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Calcium in PDB 4alf: Pseudomonas Fluorescens Phox in Complex with Phosphate

Enzymatic activity of Pseudomonas Fluorescens Phox in Complex with Phosphate

All present enzymatic activity of Pseudomonas Fluorescens Phox in Complex with Phosphate:
3.1.3.1;

Protein crystallography data

The structure of Pseudomonas Fluorescens Phox in Complex with Phosphate, PDB code: 4alf 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) 16.14 / 1.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.099, 71.035, 228.501, 90.00, 90.00, 90.00
R / Rfree (%) 13.272 / 16.432

Other elements in 4alf:

The structure of Pseudomonas Fluorescens Phox in Complex with Phosphate also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Pseudomonas Fluorescens Phox in Complex with Phosphate (pdb code 4alf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Pseudomonas Fluorescens Phox in Complex with Phosphate, PDB code: 4alf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4alf

Go back to Calcium Binding Sites List in 4alf
Calcium binding site 1 out of 6 in the Pseudomonas Fluorescens Phox in Complex with Phosphate


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 Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1590

b:7.0
occ:0.99
O A:FEO1593 2.4 6.2 1.0
OE2 A:GLU273 2.4 5.5 1.0
OD2 A:ASP479 2.5 5.8 1.0
O A:HOH2636 2.5 9.4 1.0
OD1 A:ASP479 2.5 5.6 1.0
O A:HOH2152 2.5 7.4 1.0
O1 A:PO41589 2.6 7.4 1.0
O A:HOH2153 2.7 7.2 1.0
CG A:ASP479 2.8 5.7 1.0
OE2 A:GLU387 2.9 5.7 1.0
HE1 A:TRP388 3.1 5.3 1.0
CD A:GLU273 3.5 4.8 1.0
CA A:CA1591 3.6 6.5 1.0
FE2 A:FEO1593 3.6 5.2 1.0
FE1 A:FEO1593 3.6 6.2 1.0
P A:PO41589 3.7 6.9 1.0
CD A:GLU387 3.8 5.1 1.0
OE1 A:GLU273 4.0 4.5 1.0
SG A:CYS179 4.1 7.7 1.0
NE1 A:TRP388 4.1 5.2 1.0
O2 A:PO41589 4.1 7.6 1.0
O3 A:PO41589 4.2 6.2 1.0
HB3 A:GLU387 4.2 4.4 1.0
HD1 A:TRP388 4.2 5.2 1.0
OE1 A:GLU387 4.2 6.1 1.0
OE2 A:GLU532 4.3 6.5 1.0
CB A:ASP479 4.3 5.6 1.0
CD1 A:TRP388 4.6 5.4 1.0
OD2 A:ASP494 4.7 6.7 1.0
O A:HOH2188 4.7 6.2 1.0
HB3 A:ASP479 4.7 5.7 1.0
OG1 A:THR534 4.7 8.6 1.0
O A:HOH2637 4.7 9.5 1.0
HB2 A:ASP479 4.7 5.7 1.0
CG A:GLU387 4.7 4.5 1.0
OD1 A:ASP69 4.8 6.9 1.0
CG A:GLU273 4.8 4.6 1.0
HG3 A:GLU273 4.8 4.7 1.0
CA A:CA1592 4.8 7.2 1.0
HG2 A:GLU387 4.8 4.4 1.0
OD2 A:ASP69 4.9 7.1 1.0
CB A:GLU387 4.9 4.3 1.0
HB2 A:ASP494 5.0 6.6 1.0
O4 A:PO41589 5.0 8.9 1.0

Calcium binding site 2 out of 6 in 4alf

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Calcium binding site 2 out of 6 in the Pseudomonas Fluorescens Phox in Complex with Phosphate


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 Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1591

b:6.5
occ:1.00
OD2 A:ASP479 2.3 5.8 1.0
O A:HOH2554 2.3 7.6 1.0
O1 A:PO41589 2.4 7.4 1.0
OD2 A:ASP494 2.4 6.7 1.0
OE2 A:GLU387 2.5 5.7 1.0
O A:HOH2553 2.5 9.4 1.0
OE1 A:GLU387 2.6 6.1 1.0
CD A:GLU387 2.9 5.1 1.0
HB3 A:ASP494 3.1 6.6 1.0
O3 A:PO41589 3.3 6.2 1.0
CG A:ASP479 3.3 5.7 1.0
P A:PO41589 3.3 6.9 1.0
HH22 A:ARG385 3.3 8.1 1.0
CG A:ASP494 3.4 7.4 1.0
CA A:CA1590 3.6 7.0 1.0
HB2 A:ASP479 3.6 5.7 1.0
CB A:ASP494 3.7 6.5 1.0
O4 A:PO41589 3.7 8.9 1.0
HG21 A:THR403 3.8 5.5 1.0
NH2 A:ARG385 3.8 8.7 1.0
CA A:CA1592 3.9 7.2 1.0
HH21 A:ARG385 4.0 7.3 1.0
CB A:ASP479 4.0 5.6 1.0
HB2 A:ASP494 4.1 6.6 1.0
FE2 A:FEO1593 4.1 5.2 1.0
OD1 A:ASP479 4.1 5.6 1.0
O A:FEO1593 4.3 6.2 1.0
CG A:GLU387 4.4 4.5 1.0
O A:ASP494 4.4 7.8 1.0
O A:HOH2649 4.5 22.7 1.0
OG1 A:THR403 4.5 6.2 1.0
OD1 A:ASP494 4.5 8.7 1.0
HG1 A:THR403 4.5 6.1 1.0
OD2 A:ASP292 4.6 6.1 1.0
HB3 A:ASP479 4.6 5.7 1.0
OE2 A:GLU532 4.6 6.5 1.0
CG2 A:THR403 4.6 5.6 1.0
HH12 A:ARG385 4.6 8.3 1.0
O A:HOH2636 4.6 9.4 1.0
CZ A:ARG385 4.7 8.6 1.0
HG3 A:GLU387 4.7 4.4 1.0
O2 A:PO41589 4.8 7.6 1.0
HG2 A:GLU387 4.8 4.4 1.0
HB A:THR403 4.8 6.1 1.0
HG23 A:THR403 4.8 6.0 1.0
O A:HOH2652 4.8 13.7 1.0
CB A:THR403 4.9 5.7 1.0
HA A:ASP479 5.0 5.2 1.0

Calcium binding site 3 out of 6 in 4alf

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Calcium binding site 3 out of 6 in the Pseudomonas Fluorescens Phox in Complex with Phosphate


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 Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1592

b:7.2
occ:0.99
O A:HOH2188 2.4 6.2 1.0
OE1 A:GLU532 2.4 6.8 1.0
O4 A:PO41589 2.4 8.9 1.0
OD2 A:ASP494 2.4 6.7 1.0
O A:HOH2652 2.5 13.7 1.0
O A:HOH2191 2.5 12.1 1.0
O1 A:PO41589 2.6 7.4 1.0
OE2 A:GLU532 2.7 6.5 1.0
CD A:GLU532 2.9 6.3 1.0
P A:PO41589 3.0 6.9 1.0
CG A:ASP494 3.2 7.4 1.0
H12 A:EDO1596 3.4 9.8 0.7
OD1 A:ASP494 3.4 8.7 1.0
O2 A:PO41589 3.6 7.6 1.0
HE2 A:HIS551 3.6 6.5 1.0
O A:HOH2553 3.8 9.4 1.0
CA A:CA1591 3.9 6.5 1.0
O A:HOH2153 4.3 7.2 1.0
O3 A:PO41589 4.3 6.2 1.0
OE1 A:GLN550 4.3 6.3 1.0
CG A:GLU532 4.4 6.2 1.0
C1 A:EDO1596 4.4 10.7 0.7
O A:HOH2717 4.4 22.8 1.0
CB A:ASP494 4.4 6.5 1.0
HB2 A:ASP494 4.4 6.6 1.0
O A:HOH2651 4.4 14.3 0.5
H11 A:EDO1596 4.6 9.5 0.7
OD2 A:ASP479 4.6 5.8 1.0
O A:HOH2689 4.6 17.5 1.0
NE2 A:HIS551 4.6 6.7 1.0
O A:HOH2649 4.6 22.7 1.0
O A:HOH2636 4.7 9.4 1.0
HE1 A:TYR91 4.7 5.8 1.0
HB3 A:GLU532 4.7 5.9 1.0
HG2 A:GLU532 4.7 6.2 1.0
HB3 A:ASP494 4.7 6.6 1.0
O2 A:EDO1596 4.8 19.4 0.7
CA A:CA1590 4.8 7.0 1.0
HG3 A:GLU532 4.9 6.4 1.0
OH A:TYR91 4.9 7.4 1.0
OE1 A:GLU90 5.0 6.2 1.0

