Zinc in PDB 3v1c: Crystal Structure of De Novo Designed MID1-Zinc

The structure of Crystal Structure of De Novo Designed MID1-Zinc, PDB code: 3v1c 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)	19.29 / 1.13
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.312, 29.800, 105.412, 90.00, 90.00, 90.00
R / Rfree (%)	14.7 / 17.6

The binding sites of Zinc atom in the Crystal Structure of De Novo Designed MID1-Zinc (pdb code 3v1c). 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, PDB code: 3v1c:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:8.7 occ:1.00 O41 A:TLA102 1.9 11.7 1.0 ND1 B:HIS39 2.0 7.6 1.0 NE2 A:HIS16 2.0 9.2 1.0 NE2 A:HIS12 2.0 8.4 1.0 C4 A:TLA102 2.7 11.5 1.0 O4 A:TLA102 2.9 12.9 1.0 CE1 B:HIS39 2.9 7.7 1.0 CD2 A:HIS12 2.9 8.8 1.0 CE1 A:HIS16 3.0 9.6 1.0 CE1 A:HIS12 3.0 9.3 1.0 CD2 A:HIS16 3.0 8.2 1.0 CG B:HIS39 3.0 6.7 1.0 HE1 B:HIS39 3.1 9.2 1.0 HE1 A:HIS16 3.1 11.5 1.0 HD2 A:HIS12 3.1 10.5 1.0 HA B:HIS39 3.1 7.3 1.0 HB2 B:HIS39 3.1 8.3 1.0 HE1 A:HIS12 3.2 11.2 1.0 HD2 A:HIS16 3.3 9.8 1.0 CB B:HIS39 3.5 6.9 1.0 CA B:HIS39 3.8 6.1 1.0 ND1 A:HIS12 4.1 9.1 1.0 NE2 B:HIS39 4.1 7.5 1.0 CG A:HIS12 4.1 7.9 1.0 ND1 A:HIS16 4.1 9.3 1.0 C3 A:TLA102 4.1 13.8 1.0 CD2 B:HIS39 4.1 7.9 1.0 CG A:HIS16 4.2 8.1 1.0 H3 A:TLA102 4.4 16.6 1.0 O B:HOH228 4.4 16.5 0.8 HB3 B:HIS39 4.4 8.3 1.0 O B:HIS39 4.5 7.7 1.0 H2 A:TLA102 4.5 16.0 1.0 HE1 B:MET38 4.6 13.4 0.4 C B:HIS39 4.6 6.8 1.0 HZ2 A:LYS19 4.7 14.9 1.0 OE1 B:GLN43 4.8 19.4 1.0 O A:HOH211 4.8 14.5 1.0 HE2 B:HIS39 4.8 9.0 1.0 HD1 A:HIS12 4.8 10.9 1.0 C2 A:TLA102 4.8 13.3 1.0 HD1 A:HIS16 4.9 11.1 1.0 N B:HIS39 4.9 6.4 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:8.4 occ:1.00 NE2 B:HIS16 2.0 8.9 1.0 NE2 B:HIS12 2.0 8.5 1.0 ND1 A:HIS39 2.0 10.3 1.0 CE1 B:HIS12 2.9 9.6 1.0 CE1 B:HIS16 3.0 10.4 1.0 HB2 A:HIS39 3.0 11.1 1.0 CE1 A:HIS39 3.0 11.9 1.0 CD2 B:HIS16 3.0 8.0 1.0 CD2 B:HIS12 3.1 8.1 1.0 HE1 B:HIS12 3.1 11.6 1.0 CG A:HIS39 3.1 10.5 1.0 HE1 B:HIS16 3.1 12.4 1.0 HE1 A:HIS39 3.1 14.3 1.0 HD2 B:HIS16 3.2 9.6 1.0 HD2 B:HIS12 3.3 9.8 1.0 HA A:HIS39 3.4 10.4 1.0 CB A:HIS39 3.4 9.3 1.0 CA A:HIS39 3.9 8.7 1.0 ND1 B:HIS12 4.0 9.6 1.0 ND1 B:HIS16 4.1 10.8 1.0 NE2 A:HIS39 4.1 13.2 1.0 CG B:HIS12 4.1 7.0 1.0 CG B:HIS16 4.2 8.5 1.0 CD2 A:HIS39 4.2 12.1 1.0 O A:HOH252 4.3 31.1 1.0 HB3 A:HIS39 4.3 11.1 1.0 O A:HOH253 4.5 22.0 1.0 O A:HIS39 4.8 10.8 1.0 C A:HIS39 4.8 9.8 1.0 HD1 B:HIS12 4.8 11.5 1.0 HD1 B:HIS16 4.9 13.0 1.0 HE2 A:HIS39 4.9 15.8 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