Atomistry » Calcium » PDB 3zni-4a08 » 3zwu
Atomistry »
  Calcium »
    PDB 3zni-4a08 »
      3zwu »

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

Go back to Calcium Binding Sites List in 3zwu
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

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy