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Calcium in PDB 6b67: Human PP2CALPHA (PPM1A) Complexed with Cyclic Peptide C(Mpsipyva)

Enzymatic activity of Human PP2CALPHA (PPM1A) Complexed with Cyclic Peptide C(Mpsipyva)

All present enzymatic activity of Human PP2CALPHA (PPM1A) Complexed with Cyclic Peptide C(Mpsipyva):
3.1.3.16;

Protein crystallography data

The structure of Human PP2CALPHA (PPM1A) Complexed with Cyclic Peptide C(Mpsipyva), PDB code: 6b67 was solved by F.Dyda, D.Kosek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 159.030, 89.570, 70.050, 90.00, 113.86, 90.00
R / Rfree (%) 16.9 / 22.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Human PP2CALPHA (PPM1A) Complexed with Cyclic Peptide C(Mpsipyva) (pdb code 6b67). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Human PP2CALPHA (PPM1A) Complexed with Cyclic Peptide C(Mpsipyva), PDB code: 6b67:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 6b67

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Calcium binding site 1 out of 10 in the Human PP2CALPHA (PPM1A) Complexed with Cyclic Peptide C(Mpsipyva)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human PP2CALPHA (PPM1A) Complexed with Cyclic Peptide C(Mpsipyva) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:12.8
occ:1.00
 O A:GLY61 2.1 12.7 1.0
O3P D:SEP2 2.1 17.0 1.0
O A:HOH424 2.3 13.9 1.0
OD1 A:ASP60 2.3 20.1 1.0
O D:HOH101 2.3 12.2 1.0
O A:HOH405 2.4 17.0 1.0
C A:GLY61 3.3 10.2 1.0
CG A:ASP60 3.5 16.0 1.0
P D:SEP2 3.5 18.6 1.0
O2P D:SEP2 3.6 20.5 1.0
O A:HOH453 3.7 20.9 1.0
N A:GLY61 4.0 10.5 1.0
O1P D:SEP2 4.0 16.6 1.0
OD2 A:ASP60 4.1 10.5 1.0
O A:HOH510 4.1 22.3 1.0
O A:HOH459 4.1 27.3 1.0
C A:ASP60 4.1 10.2 1.0
CA A:CA302 4.2 21.1 1.0
N A:HIS62 4.2 8.9 1.0
CA A:GLY61 4.2 7.2 1.0
OD1 A:ASP38 4.3 13.6 1.0
CA A:HIS62 4.3 9.7 1.0
CB A:GLU37 4.4 8.7 1.0
OD1 A:ASN283 4.4 11.8 1.0
O A:ASP60 4.5 10.7 1.0
O A:HOH515 4.5 14.4 1.0
OE1 A:GLU37 4.5 15.6 1.0
CB A:HIS62 4.5 10.3 1.0
OG D:SEP2 4.6 19.8 1.0
CB A:ASP60 4.6 5.6 1.0
CA A:ASP60 4.6 10.2 1.0
OD1 A:ASP282 4.8 13.3 1.0
O A:GLU37 5.0 10.0 1.0

Calcium binding site 2 out of 10 in 6b67

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Calcium binding site 2 out of 10 in the Human PP2CALPHA (PPM1A) Complexed with Cyclic Peptide C(Mpsipyva)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human PP2CALPHA (PPM1A) Complexed with Cyclic Peptide C(Mpsipyva) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:21.1
occ:1.00
 O A:HOH453 2.3 20.9 1.0
OD1 A:ASP239 2.4 21.8 1.0
OD2 A:ASP282 2.4 16.0 1.0
OD2 A:ASP60 2.4 10.5 1.0
O A:HOH510 2.5 22.3 1.0
O A:HOH405 2.6 17.0 1.0
CG A:ASP60 3.3 16.0 1.0
CG A:ASP282 3.4 14.3 1.0
CG A:ASP239 3.5 15.0 1.0
OD1 A:ASP60 3.5 20.1 1.0
OD1 A:ASP282 3.7 13.3 1.0
OD2 A:ASP239 3.9 26.3 1.0
O3P D:SEP2 4.1 17.0 1.0
CA A:CA301 4.2 12.8 1.0
O A:HOH419 4.2 19.9 1.0
O A:HOH420 4.2 11.6 1.0
O1P D:SEP2 4.2 16.6 1.0
N A:GLY240 4.4 12.4 1.0
O A:HOH592 4.7 36.2 1.0
CB A:ASP282 4.7 9.3 1.0
CB A:ASP60 4.7 5.6 1.0
CB A:ASP239 4.8 9.9 1.0
N A:ASP239 4.8 14.1 1.0
O A:HOH459 4.8 27.3 1.0
C A:ASP239 4.9 13.8 1.0
O A:ASN283 4.9 8.9 1.0
P D:SEP2 5.0 18.6 1.0
SG A:CYS238 5.0 15.5 1.0

