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Zinc in PDB 4guo: Structure of P73 Dna Binding Domain Complex with 12 Bp Dna

Protein crystallography data

The structure of Structure of P73 Dna Binding Domain Complex with 12 Bp Dna, PDB code: 4guo was solved by A.S Ethayathulla, H.Viadiu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.01 / 3.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.250, 104.329, 123.324, 90.00, 96.38, 90.00
R / Rfree (%) 20.8 / 27

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of P73 Dna Binding Domain Complex with 12 Bp Dna (pdb code 4guo). 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 P73 Dna Binding Domain Complex with 12 Bp Dna, PDB code: 4guo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4guo

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Zinc binding site 1 out of 8 in the Structure of P73 Dna Binding Domain Complex with 12 Bp Dna


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 Complex with 12 Bp Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:87.6
occ:1.00
 ND1 A:HIS197 2.1 96.2 1.0
SG A:CYS258 2.3 80.3 1.0
SG A:CYS262 2.3 81.6 1.0
SG A:CYS194 2.3 88.8 1.0
CG A:HIS197 3.0 97.8 1.0
CE1 A:HIS197 3.0 100.0 1.0
CB A:CYS262 3.3 79.4 1.0
CB A:HIS197 3.3 99.7 1.0
CB A:CYS194 3.4 93.6 1.0
CB A:CYS258 3.4 77.8 1.0
CA A:CYS258 3.9 75.7 1.0
NE2 A:HIS197 4.0 1.0 1.0
CD2 A:HIS197 4.0 0.6 1.0
N A:CYS194 4.1 89.4 1.0
CA A:CYS194 4.3 93.5 1.0
N A:ASN259 4.4 72.6 1.0
N A:HIS197 4.5 0.9 1.0
CA A:HIS197 4.5 0.8 1.0
O A:MET257 4.6 84.4 1.0
C A:CYS258 4.6 73.6 1.0
CA A:CYS262 4.7 76.2 1.0
O A:CYS194 4.8 0.5 1.0
C A:CYS194 4.9 98.3 1.0

Zinc binding site 2 out of 8 in 4guo

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Zinc binding site 2 out of 8 in the Structure of P73 Dna Binding Domain Complex with 12 Bp Dna


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 Complex with 12 Bp Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:63.2
occ:1.00
 ND1 B:HIS197 2.1 70.3 1.0
SG B:CYS258 2.3 65.8 1.0
SG B:CYS262 2.3 69.1 1.0
SG B:CYS194 2.3 67.7 1.0
CE1 B:HIS197 2.9 74.6 1.0
CG B:HIS197 3.2 71.5 1.0
CB B:CYS262 3.2 70.2 1.0
CB B:CYS194 3.3 67.7 1.0
CB B:CYS258 3.3 60.7 1.0
CB B:HIS197 3.7 69.2 1.0
CA B:CYS258 3.9 61.7 1.0
NE2 B:HIS197 4.0 75.9 1.0
N B:CYS194 4.1 68.7 1.0
CD2 B:HIS197 4.2 76.0 1.0
O B:HOH508 4.3 93.8 1.0
CA B:CYS194 4.3 68.2 1.0
N B:ASN259 4.3 60.3 1.0
CA B:CYS262 4.6 69.7 1.0
C B:CYS258 4.6 61.8 1.0
N B:HIS197 4.7 64.7 1.0
CA B:HIS197 4.8 66.9 1.0
O B:MET257 4.8 57.0 1.0
O B:ASN259 4.8 67.8 1.0
O B:CYS194 4.9 68.1 1.0
C B:CYS194 5.0 68.1 1.0

Zinc binding site 3 out of 8 in 4guo

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Zinc binding site 3 out of 8 in the Structure of P73 Dna Binding Domain Complex with 12 Bp Dna


