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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 3mib:

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

Copper (Cu) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total only one binding site of Nickel was determined in the Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Nitrite, PDB code: 3mib:

Nickel binding site 1 out of 1 in 3mib

Go back to Nickel Binding Sites List in 3mib
Nickel binding site 1 out of 1 in the Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) with Bound Nitrite


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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:Ni359

b:51.0
occ:1.00
 O A:HOH486 1.9 54.8 1.0
O2 A:NO22 1.9 57.9 1.0
O A:HOH463 2.0 49.2 1.0
NE2 A:HIS235 2.0 54.8 1.0
O1 A:NO22 2.6 59.3 1.0
N A:NO22 2.8 59.2 1.0
CD2 A:HIS235 2.9 55.6 1.0
CE1 A:HIS235 3.1 55.0 1.0
CB A:ASP282 4.0 64.9 1.0
CG A:HIS235 4.1 56.9 1.0
ND1 A:HIS235 4.1 55.6 1.0
OD1 A:ASP282 4.2 66.2 1.0
CG A:ASP282 4.3 65.4 1.0
O A:HOH40 4.4 64.6 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 Aug 18 18:47:00 2025

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