Copper in PDB 1nol: Oxygenated Hemocyanin (Subunit Type II)

The structure of Oxygenated Hemocyanin (Subunit Type II), PDB code: 1nol was solved by B.Hazes, W.G.J.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.40
Space group	R 3 2
Cell size a, b, c (Å), α, β, γ (°)	117.002, 117.002, 117.002, 60.02, 60.02, 60.02
R / Rfree (%)	18.1 / n/a

The structure of Oxygenated Hemocyanin (Subunit Type II) also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Copper atom in the Oxygenated Hemocyanin (Subunit Type II) (pdb code 1nol). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Oxygenated Hemocyanin (Subunit Type II), PDB code: 1nol:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in the Oxygenated Hemocyanin (Subunit Type II)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Oxygenated Hemocyanin (Subunit Type II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu629 b:10.7 occ:1.00 O1 A:PER631 1.8 7.6 1.0 O2 A:PER631 1.9 7.2 1.0 NE2 A:HIS173 1.9 8.1 1.0 NE2 A:HIS177 2.0 6.8 1.0 NE2 A:HIS204 2.3 2.5 1.0 CE1 A:HIS173 2.6 9.1 1.0 CE1 A:HIS177 2.9 7.8 1.0 CD2 A:HIS177 3.0 7.5 1.0 CD2 A:HIS173 3.1 9.1 1.0 CD2 A:HIS204 3.2 6.4 1.0 CE1 A:HIS204 3.3 5.0 1.0 CU A:CU630 3.6 11.5 1.0 ND1 A:HIS173 3.8 8.3 1.0 ND1 A:HIS177 4.0 7.1 1.0 CG A:HIS173 4.0 7.8 1.0 CG A:HIS177 4.1 6.4 1.0 ND1 A:HIS204 4.3 5.5 1.0 CG A:HIS204 4.4 4.7 1.0 CE2 A:PHE360 4.6 4.3 1.0 NE2 A:HIS364 4.8 2.0 1.0 CE1 A:PHE49 4.8 8.0 1.0 CZ A:PHE360 4.8 3.1 1.0 CZ A:PHE49 4.9 7.0 1.0 CG2 A:THR351 4.9 6.7 1.0 NE2 A:HIS324 4.9 5.3 1.0 CE1 A:HIS324 5.0 2.0 1.0

Copper binding site 2 out of 2 in the Oxygenated Hemocyanin (Subunit Type II)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Oxygenated Hemocyanin (Subunit Type II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu630 b:11.5 occ:1.00 NE2 A:HIS364 1.9 2.0 1.0 O1 A:PER631 2.0 7.6 1.0 NE2 A:HIS324 2.0 5.3 1.0 O2 A:PER631 2.1 7.2 1.0 NE2 A:HIS328 2.3 7.7 1.0 CE1 A:HIS364 2.4 2.0 1.0 CE1 A:HIS324 2.7 2.0 1.0 CD2 A:HIS324 3.1 3.8 1.0 CD2 A:HIS364 3.2 6.6 1.0 CE1 A:HIS328 3.2 7.2 1.0 CD2 A:HIS328 3.3 6.5 1.0 ND1 A:HIS364 3.6 5.1 1.0 CU A:CU629 3.6 10.7 1.0 ND1 A:HIS324 3.9 4.6 1.0 CG A:HIS364 4.0 4.5 1.0 CG A:HIS324 4.1 3.9 1.0 CD2 A:HIS204 4.1 6.4 1.0 NE2 A:HIS204 4.2 2.5 1.0 CE2 A:PHE360 4.3 4.3 1.0 CE1 A:PHE49 4.3 8.0 1.0 ND1 A:HIS328 4.3 7.5 1.0 CG A:HIS328 4.4 5.9 1.0 CZ A:PHE360 4.7 3.1 1.0 CZ A:PHE49 4.8 7.0 1.0

B.Hazes, K.A.Magnus, C.Bonaventura, J.Bonaventura, Z.Dauter, K.H.Kalk, W.G.Hol. Crystal Structure of Deoxygenated Limulus Polyphemus Subunit II Hemocyanin at 2.18 A Resolution: Clues For A Mechanism For Allosteric Regulation. Protein Sci. V. 2 597 1993.
ISSN: ISSN 0961-8368
PubMed: 8518732