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Calcium in PDB 5hp5: Srtucture of Human Peptidylarginine Deiminase Type I (PAD1)

Enzymatic activity of Srtucture of Human Peptidylarginine Deiminase Type I (PAD1)

All present enzymatic activity of Srtucture of Human Peptidylarginine Deiminase Type I (PAD1):
3.5.3.15;

Protein crystallography data

The structure of Srtucture of Human Peptidylarginine Deiminase Type I (PAD1), PDB code: 5hp5 was solved by M.Unno, A.Nagai, S.Saijo, N.Shimizu, S.Kinjo, R.Mashimo, K.Kizawa, H.Takahara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.73 / 3.20
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 90.815, 90.815, 373.049, 90.00, 90.00, 120.00
R / Rfree (%) 21.3 / 27.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Srtucture of Human Peptidylarginine Deiminase Type I (PAD1) (pdb code 5hp5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Srtucture of Human Peptidylarginine Deiminase Type I (PAD1), PDB code: 5hp5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5hp5

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Calcium binding site 1 out of 8 in the Srtucture of Human Peptidylarginine Deiminase Type I (PAD1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Srtucture of Human Peptidylarginine Deiminase Type I (PAD1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:64.5
occ:1.00
 OD2 A:ASP157 2.4 81.6 1.0
OD2 A:ASP179 2.5 75.9 1.0
OD1 A:ASP157 2.9 72.8 1.0
OD2 A:ASP155 2.9 64.9 1.0
NZ A:LYS364 2.9 89.0 1.0
CG A:ASP157 3.0 80.0 1.0
OD1 A:ASP179 3.0 78.0 1.0
O A:PRO389 3.1 77.8 1.0
CG A:ASP179 3.1 73.6 1.0
OD1 A:ASP390 3.2 53.6 1.0
CE A:LYS364 3.4 83.0 1.0
CA A:CA702 4.0 64.5 1.0
CG A:ASP155 4.1 70.0 1.0
C A:PRO389 4.1 74.4 1.0
CG A:ASP390 4.3 74.0 1.0
CA A:ASP390 4.5 70.4 1.0
CB A:ASP157 4.5 82.0 1.0
CB A:ASP179 4.6 70.4 1.0
N A:ASP390 4.7 66.4 1.0
CD A:LYS364 4.7 82.1 1.0
O A:ALA175 4.7 75.3 1.0
OD1 A:ASP155 4.8 73.4 1.0

Calcium binding site 2 out of 8 in 5hp5

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Calcium binding site 2 out of 8 in the Srtucture of Human Peptidylarginine Deiminase Type I (PAD1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Srtucture of Human Peptidylarginine Deiminase Type I (PAD1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:64.5
occ:1.00
 OD1 A:ASP176 2.4 63.4 1.0
OD1 A:ASP157 2.4 72.8 1.0
OD1 A:ASP155 2.5 73.4 1.0
OD1 A:ASN153 2.5 68.2 1.0
OD2 A:ASP165 2.6 71.0 1.0
OD2 A:ASP179 2.6 75.9 1.0
OD2 A:ASP155 3.0 64.9 1.0
CG A:ASP155 3.1 70.0 1.0
CG A:ASP179 3.1 73.6 1.0
CG A:ASN153 3.4 63.5 1.0
CG A:ASP157 3.5 80.0 1.0
CB A:ASP179 3.5 70.4 1.0
CG A:ASP176 3.6 69.2 1.0
ND2 A:ASN153 3.6 69.3 1.0
CG A:ASP165 3.8 78.2 1.0
OD1 A:ASP179 3.9 78.0 1.0
CA A:CA701 4.0 64.5 1.0
CA A:ASP176 4.1 72.6 1.0
O A:ASP176 4.3 70.3 1.0
CB A:ASP176 4.3 70.5 1.0
OD2 A:ASP157 4.3 81.6 1.0
CB A:ASP157 4.4 82.0 1.0
OD2 A:ASP176 4.5 73.0 1.0
O A:ASP155 4.5 72.5 1.0
CB A:ASP155 4.5 62.7 1.0
CB A:ASP165 4.5 73.7 1.0
C A:ASP176 4.7 72.2 1.0
OD1 A:ASP165 4.7 82.0 1.0
N A:ASP157 4.8 68.0 1.0
CB A:ASN153 4.8 63.2 1.0
C A:ASP155 4.8 72.8 1.0
N A:ASP155 5.0 65.2 1.0
CA A:ASP179 5.0 66.6 1.0

