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Calcium in PDB 3zwu: Pseudomonas Fluorescens Phox in Complex with Vanadate, A Transition State Analogue

Enzymatic activity of Pseudomonas Fluorescens Phox in Complex with Vanadate, A Transition State Analogue

All present enzymatic activity of Pseudomonas Fluorescens Phox in Complex with Vanadate, A Transition State Analogue:
3.1.3.1;

Protein crystallography data

The structure of Pseudomonas Fluorescens Phox in Complex with Vanadate, A Transition State Analogue, PDB code: 3zwu 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) 38.42 / 1.39
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.790, 71.470, 227.830, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 17.13

Other elements in 3zwu:

The structure of Pseudomonas Fluorescens Phox in Complex with Vanadate, A Transition State Analogue also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Pseudomonas Fluorescens Phox in Complex with Vanadate, A Transition State Analogue (pdb code 3zwu). 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 Vanadate, A Transition State Analogue, PDB code: 3zwu:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3zwu

Go back to Calcium Binding Sites List in 3zwu
Calcium binding site 1 out of 6 in the Pseudomonas Fluorescens Phox in Complex with Vanadate, A Transition State Analogue


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 Vanadate, A Transition State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1591

b:9.7
occ:0.95
OE2 A:GLU273 2.3 9.6 1.0
O A:FEO1594 2.4 8.8 1.0
OD2 A:ASP479 2.4 10.3 1.0
O A:HOH2815 2.4 13.0 1.0
OD1 A:ASP479 2.5 9.4 1.0
O A:HOH2195 2.5 10.8 1.0
O2 A:VO4700 2.6 8.2 0.7
O A:HOH2196 2.7 11.1 1.0
CG A:ASP479 2.8 9.2 1.0
OE2 A:GLU387 2.9 11.1 1.0
CD A:GLU273 3.4 10.1 1.0
FE2 A:FEO1594 3.6 10.0 1.0
CA A:CA1592 3.6 10.0 0.9
FE1 A:FEO1594 3.6 9.8 1.0
V A:VO4700 3.7 14.6 0.7
CD A:GLU387 3.7 16.0 1.0
OE1 A:GLU273 3.9 10.1 1.0
SG A:CYS179 4.0 11.8 1.0
NE1 A:TRP388 4.0 8.7 1.0
OE2 A:GLU532 4.2 12.8 1.0
OE1 A:GLU387 4.2 11.2 1.0
CB A:ASP479 4.3 9.7 1.0
O4 A:VO4700 4.3 12.3 0.7
O3 A:VO4700 4.4 9.0 0.7
CD1 A:TRP388 4.5 9.4 1.0
OG1 A:THR534 4.7 11.9 1.0
CG A:GLU273 4.7 10.4 1.0
OD2 A:ASP494 4.7 13.5 1.0
O A:HOH2244 4.7 11.3 1.0
CG A:GLU387 4.7 11.0 1.0
O A:HOH2816 4.7 14.1 1.0
OD1 A:ASP69 4.8 10.1 1.0
OD2 A:ASP69 4.8 11.3 1.0
CA A:CA1593 4.9 10.6 0.7
CB A:GLU387 4.9 8.2 1.0

Calcium binding site 2 out of 6 in 3zwu

Go back to Calcium Binding Sites List in 3zwu
Calcium binding site 2 out of 6 in the Pseudomonas Fluorescens Phox in Complex with Vanadate, A Transition State Analogue


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 Vanadate, A Transition State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1592

b:10.0
occ:0.94
OD2 A:ASP479 2.3 10.3 1.0
O A:HOH2722 2.4 10.4 1.0
O2 A:VO4700 2.4 8.2 0.7
OD2 A:ASP494 2.4 13.5 1.0
O A:HOH2721 2.4 17.3 1.0
OE1 A:GLU387 2.5 11.2 1.0
OE2 A:GLU387 2.6 11.1 1.0
CD A:GLU387 2.9 16.0 1.0
CG A:ASP479 3.3 9.2 1.0
O4 A:VO4700 3.4 12.3 0.7
V A:VO4700 3.4 14.6 0.7
CG A:ASP494 3.4 13.7 1.0
CA A:CA1591 3.6 9.7 0.9
CB A:ASP494 3.7 9.7 1.0
NH2 A:ARG385 3.8 19.2 1.0
O1 A:VO4700 3.8 12.0 0.7
CA A:CA1593 3.9 10.6 0.7
CB A:ASP479 4.0 9.7 1.0
O A:FEO1594 4.0 8.8 1.0
FE2 A:FEO1594 4.1 10.0 1.0
OD1 A:ASP479 4.1 9.4 1.0
CG A:GLU387 4.4 11.0 1.0
O A:ASP494 4.4 12.8 1.0
OG1 A:THR403 4.5 11.8 1.0
OD2 A:ASP292 4.5 10.7 1.0
OD1 A:ASP494 4.5 12.6 1.0
OE2 A:GLU532 4.6 12.8 1.0
CG2 A:THR403 4.6 11.1 1.0
O A:HOH2815 4.7 13.0 1.0
CZ A:ARG385 4.7 26.3 1.0
O A:HOH2720 4.8 26.4 1.0
CB A:THR403 4.9 13.6 1.0
O A:HOH2832 5.0 28.5 1.0

