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Copper in PDB 4e4z: Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) in Complex with Hydrogen Peroxide (1.98 A)

Enzymatic activity of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) in Complex with Hydrogen Peroxide (1.98 A)

All present enzymatic activity of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) in Complex with Hydrogen Peroxide (1.98 A):
1.14.17.3;

Protein crystallography data

The structure of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) in Complex with Hydrogen Peroxide (1.98 A), PDB code: 4e4z was solved by K.Rudzka, L.M.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.22 / 1.98
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.503, 68.513, 81.472, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 24.4

Other elements in 4e4z:

The structure of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) in Complex with Hydrogen Peroxide (1.98 A) also contains other interesting chemical elements:

Nickel (Ni) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) in Complex with Hydrogen Peroxide (1.98 A) (pdb code 4e4z). 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) in Complex with Hydrogen Peroxide (1.98 A), PDB code: 4e4z:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 4e4z

Go back to Copper Binding Sites List in 4e4z
Copper binding site 1 out of 2 in the Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) in Complex with Hydrogen Peroxide (1.98 A)


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) in Complex with Hydrogen Peroxide (1.98 A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:57.4
occ:1.00
 ND1 A:HIS107 1.9 67.3 1.0
ND1 A:HIS108 2.0 49.5 1.0
ND1 A:HIS172 2.2 62.0 1.0
CE1 A:HIS107 2.8 68.0 1.0
CG A:HIS107 2.9 61.4 1.0
CE1 A:HIS172 2.9 63.8 1.0
CG A:HIS108 3.0 48.6 1.0
CE1 A:HIS108 3.1 48.8 1.0
CB A:HIS108 3.2 47.8 1.0
CG A:HIS172 3.3 62.0 1.0
N A:HIS108 3.4 48.5 1.0
CB A:HIS107 3.4 57.9 1.0
C A:HIS107 3.6 54.1 1.0
CB A:HIS172 3.7 54.0 1.0
CA A:HIS108 3.9 44.2 1.0
NE2 A:HIS107 3.9 68.1 1.0
CD2 A:HIS107 4.0 60.0 1.0
O A:HIS107 4.0 49.1 1.0
CD2 A:HIS108 4.1 45.6 1.0
NE2 A:HIS172 4.2 65.5 1.0
CA A:HIS107 4.2 52.0 1.0
NE2 A:HIS108 4.2 45.6 1.0
O A:HOH540 4.2 55.1 1.0
CD2 A:HIS172 4.3 65.4 1.0
O A:HIS172 4.8 46.9 1.0
OH A:TYR79 4.8 63.0 1.0
C A:HIS108 4.9 45.7 1.0

Copper binding site 2 out of 2 in 4e4z

Go back to Copper Binding Sites List in 4e4z
Copper binding site 2 out of 2 in the Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) in Complex with Hydrogen Peroxide (1.98 A)


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) in Complex with Hydrogen Peroxide (1.98 A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:42.2
occ:1.00
 O2 A:PEO404 2.0 49.4 1.0
NE2 A:HIS242 2.0 38.8 1.0
NE2 A:HIS244 2.1 36.3 1.0
O1 A:PEO404 2.1 46.9 1.0
SD A:MET314 2.4 35.8 1.0
O A:HOH539 2.6 64.2 1.0
CD2 A:HIS244 2.9 34.0 1.0
CE1 A:HIS242 3.0 38.3 1.0
CD2 A:HIS242 3.0 33.6 1.0
CE1 A:HIS244 3.1 36.8 1.0
CG A:MET314 3.5 32.9 1.0
CE A:MET314 3.6 35.7 1.0
CB A:MET314 3.9 29.3 1.0
ND1 A:HIS242 4.2 36.7 1.0
CG A:HIS244 4.2 35.5 1.0
CG A:HIS242 4.2 34.1 1.0
ND1 A:HIS244 4.2 35.2 1.0
CG A:GLU128 4.7 88.2 1.0
O A:HOH624 4.7 49.1 1.0
O A:HOH622 4.8 64.6 1.0
OE2 A:GLU128 4.9 87.0 1.0
CB A:GLU128 4.9 82.1 1.0
CD A:GLU128 5.0 90.6 1.0

Reference:

K.Rudzka, D.M.Moreno, B.Eipper, R.Mains, D.A.Estrin, L.M.Amzel. Coordination of Peroxide to the Cu(M) Center of Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm): Structural and Computational Study. J.Biol.Inorg.Chem. V. 18 223 2013.
ISSN: ISSN 0949-8257
PubMed: 23247335
DOI: 10.1007/S00775-012-0967-Z
Page generated: Wed Jul 31 02:44:15 2024

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