Zinc in PDB 2in4: Crystal Structure of Myoglobin with Charge Neutralized Heme, Zndmb-Dme

The structure of Crystal Structure of Myoglobin with Charge Neutralized Heme, Zndmb-Dme, PDB code: 2in4 was solved by K.E.Wheeler, J.M.Nocek, D.A.Cull, L.A.Yatsunyk, A.C.Rosenzweig, B.M.Hoffman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.99 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.604, 30.577, 56.485, 90.00, 97.66, 90.00
R / Rfree (%)	17.5 / 23.2

The binding sites of Zinc atom in the Crystal Structure of Myoglobin with Charge Neutralized Heme, Zndmb-Dme (pdb code 2in4). 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 Myoglobin with Charge Neutralized Heme, Zndmb-Dme, PDB code: 2in4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Myoglobin with Charge Neutralized Heme, Zndmb-Dme


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 Myoglobin with Charge Neutralized Heme, Zndmb-Dme within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:15.2 occ:0.60 ZN A:HE5201 0.0 15.2 0.6 ZN A:HE5201 0.4 12.1 0.4 NC A:HE5201 1.8 12.0 0.4 ND A:HE5201 2.1 12.1 0.4 ND A:HE5201 2.2 15.3 0.6 NC A:HE5201 2.2 15.6 0.6 NB A:HE5201 2.2 15.1 0.6 NA A:HE5201 2.2 15.9 0.6 NE2 A:HIS93 2.2 14.4 1.0 NB A:HE5201 2.3 12.3 0.4 NA A:HE5201 2.6 12.3 0.4 C4C A:HE5201 2.7 11.7 0.4 C1C A:HE5201 2.8 11.8 0.4 C1D A:HE5201 2.9 12.4 0.4 CE1 A:HIS93 3.0 13.6 1.0 C4D A:HE5201 3.1 15.6 0.6 C1C A:HE5201 3.1 14.9 0.6 CHD A:HE5201 3.1 11.8 0.4 C1B A:HE5201 3.1 14.8 0.6 C4C A:HE5201 3.1 14.7 0.6 C1D A:HE5201 3.1 14.9 0.6 C4A A:HE5201 3.1 15.4 0.6 C1A A:HE5201 3.1 15.8 0.6 C4B A:HE5201 3.2 14.8 0.6 C4B A:HE5201 3.2 12.2 0.4 C4D A:HE5201 3.2 12.1 0.4 CD2 A:HIS93 3.3 13.6 1.0 CHC A:HE5201 3.4 11.6 0.4 C1B A:HE5201 3.4 12.0 0.4 CHA A:HE5201 3.5 15.2 0.6 CHD A:HE5201 3.5 14.9 0.6 C1A A:HE5201 3.5 12.5 0.4 CHB A:HE5201 3.5 15.2 0.6 CHC A:HE5201 3.5 14.6 0.6 C4A A:HE5201 3.6 12.0 0.4 CHA A:HE5201 3.7 12.2 0.4 CHB A:HE5201 3.9 12.0 0.4 C3C A:HE5201 3.9 11.5 0.4 C2C A:HE5201 4.0 11.8 0.4 C2D A:HE5201 4.2 12.3 0.4 ND1 A:HIS93 4.2 15.0 1.0 C3D A:HE5201 4.3 12.7 0.4 C3C A:HE5201 4.3 15.4 0.6 C3D A:HE5201 4.3 16.1 0.6 C3B A:HE5201 4.3 14.7 0.6 C2D A:HE5201 4.3 15.7 0.6 C3A A:HE5201 4.4 16.1 0.6 C2C A:HE5201 4.4 14.8 0.6 C2A A:HE5201 4.4 16.2 0.6 C2B A:HE5201 4.4 14.4 0.6 CG A:HIS93 4.4 14.9 1.0 NE2 A:HIS64 4.4 20.4 1.0 C3B A:HE5201 4.4 12.2 0.4 CG2 A:VAL68 4.5 13.4 1.0 C2B A:HE5201 4.6 12.4 0.4 C2A A:HE5201 4.8 12.9 0.4 C3A A:HE5201 4.8 12.5 0.4 CE1 A:HIS64 4.8 18.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Myoglobin with Charge Neutralized Heme, Zndmb-Dme