Calcium binding site 3 out of 8 in 5hp5

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Calcium binding site 3 out of 8 in the Srtucture of Human Peptidylarginine Deiminase Type I (PAD1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Srtucture of Human Peptidylarginine Deiminase Type I (PAD1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:65.7
occ:1.00
 OE1 A:GLN351 2.3 60.5 1.0
O A:LEU412 2.4 68.1 1.0
O A:HOH802 2.5 59.2 1.0
O A:HOH804 2.5 53.7 1.0
O A:PHE409 2.6 59.7 1.0
OE1 A:GLU355 3.3 59.8 1.0
C A:LEU412 3.4 55.0 1.0
CD A:GLN351 3.5 62.2 1.0
C A:PHE409 3.8 60.9 1.0
CA A:GLY410 3.9 59.1 1.0
O A:GLY410 4.0 57.0 1.0
OD2 A:ASP413 4.0 76.9 1.0
C A:GLY410 4.0 59.0 1.0
N A:ASP413 4.2 61.5 1.0
N A:LEU412 4.2 56.1 1.0
CA A:ASP413 4.2 65.6 1.0
N A:GLY410 4.3 60.2 1.0
CE1 A:HIS644 4.3 69.1 1.0
CG A:ASP413 4.3 76.2 1.0
CA A:LEU412 4.3 48.1 1.0
NE2 A:GLN351 4.4 62.5 1.0
CG A:GLN351 4.5 69.0 1.0
CB A:ASP413 4.5 67.9 1.0
NE2 A:HIS644 4.5 65.2 1.0
CD A:GLU355 4.5 63.8 1.0
CB A:LEU412 4.8 53.2 1.0
N A:ASN411 4.9 56.7 1.0
O A:GLN351 4.9 65.4 1.0
OD1 A:ASP413 5.0 76.6 1.0

Calcium binding site 4 out of 8 in 5hp5

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Calcium binding site 4 out of 8 in the Srtucture of Human Peptidylarginine Deiminase Type I (PAD1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Srtucture of Human Peptidylarginine Deiminase Type I (PAD1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:80.0
occ:1.00
 OD2 A:ASP371 2.5 69.6 1.0
O A:HOH801 2.5 69.0 1.0
OD1 A:ASN375 2.5 89.9 1.0
O A:SER372 2.9 74.7 1.0
OD1 A:ASP371 3.0 68.0 1.0
CG A:ASP371 3.1 67.6 1.0
OE2 A:GLU353 3.3 82.0 1.0
CG A:ASN375 3.7 89.4 1.0
O A:LYS379 3.9 77.6 1.0
C A:SER372 4.0 69.9 1.0
CA A:LYS379 4.4 75.8 1.0
N A:ASN375 4.4 75.5 1.0
ND2 A:ASN375 4.5 91.1 1.0
CA A:ASN375 4.6 78.8 1.0
CB A:ASP371 4.6 61.1 1.0
CD A:GLU353 4.6 79.8 1.0
C A:LYS379 4.6 82.5 1.0
CB A:ASN375 4.7 83.5 1.0
CA A:PRO373 4.8 69.1 1.0
C A:PRO373 4.8 69.2 1.0
N A:PRO373 4.8 62.2 1.0
C A:ASP371 4.8 57.3 1.0
CB A:LYS379 4.8 75.9 1.0
N A:SER372 4.8 57.3 1.0
OH A:TYR393 4.9 58.6 1.0
O A:ASP371 4.9 57.7 1.0

