Zinc in PDB 9bdy: At-Centric Nf-Kappab Rela Binding Dna

The structure of At-Centric Nf-Kappab Rela Binding Dna, PDB code: 9bdy was solved by T.Biswas, S.Shahabi, O.V.Tsodikov, G.Ghosh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.479, 46.447, 98.381, 90.01, 89.92, 60.01
R / Rfree (%)	30.2 / 36.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 102;

Binding sites:

The binding sites of Zinc atom in the At-Centric Nf-Kappab Rela Binding Dna (pdb code 9bdy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 102 binding sites of Zinc where determined in the At-Centric Nf-Kappab Rela Binding Dna, PDB code: 9bdy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 102 in the At-Centric Nf-Kappab Rela Binding Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of At-Centric Nf-Kappab Rela Binding Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:62.8 occ:1.00 N7 A:DG3 2.1 62.2 1.0 C8 A:DG3 3.1 58.8 1.0 C5 A:DG3 3.1 60.8 1.0 O A:HOH306 3.2 59.1 1.0 O6 A:DG3 3.4 57.4 1.0 C6 A:DG3 3.6 58.9 1.0 O6 A:DG4 4.3 56.0 1.0 N9 A:DG3 4.3 58.5 1.0 C4 A:DG3 4.3 58.6 1.0 N7 A:DG2 4.9 60.1 1.0 C8 A:DG2 4.9 54.3 1.0 N1 A:DG3 5.0 59.8 1.0 N4 B:DC109 5.0 55.5 1.0

Zinc binding site 2 out of 102 in the At-Centric Nf-Kappab Rela Binding Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of At-Centric Nf-Kappab Rela Binding Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:67.5 occ:1.00 N7 A:DG2 2.1 60.1 1.0 O A:HOH309 2.1 54.5 1.0 O A:HOH306 2.1 59.1 1.0 C8 A:DG2 3.0 54.3 1.0 C5 A:DG2 3.1 60.6 1.0 O6 A:DG2 3.5 56.9 1.0 C6 A:DG2 3.7 57.5 1.0 O3' A:DC1 4.2 73.9 1.0 N9 A:DG2 4.2 56.6 1.0 C4 A:DG2 4.3 58.6 1.0 O E:HOH310 4.6 47.6 1.0 O6 A:DG3 4.7 57.4 1.0 O D:HOH303 4.9 40.0 1.0

Zinc binding site 3 out of 102 in the At-Centric Nf-Kappab Rela Binding Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of At-Centric Nf-Kappab Rela Binding Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:46.8 occ:1.00 O A:HOH308 2.1 50.0 1.0 O A:HOH311 2.1 55.9 1.0 O A:HOH301 2.1 35.4 1.0 O A:HOH307 2.1 38.6 1.0 N7 A:DG12 2.1 40.0 1.0 C8 A:DG12 3.1 41.1 1.0 C5 A:DG12 3.2 39.8 1.0 O6 A:DG12 3.5 45.0 1.0 C6 A:DG12 3.7 43.0 1.0 OP2 A:DG12 4.0 52.5 1.0 N9 A:DG12 4.3 41.7 1.0 C4 A:DG12 4.3 38.2 1.0

Zinc binding site 4 out of 102 in the At-Centric Nf-Kappab Rela Binding Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of At-Centric Nf-Kappab Rela Binding Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:52.3 occ:1.00 OP1 E:DG12 1.9 47.5 1.0 OP1 B:DG112 2.0 48.8 1.0 OXT B:ACT202 2.1 59.6 1.0 O E:ACT204 2.1 60.8 1.0 OXT E:ACT204 2.5 57.7 1.0 C E:ACT204 2.6 65.3 1.0 O B:ACT202 2.6 58.3 1.0 C B:ACT202 2.7 64.5 1.0 P B:DG112 3.1 46.4 1.0 P E:DG12 3.2 47.3 1.0 O3' B:DC111 3.4 46.1 1.0 O3' E:DC11 3.5 46.5 1.0 OP2 B:DG112 3.9 50.2 1.0 CH3 E:ACT204 4.0 63.3 1.0 OP2 E:DG12 4.1 50.3 1.0 CH3 B:ACT202 4.2 64.7 1.0 O5' E:DG12 4.3 44.7 1.0 O5' B:DG112 4.4 43.6 1.0 C5' E:DG12 4.5 43.4 1.0 C5' B:DG112 4.7 44.7 1.0 C3' B:DC111 4.8 50.0 1.0 C3' E:DC11 4.9 49.2 1.0

Zinc binding site 5 out of 102 in the At-Centric Nf-Kappab Rela Binding Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of At-Centric Nf-Kappab Rela Binding Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:65.9 occ:1.00 O B:HOH311 2.1 48.4 1.0 N7 B:DG103 2.1 51.8 1.0 C5 B:DG103 3.1 51.1 1.0 C8 B:DG103 3.1 51.3 1.0 O6 B:DG103 3.3 46.7 1.0 O B:HOH305 3.3 59.1 1.0 C6 B:DG103 3.5 47.9 1.0 O B:HOH309 3.8 60.0 1.0 O B:HOH302 4.0 42.7 1.0 C4 B:DG103 4.3 51.4 1.0 N9 B:DG103 4.3 53.1 1.0 C8 B:DG102 4.3 59.1 1.0 N7 B:DG102 4.3 61.1 1.0 N6 B:DA104 4.5 44.7 1.0 N9 B:DG102 4.8 57.6 1.0 C5 B:DG102 4.8 57.0 1.0 ZN B:ZN204 4.8 64.0 1.0 N1 B:DG103 4.9 50.7 1.0