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 Myoglobin with Charge Neutralized Heme, Zndmb-Dme within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:12.1 occ:0.40 ZN A:HE5201 0.0 12.1 0.4 ZN A:HE5201 0.4 15.2 0.6 ND A:HE5201 1.8 15.3 0.6 NC A:HE5201 2.1 15.6 0.6 NC A:HE5201 2.2 12.0 0.4 ND A:HE5201 2.2 12.1 0.4 NB A:HE5201 2.2 12.3 0.4 NE2 A:HIS93 2.2 14.4 1.0 NA A:HE5201 2.2 12.3 0.4 NA A:HE5201 2.3 15.9 0.6 NB A:HE5201 2.6 15.1 0.6 C1D A:HE5201 2.7 14.9 0.6 C4D A:HE5201 2.8 15.6 0.6 C4C A:HE5201 2.9 14.7 0.6 CE1 A:HIS93 3.0 13.6 1.0 C1B A:HE5201 3.1 12.0 0.4 CHD A:HE5201 3.1 14.9 0.6 C1C A:HE5201 3.1 11.8 0.4 C4D A:HE5201 3.1 12.1 0.4 C4A A:HE5201 3.1 12.0 0.4 C1D A:HE5201 3.1 12.4 0.4 C4C A:HE5201 3.1 11.7 0.4 C4B A:HE5201 3.2 12.2 0.4 C1A A:HE5201 3.2 12.5 0.4 C1A A:HE5201 3.2 15.8 0.6 C1C A:HE5201 3.2 14.9 0.6 CD2 A:HIS93 3.2 13.6 1.0 CHA A:HE5201 3.3 15.2 0.6 C4A A:HE5201 3.4 15.4 0.6 CHA A:HE5201 3.5 12.2 0.4 CHB A:HE5201 3.5 12.0 0.4 C4B A:HE5201 3.5 14.8 0.6 CHD A:HE5201 3.5 11.8 0.4 CHC A:HE5201 3.5 11.6 0.4 C1B A:HE5201 3.6 14.8 0.6 CHC A:HE5201 3.7 14.6 0.6 CHB A:HE5201 3.9 15.2 0.6 C2D A:HE5201 3.9 15.7 0.6 C3D A:HE5201 4.0 16.1 0.6 C3C A:HE5201 4.2 15.4 0.6 ND1 A:HIS93 4.2 15.0 1.0 NE2 A:HIS64 4.3 20.4 1.0 CG A:HIS93 4.3 14.9 1.0 C3C A:HE5201 4.3 11.5 0.4 C2C A:HE5201 4.3 14.8 0.6 C3B A:HE5201 4.3 12.2 0.4 C3D A:HE5201 4.3 12.7 0.4 C2D A:HE5201 4.3 12.3 0.4 C3A A:HE5201 4.3 12.5 0.4 C2C A:HE5201 4.4 11.8 0.4 C2B A:HE5201 4.4 12.4 0.4 C2A A:HE5201 4.4 12.9 0.4 C2A A:HE5201 4.5 16.2 0.6 C3A A:HE5201 4.6 16.1 0.6 CG2 A:VAL68 4.7 13.4 1.0 C3B A:HE5201 4.7 14.7 0.6 CE1 A:HIS64 4.7 18.7 1.0 C2B A:HE5201 4.8 14.4 0.6

K.E.Wheeler, J.M.Nocek, D.A.Cull, L.A.Yatsunyk, A.C.Rosenzweig, B.M.Hoffman. Dynamic Docking of Cytochrome B5 with Myoglobin and Alpha-Hemoglobin: Heme-Neutralization "Squares" and the Binding of Electron-Transfer-Reactive Configurations. J.Am.Chem.Soc. V. 129 3906 2007.
ISSN: ISSN 0002-7863
PubMed: 17343378
DOI: 10.1021/JA067598G