Calcium binding site 5 out of 8 in 5hp5

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Calcium binding site 5 out of 8 in the Srtucture of Human Peptidylarginine Deiminase Type I (PAD1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Srtucture of Human Peptidylarginine Deiminase Type I (PAD1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:68.6
occ:1.00
 OD2 B:ASP179 2.4 69.8 1.0
OD1 B:ASP157 2.5 78.5 1.0
OD2 B:ASP157 2.7 71.0 1.0
CG B:ASP157 2.9 76.4 1.0
OD1 B:ASP179 3.0 85.7 1.0
CG B:ASP179 3.0 75.3 1.0
OD2 B:ASP155 3.0 68.8 1.0
OD1 B:ASP390 3.2 56.0 1.0
O B:PRO389 3.2 76.0 1.0
NZ B:LYS364 3.4 84.6 1.0
CA B:CA702 4.0 60.9 1.0
CG B:ASP155 4.2 68.1 1.0
C B:PRO389 4.2 71.9 1.0
CB B:ASP157 4.4 81.1 1.0
CG B:ASP390 4.5 73.2 1.0
CB B:ASP179 4.5 76.4 1.0
CE B:LYS364 4.6 79.3 1.0
CA B:ASP390 4.7 64.2 1.0
OD1 B:ASP155 4.8 71.7 1.0
N B:ASP390 4.9 60.5 1.0
O B:ALA175 4.9 82.5 1.0

Calcium binding site 6 out of 8 in 5hp5

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Calcium binding site 6 out of 8 in the Srtucture of Human Peptidylarginine Deiminase Type I (PAD1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Srtucture of Human Peptidylarginine Deiminase Type I (PAD1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:60.9
occ:1.00
 OD1 B:ASP176 2.4 67.3 1.0
OD2 B:ASP179 2.4 69.8 1.0
OD1 B:ASP155 2.4 71.7 1.0
OD2 B:ASP157 2.5 71.0 1.0
OD2 B:ASP165 2.5 73.7 1.0
OD1 B:ASN153 2.5 69.4 1.0
OD2 B:ASP155 3.1 68.8 1.0
CG B:ASP155 3.1 68.1 1.0
CG B:ASN153 3.4 66.2 1.0
ND2 B:ASN153 3.5 69.4 1.0
CG B:ASP179 3.5 75.3 1.0
CG B:ASP176 3.5 72.5 1.0
CG B:ASP157 3.6 76.4 1.0
CG B:ASP165 3.7 76.3 1.0
CB B:ASP179 3.9 76.4 1.0
CA B:CA701 4.0 68.6 1.0
CA B:ASP176 4.2 77.8 1.0
CB B:ASP157 4.3 81.1 1.0
O B:ASP155 4.3 71.1 1.0
CB B:ASP165 4.3 71.9 1.0
OD2 B:ASP176 4.3 77.5 1.0
CB B:ASP176 4.4 75.5 1.0
CB B:ASP155 4.5 60.9 1.0
O B:ASP176 4.5 74.5 1.0
OD1 B:ASP157 4.5 78.5 1.0
OD1 B:ASP179 4.6 85.7 1.0
N B:ASP157 4.7 67.1 1.0
OD1 B:ASP165 4.7 82.7 1.0
C B:ASP155 4.8 71.4 1.0
CB B:ASN153 4.8 64.5 1.0
C B:ASP176 4.9 76.7 1.0
N B:ASP155 4.9 70.9 1.0
CA B:ASP155 5.0 67.3 1.0

