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Calcium in PDB 4equ: Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7

Enzymatic activity of Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7

All present enzymatic activity of Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7:
2.7.11.1;

Protein crystallography data

The structure of Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7, PDB code: 4equ was solved by E.A.Merritt, E.T.Larson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.810, 49.040, 133.760, 90.00, 101.42, 90.00
R / Rfree (%) 22.3 / 24.6

Other elements in 4equ:

The structure of Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7 also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7 (pdb code 4equ). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7, PDB code: 4equ:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4equ

Go back to Calcium Binding Sites List in 4equ
Calcium binding site 1 out of 5 in the Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:69.1
occ:1.00
 OE2 A:GLU316 2.1 64.2 1.0
O A:HOH509 2.3 47.2 1.0
O A:HOH510 2.5 68.7 1.0
OE1 A:GLU313 3.4 69.1 1.0
CD A:GLU316 3.4 65.5 1.0
O A:HOH518 3.7 57.2 1.0
CG A:GLU316 4.2 62.1 1.0
OE1 A:GLU316 4.3 68.7 1.0
CD A:GLU313 4.5 65.1 1.0
OE2 A:GLU313 4.9 72.1 1.0

Calcium binding site 2 out of 5 in 4equ

Go back to Calcium Binding Sites List in 4equ
Calcium binding site 2 out of 5 in the Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:92.4
occ:1.00
 O A:HOH519 2.2 71.0 1.0
O A:HOH520 2.6 56.7 1.0
OE1 A:GLU234 2.6 66.2 1.0
O A:HOH522 2.6 78.1 1.0
O A:HOH523 2.7 61.8 1.0
OE2 A:GLU234 2.8 64.9 1.0
CD A:GLU234 3.0 60.3 1.0
O A:HOH521 3.1 58.3 1.0
CG A:GLU234 4.5 55.3 1.0

Calcium binding site 3 out of 5 in 4equ

Go back to Calcium Binding Sites List in 4equ
Calcium binding site 3 out of 5 in the Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:30.6
occ:0.50
 OE2 B:GLU316 2.1 49.4 1.0
O B:HOH526 2.2 44.7 1.0
CD B:GLU316 3.3 47.9 1.0
OE1 B:GLU313 3.3 53.3 1.0
O B:HOH529 3.8 36.0 1.0
CG B:GLU316 4.1 45.9 1.0
OE1 B:GLU316 4.3 47.9 1.0
CD B:GLU313 4.4 51.6 1.0
OE2 B:GLU313 4.9 53.1 1.0

Calcium binding site 4 out of 5 in 4equ

Go back to Calcium Binding Sites List in 4equ
Calcium binding site 4 out of 5 in the Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:61.5
occ:0.50
 O B:HOH527 2.6 60.9 1.0
OE2 B:GLU168 3.1 60.1 1.0
O B:HOH542 3.2 47.5 1.0
OE1 B:GLU168 3.3 58.8 1.0
CD B:GLU168 3.6 54.5 1.0
OD2 B:ASP170 4.3 38.5 1.0
NH2 B:ARG172 4.4 32.9 1.0

Calcium binding site 5 out of 5 in 4equ

Go back to Calcium Binding Sites List in 4equ
Calcium binding site 5 out of 5 in the Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:69.8
occ:1.00
 O B:HOH530 2.2 67.8 1.0
OE2 B:GLU234 2.5 63.8 1.0
OE1 B:GLU234 2.6 60.3 1.0
O B:HOH531 2.7 63.8 1.0
O B:HOH533 2.8 66.8 1.0
O B:HOH534 2.8 59.9 1.0
CD B:GLU234 2.9 54.7 1.0
O B:HOH532 3.3 65.5 1.0
CG B:GLU234 4.4 48.2 1.0

Reference:

P.Ranjitkar, B.G.Perera, D.L.Swaney, S.B.Hari, E.T.Larson, R.Krishnamurty, E.A.Merritt, J.Villen, D.J.Maly. Affinity-Based Probes Based on Type II Kinase Inhibitors. J.Am.Chem.Soc. V. 134 19017 2012.
ISSN: ISSN 0002-7863
PubMed: 23088519
DOI: 10.1021/JA306035V
Page generated: Tue Jul 8 19:51:43 2025

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