Zinc in PDB 7ezj: Crystal Structure of P73 Dna Binding Domain Complex Bound with 1 Bp and 2 Bp Spacer Dna Response Elements.

The structure of Crystal Structure of P73 Dna Binding Domain Complex Bound with 1 Bp and 2 Bp Spacer Dna Response Elements., PDB code: 7ezj was solved by T.Koley, S.Roy Chowdhury, M.Kumar, P.Kaur, T.P.Singh, H.Viadiu, A.S.Ethayathulla, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.93 / 2.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	139.697, 105.496, 155.504, 90, 112.36, 90
R / Rfree (%)	24.1 / 30.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of P73 Dna Binding Domain Complex Bound with 1 Bp and 2 Bp Spacer Dna Response Elements. (pdb code 7ezj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Crystal Structure of P73 Dna Binding Domain Complex Bound with 1 Bp and 2 Bp Spacer Dna Response Elements., PDB code: 7ezj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the Crystal Structure of P73 Dna Binding Domain Complex Bound with 1 Bp and 2 Bp Spacer Dna Response Elements.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of P73 Dna Binding Domain Complex Bound with 1 Bp and 2 Bp Spacer Dna Response Elements. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:84.4 occ:1.00 ND1 A:HIS197 2.3 92.7 1.0 SG A:CYS194 2.3 83.3 1.0 SG A:CYS262 2.3 63.6 1.0 SG A:CYS258 2.3 77.5 1.0 CE1 A:HIS197 3.1 92.3 1.0 CB A:CYS262 3.1 69.3 1.0 CB A:CYS194 3.3 77.0 1.0 CG A:HIS197 3.4 90.8 1.0 CB A:CYS258 3.4 75.8 1.0 CA A:CYS258 3.8 71.4 1.0 CB A:HIS197 3.8 90.4 1.0 N A:CYS194 3.9 78.3 1.0 CA A:CYS194 4.1 79.9 1.0 NE2 A:HIS197 4.2 92.4 1.0 N A:ASN259 4.3 66.5 1.0 CD2 A:HIS197 4.4 91.8 1.0 C A:CYS258 4.4 70.7 1.0 CA A:CYS262 4.6 68.3 1.0 N A:HIS197 4.6 99.2 1.0 O A:MET257 4.7 80.2 1.0 O A:CYS194 4.7 89.7 1.0 C A:CYS194 4.8 89.5 1.0 CA A:HIS197 4.9 96.3 1.0

Zinc binding site 2 out of 16 in the Crystal Structure of P73 Dna Binding Domain Complex Bound with 1 Bp and 2 Bp Spacer Dna Response Elements.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of P73 Dna Binding Domain Complex Bound with 1 Bp and 2 Bp Spacer Dna Response Elements. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:59.6 occ:1.00 ND1 B:HIS197 2.0 69.7 1.0 SG B:CYS194 2.2 59.3 1.0 SG B:CYS262 2.3 68.6 1.0 CE1 B:HIS197 2.6 64.5 1.0 SG B:CYS258 2.8 30.0 1.0 CB B:CYS258 3.0 30.0 1.0 CG B:HIS197 3.2 67.2 1.0 CB B:CYS262 3.3 69.9 1.0 CB B:CYS194 3.3 68.1 1.0 CA B:CYS258 3.7 64.0 1.0 NE2 B:HIS197 3.8 63.6 1.0 CB B:HIS197 3.8 64.4 1.0 N B:CYS194 4.0 71.8 1.0 CD2 B:HIS197 4.1 65.8 1.0 CA B:CYS194 4.2 73.3 1.0 N B:ASN259 4.3 63.7 1.0 C B:CYS258 4.5 62.9 1.0 N B:HIS197 4.6 64.8 1.0 CA B:CYS262 4.7 75.7 1.0 O B:MET257 4.8 56.6 1.0 N B:CYS258 4.8 59.6 1.0 CA B:HIS197 4.9 64.6 1.0 C B:CYS194 5.0 71.5 1.0 O B:CYS194 5.0 68.9 1.0

