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Sodium in PDB 3mic: Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Azide Obtained By Co-Crystallization

Enzymatic activity of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Azide Obtained By Co-Crystallization

All present enzymatic activity of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Azide Obtained By Co-Crystallization:
1.14.17.3;

Protein crystallography data

The structure of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Azide Obtained By Co-Crystallization, PDB code: 3mic 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 / 2.42
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.454, 68.579, 81.409, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 26.4

Other elements in 3mic:

The structure of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Azide Obtained By Co-Crystallization also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Copper (Cu) 2 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 2 in 3mic

Go back to Sodium Binding Sites List in 3mic
Sodium binding site 1 out of 2 in the Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Azide Obtained By Co-Crystallization


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Azide Obtained By Co-Crystallization within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na360

b:55.2
occ:1.00
 N2 A:AZI1 2.3 51.7 1.0
N1 A:AZI1 2.4 47.8 1.0
O A:ASP127 2.6 49.6 1.0
N3 A:AZI1 2.7 51.1 1.0
O A:GLY308 2.9 47.2 1.0
C A:GLY308 3.5 46.8 1.0
C A:ASP127 3.7 49.2 1.0
CB A:GLU128 3.8 50.7 1.0
CU A:CU358 3.8 42.0 1.0
CA A:GLY308 3.9 46.3 1.0
CE A:MET314 4.1 40.2 1.0
NE2 A:HIS244 4.3 41.3 1.0
N A:GLU128 4.3 50.0 1.0
CA A:GLU128 4.3 50.3 1.0
N A:THR309 4.3 47.0 1.0
CE1 A:HIS244 4.4 39.8 1.0
O A:GLU128 4.4 50.4 1.0
C A:GLU128 4.4 50.4 1.0
SD A:MET314 4.5 41.7 1.0
OE2 A:GLU128 4.7 53.4 1.0
CA A:THR309 4.7 47.1 1.0
CB A:ASP127 4.8 48.9 1.0
CA A:ASP127 4.8 48.8 1.0
C A:THR309 4.8 47.5 1.0
O A:THR309 4.9 47.7 1.0
O A:GLY307 4.9 45.1 1.0

Sodium binding site 2 out of 2 in 3mic

Go back to Sodium Binding Sites List in 3mic
Sodium binding site 2 out of 2 in the Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Azide Obtained By Co-Crystallization


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Azide Obtained By Co-Crystallization within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na361

b:79.9
occ:1.00
 N3 A:AZI2 2.9 71.3 1.0
O A:PHE343 3.1 45.0 1.0
NH2 A:ARG292 3.4 41.3 1.0
NH1 A:ARG292 3.5 41.3 1.0
N2 A:AZI2 3.8 71.6 1.0
CZ A:ARG292 3.9 41.3 1.0
C A:PHE343 4.0 45.2 1.0
CG2 A:ILE346 4.1 45.1 1.0
CA A:ARG344 4.2 45.5 1.0
N A:ARG344 4.5 45.3 1.0
C A:ARG344 4.9 45.5 1.0
N1 A:AZI2 4.9 71.2 1.0
ND2 A:ASN351 4.9 50.3 1.0
CB A:PHE343 4.9 45.0 1.0
O A:ARG344 5.0 45.5 1.0

Reference:

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
Page generated: Mon Oct 7 11:30:32 2024

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