Zinc in PDB 3v1f: Crystal Structure of De Novo Designed MID1-Zinc H35E Mutant

The structure of Crystal Structure of De Novo Designed MID1-Zinc H35E Mutant, PDB code: 3v1f was solved by B.S.Der, M.Machius, M.J.Miley, B.Kuhlman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.34 / 1.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.241, 46.528, 62.277, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 18.6

The binding sites of Zinc atom in the Crystal Structure of De Novo Designed MID1-Zinc H35E Mutant (pdb code 3v1f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of De Novo Designed MID1-Zinc H35E Mutant, PDB code: 3v1f:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of De Novo Designed MID1-Zinc H35E Mutant


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 De Novo Designed MID1-Zinc H35E Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn704 b:14.6 occ:1.00 OE2 A:GLU35 2.0 14.0 1.0 NE2 B:HIS12 2.0 14.1 1.0 NE2 B:HIS16 2.0 15.5 1.0 ND1 A:HIS39 2.1 17.0 1.0 CD A:GLU35 2.8 13.7 1.0 CE1 B:HIS12 2.9 15.1 1.0 HB2 A:HIS39 3.0 18.8 1.0 CE1 B:HIS16 3.0 16.8 1.0 OE1 A:GLU35 3.0 15.2 1.0 CE1 A:HIS39 3.0 18.4 1.0 CD2 B:HIS12 3.0 14.2 1.0 HE1 B:HIS12 3.1 18.1 1.0 CD2 B:HIS16 3.1 14.9 1.0 CG A:HIS39 3.1 16.8 1.0 HE1 B:HIS16 3.1 20.1 1.0 HE1 A:HIS39 3.2 22.1 1.0 HD2 B:HIS16 3.3 17.9 1.0 HD2 B:HIS12 3.3 17.1 1.0 HA A:HIS39 3.4 18.0 1.0 CB A:HIS39 3.4 15.7 1.0 CA A:HIS39 3.9 15.0 1.0 O A:HOH60 3.9 20.5 1.0 O A:HOH77 4.0 24.2 1.0 ND1 B:HIS12 4.0 15.1 1.0 ND1 B:HIS16 4.1 17.5 1.0 CG B:HIS12 4.1 13.4 1.0 NE2 A:HIS39 4.1 20.5 1.0 CG B:HIS16 4.2 15.1 1.0 CD2 A:HIS39 4.2 19.1 1.0 CG A:GLU35 4.2 13.3 1.0 HB3 A:HIS39 4.3 18.8 1.0 H A:HIS39 4.3 16.9 1.0 O A:GLU35 4.3 13.4 1.0 N A:HIS39 4.4 14.1 1.0 HG3 A:GLU35 4.4 15.9 1.0 HG2 A:GLU35 4.6 15.9 1.0 O B:HOH91 4.7 26.9 1.0 HD1 B:HIS12 4.8 18.1 1.0 O A:HOH62 4.8 25.6 1.0 HD1 B:HIS16 4.9 21.0 1.0 O A:HOH91 4.9 44.5 1.0 HE2 A:HIS39 4.9 24.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of De Novo Designed MID1-Zinc H35E Mutant


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 De Novo Designed MID1-Zinc H35E Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn703 b:13.3 occ:1.00 OE2 B:GLU35 2.0 12.9 1.0 NE2 A:HIS12 2.0 13.2 1.0 NE2 A:HIS16 2.0 14.7 1.0 ND1 B:HIS39 2.0 16.2 1.0 CD B:GLU35 2.8 12.4 1.0 CE1 A:HIS12 2.9 14.1 1.0 CE1 A:HIS16 2.9 15.9 1.0 CE1 B:HIS39 3.0 18.2 1.0 OE1 B:GLU35 3.0 13.5 1.0 HB2 B:HIS39 3.0 17.6 1.0 CD2 A:HIS12 3.0 13.3 1.0 HE1 A:HIS16 3.1 19.1 1.0 HE1 A:HIS12 3.1 16.9 1.0 CG B:HIS39 3.1 16.8 1.0 CD2 A:HIS16 3.1 13.7 1.0 HE1 B:HIS39 3.1 21.8 1.0 HD2 A:HIS12 3.3 16.0 1.0 HD2 A:HIS16 3.3 16.4 1.0 HA B:HIS39 3.4 16.8 1.0 CB B:HIS39 3.4 14.7 1.0 CA B:HIS39 3.9 14.0 1.0 O B:HOH67 3.9 21.5 1.0 O B:HOH72 4.0 17.9 1.0 ND1 A:HIS12 4.0 14.0 1.0 ND1 A:HIS16 4.1 16.7 1.0 NE2 B:HIS39 4.1 20.2 1.0 CG A:HIS12 4.1 13.0 1.0 CD2 B:HIS39 4.2 19.1 1.0 CG A:HIS16 4.2 14.4 1.0 CG B:GLU35 4.2 12.2 1.0 HB3 B:HIS39 4.3 17.6 1.0 H B:HIS39 4.3 15.4 1.0 N B:HIS39 4.4 12.9 1.0 O B:GLU35 4.4 11.5 1.0 HG3 B:GLU35 4.4 14.6 1.0 HG2 B:GLU35 4.6 14.6 1.0 HD1 A:HIS12 4.8 16.8 1.0 O B:HOH66 4.8 26.1 1.0 O B:HOH116 4.8 42.6 1.0 HD1 A:HIS16 4.8 20.0 1.0 HE2 B:HIS39 4.9 24.2 1.0 O A:HOH72 4.9 27.7 1.0 O A:HOH81 5.0 39.9 1.0 O A:HOH165 5.0 40.6 1.0

B.S.Der, M.Machius, M.J.Miley, J.L.Mills, T.Szyperski, B.Kuhlman. Metal-Mediated Affinity and Orientation Specificity in A Computationally Designed Protein Homodimer. J.Am.Chem.Soc. V. 134 375 2012.
ISSN: ISSN 0002-7863
PubMed: 22092237
DOI: 10.1021/JA208015J