Copper in PDB 3mib: Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Nitrite

All present enzymatic activity of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Nitrite:
1.14.17.3;

The structure of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Nitrite, PDB code: 3mib was solved by E.E.Chufan, B.A.Eipper, R.E.Mains, L.M.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.00 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.612, 68.617, 80.254, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 24.4

The structure of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Nitrite also contains other interesting chemical elements:

Nickel

(Ni)

1 atom

The binding sites of Copper atom in the Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Nitrite (pdb code 3mib). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Nitrite, PDB code: 3mib:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in the Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Nitrite


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Nitrite within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu357 b:71.2 occ:1.00 ND1 A:HIS107 2.0 66.3 1.0 ND1 A:HIS108 2.0 65.4 1.0 ND1 A:HIS172 2.0 63.7 1.0 CE1 A:HIS172 2.8 62.6 1.0 CG A:HIS107 2.9 64.2 1.0 CE1 A:HIS107 2.9 65.0 1.0 CG A:HIS108 3.0 62.9 1.0 CE1 A:HIS108 3.0 64.2 1.0 CG A:HIS172 3.2 61.0 1.0 CB A:HIS107 3.3 63.2 1.0 CB A:HIS108 3.3 61.8 1.0 N A:HIS108 3.4 62.1 1.0 CB A:HIS172 3.6 59.5 1.0 C A:HIS107 3.7 62.6 1.0 CA A:HIS108 3.9 61.6 1.0 NE2 A:HIS107 4.0 64.7 1.0 CD2 A:HIS107 4.0 64.6 1.0 NE2 A:HIS172 4.0 62.2 1.0 NE2 A:HIS108 4.1 64.8 1.0 CD2 A:HIS108 4.1 63.8 1.0 CA A:HIS107 4.1 63.0 1.0 CD2 A:HIS172 4.2 61.6 1.0 O A:HIS107 4.2 62.6 1.0 O A:HOH384 4.3 67.6 1.0 O A:HOH409 4.4 87.3 1.0 OH A:TYR79 4.8 61.3 1.0 C A:HIS108 4.9 61.1 1.0 O A:HIS172 4.9 59.1 1.0 O A:HIS108 5.0 60.8 1.0

Copper binding site 2 out of 2 in the Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Nitrite


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Nitrite within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu358 b:55.4 occ:1.00 O1 A:NO21 1.9 63.4 1.0 NE2 A:HIS242 2.0 55.0 1.0 NE2 A:HIS244 2.0 57.2 1.0 SD A:MET314 2.5 61.0 1.0 O2 A:NO21 2.7 65.0 1.0 N A:NO21 2.7 64.5 1.0 CD2 A:HIS244 2.9 56.3 1.0 CD2 A:HIS242 3.0 54.2 1.0 CE1 A:HIS242 3.0 54.4 1.0 CE1 A:HIS244 3.1 56.4 1.0 CG A:MET314 3.6 59.8 1.0 CE A:MET314 3.7 59.3 1.0 CB A:MET314 3.9 59.6 1.0 CG A:HIS244 4.1 56.8 1.0 ND1 A:HIS242 4.1 54.2 1.0 ND1 A:HIS244 4.1 56.8 1.0 CG A:HIS242 4.1 54.9 1.0

E.E.Chufan, S.T.Prigge, X.Siebert, B.A.Eipper, R.E.Mains, L.M.Amzel. Differential Reactivity Between the Two Copper Sites of Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) J.Am.Chem.Soc. V. 132 15565 2010.
ISSN: ISSN 0002-7863
PubMed: 20958070
DOI: 10.1021/JA103117R