Zinc in PDB 9be1: Cg-Centric Nf-Kappab Rela Binding Dna

The structure of Cg-Centric Nf-Kappab Rela Binding Dna, PDB code: 9be1 was solved by T.Biswas, S.Shahabi, O.V.Tsodikov, V.Wang, G.Ghosh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.999, 47.031, 98.682, 90.03, 89.96, 59.99
R / Rfree (%)	29.8 / 34.9

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 - 103;

Binding sites:

The binding sites of Zinc atom in the Cg-Centric Nf-Kappab Rela Binding Dna (pdb code 9be1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 103 binding sites of Zinc where determined in the Cg-Centric Nf-Kappab Rela Binding Dna, PDB code: 9be1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 103 in the Cg-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 Cg-Centric Nf-Kappab Rela Binding Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:67.6 occ:1.00 N7 A:DG3 2.1 49.6 1.0 C8 A:DG3 3.1 45.7 1.0 O A:HOH406 3.1 54.8 1.0 C5 A:DG3 3.1 44.1 1.0 O6 A:DG3 3.4 43.3 1.0 C6 A:DG3 3.6 42.4 1.0 N9 A:DG3 4.3 45.9 1.0 C4 A:DG3 4.3 44.3 1.0 O A:HOH411 4.5 57.5 1.0 O6 A:DG4 4.5 41.8 1.0 C8 A:DG2 4.6 45.9 1.0 N7 A:DG2 4.6 47.9 1.0 N9 A:DG2 5.0 46.5 1.0

Zinc binding site 2 out of 103 in the Cg-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 Cg-Centric Nf-Kappab Rela Binding Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:61.6 occ:1.00 O A:HOH409 2.1 51.3 1.0 O A:HOH406 2.1 54.8 1.0 N7 A:DG2 2.1 47.9 1.0 C8 A:DG2 3.0 45.9 1.0 C5 A:DG2 3.1 43.7 1.0 O6 A:DG2 3.4 43.7 1.0 C6 A:DG2 3.7 42.0 1.0 O3' A:DC1 4.0 71.3 1.0 N9 A:DG2 4.3 46.5 1.0 O E:HOH326 4.3 52.9 1.0 C4 A:DG2 4.3 44.1 1.0 O6 A:DG3 4.5 43.3 1.0

Zinc binding site 3 out of 103 in the Cg-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 Cg-Centric Nf-Kappab Rela Binding Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:37.0 occ:1.00 O A:HOH416 2.1 37.3 1.0 O A:HOH414 2.1 33.7 1.0 O A:HOH415 2.1 32.3 1.0 N7 A:DG12 2.1 38.4 1.0 O A:HOH401 2.1 26.7 1.0 C8 A:DG12 3.0 39.1 1.0 C5 A:DG12 3.2 38.0 1.0 O6 A:DG12 3.5 40.1 1.0 C6 A:DG12 3.7 38.5 1.0 OP2 A:DG12 3.8 41.5 1.0 N9 A:DG12 4.2 38.3 1.0 C4 A:DG12 4.3 37.6 1.0 O A:HOH423 4.7 54.2 1.0

Zinc binding site 4 out of 103 in the Cg-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 Cg-Centric Nf-Kappab Rela Binding Dna within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn202 b:66.1 occ:1.00 O P:HOH321 2.1 55.8 1.0 N7 P:DG103 2.1 44.3 1.0 C8 P:DG103 3.1 42.3 1.0 O P:HOH312 3.1 53.0 1.0 C5 P:DG103 3.1 40.4 1.0 O6 P:DG103 3.4 39.3 1.0 C6 P:DG103 3.6 39.2 1.0 O A:HOH422 3.9 31.3 1.0 N9 P:DG103 4.3 44.0 1.0 C4 P:DG103 4.3 41.2 1.0 O P:HOH303 4.4 46.0 1.0 C8 P:DG102 4.4 44.8 1.0 N6 P:DA104 4.5 41.4 1.0 N7 P:DG102 4.5 45.4 1.0 O P:HOH313 4.5 46.9 1.0 O P:HOH327 4.9 52.8 1.0 N9 P:DG102 4.9 45.0 1.0 ZN P:ZN203 5.0 58.3 1.0

Zinc binding site 5 out of 103 in the Cg-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 Cg-Centric Nf-Kappab Rela Binding Dna within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn203 b:58.3 occ:1.00 O P:HOH317 2.1 57.0 1.0 O P:HOH312 2.1 53.0 1.0 N7 P:DG102 2.1 45.4 1.0 C8 P:DG102 3.0 44.8 1.0 C5 P:DG102 3.2 42.1 1.0 O6 P:DG102 3.5 40.5 1.0 C6 P:DG102 3.7 40.2 1.0 N9 P:DG102 4.2 45.0 1.0 C4 P:DG102 4.3 43.5 1.0 O6 P:DG103 4.4 39.3 1.0 O P:HOH321 4.5 55.8 1.0 OP2 P:DG102 4.6 56.4 1.0 ZN P:ZN202 5.0 66.1 1.0 C6 P:DG103 5.0 39.2 1.0