Calcium binding site 3 out of 10 in 6b67

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Calcium binding site 3 out of 10 in the Human PP2CALPHA (PPM1A) Complexed with Cyclic Peptide C(Mpsipyva)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human PP2CALPHA (PPM1A) Complexed with Cyclic Peptide C(Mpsipyva) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:36.6
occ:1.00
 O D:HOH105 2.4 36.3 1.0
O A:HOH504 2.4 34.4 1.0
O A:HOH584 2.5 36.3 1.0
O A:HOH581 2.5 36.9 1.0
OD2 A:ASP243 2.6 25.7 1.0
OD2 A:ASP239 2.7 26.3 1.0
OD1 A:ASP243 2.8 24.7 1.0
CG A:ASP243 3.1 23.0 1.0
CG A:ASP239 3.7 15.0 1.0
OE1 A:GLU146 3.9 95.4 1.0
CB A:ASP239 4.1 9.9 1.0
O A:HOH419 4.2 19.9 1.0
O A:HOH592 4.4 36.2 1.0
CB A:ASP243 4.6 18.8 1.0
OD1 A:ASP239 4.8 21.8 1.0
NZ A:LYS165 4.8 53.0 1.0
CE A:LYS165 4.8 47.7 1.0
O10 D:48V7 4.9 26.6 1.0

Calcium binding site 4 out of 10 in 6b67

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Calcium binding site 4 out of 10 in the Human PP2CALPHA (PPM1A) Complexed with Cyclic Peptide C(Mpsipyva)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human PP2CALPHA (PPM1A) Complexed with Cyclic Peptide C(Mpsipyva) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:54.0
occ:1.00
 O A:HOH416 2.3 53.1 1.0
O A:HOH568 2.4 52.5 1.0
OE1 B:GLN16 2.5 31.3 1.0
OE1 B:GLU265 2.5 30.0 1.0
OE1 A:GLU265 2.7 26.1 1.0
CD B:GLU265 3.3 13.4 1.0
CD B:GLN16 3.4 21.5 1.0
CD A:GLU265 3.8 5.9 1.0
NE2 B:GLN16 3.8 33.2 1.0
O B:HOH570 3.8 29.6 1.0
OE2 B:GLU265 3.9 16.0 1.0
OD2 B:ASP263 4.0 26.6 1.0
CG B:GLU265 4.1 16.9 1.0
CB B:GLU265 4.4 15.6 1.0
OE2 A:GLU265 4.4 14.7 1.0
CG B:GLN16 4.5 23.1 1.0
OD2 A:ASP263 4.6 19.6 1.0
CG B:ASP263 4.6 26.8 1.0
OD1 B:ASP263 4.7 35.3 1.0
OE1 A:GLN16 4.7 21.5 1.0
CG A:GLU265 4.8 6.9 1.0
OD1 A:ASP263 4.8 14.5 1.0
CB A:GLU265 4.8 10.3 1.0
O B:HOH585 4.9 28.6 1.0

Calcium binding site 5 out of 10 in 6b67

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Calcium binding site 5 out of 10 in the Human PP2CALPHA (PPM1A) Complexed with Cyclic Peptide C(Mpsipyva)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Human PP2CALPHA (PPM1A) Complexed with Cyclic Peptide C(Mpsipyva) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:18.3
occ:1.00
 O B:GLY61 2.1 15.1 1.0
O2P E:SEP2 2.1 26.4 1.0
OD2 B:ASP60 2.3 14.1 1.0
O B:HOH438 2.4 18.9 1.0
O B:HOH406 2.4 22.0 1.0
O E:HOH101 2.4 16.7 1.0
P E:SEP2 3.1 24.4 1.0
O3P E:SEP2 3.2 26.9 1.0
C B:GLY61 3.3 13.1 1.0
CG B:ASP60 3.5 15.7 1.0
O B:HOH523 3.9 25.1 1.0
O1P E:SEP2 3.9 22.4 1.0
O B:HOH414 4.1 26.6 1.0
N B:GLY61 4.1 12.9 1.0
OD1 B:ASP60 4.1 14.6 1.0
CA B:CA302 4.2 26.0 1.0
C B:ASP60 4.2 12.6 1.0
N B:HIS62 4.2 11.8 1.0
CA B:GLY61 4.3 11.8 1.0
CA B:HIS62 4.3 12.3 1.0
CB B:HIS62 4.4 11.9 1.0
OE2 B:GLU37 4.4 19.8 1.0
CB B:GLU37 4.4 6.4 1.0
OD1 B:ASP38 4.5 14.2 1.0
O B:HOH480 4.5 16.3 1.0
OG E:SEP2 4.5 25.7 1.0
O B:ASP60 4.6 11.2 1.0
OD1 B:ASN283 4.6 18.4 1.0
CB B:ASP60 4.7 12.7 1.0
CA B:ASP60 4.7 12.9 1.0
OD1 B:ASP282 4.8 12.8 1.0
NH1 B:ARG33 4.8 17.9 1.0
O E:HOH102 4.9 24.7 1.0
O B:HOH469 4.9 28.4 1.0

