Calcium in PDB 4yga: CDPK1, From Toxoplasma Gondii, Bound to Inhibitory Vhh-1B7

The structure of CDPK1, From Toxoplasma Gondii, Bound to Inhibitory Vhh-1B7, PDB code: 4yga was solved by K.E.Knockenhauer, T.U.Schwartz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.67 / 2.94
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	76.920, 91.067, 106.641, 88.71, 108.27, 90.26
R / Rfree (%)	22.6 / 26.2

Pages:

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

Binding sites:

The binding sites of Calcium atom in the CDPK1, From Toxoplasma Gondii, Bound to Inhibitory Vhh-1B7 (pdb code 4yga). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the CDPK1, From Toxoplasma Gondii, Bound to Inhibitory Vhh-1B7, PDB code: 4yga:
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 CDPK1, From Toxoplasma Gondii, Bound to Inhibitory Vhh-1B7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of CDPK1, From Toxoplasma Gondii, Bound to Inhibitory Vhh-1B7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:80.3 occ:1.00 OD1 A:ASN370 2.4 86.8 1.0 O A:GLN374 2.4 86.2 1.0 OD1 A:ASP372 2.5 0.2 1.0 OE2 A:GLU379 2.5 0.8 1.0 OD2 A:ASP372 2.7 0.4 1.0 OD1 A:ASP368 2.8 65.5 1.0 CG A:ASP372 2.9 99.9 1.0 OE1 A:GLU379 2.9 0.6 1.0 CD A:GLU379 3.0 0.8 1.0 CG A:ASN370 3.3 83.4 1.0 C A:GLN374 3.5 83.4 1.0 ND2 A:ASN370 3.5 83.6 1.0 CG A:ASP368 4.0 77.0 1.0 CA A:GLN374 4.2 75.5 1.0 N A:GLN374 4.2 85.5 1.0 CB A:ASP372 4.3 92.3 1.0 OD2 A:ASP376 4.3 0.4 1.0 N A:LEU375 4.4 89.6 1.0 CB A:GLN374 4.4 75.5 1.0 CG A:GLU379 4.5 0.8 1.0 CA A:LEU375 4.5 89.5 1.0 N A:ASP372 4.5 81.4 1.0 OD2 A:ASP368 4.6 78.3 1.0 N A:ASP376 4.6 95.2 1.0 CB A:ASN370 4.6 76.8 1.0 CG A:ASP376 4.6 0.6 1.0 N A:ASN370 4.7 88.4 1.0 C A:LEU375 4.9 88.5 1.0 N A:GLY371 4.9 82.5 1.0 CA A:ASP368 5.0 85.0 1.0 CA A:ASP372 5.0 86.1 1.0 OD1 A:ASP376 5.0 0.2 1.0

Calcium binding site 2 out of 16 in the CDPK1, From Toxoplasma Gondii, Bound to Inhibitory Vhh-1B7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of CDPK1, From Toxoplasma Gondii, Bound to Inhibitory Vhh-1B7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:81.4 occ:1.00 OD1 A:ASP417 2.3 0.8 1.0 O A:TYR421 2.3 60.5 1.0 OD1 A:ASP415 2.4 0.4 1.0 OE1 A:GLU426 2.5 56.9 1.0 OE2 A:GLU426 2.6 76.2 1.0 OD1 A:ASN419 2.6 85.8 1.0 CD A:GLU426 2.8 73.0 1.0 CG A:ASP417 3.1 0.1 1.0 OD2 A:ASP417 3.1 0.1 1.0 CG A:ASN419 3.4 85.3 1.0 C A:TYR421 3.5 74.3 1.0 CG A:ASP415 3.6 0.4 1.0 ND2 A:ASN419 3.6 91.7 1.0 CG A:GLU423 4.0 79.3 1.0 OE1 A:GLU423 4.2 0.3 1.0 N A:GLU423 4.2 73.2 1.0 CA A:ILE422 4.2 75.3 1.0 OD2 A:ASP415 4.2 0.4 1.0 N A:ILE422 4.3 68.9 1.0 CG A:GLU426 4.3 79.4 1.0 OH B:TYR107 4.3 84.4 1.0 CD A:GLU423 4.4 89.7 1.0 CA A:TYR421 4.5 85.9 1.0 N A:TYR421 4.5 91.4 1.0 CB A:ASP417 4.5 0.3 1.0 N A:ASP417 4.6 0.2 1.0 C A:ILE422 4.7 79.8 1.0 CB A:ASP415 4.7 0.0 1.0 N A:ASN419 4.7 0.6 1.0 CB A:ASN419 4.8 83.7 1.0 CA A:ASP415 4.8 0.0 1.0 CB A:TYR421 4.8 86.8 1.0 C A:ASP415 4.9 98.3 1.0 N A:LYS418 4.9 0.9 1.0 N A:PHE416 4.9 85.2 1.0 CB A:GLU423 5.0 69.2 1.0 CE1 B:TYR107 5.0 66.7 1.0

