Atomistry » Magnesium » PDB 1rc5-1rtd » 1rky
Atomistry »
  Magnesium »
    PDB 1rc5-1rtd »
      1rky »

Magnesium in PDB 1rky: Pplo + Xe

Enzymatic activity of Pplo + Xe

All present enzymatic activity of Pplo + Xe:
1.4.3.13;

Protein crystallography data

The structure of Pplo + Xe, PDB code: 1rky was solved by J.M.Guss, A.P.Duff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.47 / 1.68
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 140.144, 66.702, 108.620, 90.00, 119.24, 90.00
R / Rfree (%) 15.1 / 18.2

Other elements in 1rky:

The structure of Pplo + Xe also contains other interesting chemical elements:

Xenon (Xe) 8 atoms
Calcium (Ca) 2 atoms
Chlorine (Cl) 6 atoms
Copper (Cu) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pplo + Xe (pdb code 1rky). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Pplo + Xe, PDB code: 1rky:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 1rky

Go back to Magnesium Binding Sites List in 1rky
Magnesium binding site 1 out of 3 in the Pplo + Xe


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pplo + Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg804

b:31.6
occ:1.00
O A:HOH2611 2.0 29.5 1.0
O A:HOH2534 2.0 33.2 1.0
O A:HOH2306 2.0 30.8 1.0
O A:HOH2589 2.1 32.5 1.0
O A:HOH2614 2.1 27.0 1.0
O A:HOH2609 2.1 35.0 1.0
O A:SER63 3.9 25.3 1.0
OD2 A:ASP425 4.0 39.1 1.0
OG A:SER63 4.1 30.0 1.0
OG1 A:THR62 4.3 27.6 1.0
O A:HOH2607 4.3 57.3 1.0
O A:HOH2222 4.3 42.6 1.0
O A:HOH2127 4.4 33.2 1.0
O A:HOH2155 4.4 34.8 1.0
O A:HOH2527 4.4 45.8 1.0
CA A:ALA65 4.5 31.2 1.0
O A:LEU64 4.5 28.4 1.0
N A:ALA65 4.6 31.7 1.0
C A:LEU64 4.7 28.0 1.0
C A:SER63 4.7 26.9 1.0
CB A:ALA65 4.9 33.3 1.0
CG2 A:THR62 4.9 30.0 1.0
CG A:ASP425 5.0 36.9 1.0

Magnesium binding site 2 out of 3 in 1rky

Go back to Magnesium Binding Sites List in 1rky
Magnesium binding site 2 out of 3 in the Pplo + Xe


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pplo + Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg805

b:37.4
occ:0.50
O A:HOH2362 2.1 47.1 1.0
OD2 A:ASP117 4.0 62.0 1.0
OD1 A:ASP117 4.4 47.8 1.0
CG A:ASP117 4.6 52.8 1.0

Magnesium binding site 3 out of 3 in 1rky

Go back to Magnesium Binding Sites List in 1rky
Magnesium binding site 3 out of 3 in the Pplo + Xe


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pplo + Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg806

b:59.0
occ:0.60
O A:HOH2617 2.0 49.5 1.0
O A:HOH2313 2.1 45.7 1.0
O A:HOH2440 2.3 43.8 1.0
O A:HOH2380 2.3 47.0 1.0
OD2 A:ASP336 3.9 28.0 1.0
OD1 A:ASP336 4.2 30.6 1.0
CB A:ASP338 4.5 38.2 1.0
OE2 A:GLU339 4.5 37.6 1.0
OD2 A:ASP338 4.5 78.7 1.0
CG A:ASP336 4.6 31.1 1.0
OE2 A:GLU54 4.6 41.2 0.5
CG A:GLU339 4.6 30.6 1.0
O A:HOH2531 4.6 56.2 1.0
CG A:GLU54 4.8 24.3 0.5
CG A:ASP338 5.0 81.7 1.0
CG A:GLU54 5.0 40.5 0.5

Reference:

A.P.Duff, D.M.Trambaiolo, A.E.Cohen, P.J.Ellis, G.A.Juda, E.M.Shepard, D.B.Langley, D.M.Dooley, H.C.Freeman, J.M.Guss. Using Xenon As A Probe For Dioxygen-Binding Sites in Copper Amine Oxidases J.Mol.Biol. V. 344 599 2004.
ISSN: ISSN 0022-2836
PubMed: 15533431
DOI: 10.1016/J.JMB.2004.09.075
Page generated: Mon Dec 14 06:42:46 2020

Last articles

Zn in 7M6U
Zn in 7NNG
Zn in 7NEE
Zn in 7NEU
Zn in 7M3K
Zn in 7KWD
Zn in 7KYH
Zn in 7KNG
Zn in 7KY2
Zn in 7KYF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy