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Copper in PDB 1opm: Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Substrate

Enzymatic activity of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Substrate

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

Protein crystallography data

The structure of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Substrate, PDB code: 1opm was solved by S.T.Prigge, L.M.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.399, 68.840, 81.047, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 25.9

Other elements in 1opm:

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

Nickel (Ni) 1 atom
Iodine (I) 4 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Substrate (pdb code 1opm). 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 Substrate, PDB code: 1opm:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 1opm

Go back to Copper Binding Sites List in 1opm
Copper binding site 1 out of 2 in the Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Substrate


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 Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu357

b:75.0
occ:1.00
ND1 A:HIS107 2.0 65.3 1.0
ND1 A:HIS108 2.1 56.6 1.0
CE1 A:HIS107 2.5 63.7 1.0
ND1 A:HIS172 2.6 66.2 1.0
CG A:HIS108 3.0 51.4 1.0
CG A:HIS107 3.2 59.8 1.0
CB A:HIS108 3.2 50.6 1.0
CE1 A:HIS108 3.2 55.3 1.0
CG A:HIS172 3.4 63.7 1.0
CE1 A:HIS172 3.5 65.0 1.0
CB A:HIS172 3.7 56.1 1.0
NE2 A:HIS107 3.7 63.1 1.0
N A:HIS108 3.8 47.5 1.0
CB A:HIS107 3.9 54.8 1.0
CD2 A:HIS107 4.0 59.5 1.0
CA A:HIS108 4.1 46.1 1.0
C A:HIS107 4.1 51.2 1.0
CD2 A:HIS108 4.2 54.6 1.0
O A:HOH438 4.2 62.3 1.0
NE2 A:HIS108 4.3 55.5 1.0
O A:HOH608 4.4 68.0 1.0
O A:HIS107 4.5 49.6 1.0
CD2 A:HIS172 4.5 65.8 1.0
NE2 A:HIS172 4.5 68.5 1.0
OH A:TYR79 4.6 73.3 1.0
CA A:HIS107 4.7 50.5 1.0
C A:HIS108 4.9 40.7 1.0
O A:HIS172 5.0 52.4 1.0

Copper binding site 2 out of 2 in 1opm

Go back to Copper Binding Sites List in 1opm
Copper binding site 2 out of 2 in the Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Substrate


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 Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu358

b:43.3
occ:1.00
O A:HOH803 2.0 47.9 1.0
NE2 A:HIS242 2.2 31.7 1.0
NE2 A:HIS244 2.2 32.7 1.0
SD A:MET314 2.4 33.4 1.0
CE1 A:HIS242 3.1 19.6 1.0
CD2 A:HIS244 3.1 25.6 1.0
CD2 A:HIS242 3.2 28.5 1.0
CE A:MET314 3.2 31.0 1.0
CE1 A:HIS244 3.3 29.0 1.0
CG A:MET314 3.4 27.3 1.0
CB A:MET314 3.9 28.4 1.0
ND1 A:HIS242 4.2 26.3 1.0
CAT A:IYG801 4.3 40.9 1.0
NT A:IYG801 4.3 42.1 1.0
CG A:HIS244 4.3 28.8 1.0
CG A:HIS242 4.3 25.3 1.0
ND1 A:HIS244 4.4 32.4 1.0
O A:HOH604 4.4 60.6 1.0
O A:HOH594 4.5 57.3 1.0
C A:IYG801 4.8 39.3 1.0
CT A:IYG801 4.9 42.7 1.0
OT1 A:IYG801 4.9 40.6 1.0

Reference:

S.T.Prigge, A.S.Kolhekar, B.A.Eipper, R.E.Mains, L.M.Amzel. Substrate-Mediated Electron Transfer in Peptidylglycine Alpha-Hydroxylating Monooxygenase. Nat.Struct.Biol. V. 6 976 1999.
ISSN: ISSN 1072-8368
PubMed: 10504734
DOI: 10.1038/13351
Page generated: Sun Dec 13 11:01:13 2020

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