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Calcium in PDB 6y81: Fragment KCL_1088 in Complex with Map Kinase P38-Alpha

Enzymatic activity of Fragment KCL_1088 in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Fragment KCL_1088 in Complex with Map Kinase P38-Alpha:
2.7.11.24;

Protein crystallography data

The structure of Fragment KCL_1088 in Complex with Map Kinase P38-Alpha, PDB code: 6y81 was solved by G.F.De Nicola, C.E.Nichols, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.87 / 1.54
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 80.818, 102.350, 104.261, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 21.6

Other elements in 6y81:

The structure of Fragment KCL_1088 in Complex with Map Kinase P38-Alpha also contains other interesting chemical elements:

Fluorine (F) 1 atom
Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Fragment KCL_1088 in Complex with Map Kinase P38-Alpha (pdb code 6y81). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Fragment KCL_1088 in Complex with Map Kinase P38-Alpha, PDB code: 6y81:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6y81

Go back to Calcium Binding Sites List in 6y81
Calcium binding site 1 out of 6 in the Fragment KCL_1088 in Complex with Map Kinase P38-Alpha


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Fragment KCL_1088 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:18.7
occ:1.00
 O A:GLU356 2.3 23.5 1.0
OD1 A:ASP354 2.5 20.0 1.0
OD2 A:ASP354 2.6 20.9 1.0
CG A:ASP354 2.9 22.8 1.0
C A:GLU356 3.4 20.3 1.0
N A:GLU357 4.3 21.8 1.0
O A:HOH513 4.3 23.4 1.0
CA A:GLU356 4.3 22.6 1.0
N A:GLU356 4.3 20.8 1.0
CA A:GLU357 4.4 22.1 1.0
CB A:ASP354 4.4 17.6 1.0
CB A:GLU356 4.6 22.3 1.0
O A:HOH703 4.6 32.6 1.0

Calcium binding site 2 out of 6 in 6y81

Go back to Calcium Binding Sites List in 6y81
Calcium binding site 2 out of 6 in the Fragment KCL_1088 in Complex with Map Kinase P38-Alpha


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Fragment KCL_1088 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:20.5
occ:1.00
 OD2 A:ASP313 2.3 22.9 1.0
O A:HOH529 2.4 28.2 1.0
O A:HOH571 2.4 19.1 1.0
OE2 A:GLU359 2.6 30.4 1.0
CG A:ASP313 3.4 23.1 1.0
CD A:GLU359 3.6 40.8 1.0
CB A:ASP313 3.8 18.9 1.0
OE1 A:GLU359 4.0 44.9 1.0
O A:HOH698 4.4 47.5 1.0
OD2 A:ASP316 4.5 22.7 1.0
OD1 A:ASP313 4.5 23.5 1.0
O A:HOH535 4.6 24.1 1.0
CB A:ASP316 4.8 18.7 1.0
CG A:GLU359 4.9 34.9 1.0
O A:HOH650 4.9 36.5 1.0

Calcium binding site 3 out of 6 in 6y81

Go back to Calcium Binding Sites List in 6y81
Calcium binding site 3 out of 6 in the Fragment KCL_1088 in Complex with Map Kinase P38-Alpha


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Fragment KCL_1088 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:50.7
occ:1.00
 O A:HOH682 2.5 48.1 1.0
OD2 A:ASP315 2.8 56.5 1.0
O A:HOH698 3.4 47.5 1.0
CG A:ASP315 3.7 48.5 1.0
CB A:ASP315 4.0 35.6 1.0
OD1 A:ASP313 4.5 23.5 1.0
OD1 A:ASP315 4.9 49.4 1.0

Calcium binding site 4 out of 6 in 6y81

Go back to Calcium Binding Sites List in 6y81
Calcium binding site 4 out of 6 in the Fragment KCL_1088 in Complex with Map Kinase P38-Alpha


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Fragment KCL_1088 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:43.8
occ:0.47
 O A:HOH637 2.6 38.6 1.0
O A:HOH580 2.7 46.1 1.0
OE2 A:GLU163 4.5 32.2 1.0
O A:HOH566 4.5 35.4 1.0
O A:HOH713 4.7 41.2 0.5
OE2 A:GLU356 4.7 36.3 1.0
O A:HOH703 4.9 32.6 1.0
OE1 A:GLU163 4.9 32.8 1.0

Calcium binding site 5 out of 6 in 6y81

Go back to Calcium Binding Sites List in 6y81
Calcium binding site 5 out of 6 in the Fragment KCL_1088 in Complex with Map Kinase P38-Alpha


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Fragment KCL_1088 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:54.0
occ:1.00
 OD1 A:ASP283 2.5 32.7 1.0
CG A:ASP283 3.5 27.1 1.0
CB A:ASP283 3.8 22.6 1.0
CA A:ASP283 4.1 22.9 1.0
O A:HOH641 4.3 34.4 1.0
OD2 A:ASP283 4.6 27.6 1.0
N A:ASP283 4.9 23.6 1.0

Calcium binding site 6 out of 6 in 6y81

Go back to Calcium Binding Sites List in 6y81
Calcium binding site 6 out of 6 in the Fragment KCL_1088 in Complex with Map Kinase P38-Alpha


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Fragment KCL_1088 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:63.6
occ:1.00
 N A:ASN269 3.3 31.1 1.0
CA A:MET268 3.7 29.9 1.0
CB A:MET268 3.7 32.1 1.0
ND2 A:ASN272 3.7 49.9 1.0
C A:MET268 4.0 30.7 1.0
CG A:MET268 4.0 32.9 1.0
CE A:MET268 4.1 41.9 1.0
CB A:ASN272 4.1 40.5 1.0
O A:ASN269 4.1 28.8 1.0
CB A:ASN269 4.2 35.5 1.0
CA A:ASN269 4.2 30.6 1.0
CG A:ASN272 4.4 46.2 1.0
C A:ASN269 4.6 28.2 1.0
SD A:MET268 4.9 40.5 1.0

Reference:

G.F.De Nicola, C.E.Nichols. Fragment KCL_1088 in Complex with Map Kinase P38-Alpha To Be Published.
Page generated: Wed Jul 9 20:17:19 2025

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