Zinc in PDB 6vtx: Crystal Structure of Human KLF4 Zinc Finger Dna Binding Domain in Complex with Nanog Dna

The structure of Crystal Structure of Human KLF4 Zinc Finger Dna Binding Domain in Complex with Nanog Dna, PDB code: 6vtx was solved by R.Sharma, S.Sharma, K.J.Choi, A.C.M.Ferreon, J.C.Ferreon, B.Sankaran, K.R.Mackenzie, C.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.45 / 2.14
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.964, 46.688, 45.2, 90, 113.5, 90
R / Rfree (%)	21.7 / 24.7

The structure of Crystal Structure of Human KLF4 Zinc Finger Dna Binding Domain in Complex with Nanog Dna also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Human KLF4 Zinc Finger Dna Binding Domain in Complex with Nanog Dna (pdb code 6vtx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Human KLF4 Zinc Finger Dna Binding Domain in Complex with Nanog Dna, PDB code: 6vtx:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Human KLF4 Zinc Finger Dna Binding Domain in Complex with Nanog Dna


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 Human KLF4 Zinc Finger Dna Binding Domain in Complex with Nanog Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:27.8 occ:1.00 NE2 A:HIS480 2.1 26.5 1.0 NE2 A:HIS484 2.1 28.2 1.0 SG A:CYS467 2.3 26.4 1.0 SG A:CYS462 2.3 30.5 1.0 CD2 A:HIS484 2.8 24.3 1.0 CD2 A:HIS480 3.1 20.5 1.0 CE1 A:HIS480 3.1 32.7 1.0 CB A:CYS467 3.2 30.7 1.0 CB A:CYS462 3.3 26.2 1.0 CE1 A:HIS484 3.3 42.6 1.0 CG A:HIS484 4.1 29.6 1.0 CB A:TRP464 4.1 30.8 1.0 ND1 A:HIS480 4.2 27.6 1.0 CG A:HIS480 4.2 25.4 1.0 ND1 A:HIS484 4.3 39.9 1.0 CA A:CYS467 4.6 34.3 1.0 CB A:TRP469 4.6 32.8 1.0 CA A:CYS462 4.7 31.1 1.0 CD1 A:TRP469 4.9 30.9 1.0 CG A:TRP464 5.0 31.9 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Human KLF4 Zinc Finger Dna Binding Domain in Complex with Nanog Dna


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 Human KLF4 Zinc Finger Dna Binding Domain in Complex with Nanog Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:40.8 occ:1.00 NE2 A:HIS508 2.1 37.4 1.0 NE2 A:HIS512 2.3 47.1 1.0 SG A:CYS492 2.4 47.0 1.0 SG A:CYS495 2.4 44.0 1.0 CD2 A:HIS512 2.8 40.9 1.0 CD2 A:HIS508 3.1 28.0 1.0 CE1 A:HIS508 3.1 30.1 1.0 CB A:CYS495 3.4 50.4 1.0 CB A:CYS492 3.5 49.0 1.0 CE1 A:HIS512 3.5 55.9 1.0 N A:CYS495 3.7 61.2 1.0 CG A:HIS512 4.1 53.5 1.0 CA A:CYS495 4.1 61.7 1.0 ND1 A:HIS508 4.2 33.2 1.0 CG A:HIS508 4.2 35.5 1.0 CB A:LYS494 4.2 58.3 1.0 C A:LYS494 4.4 57.4 1.0 ND1 A:HIS512 4.4 57.6 1.0 CA A:LYS494 4.7 61.3 1.0 SD A:MET509 4.8 63.4 1.0 N A:LYS494 4.8 62.7 1.0 C A:CYS495 4.9 66.8 1.0 CB A:ARG497 4.9 36.9 1.0 CA A:CYS492 4.9 59.5 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Human KLF4 Zinc Finger Dna Binding Domain in Complex with Nanog Dna


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 Human KLF4 Zinc Finger Dna Binding Domain in Complex with Nanog Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:49.8 occ:1.00 NE2 A:HIS454 2.1 55.1 1.0 NE2 A:HIS450 2.3 51.7 1.0 SG A:CYS432 2.4 51.7 1.0 SG A:CYS437 2.4 54.5 1.0 O A:HOH723 2.7 59.6 1.0 CD2 A:HIS454 3.0 55.1 1.0 CD2 A:HIS450 3.1 45.3 1.0 CE1 A:HIS454 3.2 51.9 1.0 CB A:CYS432 3.3 49.1 1.0 CB A:CYS437 3.4 60.8 1.0 CE1 A:HIS450 3.4 48.4 1.0 CG A:HIS454 4.2 54.5 1.0 ND1 A:HIS454 4.2 55.4 1.0 CG A:HIS450 4.3 49.2 1.0 ND1 A:HIS450 4.4 58.5 1.0 CB A:LYS439 4.5 58.3 1.0 CB A:TYR434 4.7 47.8 1.0 CA A:CYS432 4.7 54.6 1.0 CA A:CYS437 4.8 60.1 1.0 O A:TYR434 4.9 61.7 1.0 O A:HOH734 4.9 56.4 1.0

R.Sharma, S.Sharma, K.J.Choi, A.C.M.Ferreon, J.C.Ferreon, S.Banumathi, C.W.Kim. Crystal Structure of Human KLF4 Zinc Finger Dna Binding Domain in Complex with Nanog Dna. To Be Published.