Calcium binding site 3 out of 6 in 3zwu

Go back to Calcium Binding Sites List in 3zwu
Calcium binding site 3 out of 6 in the Pseudomonas Fluorescens Phox in Complex with Vanadate, A Transition State Analogue


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 Vanadate, A Transition State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1593

b:10.6
occ:0.65
OE1 A:GLU532 2.3 11.7 1.0
O1 A:VO4700 2.4 12.0 0.7
O A:HOH2244 2.4 11.3 1.0
OD2 A:ASP494 2.5 13.5 1.0
O2 A:VO4700 2.5 8.2 0.7
O A:HOH2832 2.5 28.5 1.0
O A:HOH2252 2.6 16.7 1.0
OE2 A:GLU532 2.7 12.8 1.0
CD A:GLU532 2.8 12.2 1.0
V A:VO4700 3.1 14.6 0.7
CG A:ASP494 3.1 13.7 1.0
OD1 A:ASP494 3.4 12.6 1.0
O3 A:VO4700 3.8 9.0 0.7
O A:HOH2721 3.8 17.3 1.0
CA A:CA1592 3.9 10.0 0.9
O A:HOH2245 4.1 24.9 1.0
O A:HOH2196 4.2 11.1 1.0
OE1 A:GLN550 4.3 9.7 1.0
CG A:GLU532 4.3 12.0 1.0
CB A:ASP494 4.4 9.7 1.0
O A:HOH2910 4.4 31.1 1.0
O A:HOH2877 4.5 25.1 1.0
O4 A:VO4700 4.5 12.3 0.7
NE2 A:HIS551 4.5 11.6 1.0
OD2 A:ASP479 4.6 10.3 1.0
O A:HOH2815 4.7 13.0 1.0
CA A:CA1591 4.9 9.7 0.9
O A:FEO1594 4.9 8.8 1.0
OE1 A:GLU90 4.9 10.8 1.0
OH A:TYR91 5.0 12.6 1.0
CB A:GLU532 5.0 9.7 1.0

Calcium binding site 4 out of 6 in 3zwu

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Calcium binding site 4 out of 6 in the Pseudomonas Fluorescens Phox in Complex with Vanadate, A Transition State Analogue


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 Vanadate, A Transition State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1591

b:10.1
occ:1.00
OE2 B:GLU273 2.3 10.0 1.0
O B:FEO1594 2.4 9.9 1.0
OD2 B:ASP479 2.4 10.4 1.0
O B:HOH2706 2.5 11.2 1.0
O B:HOH2179 2.5 9.8 1.0
OD1 B:ASP479 2.5 11.2 1.0
O2 B:VO4700 2.6 9.8 0.7
O B:HOH2180 2.7 10.6 1.0
CG B:ASP479 2.8 11.7 1.0
OE2 B:GLU387 2.9 9.7 1.0
CD B:GLU273 3.4 9.1 1.0
FE2 B:FEO1594 3.6 9.4 1.0
CA B:CA1592 3.6 10.6 1.0
FE1 B:FEO1594 3.6 9.3 1.0
V B:VO4700 3.7 13.3 0.7
CD B:GLU387 3.7 12.8 1.0
OE1 B:GLU273 3.9 9.1 1.0
SG B:CYS179 4.0 11.3 1.0
NE1 B:TRP388 4.0 10.0 1.0
OE2 B:GLU532 4.2 10.8 1.0
OE1 B:GLU387 4.2 10.5 1.0
CB B:ASP479 4.3 8.9 1.0
O4 B:VO4700 4.3 10.8 0.7
O3 B:VO4700 4.4 8.2 0.7
CD1 B:TRP388 4.5 10.7 1.0
OG1 B:THR534 4.7 11.1 1.0
CG B:GLU273 4.7 8.6 1.0
OD2 B:ASP494 4.7 12.6 1.0
O B:HOH2213 4.7 10.4 1.0
O B:HOH2707 4.7 13.4 1.0
CG B:GLU387 4.7 8.8 1.0
OD1 B:ASP69 4.8 11.2 1.0
OD2 B:ASP69 4.8 10.7 1.0
CA B:CA1593 4.8 11.2 0.7
CB B:GLU387 4.9 8.2 1.0

