Calcium in PDB 4a9x: Pseudomonas Fluorescens Phox in Complex with the Substrate Analogue Appcp

All present enzymatic activity of Pseudomonas Fluorescens Phox in Complex with the Substrate Analogue Appcp:
3.1.3.1;

The structure of Pseudomonas Fluorescens Phox in Complex with the Substrate Analogue Appcp, PDB code: 4a9x was solved by S.C.Yong, P.Roversi, J.E.D.Lillington, O.B.Zeldin, E.F.Garman, S.M.Lea, B.C.Berks, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.80 / 1.79
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.400, 78.900, 111.630, 90.00, 90.00, 90.00
R / Rfree (%)	24.28 / 28.66

The structure of Pseudomonas Fluorescens Phox in Complex with the Substrate Analogue Appcp also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Calcium atom in the Pseudomonas Fluorescens Phox in Complex with the Substrate Analogue Appcp (pdb code 4a9x). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Pseudomonas Fluorescens Phox in Complex with the Substrate Analogue Appcp, PDB code: 4a9x:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Pseudomonas Fluorescens Phox in Complex with the Substrate Analogue Appcp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pseudomonas Fluorescens Phox in Complex with the Substrate Analogue Appcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1591 b:17.9 occ:1.00 O A:FEO1594 2.2 11.4 1.0 OE2 A:GLU273 2.4 4.0 1.0 OD1 A:ASP479 2.4 11.1 1.0 OD2 A:ASP479 2.5 9.2 1.0 O A:HOH2107 2.6 12.8 1.0 CG A:ASP479 2.8 11.3 1.0 O A:HOH2106 2.8 14.2 1.0 O A:HOH2108 2.8 13.7 1.0 OE1 A:GLU387 3.1 14.4 1.0 HE1 A:TRP388 3.1 10.4 1.0 CD A:GLU273 3.4 11.5 1.0 O1G A:ACP1000 3.4 19.9 1.0 FE2 A:FEO1594 3.5 13.3 1.0 FE1 A:FEO1594 3.6 12.6 1.0 CA A:CA1592 3.8 14.8 1.0 OE1 A:GLU273 3.8 14.5 1.0 CD A:GLU387 3.8 18.1 1.0 SG A:CYS179 3.9 13.1 1.0 NE1 A:TRP388 3.9 11.0 1.0 HB3 A:GLU387 4.0 9.3 1.0 HD1 A:TRP388 4.0 11.6 1.0 HG1 A:THR534 4.1 13.6 1.0 OE2 A:GLU532 4.3 16.6 1.0 PG A:ACP1000 4.3 21.2 1.0 CB A:ASP479 4.3 7.2 1.0 OE2 A:GLU387 4.3 16.4 1.0 O3G A:ACP1000 4.4 24.9 1.0 CD1 A:TRP388 4.4 12.4 1.0 O2G A:ACP1000 4.5 14.7 1.0 OD1 A:ASP69 4.7 10.1 1.0 O A:HOH2472 4.7 13.9 1.0 HB3 A:ASP479 4.7 7.3 1.0 CG A:GLU273 4.7 9.1 1.0 HB2 A:ASP479 4.7 6.4 1.0 HG3 A:GLU273 4.7 9.8 1.0 CG A:GLU387 4.8 6.8 1.0 OD2 A:ASP494 4.8 11.8 1.0 OG1 A:THR534 4.8 14.4 1.0 O A:HOH2130 4.9 19.1 1.0 OD2 A:ASP69 4.9 13.5 1.0 CB A:GLU387 4.9 10.4 1.0 HG2 A:GLU387 5.0 6.6 1.0 OE2 A:GLU194 5.0 10.7 1.0