Zinc binding site 6 out of 102 in the At-Centric Nf-Kappab Rela Binding Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of At-Centric Nf-Kappab Rela Binding Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn204 b:64.0 occ:1.00 O B:HOH304 2.1 51.8 1.0 O B:HOH305 2.1 59.1 1.0 N7 B:DG102 2.1 61.1 1.0 C8 B:DG102 3.0 59.1 1.0 C5 B:DG102 3.2 57.0 1.0 O6 B:DG102 3.5 51.6 1.0 C6 B:DG102 3.7 51.9 1.0 N9 B:DG102 4.2 57.6 1.0 C4 B:DG102 4.3 58.3 1.0 O A:HOH314 4.5 59.3 1.0 O6 B:DG103 4.5 46.7 1.0 OP2 B:DG102 4.7 74.8 1.0 ZN B:ZN203 4.8 65.9 1.0

Zinc binding site 7 out of 102 in the At-Centric Nf-Kappab Rela Binding Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of At-Centric Nf-Kappab Rela Binding Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn205 b:48.0 occ:1.00 O B:HOH301 2.1 45.9 1.0 O B:HOH306 2.1 43.7 1.0 O B:HOH303 2.1 38.4 1.0 N7 B:DG112 2.1 41.8 1.0 C8 B:DG112 3.0 41.1 1.0 C5 B:DG112 3.2 40.1 1.0 O6 B:DG112 3.6 44.1 1.0 C6 B:DG112 3.8 41.2 1.0 OP2 B:DG112 4.0 50.2 1.0 N9 B:DG112 4.2 40.8 1.0 C4 B:DG112 4.3 39.2 1.0 ZN D:ZN205 4.8 135.2 1.0 C5' D:DA104 4.8 53.1 1.0

Zinc binding site 8 out of 102 in the At-Centric Nf-Kappab Rela Binding Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of At-Centric Nf-Kappab Rela Binding Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn206 b:109.9 occ:1.00 OP1 B:DA105 2.7 70.9 1.0 O3' B:DA104 2.7 55.0 1.0 P B:DA105 3.0 66.7 1.0 C3' B:DA104 3.2 51.9 1.0 OP2 B:DA105 3.4 65.5 1.0 OP1 S:DG3 3.8 44.0 0.5 C4' B:DA104 3.8 51.7 1.0 OP2 S:DG3 4.1 47.7 0.5 C5' B:DA104 4.1 51.4 1.0 P S:DG3 4.4 44.6 0.5 O5' B:DA105 4.5 58.8 1.0 C2' B:DA104 4.6 51.2 1.0 O5' B:DA104 4.9 51.5 1.0 C5' B:DA105 5.0 57.9 1.0

Zinc binding site 9 out of 102 in the At-Centric Nf-Kappab Rela Binding Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of At-Centric Nf-Kappab Rela Binding Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn201 b:69.5 occ:1.00 N7 E:DG3 2.1 57.9 1.0 C8 E:DG3 3.1 56.2 1.0 C5 E:DG3 3.1 57.3 1.0 O6 E:DG3 3.3 56.5 1.0 C6 E:DG3 3.6 55.5 1.0 O E:HOH309 3.7 48.8 1.0 O E:HOH305 3.8 34.0 1.0 O6 E:DG4 4.3 47.7 1.0 N9 E:DG3 4.3 57.6 1.0 C4 E:DG3 4.3 58.8 1.0 N7 E:DG2 4.7 53.5 1.0 C8 E:DG2 4.7 49.2 1.0 O E:HOH313 4.9 40.1 1.0 ZN E:ZN202 4.9 69.9 1.0 N1 E:DG3 5.0 56.0 1.0

Zinc binding site 10 out of 102 in the At-Centric Nf-Kappab Rela Binding Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of At-Centric Nf-Kappab Rela Binding Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn202 b:69.9 occ:1.00 N7 E:DG2 2.1 53.5 1.0 O E:HOH309 2.1 48.8 1.0 O E:HOH302 2.1 60.0 1.0 O E:HOH311 2.1 63.6 1.0 C8 E:DG2 3.1 49.2 1.0 C5 E:DG2 3.1 52.5 1.0 O6 E:DG2 3.3 52.2 1.0 C6 E:DG2 3.5 51.4 1.0 N9 E:DG2 4.2 52.2 1.0 C4 E:DG2 4.3 52.1 1.0 O6 E:DG3 4.4 56.5 1.0 ZN E:ZN201 4.9 69.5 1.0 N1 E:DG2 4.9 50.7 1.0 C6 E:DG3 5.0 55.5 1.0

T.Li, S.Shahabi, T.Biswas, O.V.Tsodikov, W.Pan, D.B.Huang, V.Y.Wang, Y.Wang, G.Ghosh. Transient Interactions Modulate the Affinity of Nf-Kappa B Transcription Factors For Dna. Proc.Natl.Acad.Sci.Usa V. 121 55121 2024.
ISSN: ESSN 1091-6490
PubMed: 38805268
DOI: 10.1073/PNAS.2405555121