Calcium binding site 3 out of 16 in the CDPK1, From Toxoplasma Gondii, Bound to Inhibitory Vhh-1B7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of CDPK1, From Toxoplasma Gondii, Bound to Inhibitory Vhh-1B7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:81.0 occ:1.00 OE1 A:GLU462 2.4 98.1 1.0 OG A:SER455 2.5 0.6 1.0 O A:LYS457 2.5 0.4 1.0 OD1 A:ASP451 2.5 84.7 1.0 OD1 A:ASP453 2.6 0.7 1.0 OD2 A:ASP453 2.9 0.2 1.0 CG A:ASP453 3.1 0.5 1.0 CD A:GLU462 3.2 95.4 1.0 OE2 A:GLU462 3.5 94.6 1.0 CB A:SER455 3.6 0.2 1.0 C A:LYS457 3.7 99.6 1.0 CG A:ASP451 3.7 82.8 1.0 OG A:SER459 3.8 0.4 1.0 N A:SER455 4.0 0.6 1.0 OE2 A:GLU491 4.3 0.4 1.0 OD2 A:ASP451 4.4 77.9 1.0 CA A:SER455 4.4 0.5 1.0 N A:SER459 4.4 0.8 1.0 N A:LYS457 4.5 97.1 1.0 CB A:ASP453 4.5 0.4 1.0 CG A:GLU462 4.5 88.3 1.0 CA A:LYS457 4.6 96.3 1.0 N A:ILE458 4.6 97.6 1.0 CA A:ILE458 4.6 88.6 1.0 N A:ASP453 4.7 0.9 1.0 N A:ASN454 4.7 0.1 1.0 CB A:ASP451 4.7 83.5 1.0 CA A:ASP451 4.8 84.7 1.0 N A:GLY456 4.9 0.4 1.0 CB A:SER459 4.9 0.2 1.0 C A:ASP453 4.9 0.4 1.0 CA A:ASP453 4.9 0.8 1.0 C A:ILE458 5.0 95.0 1.0

Calcium binding site 4 out of 16 in the CDPK1, From Toxoplasma Gondii, Bound to Inhibitory Vhh-1B7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of CDPK1, From Toxoplasma Gondii, Bound to Inhibitory Vhh-1B7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:94.8 occ:1.00 OD1 A:ASN487 2.4 0.7 1.0 O A:GLU491 2.4 87.3 1.0 OE1 A:GLU496 2.4 94.4 1.0 OD1 A:ASP485 2.4 83.4 1.0 OD1 A:ASP489 2.5 0.5 1.0 OD2 A:ASP489 2.9 98.5 1.0 OE2 A:GLU496 2.9 92.3 1.0 CG A:ASP489 2.9 0.7 1.0 CD A:GLU496 3.0 87.2 1.0 CG A:ASN487 3.5 0.9 1.0 C A:GLU491 3.5 85.6 1.0 CG A:ASP485 3.6 91.4 1.0 ND2 A:ASN487 4.0 0.5 1.0 N A:ASP489 4.2 0.7 1.0 N A:GLU491 4.2 98.3 1.0 OD2 A:ASP493 4.2 0.9 1.0 CB A:ASP489 4.3 0.1 1.0 N A:ASN487 4.3 1.0 1.0 N A:VAL492 4.3 72.0 1.0 CA A:VAL492 4.4 74.7 1.0 CA A:ASP485 4.4 87.1 1.0 CA A:GLU491 4.4 98.2 1.0 OD2 A:ASP485 4.4 0.2 1.0 N A:LYS486 4.4 0.1 1.0 CG A:GLU496 4.5 80.5 1.0 N A:ASN488 4.5 0.1 1.0 CB A:ASP485 4.5 85.0 1.0 N A:ASP493 4.6 78.6 1.0 C A:ASP485 4.7 98.1 1.0 CB A:ASN487 4.7 0.8 1.0 CA A:ASP489 4.7 0.8 1.0 N A:GLY490 4.7 98.7 1.0 CA A:ASN487 4.9 0.3 1.0 C A:ASN487 4.9 0.9 1.0 CG A:ASP493 4.9 0.3 1.0 C A:VAL492 5.0 75.4 1.0