Calcium binding site 2 out of 3 in the Pseudomonas Fluorescens Phox in Complex with the Substrate Analogue Appcp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pseudomonas Fluorescens Phox in Complex with the Substrate Analogue Appcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1592 b:14.8 occ:1.00 OD2 A:ASP494 2.3 11.8 1.0 OD2 A:ASP479 2.3 9.2 1.0 O1G A:ACP1000 2.3 19.9 1.0 O A:HOH2414 2.5 16.3 1.0 O1B A:ACP1000 2.5 17.1 1.0 OE1 A:GLU387 2.7 14.4 1.0 OE2 A:GLU387 2.7 16.4 1.0 CD A:GLU387 3.1 18.1 1.0 HH22 A:ARG385 3.1 20.9 1.0 HB3 A:ASP494 3.1 14.1 1.0 CG A:ASP494 3.3 16.4 1.0 CG A:ASP479 3.3 11.3 1.0 PG A:ACP1000 3.4 21.2 1.0 HB2 A:ASP479 3.6 6.4 1.0 O3G A:ACP1000 3.6 24.9 1.0 PB A:ACP1000 3.6 21.8 1.0 HG23 A:THR403 3.7 10.1 1.0 CB A:ASP494 3.7 13.7 1.0 CA A:CA1591 3.8 17.9 1.0 NH2 A:ARG385 3.8 20.8 1.0 CA A:CA1593 3.8 18.4 1.0 HH21 A:ARG385 4.0 20.6 1.0 CB A:ASP479 4.1 7.2 1.0 O A:FEO1594 4.1 11.4 1.0 OD1 A:ASP479 4.1 11.1 1.0 C3B A:ACP1000 4.2 21.2 1.0 FE2 A:FEO1594 4.2 13.3 1.0 HB2 A:ASP494 4.2 14.4 1.0 O2B A:ACP1000 4.3 21.9 1.0 O A:ASP494 4.3 15.1 1.0 O A:HOH2413 4.4 16.8 1.0 OD1 A:ASP494 4.4 15.4 1.0 HH12 A:ARG385 4.4 6.5 1.0 OG1 A:THR403 4.5 12.5 1.0 HG1 A:THR403 4.5 11.8 1.0 CG A:GLU387 4.6 6.8 1.0 OE2 A:GLU532 4.6 16.6 1.0 HB3 A:ASP479 4.6 7.3 1.0 OD2 A:ASP292 4.6 14.7 1.0 CG2 A:THR403 4.7 8.7 1.0 CZ A:ARG385 4.7 16.0 1.0 HOB2 A:ACP1000 4.7 21.0 1.0 O2G A:ACP1000 4.8 14.7 1.0 O3A A:ACP1000 4.8 26.0 1.0 HB A:THR403 4.9 9.6 1.0 H3B2 A:ACP1000 4.9 21.1 1.0 O A:HOH2107 4.9 12.8 1.0 NH1 A:ARG385 4.9 7.3 1.0 HG3 A:GLU387 5.0 6.6 1.0 CB A:THR403 5.0 8.8 1.0

Calcium binding site 3 out of 3 in the Pseudomonas Fluorescens Phox in Complex with the Substrate Analogue Appcp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Pseudomonas Fluorescens Phox in Complex with the Substrate Analogue Appcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1593 b:18.4 occ:1.00 OE1 A:GLU532 2.3 10.6 1.0 OD2 A:ASP494 2.4 11.8 1.0 O A:HOH2134 2.4 15.8 1.0 O1G A:ACP1000 2.4 19.9 1.0 O A:HOH2484 2.5 27.5 1.0 O A:HOH2130 2.5 19.1 1.0 O2B A:ACP1000 2.7 21.9 1.0 OE2 A:GLU532 3.0 16.6 1.0 CD A:GLU532 3.0 11.9 1.0 CG A:ASP494 3.1 16.4 1.0 PB A:ACP1000 3.3 21.8 1.0 HOB2 A:ACP1000 3.3 21.0 1.0 PG A:ACP1000 3.3 21.2 1.0 OD1 A:ASP494 3.4 15.4 1.0 H3B1 A:ACP1000 3.5 21.4 1.0 C3B A:ACP1000 3.5 21.2 1.0 HE2 A:HIS551 3.6 13.6 1.0 CA A:CA1592 3.8 14.8 1.0 O2G A:ACP1000 3.8 14.7 1.0 O1B A:ACP1000 3.8 17.1 1.0 CB A:ASP494 4.4 13.7 1.0 OE1 A:GLN550 4.4 17.6 1.0 O A:HOH2106 4.4 14.2 1.0 HB2 A:ASP494 4.4 14.4 1.0 O A:HOH2529 4.4 22.7 1.0 CG A:GLU532 4.4 16.2 1.0 NE2 A:HIS551 4.5 14.1 1.0 OD2 A:ASP479 4.6 9.2 1.0 H3B2 A:ACP1000 4.6 21.1 1.0 HB3 A:GLU532 4.6 11.5 1.0 HOG2 A:ACP1000 4.7 14.1 1.0 O A:HOH2512 4.7 33.6 1.0 HE2 A:TYR91 4.7 13.3 1.0 O3G A:ACP1000 4.8 24.9 1.0 HB3 A:ASP494 4.8 14.1 1.0 O3A A:ACP1000 4.8 26.0 1.0 HG2 A:GLU532 4.9 15.3 1.0 O A:HOH2107 4.9 12.8 1.0 HB2 A:GLU532 5.0 9.7 1.0 CB A:GLU532 5.0 11.1 1.0

S.C.Yong, P.Roversi, J.Lillington, F.Rodriguez, M.Krehenbrink, O.B.Zeldin, E.F.Garman, S.M.Lea, B.C.Berks. A Complex Iron-Calcium Cofactor Catalyzing Phosphotransfer Chemistry Science V. 345 1170 2014.
ISSN: ISSN 0036-8075
PubMed: 25190793
DOI: 10.1126/SCIENCE.1254237