Zinc binding site 3 out of 16 in the Crystal Structure of P73 Dna Binding Domain Complex Bound with 1 Bp and 2 Bp Spacer Dna Response Elements.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of P73 Dna Binding Domain Complex Bound with 1 Bp and 2 Bp Spacer Dna Response Elements. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:63.8 occ:1.00 ND1 C:HIS197 1.9 63.1 1.0 SG C:CYS258 2.3 53.2 1.0 SG C:CYS262 2.3 55.5 1.0 SG C:CYS194 2.4 54.6 1.0 CE1 C:HIS197 2.7 62.4 1.0 CG C:HIS197 3.0 59.2 1.0 CB C:CYS262 3.1 61.3 1.0 CB C:CYS194 3.2 59.5 1.0 CB C:CYS258 3.3 56.0 1.0 CB C:HIS197 3.5 59.5 1.0 CA C:CYS258 3.8 60.0 1.0 NE2 C:HIS197 3.8 59.7 1.0 N C:CYS194 3.9 63.8 1.0 CD2 C:HIS197 4.0 60.3 1.0 CA C:CYS194 4.1 65.4 1.0 N C:HIS197 4.3 68.9 1.0 N C:ASN259 4.5 59.7 1.0 CA C:CYS262 4.5 61.9 1.0 CA C:HIS197 4.6 65.0 1.0 O C:MET257 4.6 55.5 1.0 C C:CYS258 4.6 58.4 1.0 O C:CYS194 4.8 61.1 1.0 C C:CYS194 4.8 63.0 1.0 N C:CYS258 4.9 55.5 1.0 O C:ASN259 5.0 62.2 1.0

Zinc binding site 4 out of 16 in the Crystal Structure of P73 Dna Binding Domain Complex Bound with 1 Bp and 2 Bp Spacer Dna Response Elements.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of P73 Dna Binding Domain Complex Bound with 1 Bp and 2 Bp Spacer Dna Response Elements. within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:63.8 occ:1.00 ND1 D:HIS197 2.0 66.5 1.0 SG D:CYS194 2.3 75.0 1.0 SG D:CYS262 2.3 67.7 1.0 SG D:CYS258 2.3 69.7 1.0 CE1 D:HIS197 2.8 68.1 1.0 CG D:HIS197 3.2 68.1 1.0 CB D:CYS262 3.2 74.0 1.0 CB D:CYS194 3.3 69.4 1.0 CB D:CYS258 3.3 56.8 1.0 N D:CYS194 3.7 59.6 1.0 CB D:HIS197 3.8 65.8 1.0 NE2 D:HIS197 4.0 64.2 1.0 CA D:CYS258 4.0 61.0 1.0 CA D:CYS194 4.0 66.4 1.0 CD2 D:HIS197 4.2 65.5 1.0 N D:ASN259 4.5 59.8 1.0 N D:HIS197 4.5 64.8 1.0 CA D:CYS262 4.6 79.0 1.0 O D:CYS194 4.7 67.3 1.0 C D:CYS194 4.7 66.7 1.0 CA D:HIS197 4.8 67.3 1.0 C D:CYS258 4.8 61.9 1.0 C D:ARG193 4.9 60.8 1.0 O D:MET257 4.9 57.1 1.0

Zinc binding site 5 out of 16 in the Crystal Structure of P73 Dna Binding Domain Complex Bound with 1 Bp and 2 Bp Spacer Dna Response Elements.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of P73 Dna Binding Domain Complex Bound with 1 Bp and 2 Bp Spacer Dna Response Elements. within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn401 b:76.3 occ:1.00 ND1 I:HIS197 1.9 88.3 1.0 SG I:CYS258 2.3 104.1 1.0 SG I:CYS262 2.3 67.4 1.0 SG I:CYS194 2.3 86.1 1.0 CE1 I:HIS197 2.4 81.0 1.0 CB I:CYS262 3.0 69.8 1.0 CG I:HIS197 3.1 88.9 1.0 CB I:CYS258 3.2 75.6 1.0 CA I:CYS258 3.3 74.7 1.0 CB I:CYS194 3.4 83.0 1.0 NE2 I:HIS197 3.6 88.5 1.0 CB I:HIS197 3.8 88.0 1.0 N I:ASN259 3.8 71.2 1.0 CD2 I:HIS197 3.9 85.5 1.0 N I:CYS194 4.0 77.1 1.0 C I:CYS258 4.1 68.8 1.0 CA I:CYS194 4.3 82.8 1.0 N I:CYS258 4.5 81.6 1.0 CA I:CYS262 4.5 68.2 1.0 O I:ASN259 4.7 62.6 1.0 O I:MET257 4.7 87.0 1.0 N I:HIS197 4.7 96.1 1.0 CA I:HIS197 4.9 91.4 1.0 CA I:ASN259 5.0 66.9 1.0

