Zinc in PDB 4yj0: Crystal Structure of the Dm Domain of Human DMRT1 Bound to 25MER Target Dna

The structure of Crystal Structure of the Dm Domain of Human DMRT1 Bound to 25MER Target Dna, PDB code: 4yj0 was solved by M.W.Murphy, J.K.Lee, S.Rojo, M.D.Gearhart, K.Kurahashi, S.Banerjee, G.Loeuille, A.Bashamboo, K.Mcelreavey, D.Zarkower, H.Aihara, V.J.Bardwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.73 / 3.81
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	83.185, 138.926, 141.574, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 26.2

The binding sites of Zinc atom in the Crystal Structure of the Dm Domain of Human DMRT1 Bound to 25MER Target Dna (pdb code 4yj0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the Dm Domain of Human DMRT1 Bound to 25MER Target Dna, PDB code: 4yj0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of the Dm Domain of Human DMRT1 Bound to 25MER Target 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 the Dm Domain of Human DMRT1 Bound to 25MER Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:0.1 occ:1.00 NE2 A:HIS82 2.4 0.2 1.0 SG A:CYS102 2.4 0.6 1.0 SG A:CYS105 2.9 0.9 1.0 SG A:CYS100 3.1 99.2 1.0 CE1 A:HIS82 3.2 0.9 1.0 CD2 A:HIS82 3.5 0.8 1.0 CB A:CYS102 3.6 0.9 1.0 CD1 A:TRP97 3.9 0.7 1.0 CB A:CYS105 4.0 0.5 1.0 CG A:TRP97 4.4 0.3 1.0 ND1 A:HIS82 4.4 0.1 1.0 CB A:CYS100 4.4 0.3 1.0 NE1 A:TRP97 4.4 0.1 1.0 CG A:HIS82 4.6 0.4 1.0 CB A:TRP97 4.8 0.2 1.0 CA A:CYS102 4.8 0.5 1.0 N A:CYS102 4.8 0.3 1.0 N A:CYS105 4.8 0.6 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of the Dm Domain of Human DMRT1 Bound to 25MER Target 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 the Dm Domain of Human DMRT1 Bound to 25MER Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:0.2 occ:1.00 SG A:CYS79 2.4 0.8 1.0 SG A:CYS95 2.5 0.6 1.0 SG A:CYS76 2.7 0.2 1.0 CD2 A:HIS91 2.8 0.4 1.0 NE2 A:HIS91 3.1 0.7 1.0 CB A:CYS79 3.4 0.2 1.0 CB A:CYS76 3.5 0.3 1.0 CB A:CYS95 3.6 0.6 1.0 N A:CYS79 3.7 0.9 1.0 O A:CYS95 3.7 0.8 1.0 CA A:CYS95 3.8 0.4 1.0 CA A:CYS79 4.1 0.5 1.0 CG A:HIS91 4.1 0.8 1.0 C A:CYS95 4.3 0.5 1.0 CE1 A:HIS91 4.4 0.4 1.0 CB A:ARG78 4.4 97.4 1.0 C A:ARG78 4.6 0.7 1.0 OG A:SER86 4.6 0.8 1.0 O A:SER86 4.8 0.9 1.0 N A:ARG78 4.8 0.3 1.0 ND1 A:HIS91 4.9 0.6 1.0 CA A:ARG78 4.9 0.6 1.0 CA A:CYS76 4.9 0.4 1.0 CB A:SER86 5.0 0.9 1.0 O A:HIS91 5.0 0.9 1.0 CB A:HIS91 5.0 0.2 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of the Dm Domain of Human DMRT1 Bound to 25MER Target 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 the Dm Domain of Human DMRT1 Bound to 25MER Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:99.5 occ:1.00 NE2 B:HIS82 2.3 0.6 1.0 SG B:CYS100 2.3 0.8 1.0 SG B:CYS105 2.4 0.6 1.0 CE1 B:HIS82 2.6 0.7 1.0 SG B:CYS102 2.8 0.6 1.0 CB B:CYS105 3.4 1.0 1.0 CD2 B:HIS82 3.6 0.7 1.0 CB B:CYS100 3.6 0.1 1.0 ND1 B:HIS82 3.8 0.9 1.0 CB B:CYS102 4.0 0.5 1.0 N B:CYS102 4.3 0.0 1.0 CG B:HIS82 4.3 0.9 1.0 N B:CYS105 4.6 0.7 1.0 CA B:CYS105 4.6 0.1 1.0 CA B:CYS102 4.7 0.8 1.0 CD1 B:TRP97 4.8 0.5 1.0 CA B:CYS100 4.8 0.4 1.0 C B:CYS100 4.8 0.1 1.0 N B:GLN101 4.8 0.2 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of the Dm Domain of Human DMRT1 Bound to 25MER Target Dna


