIS197 4.9 69.3 1.0
C A:CYS258 5.0 68.4 1.0

Zinc binding site 2 out of 6 in 3vd2

Go back to Zinc Binding Sites List in 3vd2
Zinc binding site 2 out of 6 in the Structure of P73 Dna Binding Domain Tetramer Modulates P73 Transactivation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of P73 Dna Binding Domain Tetramer Modulates P73 Transactivation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:89.5
occ:1.00
 ND1 B:HIS197 2.0 83.4 1.0
SG B:CYS194 2.3 68.4 1.0
SG B:CYS258 2.3 75.4 1.0
SG B:CYS262 2.3 85.5 1.0
CB B:CYS262 2.4 80.9 1.0
CB B:CYS194 2.4 69.1 1.0
CE1 B:HIS197 2.8 84.8 1.0
CG B:HIS197 3.1 83.1 1.0
CB B:CYS258 3.5 75.5 1.0
CB B:HIS197 3.6 82.4 1.0
CA B:CYS194 3.8 69.1 1.0
CA B:CYS262 3.8 80.0 1.0
NE2 B:HIS197 4.0 85.7 1.0
N B:CYS194 4.0 67.6 1.0
CD2 B:HIS197 4.1 84.2 1.0
C B:CYS262 4.2 79.1 1.0
CA B:CYS258 4.3 75.0 1.0
O B:VAL263 4.5 78.0 1.0
C B:CYS194 4.5 69.7 1.0
N B:HIS197 4.5 77.5 1.0
O B:CYS262 4.6 78.5 1.0
O B:CYS194 4.6 71.0 1.0
N B:VAL263 4.7 78.4 1.0
N B:ASN259 4.7 75.9 1.0
CA B:HIS197 4.7 82.6 1.0
N B:CYS262 4.9 79.8 1.0
C B:CYS258 4.9 75.2 1.0

Zinc binding site 3 out of 6 in 3vd2

Go back to Zinc Binding Sites List in 3vd2
Zinc binding site 3 out of 6 in the Structure of P73 Dna Binding Domain Tetramer Modulates P73 Transactivation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of P73 Dna Binding Domain Tetramer Modulates P73 Transactivation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:58.8
occ:1.00
 ND1 C:HIS197 2.0 67.4 1.0
SG C:CYS258 2.3 60.1 1.0
SG C:CYS262 2.3 73.6 1.0
SG C:CYS194 2.3 79.5 1.0
CE1 C:HIS197 2.5 67.6 1.0
CB C:CYS262 3.0 74.7 1.0
CG C:HIS197 3.3 67.4 1.0
CB C:CYS258 3.5 65.5 1.0
CB C:CYS194 3.7 78.1 1.0
CA C:CYS258 3.7 67.3 1.0
NE2 C:HIS197 3.8 67.5 1.0
CB C:HIS197 4.0 67.8 1.0
CD2 C:HIS197 4.2 67.6 1.0
N C:ASN259 4.2 69.4 1.0
O C:MET257 4.3 68.6 1.0
CA C:CYS262 4.4 74.8 1.0
N C:CYS194 4.4 76.5 1.0
C C:CYS258 4.5 68.5 1.0
CA C:CYS194 4.6 77.5 1.0
N C:HIS197 4.6 69.9 1.0
O C:CYS194 4.7 78.4 1.0
N C:CYS258 4.9 67.6 1.0
CG C:ARG193 4.9 79.2 1.0
CA C:HIS197 4.9 68.7 1.0

Zinc binding site 4 out of 6 in 3vd2

Go back to Zinc Binding Sites List in 3vd2
Zinc binding site 4 out of 6 in the Structure of P73 Dna Binding Domain Tetramer Modulates P73 Transactivation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of P73 Dna Binding Domain Tetramer Modulates P73 Transactivation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:84.3
occ:1.00
 ND1 D:HIS197 2.0 83.1 1.0
SG D:CYS262 2.2 89.3 1.0
SG D:CYS194 2.3 73.4 1.0
SG D:CYS258 2.3 79.4 1.0
CE1 D:HIS197 2.7 85.1 1.0
CB D:CYS262 2.9 88.2 1.0
CB D:CYS194 3.0 71.4 1.0
CG D:HIS197 3.1 82.9 1.0
CB D:CYS258 3.3 79.3 1.0
CB D:HIS197 3.7 81.0 1.0
CA D:CYS258 3.9 78.8 1.0
NE2 D:HIS197 3.9 86.7 1.0
CA D:CYS262 4.1 87.7 1.0
CA D:CYS194 4.1 70.3 1.0
CD2 D:HIS197 4.1 85.2 1.0
N D:CYS194 4.2 70.8 1.0
N D:HIS197 4.3 77.4 1.0
O D:MET257 4.5 78.0 1.0
O D:CYS194 4.6 69.2 1.0
C D:CYS258 4.6 79.2 1.0
N D:ASN259 4.6 79.3 1.0
CA D:HIS197 4.6 80.2 1.0
C D:CYS194 4.7 69.3 1.0
C D:CYS262 4.9 88.5 1.0