Zinc binding site 6 out of 16 in the Crystal Structure of P73 Dna Binding Domain Complex Bound with 1 Bp and 2 Bp Spacer Dna Response Elements.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of P73 Dna Binding Domain Complex Bound with 1 Bp and 2 Bp Spacer Dna Response Elements. within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn401 b:81.2 occ:1.00 ND1 J:HIS197 2.0 91.5 1.0 SG J:CYS262 2.3 60.0 1.0 SG J:CYS194 2.3 83.6 1.0 SG J:CYS258 2.3 90.6 1.0 CE1 J:HIS197 2.9 91.3 1.0 CG J:HIS197 2.9 90.6 1.0 CB J:CYS262 3.1 71.8 1.0 CB J:CYS258 3.3 78.8 1.0 CB J:HIS197 3.3 92.7 1.0 CB J:CYS194 3.4 84.8 1.0 CA J:CYS258 3.9 78.0 1.0 NE2 J:HIS197 3.9 92.6 1.0 CD2 J:HIS197 4.0 91.0 1.0 N J:CYS194 4.0 91.1 1.0 CA J:CYS194 4.3 87.9 1.0 N J:HIS197 4.3 98.1 1.0 CA J:HIS197 4.4 95.7 1.0 N J:ASN259 4.5 72.2 1.0 CA J:CYS262 4.5 76.7 1.0 O J:MET257 4.7 79.9 1.0 C J:CYS258 4.7 69.5 1.0 O J:CYS194 4.7 94.2 1.0 C J:CYS194 4.9 91.8 1.0

Zinc binding site 7 out of 16 in the Crystal Structure of P73 Dna Binding Domain Complex Bound with 1 Bp and 2 Bp Spacer Dna Response Elements.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of P73 Dna Binding Domain Complex Bound with 1 Bp and 2 Bp Spacer Dna Response Elements. within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn401 b:101.4 occ:1.00 SG K:CYS258 2.3 114.3 1.0 SG K:CYS262 2.3 97.9 1.0 SG K:CYS194 2.4 104.6 1.0 ND1 K:HIS197 2.4 120.5 1.0 CB K:CYS262 2.9 108.2 1.0 CE1 K:HIS197 3.1 116.4 1.0 CG K:HIS197 3.6 119.5 1.0 CB K:CYS258 3.6 113.5 1.0 CA K:CYS258 3.8 116.9 1.0 N K:ASN259 3.9 119.5 1.0 CB K:CYS194 3.9 107.8 1.0 CB K:HIS197 4.2 124.8 1.0 NE2 K:HIS197 4.3 116.3 1.0 C K:CYS258 4.3 115.7 1.0 CA K:CYS262 4.4 106.3 1.0 N K:CYS194 4.5 108.9 1.0 CD2 K:HIS197 4.6 118.1 1.0 O K:ASN259 4.6 106.9 1.0 CD1 K:ILE155 4.7 112.5 1.0 OD1 K:ASN259 4.8 126.8 1.0 CA K:CYS194 4.8 113.9 1.0 O K:MET257 4.8 113.2 1.0 CA K:ASN259 4.9 115.8 1.0 CB K:ASN259 5.0 117.5 1.0

Zinc binding site 8 out of 16 in the Crystal Structure of P73 Dna Binding Domain Complex Bound with 1 Bp and 2 Bp Spacer Dna Response Elements.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of P73 Dna Binding Domain Complex Bound with 1 Bp and 2 Bp Spacer Dna Response Elements. within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn401 b:63.2 occ:1.00 ND1 L:HIS197 2.0 77.7 1.0 SG L:CYS262 2.3 70.0 1.0 SG L:CYS194 2.3 30.0 1.0 SG L:CYS258 2.3 75.8 1.0 CE1 L:HIS197 2.6 74.4 1.0 CG L:HIS197 3.2 63.9 1.0 CB L:CYS262 3.3 62.0 1.0 CB L:CYS194 3.4 30.0 1.0 CB L:CYS258 3.5 73.2 1.0 CA L:CYS258 3.8 62.6 1.0 NE2 L:HIS197 3.9 59.4 1.0 CB L:HIS197 3.9 67.3 1.0 N L:CYS194 4.0 62.7 1.0 CD2 L:HIS197 4.2 57.2 1.0 CA L:CYS194 4.2 63.2 1.0 O L:CYS194 4.3 72.7 1.0 O L:MET257 4.4 69.4 1.0 N L:ASN259 4.4 60.2 1.0 C L:CYS258 4.5 56.5 1.0 CA L:CYS262 4.6 59.3 1.0 N L:HIS197 4.6 71.2 1.0 CD L:ARG193 4.6 72.5 1.0 C L:CYS194 4.7 70.0 1.0 CG L:ARG193 4.8 73.3 1.0 CA L:HIS197 4.9 74.5 1.0 N L:CYS258 5.0 61.5 1.0