Calcium binding site 6 out of 10 in 6b67

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Calcium binding site 6 out of 10 in the Human PP2CALPHA (PPM1A) Complexed with Cyclic Peptide C(Mpsipyva)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Human PP2CALPHA (PPM1A) Complexed with Cyclic Peptide C(Mpsipyva) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:26.0
occ:1.00
 OD1 B:ASP239 2.3 23.8 1.0
OD2 B:ASP282 2.3 20.4 1.0
O B:HOH469 2.5 28.4 1.0
OD1 B:ASP60 2.5 14.6 1.0
O B:HOH414 2.5 26.6 1.0
O B:HOH441 2.5 26.8 1.0
O B:HOH406 2.6 22.0 1.0
CG B:ASP239 3.3 20.8 1.0
CG B:ASP282 3.3 19.2 1.0
CG B:ASP60 3.5 15.7 1.0
O2P E:SEP2 3.5 26.4 1.0
OD2 B:ASP239 3.6 31.8 1.0
OD1 B:ASP282 3.6 12.8 1.0
OD2 B:ASP60 3.7 14.1 1.0
O1P E:SEP2 3.8 22.4 1.0
O B:HOH404 4.1 25.6 1.0
O B:HOH410 4.2 13.5 1.0
CA B:CA301 4.2 18.3 1.0
P E:SEP2 4.4 24.4 1.0
O B:HOH523 4.5 25.1 1.0
N B:GLY240 4.6 17.5 1.0
CB B:ASP282 4.6 18.9 1.0
CB B:ASP239 4.6 12.8 1.0
N B:ASP239 4.8 15.7 1.0
CB B:ASP60 4.9 12.7 1.0

Calcium binding site 7 out of 10 in 6b67

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Calcium binding site 7 out of 10 in the Human PP2CALPHA (PPM1A) Complexed with Cyclic Peptide C(Mpsipyva)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Human PP2CALPHA (PPM1A) Complexed with Cyclic Peptide C(Mpsipyva) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:35.8
occ:1.00
 O B:HOH549 2.4 33.1 1.0
O E:HOH112 2.4 34.1 1.0
O B:HOH578 2.5 35.7 1.0
OD2 B:ASP243 2.6 26.1 1.0
OD1 B:ASP243 2.6 25.2 1.0
OD2 B:ASP239 2.7 31.8 1.0
CG B:ASP243 3.0 24.6 1.0
O E:HOH108 3.5 38.0 1.0
CG B:ASP239 3.7 20.8 1.0
CB B:ASP239 4.0 12.8 1.0
O B:HOH404 4.1 25.6 1.0
O10 E:48V7 4.4 29.1 1.0
O B:HOH441 4.4 26.8 1.0
CB B:ASP243 4.5 19.9 1.0
O B:HOH599 4.6 36.3 1.0
NZ B:LYS165 4.6 29.8 1.0
OD1 B:ASP239 4.7 23.8 1.0
O B:HOH461 4.8 31.7 1.0
O B:HOH431 4.8 25.1 1.0
O B:ASP239 5.0 16.9 1.0

Calcium binding site 8 out of 10 in 6b67

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Calcium binding site 8 out of 10 in the Human PP2CALPHA (PPM1A) Complexed with Cyclic Peptide C(Mpsipyva)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Human PP2CALPHA (PPM1A) Complexed with Cyclic Peptide C(Mpsipyva) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:26.3
occ:1.00
 O2P F:SEP2 1.8 55.4 1.0
O C:GLY61 2.1 25.3 1.0
OD2 C:ASP60 2.3 21.3 1.0
O C:HOH413 2.4 26.3 1.0
O F:HOH102 2.4 25.6 1.0
O F:HOH101 2.4 28.8 1.0
P F:SEP2 3.0 56.0 1.0
O3P F:SEP2 3.2 54.7 1.0
C C:GLY61 3.4 21.1 1.0
CG C:ASP60 3.5 21.2 1.0
O1P F:SEP2 3.7 55.8 1.0
O C:HOH457 3.8 20.9 1.0
O C:HOH511 4.0 34.1 1.0
OD1 C:ASP60 4.0 25.9 1.0
O C:HOH467 4.1 33.7 1.0
CA C:CA302 4.1 33.6 1.0
N C:GLY61 4.1 16.0 1.0
C C:ASP60 4.2 16.1 1.0
N C:HIS62 4.3 19.1 1.0
CA C:GLY61 4.3 18.1 1.0
OG F:SEP2 4.3 60.7 1.0
OD1 C:ASP38 4.4 19.9 1.0
CB C:GLU37 4.4 25.7 1.0
OD1 C:ASN283 4.4 22.1 1.0
CA C:HIS62 4.4 19.0 1.0
OE1 C:GLU37 4.4 23.5 1.0
O C:ASP60 4.5 16.0 1.0
OD1 C:ASP282 4.6 32.2 1.0
CB C:HIS62 4.6 17.3 1.0
O C:HOH501 4.6 19.5 1.0
CB C:ASP60 4.7 10.7 1.0
CA C:ASP60 4.7 15.2 1.0
NH1 C:ARG33 4.8 24.0 1.0