Calcium binding site 5 out of 16 in the CDPK1, From Toxoplasma Gondii, Bound to Inhibitory Vhh-1B7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of CDPK1, From Toxoplasma Gondii, Bound to Inhibitory Vhh-1B7 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca601 b:96.2 occ:1.00 OE2 C:GLU379 2.4 0.5 1.0 O C:GLN374 2.4 0.7 1.0 OD2 C:ASP372 2.5 0.1 1.0 OD1 C:ASP372 2.5 1.0 1.0 ND2 C:ASN370 2.5 0.1 1.0 CG C:ASP372 2.8 0.2 1.0 OD1 C:ASP368 2.9 94.6 1.0 CD C:GLU379 3.2 0.4 1.0 OE1 C:GLU379 3.4 0.7 1.0 CG C:ASN370 3.5 0.5 1.0 C C:GLN374 3.5 0.4 1.0 OD1 C:ASN370 3.6 0.6 1.0 CG C:ASP368 4.1 0.1 1.0 OD2 C:ASP376 4.2 0.7 1.0 CB C:ASP372 4.2 0.3 1.0 CA C:GLN374 4.3 0.1 1.0 N C:GLN374 4.3 0.2 1.0 N C:LEU375 4.4 98.5 1.0 CB C:GLN374 4.4 0.0 1.0 CA C:LEU375 4.5 98.5 1.0 CG C:ASP376 4.5 0.7 1.0 N C:ASP376 4.6 0.6 1.0 CG C:GLU379 4.6 0.9 1.0 N C:ASP372 4.6 0.2 1.0 OD2 C:ASP368 4.6 0.2 1.0 CB C:ASN370 4.8 0.8 1.0 C C:LEU375 4.9 0.3 1.0 CA C:ASP372 4.9 0.3 1.0 OD1 C:ASP376 5.0 0.5 1.0

Calcium binding site 6 out of 16 in the CDPK1, From Toxoplasma Gondii, Bound to Inhibitory Vhh-1B7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of CDPK1, From Toxoplasma Gondii, Bound to Inhibitory Vhh-1B7 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca602 b:81.8 occ:1.00 O C:TYR421 2.4 92.2 1.0 OD1 C:ASP417 2.4 0.1 1.0 OD1 C:ASP415 2.6 0.8 1.0 OD1 C:ASN419 2.6 89.6 1.0 OE1 C:GLU426 2.6 97.9 1.0 OE2 C:GLU426 2.8 0.6 1.0 ND2 C:ASN419 3.0 0.3 1.0 CD C:GLU426 3.1 0.6 1.0 CG C:ASN419 3.1 96.5 1.0 CG C:ASP417 3.1 0.3 1.0 OD2 C:ASP417 3.1 0.0 1.0 C C:TYR421 3.5 0.2 1.0 CG C:ASP415 3.5 0.1 1.0 OD2 C:ASP415 3.8 0.4 1.0 CG C:GLU423 3.9 0.8 1.0 N C:GLU423 4.1 97.9 1.0 OE2 C:GLU423 4.1 0.5 1.0 CA C:ILE422 4.2 0.2 1.0 CD C:GLU423 4.3 0.4 1.0 N C:ILE422 4.3 0.0 1.0 OH D:TYR107 4.5 0.4 1.0 N C:TYR421 4.5 0.9 1.0 CB C:ASN419 4.5 0.2 1.0 CA C:TYR421 4.5 0.1 1.0 N C:ASN419 4.6 0.2 1.0 CB C:ASP417 4.6 0.3 1.0 CG C:GLU426 4.6 98.3 1.0 C C:ILE422 4.7 95.3 1.0 N C:ASP417 4.7 1.0 1.0 CB C:GLU423 4.8 99.8 1.0 N C:LYS418 4.9 0.4 1.0 CB C:TYR421 4.9 0.2 1.0 CB C:ASP415 4.9 0.8 1.0