Calcium binding site 4 out of 6 in 4alf

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Calcium binding site 4 out of 6 in the Pseudomonas Fluorescens Phox in Complex with Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Pseudomonas Fluorescens Phox in Complex with Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1590

b:6.4
occ:0.98
O B:FEO1593 2.4 6.7 1.0
OD2 B:ASP479 2.5 6.2 1.0
OE2 B:GLU273 2.5 6.0 1.0
O B:HOH2592 2.5 8.3 1.0
O B:HOH2142 2.5 7.3 1.0
OD1 B:ASP479 2.5 6.8 1.0
O1 B:PO41589 2.6 7.7 1.0
O B:HOH2143 2.7 7.2 1.0
CG B:ASP479 2.9 6.0 1.0
OE2 B:GLU387 2.9 5.5 1.0
HE1 B:TRP388 3.1 5.0 1.0
CD B:GLU273 3.5 5.1 1.0
CA B:CA1591 3.6 6.6 1.0
FE2 B:FEO1593 3.6 5.6 1.0
FE1 B:FEO1593 3.6 6.1 1.0
P B:PO41589 3.7 7.5 1.0
CD B:GLU387 3.8 5.7 1.0
OE1 B:GLU273 3.9 5.1 1.0
NE1 B:TRP388 4.1 4.9 1.0
SG B:CYS179 4.1 7.8 1.0
O2 B:PO41589 4.1 7.5 1.0
O3 B:PO41589 4.1 7.4 1.0
HD1 B:TRP388 4.2 5.0 1.0
HB3 B:GLU387 4.2 5.3 1.0
OE1 B:GLU387 4.3 6.0 1.0
OE2 B:GLU532 4.3 7.6 1.0
CB B:ASP479 4.4 5.8 1.0
CD1 B:TRP388 4.5 5.0 1.0
OD2 B:ASP494 4.6 7.9 1.0
O B:HOH2171 4.7 6.2 1.0
OG1 B:THR534 4.7 6.6 1.0
HB3 B:ASP479 4.7 6.0 1.0
OD1 B:ASP69 4.7 6.9 1.0
HB2 B:ASP479 4.7 5.6 1.0
CG B:GLU387 4.8 5.3 1.0
O B:HOH2593 4.8 9.9 1.0
CG B:GLU273 4.8 5.0 1.0
CA B:CA1592 4.8 6.6 0.9
OD2 B:ASP69 4.8 8.0 1.0
HG2 B:GLU387 4.8 5.3 1.0
HG3 B:GLU273 4.8 5.0 1.0
CB B:GLU387 5.0 5.4 1.0

Calcium binding site 5 out of 6 in 4alf

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Calcium binding site 5 out of 6 in the Pseudomonas Fluorescens Phox in Complex with Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Pseudomonas Fluorescens Phox in Complex with Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1591

b:6.6
occ:1.00
OD2 B:ASP479 2.3 6.2 1.0
O B:HOH2515 2.4 6.4 1.0
O1 B:PO41589 2.4 7.7 1.0
OD2 B:ASP494 2.4 7.9 1.0
O B:HOH2514 2.4 9.8 1.0
OE2 B:GLU387 2.5 5.5 1.0
OE1 B:GLU387 2.6 6.0 1.0
CD B:GLU387 2.9 5.7 1.0
HB3 B:ASP494 3.2 7.1 1.0
P B:PO41589 3.3 7.5 1.0
O3 B:PO41589 3.3 7.4 1.0
CG B:ASP479 3.3 6.0 1.0
HH22 B:ARG385 3.4 8.5 1.0
CG B:ASP494 3.4 7.5 1.0
CA B:CA1590 3.6 6.4 1.0
HB2 B:ASP479 3.6 5.6 1.0
O4 B:PO41589 3.7 8.9 1.0
CB B:ASP494 3.8 7.0 1.0
NH2 B:ARG385 3.9 9.1 1.0
HG21 B:THR403 3.9 6.0 1.0
CA B:CA1592 3.9 6.6 0.9
HH21 B:ARG385 4.0 8.0 1.0
FE2 B:FEO1593 4.0 5.6 1.0
CB B:ASP479 4.1 5.8 1.0
HB2 B:ASP494 4.1 6.8 1.0
OD1 B:ASP479 4.2 6.8 1.0
O B:FEO1593 4.3 6.7 1.0
O B:HOH2606 4.4 19.9 1.0
CG B:GLU387 4.4 5.3 1.0
O B:ASP494 4.5 7.3 1.0
HG1 B:THR403 4.5 6.1 1.0
OG1 B:THR403 4.5 6.1 1.0
OD1 B:ASP494 4.5 7.8 1.0
OE2 B:GLU532 4.6 7.6 1.0
OD2 B:ASP292 4.6 6.3 1.0
HB3 B:ASP479 4.6 6.0 1.0
CG2 B:THR403 4.7 6.0 1.0
O B:HOH2592 4.7 8.3 1.0
HH12 B:ARG385 4.7 9.0 1.0
O2 B:PO41589 4.7 7.5 1.0
HG3 B:GLU387 4.7 5.3 1.0
HG23 B:THR403 4.8 5.9 1.0
HG2 B:GLU387 4.8 5.3 1.0
HB B:THR403 4.8 5.9 1.0
CZ B:ARG385 4.8 8.2 1.0
O B:HOH2607 4.8 11.7 1.0
CB B:THR403 4.9 5.5 1.0

Calcium binding site 6 out of 6 in 4alf

Go back to Calcium Binding Sites List in 4alf
Calcium binding site 6 out of 6 in the Pseudomonas Fluorescens Phox in Complex with Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Pseudomonas Fluorescens Phox in Complex with Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1592

b:6.6
occ:0.94
OE1 B:GLU532 2.4 7.2 1.0
O4 B:PO41589 2.4 8.9 1.0
OD2 B:ASP494 2.4 7.9 1.0
O B:HOH2607 2.5 11.7 1.0
O B:HOH2171 2.5 6.2 1.0
O B:HOH2174 2.5 12.3 1.0
O1 B:PO41589 2.6 7.7 1.0
OE2 B:GLU532 2.7 7.6 1.0
CD B:GLU532 2.9 6.4 1.0
P B:PO41589 3.0 7.5 1.0
CG B:ASP494 3.2 7.5 1.0
HO2 B:EDO1597 3.3 12.3 0.7
OD1 B:ASP494 3.4 7.8 1.0
O2 B:PO41589 3.6 7.5 1.0
HE2 B:HIS551 3.6 6.5 1.0
O B:HOH2514 3.8 9.8 1.0
CA B:CA1591 3.9 6.6 1.0
O2 B:EDO1597 4.3 13.3 0.7
O B:HOH2143 4.3 7.2 1.0
OE1 B:GLN550 4.3 5.5 1.0
CG B:GLU532 4.4 6.9 1.0
O3 B:PO41589 4.4 7.4 1.0
O B:HOH2674 4.4 21.6 1.0
H22 B:EDO1597 4.4 13.6 0.7
CB B:ASP494 4.5 7.0 1.0
HB2 B:ASP494 4.5 6.8 1.0
O B:HOH2606 4.6 19.9 1.0
O B:HOH2643 4.6 18.3 1.0
NE2 B:HIS551 4.6 7.1 1.0
OD2 B:ASP479 4.6 6.2 1.0
O B:HOH2592 4.7 8.3 1.0
H21 B:EDO1597 4.7 13.4 0.7
HE1 B:TYR91 4.7 6.2 1.0
C2 B:EDO1597 4.7 14.4 0.7
HB3 B:GLU532 4.7 6.0 1.0
HG2 B:GLU532 4.7 6.5 1.0
HB3 B:ASP494 4.8 7.1 1.0
HH B:TYR91 4.8 7.0 1.0
CA B:CA1590 4.8 6.4 1.0
HG3 B:GLU532 4.9 6.3 1.0
OE1 B:GLU90 5.0 5.5 1.0
OH B:TYR91 5.0 7.4 1.0

Reference:

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
Page generated: Tue Jul 8 18:31:46 2025

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