Calcium binding site 9 out of 10 in 6b67

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Calcium binding site 9 out of 10 in the Human PP2CALPHA (PPM1A) Complexed with Cyclic Peptide C(Mpsipyva)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Human PP2CALPHA (PPM1A) Complexed with Cyclic Peptide C(Mpsipyva) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:33.6
occ:1.00
 O C:HOH407 2.0 64.2 1.0
O F:HOH101 2.0 28.8 1.0
OD1 C:ASP239 2.3 18.6 1.0
O C:HOH511 2.4 34.1 1.0
OD2 C:ASP282 2.4 33.3 1.0
OD1 C:ASP60 2.4 25.9 1.0
O C:HOH467 2.5 33.7 1.0
CG C:ASP60 3.4 21.2 1.0
CG C:ASP239 3.4 19.1 1.0
CG C:ASP282 3.4 31.0 1.0
OD2 C:ASP60 3.6 21.3 1.0
O1P F:SEP2 3.6 55.8 1.0
OD1 C:ASP282 3.7 32.2 1.0
OD2 C:ASP239 3.8 31.6 1.0
O2P F:SEP2 3.9 55.4 1.0
O C:HOH423 4.0 14.6 1.0
CA C:CA301 4.1 26.3 1.0
O C:HOH448 4.2 26.9 1.0
P F:SEP2 4.3 56.0 1.0
N C:GLY240 4.5 16.4 1.0
N C:ASP239 4.7 15.6 1.0
O C:HOH457 4.7 20.9 1.0
CB C:ASP239 4.7 16.8 1.0
CB C:ASP282 4.7 22.1 1.0
CB C:ASP60 4.8 10.7 1.0
C C:ASP239 4.9 15.4 1.0
CA C:ASP239 5.0 14.3 1.0
O C:ASN283 5.0 21.2 1.0
SG C:CYS238 5.0 17.5 1.0

Calcium binding site 10 out of 10 in 6b67

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Calcium binding site 10 out of 10 in the Human PP2CALPHA (PPM1A) Complexed with Cyclic Peptide C(Mpsipyva)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Human PP2CALPHA (PPM1A) Complexed with Cyclic Peptide C(Mpsipyva) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca303

b:36.8
occ:1.00
 OD2 C:ASP243 2.4 24.2 1.0
O C:HOH411 2.4 36.6 1.0
O C:HOH573 2.4 36.4 1.0
OD1 C:ASP243 2.5 27.2 1.0
OD2 C:ASP239 2.6 31.6 1.0
CG C:ASP243 2.8 25.1 1.0
CG C:ASP239 3.5 19.1 1.0
CB C:ASP239 3.7 16.8 1.0
O C:HOH548 4.0 45.6 1.0
O C:HOH448 4.3 26.9 1.0
CB C:ASP243 4.3 18.2 1.0
O C:HOH406 4.4 26.7 1.0
OE1 C:GLU146 4.5 72.4 1.0
OD1 C:ASP239 4.6 18.6 1.0
O C:ASP239 4.6 17.0 1.0
O C:HOH412 4.8 22.7 1.0
O C:HOH562 5.0 46.4 1.0

Reference:

S.Debnath, D.Kosek, H.D.Tagad, S.R.Durell, D.H.Appella, R.Acevedo, A.Grishaev, F.Dyda, E.Appella, S.J.Mazur. A Trapped Human PPM1A-Phosphopeptide Complex Reveals Structural Features Critical For Regulation of Ppm Protein Phosphatase Activity. J. Biol. Chem. V. 293 7993 2018.
ISSN: ESSN 1083-351X
PubMed: 29602904
DOI: 10.1074/JBC.RA117.001213
Page generated: Mon Jul 15 16:42:18 2024

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