Zinc binding site 9 out of 16 in the Crystal Structure of P73 Dna Binding Domain Complex Bound with 1 Bp and 2 Bp Spacer Dna Response Elements.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of P73 Dna Binding Domain Complex Bound with 1 Bp and 2 Bp Spacer Dna Response Elements. within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn401 b:85.8 occ:1.00 SG a:CYS262 2.2 75.5 1.0 ND1 a:HIS197 2.2 95.8 1.0 SG a:CYS258 2.3 87.5 1.0 SG a:CYS194 2.3 111.6 1.0 CB a:CYS262 3.0 75.9 1.0 CE1 a:HIS197 3.1 91.0 1.0 CB a:CYS194 3.1 106.9 1.0 CB a:CYS258 3.1 84.3 1.0 CG a:HIS197 3.3 95.3 1.0 N a:CYS194 3.7 115.7 1.0 CB a:HIS197 3.8 93.5 1.0 CA a:CYS194 3.9 105.3 1.0 CA a:CYS258 4.0 75.8 1.0 NE2 a:HIS197 4.2 91.6 1.0 CD2 a:HIS197 4.4 93.6 1.0 O a:CYS194 4.4 108.0 1.0 CA a:CYS262 4.5 75.3 1.0 C a:CYS194 4.6 104.1 1.0 N a:HIS197 4.6 101.1 1.0 N a:ASN259 4.7 74.9 1.0 C a:CYS258 4.8 77.8 1.0 CA a:HIS197 4.8 95.0 1.0 C a:ARG193 5.0 96.9 1.0

Zinc binding site 10 out of 16 in the Crystal Structure of P73 Dna Binding Domain Complex Bound with 1 Bp and 2 Bp Spacer Dna Response Elements.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of P73 Dna Binding Domain Complex Bound with 1 Bp and 2 Bp Spacer Dna Response Elements. within 5.0Å range: probe atom residue distance (Å) B Occ b:Zn401 b:59.9 occ:1.00 ND1 b:HIS197 2.0 69.0 1.0 SG b:CYS258 2.3 77.8 1.0 SG b:CYS194 2.3 62.7 1.0 SG b:CYS262 2.3 68.1 1.0 CE1 b:HIS197 2.5 70.1 1.0 CB b:CYS258 3.0 62.6 1.0 CB b:CYS262 3.0 74.4 1.0 CG b:HIS197 3.1 68.2 1.0 CB b:CYS194 3.2 76.1 1.0 NE2 b:HIS197 3.6 69.8 1.0 CA b:CYS258 3.7 61.3 1.0 CB b:HIS197 3.9 70.9 1.0 CD2 b:HIS197 3.9 66.0 1.0 N b:CYS194 4.1 71.3 1.0 CA b:CYS194 4.3 73.7 1.0 N b:ASN259 4.4 65.0 1.0 CA b:CYS262 4.5 76.4 1.0 C b:CYS258 4.6 66.2 1.0 N b:HIS197 4.7 63.5 1.0 O b:MET257 4.7 59.9 1.0 N b:CYS258 4.8 56.9 1.0 O b:CYS194 4.9 69.4 1.0 CA b:HIS197 4.9 65.5 1.0 O b:ASN259 5.0 66.0 1.0 C b:CYS194 5.0 69.0 1.0

T.Koley, S.Roy Chowdhury, T.Kushwaha, M.Kumar, K.K.Inampudi, P.Kaur, T.P.Singh, H.Viadiu, A.S.Ethayathulla. Deciphering the Mechanism of P73 Recognition of P53 Response Elements Using the Crystal Structure of P73-Dna Complexes and Computational Studies. Int.J.Biol.Macromol. V. 206 40 2022.
ISSN: ISSN 0141-8130
PubMed: 35217090
DOI: 10.1016/J.IJBIOMAC.2022.02.108