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 Complex with 12 Bp Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:59.7
occ:1.00
 ND1 C:HIS197 2.1 63.7 1.0
SG C:CYS194 2.3 57.7 1.0
SG C:CYS258 2.3 61.6 1.0
SG C:CYS262 2.3 64.9 1.0
CE1 C:HIS197 3.0 66.0 1.0
CG C:HIS197 3.0 69.5 1.0
CB C:CYS262 3.3 63.1 1.0
CB C:CYS194 3.3 60.1 1.0
CB C:HIS197 3.4 70.5 1.0
CB C:CYS258 3.4 58.6 1.0
CA C:CYS258 3.9 56.3 1.0
NE2 C:HIS197 4.1 69.9 1.0
CD2 C:HIS197 4.1 71.8 1.0
N C:CYS194 4.2 59.1 1.0
CA C:CYS194 4.3 60.7 1.0
N C:HIS197 4.4 73.4 1.0
N C:ASN259 4.4 61.8 1.0
CA C:HIS197 4.5 73.8 1.0
CA C:CYS262 4.6 64.7 1.0
O C:MET257 4.7 51.5 1.0
C C:CYS258 4.7 57.4 1.0
O C:CYS194 4.7 62.9 1.0
C C:CYS194 4.8 61.7 1.0

Zinc binding site 4 out of 8 in 4guo

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Zinc binding site 4 out of 8 in the Structure of P73 Dna Binding Domain Complex with 12 Bp Dna


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 Complex with 12 Bp Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:71.1
occ:1.00
 ND1 D:HIS197 2.1 76.2 1.0
SG D:CYS262 2.3 75.3 1.0
SG D:CYS194 2.3 74.3 1.0
SG D:CYS258 2.4 74.4 1.0
CE1 D:HIS197 2.8 78.6 1.0
CG D:HIS197 3.2 76.1 1.0
CB D:CYS262 3.2 72.8 1.0
CB D:CYS194 3.3 75.1 1.0
CB D:CYS258 3.5 68.1 1.0
CB D:HIS197 3.7 74.8 1.0
NE2 D:HIS197 4.0 78.9 1.0
CA D:CYS258 4.0 65.2 1.0
CD2 D:HIS197 4.2 77.6 1.0
N D:CYS194 4.2 75.7 1.0
N D:ASN259 4.3 65.5 1.0
CA D:CYS194 4.3 75.0 1.0
CA D:CYS262 4.5 74.8 1.0
O D:HOH503 4.5 58.8 1.0
N D:HIS197 4.6 73.7 1.0
C D:CYS258 4.7 65.5 1.0
CA D:HIS197 4.8 77.1 1.0
O D:ASN259 4.9 63.9 1.0
O D:CYS194 4.9 74.1 1.0
C D:CYS194 5.0 73.4 1.0

Zinc binding site 5 out of 8 in 4guo

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Zinc binding site 5 out of 8 in the Structure of P73 Dna Binding Domain Complex with 12 Bp Dna


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 Complex with 12 Bp Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn401

b:98.9
occ:1.00
 ND1 I:HIS197 2.1 94.7 1.0
SG I:CYS258 2.3 88.7 1.0
SG I:CYS262 2.3 0.1 1.0
SG I:CYS194 2.4 82.0 1.0
CE1 I:HIS197 2.8 92.8 1.0
CB I:CYS262 3.3 0.1 1.0
CG I:HIS197 3.3 97.4 1.0
CB I:CYS258 3.4 88.7 1.0
CB I:CYS194 3.6 87.6 1.0
CA I:CYS258 3.8 86.9 1.0
N I:ASN259 3.9 83.7 1.0
CB I:HIS197 3.9 0.8 1.0
NE2 I:HIS197 4.0 92.5 1.0
CD2 I:HIS197 4.2 96.0 1.0
C I:CYS258 4.3 84.0 1.0
O I:ASN259 4.5 77.8 1.0
CA I:CYS262 4.7 1.0 1.0
N I:HIS197 4.7 0.7 1.0
CA I:CYS194 4.8 91.6 1.0
CA I:ASN259 4.9 78.1 1.0
CA I:HIS197 5.0 0.3 1.0

Zinc binding site 6 out of 8 in 4guo

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Zinc binding site 6 out of 8 in the Structure of P73 Dna Binding Domain Complex with 12 Bp Dna


