Calcium in PDB 3la6: Octameric Kinase Domain of the E. Coli Tyrosine Kinase Wzc with Bound Adp

The structure of Octameric Kinase Domain of the E. Coli Tyrosine Kinase Wzc with Bound Adp, PDB code: 3la6 was solved by J.Gruszczyk, S.Nessler, V.Gueguen-Chaignon, A.Vigouroux, E.Bechet, C.Grangeasse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.74 / 3.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	245.165, 137.782, 158.958, 90.00, 92.99, 90.00
R / Rfree (%)	18.6 / 22.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Calcium atom in the Octameric Kinase Domain of the E. Coli Tyrosine Kinase Wzc with Bound Adp (pdb code 3la6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the Octameric Kinase Domain of the E. Coli Tyrosine Kinase Wzc with Bound Adp, PDB code: 3la6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 in the Octameric Kinase Domain of the E. Coli Tyrosine Kinase Wzc with Bound Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Octameric Kinase Domain of the E. Coli Tyrosine Kinase Wzc with Bound Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:79.0 occ:1.00 OG1 A:THR541 2.2 65.2 1.0 O2B A:ADP1000 2.6 64.0 1.0 O3B A:ADP1000 3.4 62.8 1.0 OD2 A:ASP564 3.5 70.4 1.0 CB A:THR541 3.6 67.8 1.0 PB A:ADP1000 3.6 62.1 1.0 OH B:TYR715 3.8 83.3 1.0 OD1 A:ASP642 4.2 86.9 1.0 OD2 A:ASP642 4.2 87.3 1.0 CG A:MET540 4.3 83.9 1.0 N A:THR541 4.4 67.0 1.0 CG2 A:THR541 4.5 63.9 1.0 O A:THR643 4.5 74.1 1.0 CA A:THR541 4.5 65.8 1.0 CG A:ASP564 4.6 67.2 1.0 CG A:ASP642 4.6 84.1 1.0 O1B A:ADP1000 4.6 62.7 1.0 O3A A:ADP1000 4.8 62.9 1.0 CB A:ASP564 4.9 68.3 1.0

Calcium binding site 2 out of 16 in the Octameric Kinase Domain of the E. Coli Tyrosine Kinase Wzc with Bound Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Octameric Kinase Domain of the E. Coli Tyrosine Kinase Wzc with Bound Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:74.0 occ:1.00 OG1 B:THR541 2.2 85.4 1.0 O2B B:ADP1000 2.5 84.2 1.0 O3B B:ADP1000 3.5 83.1 1.0 CB B:THR541 3.6 84.4 1.0 PB B:ADP1000 3.6 82.2 1.0 OD2 B:ASP564 3.6 90.0 1.0 OD2 B:ASP642 4.0 91.2 1.0 OH C:TYR715 4.1 83.0 1.0 CG B:MET540 4.2 93.5 1.0 OD1 B:ASP642 4.3 84.0 1.0 N B:THR541 4.3 79.5 1.0 CG2 B:THR541 4.4 81.4 1.0 CA B:THR541 4.4 78.7 1.0 O1B B:ADP1000 4.6 82.7 1.0 CG B:ASP642 4.6 83.3 1.0 O B:THR643 4.7 70.7 1.0 CG B:ASP564 4.7 80.5 1.0 O3A B:ADP1000 4.7 83.1 1.0 SD B:MET540 4.9 99.2 1.0 O1A B:ADP1000 5.0 82.7 1.0 CB B:ASP564 5.0 71.9 1.0

Calcium binding site 3 out of 16 in the Octameric Kinase Domain of the E. Coli Tyrosine Kinase Wzc with Bound Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Octameric Kinase Domain of the E. Coli Tyrosine Kinase Wzc with Bound Adp within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1001 b:80.5 occ:1.00 OG1 C:THR541 2.2 86.3 1.0 O2B C:ADP1000 2.3 75.4 1.0 O3B C:ADP1000 3.1 74.3 1.0 PB C:ADP1000 3.4 73.4 1.0 CB C:THR541 3.5 85.3 1.0 OD2 C:ASP564 3.8 69.9 1.0 OD2 C:ASP642 4.2 93.1 1.0 OH D:TYR715 4.3 0.8 1.0 N C:THR541 4.3 77.0 1.0 CG C:MET540 4.3 89.2 1.0 O1B C:ADP1000 4.4 73.8 1.0 CG2 C:THR541 4.4 83.4 1.0 CA C:THR541 4.4 76.0 1.0 OD1 C:ASP642 4.5 88.6 1.0 O3A C:ADP1000 4.5 74.0 1.0 O1A C:ADP1000 4.7 72.8 1.0 CG C:ASP642 4.7 85.5 1.0 O C:THR643 4.8 63.7 1.0 PA C:ADP1000 4.9 73.5 1.0 CG C:ASP564 4.9 67.5 1.0 O2A C:ADP1000 5.0 74.6 1.0