Calcium binding site 5 out of 6 in 3zwu

Go back to Calcium Binding Sites List in 3zwu
Calcium binding site 5 out of 6 in the Pseudomonas Fluorescens Phox in Complex with Vanadate, A Transition State Analogue


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 Vanadate, A Transition State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1592

b:10.6
occ:1.00
OD2 B:ASP479 2.3 10.4 1.0
O B:HOH2621 2.3 10.4 1.0
O2 B:VO4700 2.4 9.8 0.7
OD2 B:ASP494 2.4 12.6 1.0
O B:HOH2620 2.4 14.5 1.0
OE1 B:GLU387 2.5 10.5 1.0
OE2 B:GLU387 2.6 9.7 1.0
CD B:GLU387 2.9 12.8 1.0
CG B:ASP479 3.3 11.7 1.0
O4 B:VO4700 3.4 10.8 0.7
V B:VO4700 3.4 13.3 0.7
CG B:ASP494 3.4 10.7 1.0
CA B:CA1591 3.6 10.1 1.0
CB B:ASP494 3.7 8.7 1.0
NH2 B:ARG385 3.8 17.2 1.0
O1 B:VO4700 3.9 11.0 0.7
CA B:CA1593 4.0 11.2 0.7
CB B:ASP479 4.0 8.9 1.0
FE2 B:FEO1594 4.1 9.4 1.0
OD1 B:ASP479 4.1 11.2 1.0
O B:FEO1594 4.1 9.9 1.0
CG B:GLU387 4.4 8.8 1.0
O B:ASP494 4.4 10.2 1.0
OG1 B:THR403 4.5 10.1 1.0
OD2 B:ASP292 4.5 10.5 1.0
OD1 B:ASP494 4.5 10.7 1.0
O B:HOH2723 4.5 30.3 1.0
OE2 B:GLU532 4.6 10.8 1.0
CG2 B:THR403 4.6 10.1 1.0
O B:HOH2706 4.7 11.2 1.0
CZ B:ARG385 4.7 25.4 1.0
CB B:THR403 4.9 11.8 1.0
O B:HOH2724 4.9 19.1 1.0
CA B:ASP494 5.0 7.3 1.0

Calcium binding site 6 out of 6 in 3zwu

Go back to Calcium Binding Sites List in 3zwu
Calcium binding site 6 out of 6 in the Pseudomonas Fluorescens Phox in Complex with Vanadate, A Transition State Analogue


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 Vanadate, A Transition State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1593

b:11.2
occ:0.71
OE1 B:GLU532 2.2 10.8 1.0
O1 B:VO4700 2.4 11.0 0.7
O B:HOH2724 2.4 19.1 1.0
O B:HOH2213 2.5 10.4 1.0
OD2 B:ASP494 2.5 12.6 1.0
O2 B:VO4700 2.5 9.8 0.7
O B:HOH2217 2.6 17.1 1.0
OE2 B:GLU532 2.7 10.8 1.0
CD B:GLU532 2.8 12.6 1.0
V B:VO4700 3.1 13.3 0.7
CG B:ASP494 3.1 10.7 1.0
OD1 B:ASP494 3.4 10.7 1.0
O B:HOH2620 3.7 14.5 1.0
O3 B:VO4700 3.7 8.2 0.7
CA B:CA1592 4.0 10.6 1.0
O B:HOH2212 4.2 21.9 1.0
O B:HOH2180 4.2 10.6 1.0
OE1 B:GLN550 4.3 10.2 1.0
CG B:GLU532 4.3 10.0 1.0
CB B:ASP494 4.4 8.7 1.0
O B:HOH2798 4.4 28.4 1.0
O B:HOH2764 4.5 21.4 1.0
O4 B:VO4700 4.5 10.8 0.7
NE2 B:HIS551 4.5 9.9 1.0
OD2 B:ASP479 4.6 10.4 1.0
O B:HOH2706 4.7 11.2 1.0
O B:HOH2723 4.7 30.3 1.0
CA B:CA1591 4.8 10.1 1.0
O B:FEO1594 4.9 9.9 1.0
OE1 B:GLU90 4.9 10.1 1.0
CB B:GLU532 5.0 8.4 1.0
OH B:TYR91 5.0 11.4 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: Sat Dec 12 04:37:40 2020

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