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Calcium in PDB 1wd9: Calcium Bound Form of Human Peptidylarginine Deiminase TYPE4 (PAD4)

Enzymatic activity of Calcium Bound Form of Human Peptidylarginine Deiminase TYPE4 (PAD4)

All present enzymatic activity of Calcium Bound Form of Human Peptidylarginine Deiminase TYPE4 (PAD4):
3.5.3.15;

Protein crystallography data

The structure of Calcium Bound Form of Human Peptidylarginine Deiminase TYPE4 (PAD4), PDB code: 1wd9 was solved by K.Arita, H.Hashimoto, T.Shimizu, K.Nakashima, M.Yamada, M.Sato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.80 / 2.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 146.389, 60.094, 115.339, 90.00, 124.37, 90.00
R / Rfree (%) 22.4 / 26.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Calcium Bound Form of Human Peptidylarginine Deiminase TYPE4 (PAD4) (pdb code 1wd9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Calcium Bound Form of Human Peptidylarginine Deiminase TYPE4 (PAD4), PDB code: 1wd9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 1wd9

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Calcium binding site 1 out of 5 in the Calcium Bound Form of Human Peptidylarginine Deiminase TYPE4 (PAD4)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Calcium Bound Form of Human Peptidylarginine Deiminase TYPE4 (PAD4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca900

b:57.3
occ:1.00
 OE1 A:GLN349 2.3 67.7 1.0
O A:PHE407 2.4 51.2 1.0
O A:LEU410 2.5 46.2 1.0
OE1 A:GLU411 2.7 49.3 1.0
OE1 A:GLU353 2.8 55.4 1.0
C A:PHE407 3.4 51.0 1.0
CD A:GLN349 3.5 68.7 1.0
CD A:GLU411 3.6 50.2 1.0
C A:LEU410 3.7 45.6 1.0
CD A:GLU353 3.8 53.6 1.0
CA A:GLY408 3.9 50.3 1.0
N A:GLY408 4.0 50.9 1.0
OE2 A:GLU411 4.1 50.7 1.0
OE2 A:GLU353 4.2 53.2 1.0
CG A:GLN349 4.3 69.8 1.0
NE2 A:GLN349 4.4 68.7 1.0
N A:LEU410 4.4 45.7 1.0
CA A:LEU410 4.5 45.5 1.0
CE1 A:HIS644 4.6 58.3 1.0
C A:GLY408 4.6 49.7 1.0
CG A:GLU411 4.6 48.0 1.0
CA A:PHE407 4.6 51.5 1.0
CB A:PHE407 4.6 51.7 1.0
CB A:LEU410 4.7 45.2 1.0
N A:GLU411 4.7 45.8 1.0
O A:GLN349 4.7 69.2 1.0
CA A:GLU411 4.8 45.6 1.0
O A:GLY408 4.9 48.6 1.0

Calcium binding site 2 out of 5 in 1wd9

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Calcium binding site 2 out of 5 in the Calcium Bound Form of Human Peptidylarginine Deiminase TYPE4 (PAD4)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Calcium Bound Form of Human Peptidylarginine Deiminase TYPE4 (PAD4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:65.2
occ:1.00
 OD1 A:ASP155 2.4 64.6 1.0
OD2 A:ASP165 2.4 77.3 1.0
OD2 A:ASP179 2.5 62.6 1.0
OD1 A:ASP176 2.6 68.9 1.0
OD2 A:ASP157 2.8 80.0 1.0
OD1 A:ASN153 3.0 59.9 1.0
ND2 A:ASN153 3.3 58.6 1.0
CG A:ASP155 3.4 65.7 1.0
CG A:ASP165 3.4 76.5 1.0
CG A:ASN153 3.4 56.9 1.0
CG A:ASP179 3.5 59.3 1.0
OD2 A:ASP155 3.6 66.8 1.0
CG A:ASP157 3.8 79.0 1.0
CG A:ASP176 3.8 68.7 1.0
CB A:ASP165 3.8 75.8 1.0
CB A:ASP179 3.9 58.6 1.0
CA A:CA902 4.0 75.3 1.0
CA A:ASP176 4.2 69.1 1.0
CB A:ASP157 4.3 78.5 1.0
O A:ASP176 4.3 67.9 1.0
O A:ASP155 4.4 67.2 1.0
OD1 A:ASP165 4.5 78.0 1.0
CB A:ASP176 4.5 69.3 1.0
OD1 A:ASP179 4.6 56.6 1.0
N A:ASP157 4.6 76.7 1.0
C A:ASP155 4.7 67.8 1.0
OD2 A:ASP176 4.7 66.5 1.0
OD1 A:ASP157 4.7 79.1 1.0
CB A:ASN153 4.7 55.3 1.0
CB A:ASP155 4.7 65.4 1.0
C A:ASP176 4.8 68.6 1.0