Calcium binding site 4 out of 16 in the Octameric Kinase Domain of the E. Coli Tyrosine Kinase Wzc with Bound Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Octameric Kinase Domain of the E. Coli Tyrosine Kinase Wzc with Bound Adp within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1001 b:94.4 occ:1.00 OG1 D:THR541 2.4 90.2 1.0 O3B D:ADP1000 2.4 80.6 1.0 OD2 D:ASP564 3.3 93.3 1.0 OD2 D:ASP642 3.8 93.9 1.0 OH E:TYR715 3.8 82.3 1.0 PB D:ADP1000 3.9 79.9 1.0 CB D:THR541 3.9 88.2 1.0 OD1 D:ASP642 4.1 85.2 1.0 O D:THR643 4.1 74.5 1.0 O3A D:ADP1000 4.3 81.0 1.0 CG D:ASP642 4.3 85.2 1.0 CG D:ASP564 4.3 83.1 1.0 CG D:MET540 4.3 85.6 1.0 O1B D:ADP1000 4.5 80.4 1.0 CB D:ASP564 4.5 75.3 1.0 N D:THR541 4.6 78.5 1.0 CG2 D:THR541 4.6 86.9 1.0 CA D:THR541 4.7 78.0 1.0 C D:THR643 4.9 76.2 1.0 O2B D:ADP1000 4.9 81.7 1.0 SD D:MET540 5.0 91.3 1.0 CA D:PRO644 5.0 73.8 1.0 O1A D:ADP1000 5.0 83.3 1.0

Calcium binding site 5 out of 16 in the Octameric Kinase Domain of the E. Coli Tyrosine Kinase Wzc with Bound Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Octameric Kinase Domain of the E. Coli Tyrosine Kinase Wzc with Bound Adp within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca1001 b:86.6 occ:1.00 OG1 E:THR541 2.1 77.8 1.0 O3B E:ADP1000 2.3 77.2 1.0 CB E:THR541 3.5 82.6 1.0 OD2 E:ASP642 3.7 0.8 1.0 OD2 E:ASP564 3.7 95.3 1.0 PB E:ADP1000 3.7 76.4 1.0 O1B E:ADP1000 3.9 76.8 1.0 OD1 E:ASP642 4.0 99.8 1.0 OH F:TYR715 4.2 87.6 1.0 N E:THR541 4.2 80.3 1.0 CG E:MET540 4.3 89.5 1.0 CG E:ASP642 4.3 97.4 1.0 CA E:THR541 4.3 79.0 1.0 CG2 E:THR541 4.3 81.3 1.0 O E:THR643 4.4 73.5 1.0 O2B E:ADP1000 4.6 78.1 1.0 CG E:ASP564 4.7 87.6 1.0 O3A E:ADP1000 4.9 77.1 1.0 CB E:ASP564 5.0 79.5 1.0

Calcium binding site 6 out of 16 in the Octameric Kinase Domain of the E. Coli Tyrosine Kinase Wzc with Bound Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Octameric Kinase Domain of the E. Coli Tyrosine Kinase Wzc with Bound Adp within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca1001 b:83.2 occ:1.00 OG1 F:THR541 2.2 83.3 1.0 O2B F:ADP1000 2.5 75.4 1.0 O3B F:ADP1000 3.3 74.3 1.0 PB F:ADP1000 3.5 73.6 1.0 CB F:THR541 3.5 82.5 1.0 OD2 F:ASP564 3.7 75.9 1.0 OH G:TYR715 3.9 0.8 1.0 OD2 F:ASP642 4.0 87.1 1.0 N F:THR541 4.4 78.0 1.0 OD1 F:ASP642 4.4 82.3 1.0 CG F:MET540 4.4 93.1 1.0 CG2 F:THR541 4.4 76.9 1.0 CA F:THR541 4.5 76.8 1.0 O1B F:ADP1000 4.5 74.1 1.0 CG F:ASP642 4.6 80.8 1.0 O3A F:ADP1000 4.7 74.4 1.0 O F:THR643 4.7 63.1 1.0 CG F:ASP564 4.8 72.1 1.0 O1A F:ADP1000 4.9 74.7 1.0

Calcium binding site 7 out of 16 in the Octameric Kinase Domain of the E. Coli Tyrosine Kinase Wzc with Bound Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Octameric Kinase Domain of the E. Coli Tyrosine Kinase Wzc with Bound Adp within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca1001 b:89.5 occ:1.00 OG1 G:THR541 2.3 97.7 1.0 O3B G:ADP1000 2.5 87.3 1.0 OD2 G:ASP564 3.6 0.5 1.0 O1B G:ADP1000 3.6 87.1 1.0 CB G:THR541 3.7 95.7 1.0 PB G:ADP1000 3.7 86.5 1.0 OD2 G:ASP642 4.0 99.4 1.0 OH H:TYR715 4.1 0.1 1.0 OD1 G:ASP642 4.3 88.8 1.0 CG G:MET540 4.4 99.6 1.0 N G:THR541 4.5 87.3 1.0 CG2 G:THR541 4.5 93.5 1.0 CG G:ASP642 4.6 89.0 1.0 O G:THR643 4.6 79.1 1.0 CA G:THR541 4.6 86.1 1.0 CG G:ASP564 4.6 96.5 1.0 O2B G:ADP1000 4.7 88.3 1.0 O1A G:ADP1000 4.8 85.9 1.0 O3A G:ADP1000 4.9 87.2 1.0 CB G:ASP564 4.9 87.5 1.0

