Zinc in PDB 4a3n: Crystal Structure of Hmg-Box of Human SOX17

The structure of Crystal Structure of Hmg-Box of Human SOX17, PDB code: 4a3n was solved by N.Gao, H.Gao, H.Qian, S.Si, Y.Xie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.66 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	94.281, 22.525, 66.668, 90.00, 129.09, 90.00
R / Rfree (%)	20.2 / 26.7

The binding sites of Zinc atom in the Crystal Structure of Hmg-Box of Human SOX17 (pdb code 4a3n). 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 Hmg-Box of Human SOX17, PDB code: 4a3n:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Hmg-Box of Human SOX17


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 Hmg-Box of Human SOX17 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1135 b:39.7 occ:1.00 ND1 A:HIS128 2.1 36.2 1.0 NE2 A:HIS132 2.2 31.4 1.0 O A:HOH2002 2.3 19.0 1.0 CE1 A:HIS128 3.0 42.9 1.0 CG A:HIS128 3.0 35.9 1.0 CE1 A:HIS132 3.1 35.1 1.0 CD2 A:HIS132 3.2 39.9 1.0 CB A:HIS128 3.4 30.9 1.0 CA A:HIS128 3.8 44.0 1.0 NE2 A:HIS128 4.1 39.9 1.0 CD2 A:HIS128 4.2 38.9 1.0 N A:ARG70 4.2 90.3 1.0 ND1 A:HIS132 4.2 44.0 1.0 CG A:HIS132 4.3 43.6 1.0 O A:HOH2069 4.5 57.3 1.0 O A:HIS128 4.7 56.0 1.0 C A:HIS128 4.7 46.4 1.0 CG A:ARG70 4.9 95.6 1.0 N A:HIS128 4.9 40.3 1.0 CD A:PRO71 5.0 43.2 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Hmg-Box of Human SOX17


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 Hmg-Box of Human SOX17 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1136 b:50.4 occ:1.00 O A:HOH2071 2.3 12.8 1.0 ND1 A:HIS94 2.3 42.0 1.0 O A:HOH2072 2.3 21.8 1.0 CE1 A:HIS94 3.2 33.8 1.0 CG A:HIS94 3.3 41.5 1.0 CB A:HIS94 3.6 35.1 1.0 O A:HOH2022 4.0 46.3 1.0 NE2 A:HIS94 4.3 45.4 1.0 CD2 A:HIS94 4.3 44.3 1.0 CB A:GLU97 4.7 46.7 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Hmg-Box of Human SOX17


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 Hmg-Box of Human SOX17 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1137 b:88.5 occ:1.00 OE1 A:GLU122 2.6 91.4 1.0 OE1 A:GLU119 2.7 55.7 1.0 OE2 A:GLU119 2.9 56.4 1.0 O A:HOH2056 2.9 49.7 1.0 OE2 A:GLU122 3.1 83.9 1.0 CD A:GLU119 3.2 56.1 1.0 CD A:GLU122 3.2 79.8 1.0 NH1 A:ARG115 4.5 31.3 1.0 CG A:GLU122 4.6 75.0 1.0 O A:HOH2055 4.6 53.9 1.0 CG A:GLU119 4.7 45.4 1.0 O A:HOH2059 4.9 33.2 1.0

N.Gao, W.Jiang, H.Gao, Z.Cheng, H.Qian, S.Si, Y.Xie. Structural Basis of Human Transcription Factor Sry-Related Box 17 Binding to Dna. Protein Pept.Lett. V. 20 481 2013.
ISSN: ISSN 0929-8665
PubMed: 23061670
DOI: 10.2174/092986613805290336