Zinc binding site 6 out of 103 in the Cg-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 Cg-Centric Nf-Kappab Rela Binding Dna within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn204 b:41.0 occ:1.00 O P:HOH320 2.1 41.8 1.0 O P:HOH324 2.1 31.6 1.0 O P:HOH315 2.1 37.2 1.0 O P:HOH305 2.1 33.8 1.0 N7 P:DG112 2.1 39.3 1.0 C8 P:DG112 2.9 38.5 1.0 C5 P:DG112 3.2 37.7 1.0 O6 P:DG112 3.7 41.6 1.0 C6 P:DG112 3.9 38.0 1.0 OP2 P:DG112 3.9 39.3 1.0 ZN T:ZN204 4.0 117.5 1.0 N9 P:DG112 4.2 37.5 1.0 C4 P:DG112 4.3 38.3 1.0 O T:HOH316 4.4 49.9 1.0 C5' T:DA104 4.6 49.3 1.0 O P:HOH328 4.8 71.3 1.0 C4' T:DA104 5.0 50.0 1.0

Zinc binding site 7 out of 103 in the Cg-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 Cg-Centric Nf-Kappab Rela Binding Dna within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn205 b:120.9 occ:1.00 O3' P:DA104 2.8 55.2 1.0 C3' P:DA104 3.3 51.3 1.0 OP1 P:DA105 3.3 62.0 1.0 C4' P:DA104 3.4 50.3 1.0 P P:DA105 3.6 62.8 1.0 C5' P:DA104 3.8 50.1 1.0 OP2 S:DG3 3.9 41.7 0.5 O p:HOH305 4.0 44.6 1.0 OP1 S:DG3 4.1 41.1 0.5 OP2 P:DA105 4.5 63.5 1.0 P S:DG3 4.5 41.9 0.5 O4' P:DA104 4.8 48.5 1.0 O5' P:DA104 4.8 48.3 1.0 C2' P:DA104 4.8 49.1 1.0 O5' P:DA105 4.9 59.3 1.0

Zinc binding site 8 out of 103 in the Cg-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 Cg-Centric Nf-Kappab Rela Binding Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn201 b:67.8 occ:1.00 N7 E:DG3 2.1 47.1 1.0 O E:HOH304 3.0 53.2 1.0 C8 E:DG3 3.1 44.2 1.0 C5 E:DG3 3.1 42.5 1.0 O6 E:DG3 3.3 41.9 1.0 C6 E:DG3 3.6 41.2 1.0 N9 E:DG3 4.3 44.6 1.0 C4 E:DG3 4.3 42.8 1.0 O E:HOH316 4.4 47.8 1.0 C8 E:DG2 4.4 45.7 1.0 N7 E:DG2 4.4 47.3 1.0 O6 E:DG4 4.5 42.7 1.0 O E:HOH324 4.8 32.2 1.0 N9 E:DG2 4.8 45.8 1.0 ZN E:ZN202 4.9 58.0 1.0 C5 E:DG2 4.9 44.4 1.0 N1 E:DG3 5.0 40.3 1.0

Zinc binding site 9 out of 103 in the Cg-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 Cg-Centric Nf-Kappab Rela Binding Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn202 b:58.0 occ:1.00 O E:HOH312 2.1 51.4 1.0 O E:HOH304 2.1 53.2 1.0 N7 E:DG2 2.1 47.3 1.0 C8 E:DG2 3.1 45.7 1.0 C5 E:DG2 3.1 44.4 1.0 O6 E:DG2 3.4 45.2 1.0 C6 E:DG2 3.6 43.5 1.0 N9 E:DG2 4.3 45.8 1.0 C4 E:DG2 4.3 44.8 1.0 O6 E:DG3 4.5 41.9 1.0 O G:HOH226 4.6 55.5 1.0 ZN E:ZN201 4.9 67.8 1.0

Zinc binding site 10 out of 103 in the Cg-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 Cg-Centric Nf-Kappab Rela Binding Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn203 b:35.6 occ:1.00 O E:HOH318 2.1 34.0 1.0 O E:HOH311 2.1 30.9 1.0 O E:HOH314 2.1 31.4 1.0 N7 E:DG12 2.1 37.7 1.0 O E:HOH301 2.1 26.5 1.0 C8 E:DG12 3.0 38.4 1.0 C5 E:DG12 3.2 37.8 1.0 O6 E:DG12 3.5 40.8 1.0 C6 E:DG12 3.7 38.7 1.0 OP2 E:DG12 4.0 40.0 1.0 N9 E:DG12 4.2 37.9 1.0 C4 E:DG12 4.3 37.7 1.0 O A:HOH404 4.5 36.2 1.0 C5' A:DG4 4.8 48.8 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