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Sodium in PDB 3mih: Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Azide, Obtained in the Presence of Substrate

Enzymatic activity of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Azide, Obtained in the Presence of Substrate

All present enzymatic activity of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Azide, Obtained in the Presence of Substrate:
1.14.17.3;

Protein crystallography data

The structure of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Azide, Obtained in the Presence of Substrate, PDB code: 3mih 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 / 2.74
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.110, 68.800, 79.791, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 29.6

Other elements in 3mih:

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

Nickel (Ni) 1 atom
Iodine (I) 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 in the Presence of Substrate (pdb code 3mih). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Azide, Obtained in the Presence of Substrate, PDB code: 3mih:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3mih

Go back to Sodium Binding Sites List in 3mih
Sodium binding site 1 out of 4 in the Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Azide, Obtained in the Presence of Substrate


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 in the Presence of Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na363

b:92.0
occ:1.00
 N1 A:AZI1 2.7 97.0 1.0
OD2 A:ASP96 2.7 83.8 1.0
N2 A:AZI1 2.8 97.6 1.0
ND1 A:HIS192 2.9 81.2 1.0
N3 A:AZI1 3.3 97.8 1.0
CG A:ASP96 3.6 83.7 1.0
CE1 A:HIS192 3.7 81.2 1.0
CB A:ASP96 3.8 83.5 1.0
CG A:HIS192 3.9 81.1 1.0
CB A:HIS192 4.1 80.9 1.0
I A:IOD360 4.6 0.2 0.9
OD1 A:ASP96 4.8 83.8 1.0
NE2 A:HIS192 4.9 80.8 1.0
CD2 A:HIS192 5.0 81.0 1.0

Sodium binding site 2 out of 4 in 3mih

Go back to Sodium Binding Sites List in 3mih
Sodium binding site 2 out of 4 in the Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Azide, Obtained in the Presence of Substrate


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 in the Presence of Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na364

b:0.8
occ:1.00
 N3 A:AZI5 3.2 96.9 1.0
N2 A:AZI5 3.9 97.3 1.0
O A:HOH377 4.7 91.4 1.0
N1 A:AZI5 4.8 96.9 1.0

Sodium binding site 3 out of 4 in 3mih

Go back to Sodium Binding Sites List in 3mih
Sodium binding site 3 out of 4 in the Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Azide, Obtained in the Presence of Substrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Azide, Obtained in the Presence of Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na365

b:0.4
occ:1.00
 N3 A:AZI7 2.6 0.9 1.0
O A:GLY299 3.1 83.0 1.0
NE A:ARG300 3.5 84.3 1.0
N2 A:AZI7 3.7 0.1 1.0
C A:GLY299 3.8 82.9 1.0
O A:GLU298 4.0 82.5 1.0
CD2 A:LEU246 4.0 83.4 1.0
CD A:ARG300 4.1 83.8 1.0
CA A:GLY299 4.1 82.8 1.0
CG A:ARG300 4.2 83.4 1.0
CZ A:ARG300 4.5 84.6 1.0
NH2 A:ARG300 4.6 84.1 1.0
N A:ARG300 4.8 83.1 1.0
C A:GLU298 4.9 82.5 1.0
N1 A:AZI7 4.9 0.0 1.0
N A:GLY299 5.0 82.6 1.0

Sodium binding site 4 out of 4 in 3mih

Go back to Sodium Binding Sites List in 3mih
Sodium binding site 4 out of 4 in the Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Azide, Obtained in the Presence of Substrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Azide, Obtained in the Presence of Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na366

b:1.0
occ:1.00
 O A:CYS126 2.7 84.2 1.0
N3 A:AZI3 2.9 0.8 1.0
N2 A:AZI3 3.7 0.9 1.0
C A:CYS126 3.9 84.1 1.0
CB A:CYS126 4.5 83.9 1.0
CA A:GLY129 4.6 84.2 1.0
N1 A:AZI3 4.7 0.8 1.0
N A:ASP127 4.7 84.3 1.0
CA A:CYS126 4.8 84.0 1.0
CA A:ASP127 4.8 84.5 1.0
O A:GLY308 4.8 85.6 1.0
N A:GLY129 4.9 84.4 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: Tue Dec 15 06:17:37 2020

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