Calcium binding site 8 out of 16 in the Octameric Kinase Domain of the E. Coli Tyrosine Kinase Wzc with Bound Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Octameric Kinase Domain of the E. Coli Tyrosine Kinase Wzc with Bound Adp within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca1001 b:79.1 occ:1.00 OG1 H:THR541 2.3 84.2 1.0 O3B H:ADP1000 2.3 82.2 1.0 OD2 H:ASP564 3.6 88.6 1.0 CB H:THR541 3.6 82.8 1.0 PB H:ADP1000 3.7 81.3 1.0 O1B H:ADP1000 3.8 81.9 1.0 OH A:TYR715 3.9 80.8 1.0 OD2 H:ASP642 3.9 88.8 1.0 OD1 H:ASP642 4.2 84.0 1.0 CG H:MET540 4.2 93.0 1.0 O H:THR643 4.4 71.4 1.0 N H:THR541 4.4 79.8 1.0 CG H:ASP642 4.5 82.4 1.0 CA H:THR541 4.5 78.4 1.0 O2B H:ADP1000 4.5 83.2 1.0 CG2 H:THR541 4.5 77.0 1.0 CG H:ASP564 4.7 80.9 1.0 CB H:ASP564 4.9 78.4 1.0 O3A H:ADP1000 4.9 82.0 1.0 SD H:MET540 5.0 99.4 1.0

Calcium binding site 9 out of 16 in the Octameric Kinase Domain of the E. Coli Tyrosine Kinase Wzc with Bound Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Octameric Kinase Domain of the E. Coli Tyrosine Kinase Wzc with Bound Adp within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca1001 b:82.4 occ:1.00 OG1 I:THR541 2.3 92.4 1.0 O2B I:ADP1000 2.6 86.1 1.0 O3B I:ADP1000 3.5 84.9 1.0 PB I:ADP1000 3.6 84.3 1.0 CB I:THR541 3.7 88.1 1.0 OD2 I:ASP564 3.7 74.7 1.0 OH J:TYR715 3.7 91.1 1.0 OD2 I:ASP642 3.9 0.7 1.0 CG I:MET540 4.1 88.8 1.0 OD1 I:ASP642 4.1 90.6 1.0 O I:THR643 4.3 66.9 1.0 N I:THR541 4.3 76.2 1.0 CG I:ASP642 4.4 90.9 1.0 CA I:THR541 4.5 74.8 1.0 O1B I:ADP1000 4.5 84.8 1.0 CG2 I:THR541 4.6 87.5 1.0 CG I:ASP564 4.7 70.4 1.0 SD I:MET540 4.8 94.2 1.0 O3A I:ADP1000 4.9 85.1 1.0 CE I:MET540 4.9 90.9 1.0 CB I:ASP564 4.9 69.7 1.0

Calcium binding site 10 out of 16 in the Octameric Kinase Domain of the E. Coli Tyrosine Kinase Wzc with Bound Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Octameric Kinase Domain of the E. Coli Tyrosine Kinase Wzc with Bound Adp within 5.0Å range: probe atom residue distance (Å) B Occ J:Ca1001 b:81.8 occ:1.00 OG1 J:THR541 2.2 92.5 1.0 O2B J:ADP1000 2.4 76.2 1.0 O3B J:ADP1000 3.4 75.0 1.0 PB J:ADP1000 3.5 74.3 1.0 CB J:THR541 3.5 90.0 1.0 OD2 J:ASP564 3.8 90.4 1.0 OD2 J:ASP642 3.9 95.9 1.0 OH K:TYR715 3.9 79.9 1.0 CG J:MET540 4.0 87.9 1.0 OD1 J:ASP642 4.1 92.0 1.0 N J:THR541 4.2 79.8 1.0 CA J:THR541 4.4 79.0 1.0 CG J:ASP642 4.4 90.5 1.0 O1B J:ADP1000 4.4 74.8 1.0 O J:THR643 4.5 65.8 1.0 CG2 J:THR541 4.5 87.6 1.0 O3A J:ADP1000 4.7 75.4 1.0 SD J:MET540 4.8 93.5 1.0 CG J:ASP564 4.9 81.7 1.0 CE J:MET540 4.9 90.5 1.0

E.Bechet, J.Gruszczyk, R.Terreux, V.Gueguen-Chaignon, A.Vigouroux, B.Obadia, A.J.Cozzone, S.Nessler, C.Grangeasse. Identification of Structural and Molecular Determinants of the Tyrosine-Kinase Wzc and Implications in Capsular Polysaccharide Export Mol.Microbiol. V. 77 1315 2010.
ISSN: ISSN 0950-382X
PubMed: 20633230
DOI: 10.1111/J.1365-2958.2010.07291.X