Calcium binding site 7 out of 16 in the CDPK1, From Toxoplasma Gondii, Bound to Inhibitory Vhh-1B7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of CDPK1, From Toxoplasma Gondii, Bound to Inhibitory Vhh-1B7 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca603 b:89.1 occ:1.00 OD1 C:ASP451 2.4 84.3 1.0 OE2 C:GLU462 2.4 96.1 1.0 O C:LYS457 2.5 91.6 1.0 OD1 C:ASP453 2.5 0.5 1.0 OG C:SER455 2.5 95.4 1.0 OD2 C:ASP453 2.7 0.1 1.0 CG C:ASP453 2.9 0.0 1.0 CD C:GLU462 3.1 0.8 1.0 OE1 C:GLU462 3.3 0.1 1.0 CG C:ASP451 3.6 80.0 1.0 C C:LYS457 3.7 77.7 1.0 CB C:SER455 3.7 95.3 1.0 N C:SER455 4.0 99.1 1.0 OD2 C:ASP451 4.3 77.5 1.0 CB C:ASP453 4.3 0.2 1.0 N C:SER459 4.4 72.6 1.0 CG C:GLU462 4.4 93.5 1.0 CA C:SER455 4.5 95.2 1.0 N C:LYS457 4.5 74.5 1.0 CA C:ILE458 4.5 72.2 1.0 N C:ASP453 4.5 90.4 1.0 N C:ILE458 4.5 73.1 1.0 CB C:ASP451 4.6 73.5 1.0 N C:ASN454 4.6 0.4 1.0 CA C:ASP451 4.6 79.1 1.0 CA C:LYS457 4.6 77.1 1.0 CA C:ASP453 4.8 99.3 1.0 C C:ASP453 4.8 0.3 1.0 N C:GLY456 4.9 91.7 1.0 C C:ILE458 4.9 73.4 1.0 C C:ASP451 4.9 87.6 1.0 N C:SER452 4.9 86.0 1.0 CB C:SER459 5.0 85.3 1.0

Calcium binding site 8 out of 16 in the CDPK1, From Toxoplasma Gondii, Bound to Inhibitory Vhh-1B7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of CDPK1, From Toxoplasma Gondii, Bound to Inhibitory Vhh-1B7 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca604 b:82.8 occ:1.00 O C:GLU491 2.4 92.0 1.0 OE2 C:GLU496 2.4 0.1 1.0 OD1 C:ASP485 2.5 82.1 1.0 OD1 C:ASP489 2.5 0.7 1.0 OD1 C:ASN487 2.6 0.7 1.0 OD2 C:ASP489 2.6 91.9 1.0 OE1 C:GLU496 2.7 97.6 1.0 CG C:ASP489 2.8 99.0 1.0 CD C:GLU496 2.9 0.0 1.0 C C:GLU491 3.5 90.8 1.0 OD2 C:ASP493 3.6 93.7 1.0 CG C:ASN487 3.6 0.9 1.0 CG C:ASP485 3.7 82.7 1.0 ND2 C:ASN487 4.0 0.7 1.0 N C:ASP493 4.2 78.5 1.0 CA C:VAL492 4.2 73.9 1.0 CB C:ASP489 4.3 98.9 1.0 N C:VAL492 4.3 79.4 1.0 CG C:ASP493 4.3 99.0 1.0 CG C:GLU496 4.3 0.3 1.0 N C:GLU491 4.3 0.4 1.0 N C:ASP489 4.3 0.1 1.0 OD2 C:ASP485 4.4 81.7 1.0 CA C:GLU491 4.5 92.9 1.0 N C:ASN487 4.6 0.1 1.0 CA C:ASP485 4.6 78.4 1.0 CB C:ASP485 4.7 79.6 1.0 C C:VAL492 4.7 74.9 1.0 N C:LYS486 4.7 89.4 1.0 CA C:ASP489 4.8 0.5 1.0 N C:ASN488 4.8 0.2 1.0 OD1 C:ASP493 4.8 95.8 1.0 CB C:ASN487 4.9 0.8 1.0 N C:GLY490 4.9 99.0 1.0 C C:ASP485 4.9 85.0 1.0 CB C:GLU496 5.0 92.0 1.0

