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Calcium 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:

Magnesium (Mg) 3 atoms
Xenon (Xe) 8 atoms
Chlorine (Cl) 6 atoms
Copper (Cu) 1 atom

Calcium Binding Sites:

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

Calcium binding site 1 out of 2 in 1rky

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pplo + Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca802

b:23.1
occ:1.00
OD1 A:ASP539 2.3 22.5 1.0
O A:ILE684 2.3 20.3 1.0
OD1 A:ASP683 2.3 25.1 1.0
O A:LEU538 2.3 21.8 1.0
OD1 A:ASP537 2.4 22.9 1.0
O A:HOH2455 2.5 21.4 1.0
C A:LEU538 3.4 22.1 1.0
C A:ILE684 3.4 20.3 1.0
CG A:ASP539 3.5 24.1 1.0
CG A:ASP683 3.5 26.1 1.0
CG A:ASP537 3.6 25.4 1.0
N A:ILE684 3.6 22.5 1.0
NZ A:LYS105 3.8 21.9 1.0
N A:ASP539 4.1 23.7 1.0
C A:ASP537 4.1 19.3 1.0
N A:LEU538 4.1 22.9 1.0
CA A:ASP539 4.1 22.4 1.0
CA A:ILE684 4.2 22.3 1.0
C A:ASP683 4.2 21.5 1.0
OD2 A:ASP683 4.2 28.8 1.0
OD2 A:ASP537 4.3 24.9 1.0
O A:ASP537 4.3 23.1 1.0
CA A:ASP683 4.4 23.6 1.0
CA A:LEU538 4.4 24.6 1.0
OD2 A:ASP539 4.4 24.6 1.0
CB A:ASP539 4.4 23.0 1.0
CA A:ASP537 4.4 20.9 1.0
N A:VAL685 4.5 23.6 1.0
O A:THR543 4.6 26.5 1.0
CB A:ASP683 4.6 25.6 1.0
OD1 A:ASN545 4.6 25.7 1.0
CB A:ASP537 4.6 21.8 1.0
CA A:VAL685 4.9 18.1 1.0
CG2 A:VAL685 4.9 25.2 1.0
CB A:ILE684 5.0 22.5 1.0
O A:ASP683 5.0 24.2 1.0

Calcium binding site 2 out of 2 in 1rky

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pplo + Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca803

b:25.1
occ:1.00
O A:HOH2615 2.3 28.2 1.0
OE1 A:GLU677 2.3 31.0 1.0
O A:PHE673 2.4 24.7 1.0
O A:HOH2356 2.4 25.8 1.0
OD2 A:ASP675 2.4 26.9 1.0
OE2 A:GLU580 2.5 25.5 1.0
OE1 A:GLU580 2.5 25.9 1.0
CD A:GLU580 2.9 26.3 1.0
CD A:GLU677 3.3 41.9 1.0
CG A:ASP675 3.4 26.8 1.0
C A:PHE673 3.5 25.0 1.0
OD1 A:ASP675 3.8 33.0 1.0
CG A:GLU677 3.9 29.1 1.0
N A:ASP675 4.1 24.6 1.0
NZ A:LYS648 4.2 33.8 1.0
CB A:GLU677 4.2 26.5 1.0
OE1 A:GLU651 4.3 30.7 1.0
OE2 A:GLU677 4.3 36.8 1.0
CA A:PHE673 4.3 23.4 1.0
CG A:GLU580 4.4 21.3 1.0
N A:LEU674 4.4 23.5 1.0
OE2 A:GLU651 4.4 29.4 1.0
CE A:LYS648 4.5 34.6 1.0
CB A:ASP675 4.6 26.7 1.0
CA A:LEU674 4.7 23.4 1.0
N A:LYS646 4.8 23.9 1.0
CD A:GLU651 4.8 30.9 1.0
CA A:ASP675 4.8 29.2 1.0
C A:LEU674 4.9 28.5 1.0
CB A:LYS646 4.9 25.6 1.0
O A:LYS646 4.9 25.7 1.0
CB A:PHE673 4.9 24.4 1.0
CB A:THR645 5.0 25.7 1.0
N A:GLU677 5.0 25.1 1.0

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: Sat Dec 12 03:17:54 2020

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