Calcium binding site 7 out of 8 in 5hp5

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Calcium binding site 7 out of 8 in the Srtucture of Human Peptidylarginine Deiminase Type I (PAD1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Srtucture of Human Peptidylarginine Deiminase Type I (PAD1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca703

b:59.1
occ:1.00
 OE1 B:GLN351 2.4 60.0 1.0
OE1 B:GLU355 2.4 60.9 1.0
O B:PHE409 2.4 61.1 1.0
O B:HOH802 2.5 51.8 1.0
O B:HOH803 2.5 58.7 1.0
O B:LEU412 2.7 64.9 1.0
CD B:GLN351 3.4 62.0 1.0
CD B:GLU355 3.4 66.3 1.0
C B:PHE409 3.5 59.8 1.0
C B:LEU412 3.9 55.6 1.0
O B:GLN351 4.0 67.0 1.0
NE2 B:GLN351 4.1 60.1 1.0
OE2 B:GLU355 4.1 69.2 1.0
CB B:PHE409 4.2 54.7 1.0
CG B:GLU355 4.3 61.4 1.0
N B:GLY410 4.3 61.4 1.0
CG B:GLN351 4.4 69.6 1.0
CA B:PHE409 4.4 56.1 1.0
CB B:GLU355 4.4 60.3 1.0
CA B:GLY410 4.5 61.8 1.0
CB B:LEU412 4.5 55.6 1.0
CA B:LEU412 4.6 46.6 1.0
O B:MET354 4.6 59.7 1.0
N B:LEU412 4.7 54.0 1.0
CG B:LEU412 4.8 53.6 1.0
N B:ASP413 4.9 63.2 1.0
CA B:GLU355 4.9 54.7 1.0
C B:GLY410 4.9 57.7 1.0

Calcium binding site 8 out of 8 in 5hp5

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Calcium binding site 8 out of 8 in the Srtucture of Human Peptidylarginine Deiminase Type I (PAD1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Srtucture of Human Peptidylarginine Deiminase Type I (PAD1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca704

b:82.7
occ:1.00
 O B:HOH801 2.5 69.2 1.0
OD2 B:ASP371 2.6 64.8 1.0
OD1 B:ASN375 2.7 85.3 1.0
O B:SER372 2.7 70.7 1.0
OD1 B:ASP371 3.0 63.5 1.0
CG B:ASP371 3.1 63.1 1.0
OE2 B:GLU353 3.2 82.6 1.0
O B:LYS379 3.8 70.4 1.0
CG B:ASN375 3.9 83.9 1.0
C B:SER372 3.9 67.3 1.0
N B:ASN375 4.3 76.0 1.0
CA B:LYS379 4.3 74.8 1.0
CD B:GLU353 4.4 79.6 1.0
C B:LYS379 4.5 76.2 1.0
CA B:ASN375 4.6 80.2 1.0
CB B:ASP371 4.6 60.7 1.0
CA B:PRO373 4.7 70.9 1.0
C B:PRO373 4.7 70.3 1.0
N B:PRO373 4.7 64.3 1.0
ND2 B:ASN375 4.7 78.2 1.0
N B:SER372 4.8 59.0 1.0
C B:ASP371 4.8 56.5 1.0
CB B:LYS379 4.8 76.0 1.0
CB B:ASN375 4.9 82.7 1.0
N B:ARG374 4.9 64.5 1.0
OH B:TYR393 4.9 55.5 1.0
O B:HOH808 4.9 55.5 1.0
O B:ASP371 5.0 57.0 1.0
CA B:SER372 5.0 59.1 1.0
O B:PRO373 5.0 66.4 1.0

Reference:

S.Saijo, A.Nagai, S.Kinjo, R.Mashimo, M.Akimoto, K.Kizawa, T.Yabe-Wada, N.Shimizu, H.Takahara, M.Unno. Monomeric Form of Peptidylarginine Deiminase Type I Revealed By X-Ray Crystallography and Small-Angle X-Ray Scattering J.Mol.Biol. V. 428 3058 2016.
ISSN: ESSN 1089-8638
PubMed: 27393304
DOI: 10.1016/J.JMB.2016.06.018
Page generated: Sun Jul 14 20:08:56 2024

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