Calcium binding site 9 out of 16 in the CDPK1, From Toxoplasma Gondii, Bound to Inhibitory Vhh-1B7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of CDPK1, From Toxoplasma Gondii, Bound to Inhibitory Vhh-1B7 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca601 b:79.2 occ:1.00 OD1 E:ASN370 2.3 0.6 1.0 O E:GLN374 2.3 86.1 1.0 OE2 E:GLU379 2.3 99.6 1.0 OD1 E:ASP372 2.4 0.2 1.0 OD1 E:ASP368 2.6 66.1 1.0 OE1 E:GLU379 2.6 0.7 1.0 CD E:GLU379 2.8 0.3 1.0 OD2 E:ASP372 2.9 0.7 1.0 CG E:ASP372 2.9 0.1 1.0 CG E:ASN370 3.3 94.8 1.0 C E:GLN374 3.5 78.4 1.0 ND2 E:ASN370 3.6 93.0 1.0 CG E:ASP368 3.7 73.8 1.0 N E:GLN374 4.2 82.7 1.0 CG E:GLU379 4.3 0.6 1.0 N E:ASP372 4.3 76.1 1.0 CB E:ASP372 4.3 87.1 1.0 CA E:GLN374 4.3 73.1 1.0 OD2 E:ASP368 4.4 67.7 1.0 N E:LEU375 4.4 79.2 1.0 CA E:LEU375 4.5 81.4 1.0 N E:ASN370 4.6 87.1 1.0 CB E:ASN370 4.6 91.4 1.0 N E:GLY371 4.6 76.6 1.0 CB E:GLN374 4.7 72.1 1.0 CA E:ASP368 4.7 77.5 1.0 CA E:ASP372 4.8 78.7 1.0 N E:GLY373 4.8 68.2 1.0 CB E:ASP368 4.8 80.1 1.0 OD2 E:ASP376 4.8 0.9 1.0 N E:ASP376 4.9 94.2 1.0 N E:LYS369 4.9 87.3 1.0 CD2 E:LEU375 5.0 81.2 1.0

Calcium binding site 10 out of 16 in the CDPK1, From Toxoplasma Gondii, Bound to Inhibitory Vhh-1B7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of CDPK1, From Toxoplasma Gondii, Bound to Inhibitory Vhh-1B7 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca602 b:75.8 occ:1.00 OD1 E:ASP415 2.4 0.2 1.0 OD1 E:ASP417 2.5 0.2 1.0 O E:TYR421 2.5 59.1 1.0 OE2 E:GLU426 2.6 86.2 1.0 OE1 E:GLU426 2.7 75.7 1.0 OD1 E:ASN419 2.9 94.7 1.0 CD E:GLU426 3.0 78.2 1.0 CG E:ASP417 3.2 0.8 1.0 ND2 E:ASN419 3.3 90.7 1.0 OD2 E:ASP417 3.3 0.1 1.0 CG E:ASN419 3.4 87.7 1.0 CG E:ASP415 3.5 0.6 1.0 C E:TYR421 3.6 71.2 1.0 CG E:GLU423 4.0 67.1 1.0 OE1 E:GLU423 4.2 87.1 1.0 OD2 E:ASP415 4.2 95.7 1.0 N E:GLU423 4.3 64.8 1.0 OH F:TYR107 4.3 72.3 1.0 CA E:ILE422 4.4 71.5 1.0 CD E:GLU423 4.4 70.0 1.0 N E:ILE422 4.5 65.5 1.0 CG E:GLU426 4.5 72.6 1.0 CB E:ASP415 4.6 92.6 1.0 N E:TYR421 4.6 79.8 1.0 CA E:TYR421 4.6 79.7 1.0 CA E:ASP415 4.6 96.5 1.0 CB E:ASP417 4.7 97.3 1.0 N E:ASP417 4.7 99.7 1.0 C E:ASP415 4.8 90.1 1.0 CB E:ASN419 4.8 82.8 1.0 N E:ASN419 4.8 98.3 1.0 C E:ILE422 4.8 73.8 1.0 N E:PHE416 4.8 90.4 1.0 CB E:TYR421 4.9 93.1 1.0 CZ F:TYR107 4.9 60.1 1.0 CE2 F:TYR107 4.9 57.9 1.0 CB E:GLU423 5.0 57.9 1.0 N E:LYS418 5.0 99.7 1.0

J.R.Ingram, K.E.Knockenhauer, B.M.Markus, J.Mandelbaum, A.Ramek, Y.Shan, D.E.Shaw, T.U.Schwartz, H.L.Ploegh, S.Lourido. Allosteric Activation of Apicomplexan Calcium-Dependent Protein Kinases. Proc.Natl.Acad.Sci.Usa V. 112 E4975 2015.
ISSN: ESSN 1091-6490
PubMed: 26305940
DOI: 10.1073/PNAS.1505914112