Zinc binding site 5 out of 6 in 3vd2

Go back to Zinc Binding Sites List in 3vd2
Zinc binding site 5 out of 6 in the Structure of P73 Dna Binding Domain Tetramer Modulates P73 Transactivation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of P73 Dna Binding Domain Tetramer Modulates P73 Transactivation within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn401

b:76.6
occ:1.00
 ND1 I:HIS197 1.9 82.5 1.0
SG I:CYS262 2.3 83.7 1.0
SG I:CYS258 2.3 66.9 1.0
SG I:CYS194 2.3 82.1 1.0
CB I:CYS194 2.6 79.4 1.0
CE1 I:HIS197 2.6 82.5 1.0
CB I:CYS262 2.9 80.5 1.0
CG I:HIS197 3.1 82.8 1.0
CB I:CYS258 3.5 71.1 1.0
CB I:HIS197 3.7 83.6 1.0
CA I:CYS194 3.8 79.0 1.0
N I:CYS194 3.8 77.0 1.0
NE2 I:HIS197 3.8 83.4 1.0
CD2 I:HIS197 4.1 83.2 1.0
CA I:CYS258 4.1 72.8 1.0
CA I:CYS262 4.2 79.9 1.0
N I:ASN259 4.4 73.8 1.0
C I:CYS194 4.5 79.5 1.0
N I:HIS197 4.5 84.6 1.0
O I:CYS194 4.5 81.0 1.0
O I:VAL263 4.7 75.6 1.0
CA I:HIS197 4.7 85.8 1.0
C I:CYS258 4.8 73.4 1.0
C I:CYS262 4.8 79.0 1.0
O I:MET257 4.9 77.1 1.0

Zinc binding site 6 out of 6 in 3vd2

Go back to Zinc Binding Sites List in 3vd2
Zinc binding site 6 out of 6 in the Structure of P73 Dna Binding Domain Tetramer Modulates P73 Transactivation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of P73 Dna Binding Domain Tetramer Modulates P73 Transactivation within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn401

b:56.1
occ:1.00
 ND1 J:HIS197 2.0 76.5 1.0
SG J:CYS194 2.3 87.2 1.0
SG J:CYS258 2.3 63.8 1.0
SG J:CYS262 2.3 68.6 1.0
CB J:CYS194 2.4 82.9 1.0
CG J:HIS197 2.9 75.3 1.0
CE1 J:HIS197 3.1 76.2 1.0
CB J:HIS197 3.2 72.5 1.0
CB J:CYS262 3.4 69.9 1.0
CB J:CYS258 3.7 68.5 1.0
CA J:CYS194 3.7 81.9 1.0
N J:HIS197 3.9 71.7 1.0
N J:CYS194 3.9 80.3 1.0
CD2 J:HIS197 4.1 76.2 1.0
CA J:CYS258 4.1 69.7 1.0
NE2 J:HIS197 4.1 76.6 1.0
CA J:HIS197 4.2 71.2 1.0
O J:CYS194 4.5 83.3 1.0
CA J:CYS262 4.6 70.8 1.0
O J:MET257 4.6 70.7 1.0
C J:CYS194 4.6 81.6 1.0
CB J:ASN196 4.6 72.4 1.0
N J:ASN259 4.7 72.0 1.0
C J:CYS258 4.9 70.7 1.0

Reference:

A.S.Ethayathulla, P.W.Tse, P.Monti, S.Nguyen, A.Inga, G.Fronza, H.Viadiu. Structure of P73 Dna-Binding Domain Tetramer Modulates P73 Transactivation. Proc.Natl.Acad.Sci.Usa V. 109 6066 2012.
ISSN: ISSN 0027-8424
PubMed: 22474346
DOI: 10.1073/PNAS.1115463109
Page generated: Sat Oct 26 17:40:49 2024

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