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 Complex with 12 Bp Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn401

b:84.8
occ:1.00
 ND1 J:HIS197 2.1 93.4 1.0
SG J:CYS258 2.3 84.9 1.0
SG J:CYS262 2.3 79.4 1.0
SG J:CYS194 2.4 99.6 1.0
CG J:HIS197 3.0 94.7 1.0
CE1 J:HIS197 3.1 94.6 1.0
CB J:HIS197 3.3 94.5 1.0
CB J:CYS258 3.4 84.0 1.0
CB J:CYS262 3.4 86.7 1.0
CB J:CYS194 3.6 0.8 1.0
CA J:CYS258 3.8 79.3 1.0
CD2 J:HIS197 4.1 97.1 1.0
NE2 J:HIS197 4.2 96.9 1.0
N J:CYS194 4.2 0.8 1.0
N J:ASN259 4.4 77.5 1.0
CA J:CYS194 4.4 0.2 1.0
O J:MET257 4.5 81.8 1.0
CA J:HIS197 4.5 99.9 1.0
N J:HIS197 4.6 0.8 1.0
C J:CYS258 4.6 76.2 1.0
O J:CYS194 4.7 97.8 1.0
CA J:CYS262 4.8 90.9 1.0
C J:CYS194 5.0 0.1 1.0

Zinc binding site 7 out of 8 in 4guo

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Zinc binding site 7 out of 8 in the Structure of P73 Dna Binding Domain Complex with 12 Bp Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of P73 Dna Binding Domain Complex with 12 Bp Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn401

b:89.8
occ:1.00
 ND1 K:HIS197 2.1 82.8 1.0
SG K:CYS262 2.3 86.9 1.0
SG K:CYS194 2.3 83.0 1.0
SG K:CYS258 2.3 75.1 1.0
CE1 K:HIS197 2.9 81.2 1.0
CB K:CYS262 3.1 88.0 1.0
CG K:HIS197 3.1 79.1 1.0
CB K:CYS194 3.3 79.2 1.0
CB K:CYS258 3.3 74.9 1.0
CB K:HIS197 3.6 80.6 1.0
CA K:CYS258 3.9 72.0 1.0
NE2 K:HIS197 4.0 79.4 1.0
N K:CYS194 4.1 76.7 1.0
CD2 K:HIS197 4.1 79.5 1.0
CA K:CYS194 4.3 78.3 1.0
N K:ASN259 4.4 76.5 1.0
O K:HOH514 4.4 78.6 1.0
CA K:CYS262 4.5 85.3 1.0
C K:CYS258 4.6 70.0 1.0
N K:HIS197 4.6 82.2 1.0
CA K:HIS197 4.8 79.9 1.0
O K:CYS194 4.8 85.6 1.0
O K:ASN259 4.9 84.8 1.0
O K:MET257 4.9 73.7 1.0
C K:CYS194 4.9 80.5 1.0

Zinc binding site 8 out of 8 in 4guo

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Zinc binding site 8 out of 8 in the Structure of P73 Dna Binding Domain Complex with 12 Bp Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of P73 Dna Binding Domain Complex with 12 Bp Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn401

b:76.2
occ:1.00
 ND1 L:HIS197 2.1 86.4 1.0
SG L:CYS262 2.3 74.3 1.0
SG L:CYS258 2.3 70.9 1.0
SG L:CYS194 2.3 93.8 1.0
CE1 L:HIS197 2.9 87.3 1.0
CB L:CYS262 3.1 72.8 1.0
CG L:HIS197 3.2 86.5 1.0
CB L:CYS194 3.3 89.9 1.0
CB L:CYS258 3.3 71.6 1.0
CB L:HIS197 3.7 86.8 1.0
CA L:CYS258 3.9 70.2 1.0
NE2 L:HIS197 4.0 86.9 1.0
N L:CYS194 4.1 81.0 1.0
CD2 L:HIS197 4.2 85.2 1.0
CA L:CYS194 4.2 85.7 1.0
N L:ASN259 4.4 73.5 1.0
CA L:CYS262 4.5 72.7 1.0
C L:CYS258 4.6 70.4 1.0
N L:HIS197 4.7 90.0 1.0
O L:CYS194 4.8 81.4 1.0
CA L:HIS197 4.8 87.0 1.0
O L:MET257 4.9 75.8 1.0
C L:CYS194 4.9 86.6 1.0
O L:ASN259 4.9 77.1 1.0
CG L:ARG193 5.0 76.3 1.0

Reference:

A.S Ethayathulla, H.Viadiu. Structure of P73 Dna Binding Domain Complex with 12 Bp Dna To Be Published.
Page generated: Sat Oct 26 23:35:37 2024

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