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 the Dm Domain of Human DMRT1 Bound to 25MER Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:0.5 occ:1.00 SG B:CYS79 2.4 0.7 1.0 CD2 B:HIS91 2.4 0.9 1.0 NE2 B:HIS91 2.5 0.2 1.0 SG B:CYS76 2.5 0.1 1.0 SG B:CYS95 2.6 0.9 1.0 CB B:CYS95 3.4 0.2 1.0 CB B:CYS76 3.4 0.2 1.0 CG B:HIS91 3.7 0.3 1.0 CB B:CYS79 3.8 0.0 1.0 CE1 B:HIS91 3.8 0.9 1.0 CA B:CYS95 4.2 0.9 1.0 O B:HIS91 4.3 0.7 1.0 N B:CYS79 4.3 0.3 1.0 ND1 B:HIS91 4.3 0.7 1.0 CA B:CYS79 4.5 0.5 1.0 CB B:HIS91 4.8 0.8 1.0 CA B:CYS76 4.8 0.5 1.0 C B:HIS91 4.9 0.2 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of the Dm Domain of Human DMRT1 Bound to 25MER Target Dna


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 the Dm Domain of Human DMRT1 Bound to 25MER Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:0.7 occ:1.00 SG C:CYS100 1.9 1.0 1.0 NE2 C:HIS82 2.0 0.5 1.0 SG C:CYS102 2.0 1.0 1.0 SG C:CYS105 2.4 0.9 1.0 CE1 C:HIS82 2.6 0.8 1.0 CB C:CYS105 2.6 0.9 1.0 CD2 C:HIS82 3.2 0.4 1.0 CB C:CYS100 3.3 0.7 1.0 CB C:CYS102 3.4 0.8 1.0 N C:CYS102 3.5 0.4 1.0 ND1 C:HIS82 3.8 0.3 1.0 CA C:CYS105 3.8 0.2 1.0 N C:CYS105 4.0 0.3 1.0 CA C:CYS102 4.0 0.6 1.0 N C:GLN101 4.1 0.5 1.0 CG C:HIS82 4.1 0.2 1.0 O C:CYS102 4.4 0.8 1.0 C C:GLN101 4.5 0.6 1.0 CA C:CYS100 4.6 0.9 1.0 C C:CYS100 4.6 0.8 1.0 C C:CYS102 4.6 0.8 1.0 CA C:GLN101 4.7 0.4 1.0 C C:CYS105 4.9 0.6 1.0 O C:ASP99 5.0 1.0 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of the Dm Domain of Human DMRT1 Bound to 25MER Target Dna


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 the Dm Domain of Human DMRT1 Bound to 25MER Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:0.1 occ:1.00 SG C:CYS79 2.4 0.5 1.0 SG C:CYS76 2.4 0.6 1.0 SG C:CYS95 2.6 0.9 1.0 NE2 C:HIS91 2.6 0.6 1.0 CD2 C:HIS91 2.6 0.4 1.0 CB C:CYS76 3.5 0.1 1.0 CB C:CYS95 3.5 0.0 1.0 CB C:CYS79 3.5 0.6 1.0 N C:CYS79 3.8 0.7 1.0 CE1 C:HIS91 3.9 0.9 1.0 CG C:HIS91 3.9 0.7 1.0 CA C:CYS79 4.1 0.6 1.0 CA C:CYS95 4.2 0.9 1.0 ND1 C:HIS91 4.5 0.4 1.0 CB C:ARG78 4.7 94.8 1.0 C C:ARG78 4.7 0.0 1.0 O C:HIS91 4.7 0.3 1.0 OG C:SER86 4.9 0.2 1.0 CA C:CYS76 4.9 0.8 1.0

M.W.Murphy, J.K.Lee, S.Rojo, M.D.Gearhart, K.Kurahashi, S.Banerjee, G.-A.Loeuille, A.Bashamboo, K.Mcelreavey, D.Zarkower, H.Aihara, V.J.Bardwell. An Ancient Protein-Dna Interaction Underlying Metazoan Sex Determination Nat.Struct.Mol.Biol. 2015.
ISSN: ESSN 1545-9985
DOI: 10.1038/NSMB.3032