Calcium binding site 3 out of 5 in 1wd9

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Calcium binding site 3 out of 5 in the Calcium Bound Form of Human Peptidylarginine Deiminase TYPE4 (PAD4)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Calcium Bound Form of Human Peptidylarginine Deiminase TYPE4 (PAD4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:75.3
occ:1.00
 OD2 A:ASP179 2.3 62.6 1.0
OD2 A:ASP155 2.5 66.8 1.0
OD2 A:ASP157 2.6 80.0 1.0
OD1 A:ASP179 2.7 56.6 1.0
CG A:ASP179 2.9 59.3 1.0
OD1 A:ASP157 3.1 79.1 1.0
OD1 A:ASP388 3.2 69.3 1.0
CG A:ASP157 3.3 79.0 1.0
CG A:ASP388 3.4 68.7 1.0
OD2 A:ASP388 3.6 70.8 1.0
CG A:ASP155 3.6 65.7 1.0
OD1 A:ASP155 3.9 64.6 1.0
N A:ASP388 3.9 67.8 1.0
CA A:ASP388 4.0 67.7 1.0
CA A:CA901 4.0 65.2 1.0
CB A:ASP388 4.3 68.1 1.0
CB A:ASP179 4.4 58.6 1.0
CE A:LYS362 4.4 63.5 1.0
CD1 A:LEU364 4.4 51.5 1.0
CD A:LYS362 4.6 60.7 1.0
O A:GLU175 4.8 70.8 1.0
CB A:ASP157 4.8 78.5 1.0
NZ A:LYS362 4.9 65.0 1.0
CB A:ASP155 4.9 65.4 1.0

Calcium binding site 4 out of 5 in 1wd9

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Calcium binding site 4 out of 5 in the Calcium Bound Form of Human Peptidylarginine Deiminase TYPE4 (PAD4)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Calcium Bound Form of Human Peptidylarginine Deiminase TYPE4 (PAD4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:67.9
occ:1.00
 O A:SER370 2.3 64.3 1.0
OD2 A:ASP369 2.3 61.8 1.0
OD1 A:ASN373 2.6 68.5 1.0
CG A:ASP369 3.0 62.0 1.0
OD1 A:ASP369 3.4 63.1 1.0
C A:SER370 3.4 65.2 1.0
OE1 A:GLU351 3.4 65.4 1.0
O A:ARG372 3.5 74.4 1.0
OE2 A:GLU351 3.7 64.6 1.0
N A:SER370 3.8 62.6 1.0
CG A:ASN373 3.8 71.5 1.0
CD A:GLU351 3.9 64.9 1.0
C A:ASP369 4.0 61.2 1.0
CB A:ASP369 4.1 60.3 1.0
CA A:SER370 4.2 64.0 1.0
O A:LYS377 4.3 75.2 1.0
OE1 A:GLN397 4.4 68.0 1.0
N A:PRO371 4.4 66.8 1.0
CA A:ASP369 4.5 60.2 1.0
O A:ASP369 4.5 61.8 1.0
O A:GLU351 4.5 61.8 1.0
ND2 A:ASN373 4.5 70.0 1.0
C A:ARG372 4.5 73.5 1.0
CA A:PRO371 4.6 68.6 1.0
C A:PRO371 4.7 70.2 1.0
CA A:LYS377 4.7 75.2 1.0
CA A:ASN373 4.8 73.6 1.0
CB A:ASN373 4.9 73.4 1.0
CB A:SER370 5.0 64.2 1.0
C A:LYS377 5.0 74.9 1.0

Calcium binding site 5 out of 5 in 1wd9

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Calcium binding site 5 out of 5 in the Calcium Bound Form of Human Peptidylarginine Deiminase TYPE4 (PAD4)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Calcium Bound Form of Human Peptidylarginine Deiminase TYPE4 (PAD4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:71.1
occ:1.00
 O A:ASP165 2.4 74.5 1.0
O A:GLU170 2.4 75.0 1.0
OD2 A:ASP168 2.5 78.3 1.0
C A:ASP165 3.3 75.0 1.0
C A:GLU170 3.7 75.2 1.0
CG A:ASP168 3.7 75.7 1.0
OD2 A:ASP176 4.0 66.5 1.0
OD1 A:ASP168 4.1 75.1 1.0
CA A:ASP165 4.1 75.8 1.0
CB A:ASP165 4.1 75.8 1.0
O A:ASP168 4.1 74.6 1.0
N A:CYS166 4.1 74.1 1.0
CA A:CYS166 4.3 73.4 1.0
N A:GLU170 4.4 75.4 1.0
CA A:VAL171 4.5 75.3 1.0
OE1 A:GLU252 4.5 56.8 1.0
N A:VAL171 4.5 75.2 1.0
CA A:GLU170 4.6 75.4 1.0
OE2 A:GLU252 4.7 51.0 1.0
C A:ASP168 4.7 74.9 1.0
ND2 A:ASN153 4.8 58.6 1.0
N A:ASP168 4.8 74.7 1.0
CZ A:PHE214 4.9 54.6 1.0
CB A:ASP168 5.0 74.8 1.0
C A:CYS166 5.0 73.5 1.0

Reference:

K.Arita, H.Hashimoto, T.Shimizu, K.Nakashima, M.Yamada, M.Sato. Structural Basis For Ca(2+)-Induced Activation of Human PAD4 Nat.Struct.Mol.Biol. V. 11 777 2004.
ISSN: ISSN 1545-9993
PubMed: 15247907
DOI: 10.1038/NSMB799
Page generated: Sat Dec 12 03:25:55 2020

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