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Calcium in PDB 1wda: Crystal Structure of Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with Benzoyl-L-Arginine Amide

Enzymatic activity of Crystal Structure of Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with Benzoyl-L-Arginine Amide

All present enzymatic activity of Crystal Structure of Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with Benzoyl-L-Arginine Amide:
3.5.3.15;

Protein crystallography data

The structure of Crystal Structure of Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with Benzoyl-L-Arginine Amide, PDB code: 1wda 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) 42.52 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 146.133, 60.045, 115.406, 90.00, 124.23, 90.00
R / Rfree (%) 21 / 25.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with Benzoyl-L-Arginine Amide (pdb code 1wda). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with Benzoyl-L-Arginine Amide, PDB code: 1wda:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 1wda

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Calcium binding site 1 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with Benzoyl-L-Arginine Amide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with Benzoyl-L-Arginine Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca900

b:35.8
occ:1.00
 O A:PHE407 2.2 38.0 1.0
OE1 A:GLN349 2.3 31.5 1.0
O A:HOH942 2.4 40.1 1.0
O A:HOH919 2.4 37.7 1.0
O A:LEU410 2.4 37.4 1.0
OE1 A:GLU353 2.5 38.9 1.0
OE1 A:GLU411 2.6 39.3 1.0
C A:PHE407 3.4 37.1 1.0
CD A:GLN349 3.4 33.8 1.0
CD A:GLU411 3.5 42.2 1.0
CD A:GLU353 3.6 39.2 1.0
C A:LEU410 3.6 35.8 1.0
OE2 A:GLU411 3.9 43.9 1.0
OE2 A:GLU353 4.0 43.6 1.0
N A:GLY408 4.2 37.0 1.0
CA A:GLY408 4.2 37.3 1.0
NE2 A:GLN349 4.2 28.8 1.0
N A:LEU410 4.4 35.2 1.0
CA A:LEU410 4.4 35.4 1.0
CB A:PHE407 4.4 36.5 1.0
CG A:GLN349 4.4 36.0 1.0
O A:GLN349 4.5 38.8 1.0
CA A:PHE407 4.5 36.8 1.0
CB A:LEU410 4.6 35.1 1.0
CG A:GLU411 4.6 39.2 1.0
N A:GLU411 4.6 35.9 1.0
C A:GLY408 4.6 37.5 1.0
CE1 A:HIS644 4.7 38.6 1.0
CA A:GLU411 4.8 35.6 1.0
O A:GLY408 4.8 37.2 1.0
CG A:GLU353 4.9 38.2 1.0

Calcium binding site 2 out of 5 in 1wda

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Calcium binding site 2 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with Benzoyl-L-Arginine Amide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with Benzoyl-L-Arginine Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:41.6
occ:1.00
 OD2 A:ASP165 2.3 45.4 1.0
OD1 A:ASP155 2.4 41.8 1.0
OD1 A:ASN153 2.4 39.1 1.0
OD2 A:ASP179 2.4 45.0 1.0
OD1 A:ASP176 2.4 44.5 1.0
OD2 A:ASP157 2.9 47.5 1.0
CG A:ASP165 3.3 44.9 1.0
CG A:ASP155 3.3 43.0 1.0
CG A:ASN153 3.4 39.2 1.0
CG A:ASP179 3.5 44.5 1.0
OD2 A:ASP155 3.5 42.8 1.0
CG A:ASP176 3.6 46.9 1.0
ND2 A:ASN153 3.7 35.1 1.0
CB A:ASP165 3.8 45.0 1.0
CG A:ASP157 3.8 47.9 1.0
CA A:CA902 3.9 51.4 1.0
CB A:ASP179 4.0 44.2 1.0
CA A:ASP176 4.1 47.7 1.0
O A:ASP176 4.2 47.1 1.0
CB A:ASP176 4.3 47.6 1.0
CB A:ASP157 4.4 48.0 1.0
OD1 A:ASP165 4.4 42.7 1.0
OD2 A:ASP176 4.5 45.0 1.0
OD1 A:ASP179 4.5 42.8 1.0
N A:ASP157 4.6 47.2 1.0
C A:ASP176 4.7 47.7 1.0
O A:ASP155 4.7 43.3 1.0
CB A:ASP155 4.7 42.7 1.0
C A:ASP155 4.7 43.4 1.0
OD1 A:ASP157 4.8 48.5 1.0
CB A:ASN153 4.8 38.6 1.0

Calcium binding site 3 out of 5 in 1wda

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Calcium binding site 3 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with Benzoyl-L-Arginine Amide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with Benzoyl-L-Arginine Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:51.4
occ:1.00
 OD2 A:ASP157 2.3 47.5 1.0
OD2 A:ASP179 2.3 45.0 1.0
OD2 A:ASP155 2.4 42.8 1.0
OD1 A:ASP388 2.8 48.1 1.0
OD1 A:ASP179 2.8 42.8 1.0
CG A:ASP179 2.9 44.5 1.0
OD1 A:ASP157 3.0 48.5 1.0
CG A:ASP157 3.0 47.9 1.0
CG A:ASP388 3.5 46.6 1.0
CG A:ASP155 3.6 43.0 1.0
CA A:CA901 3.9 41.6 1.0
OD1 A:ASP155 4.0 41.8 1.0
OD2 A:ASP388 4.0 51.5 1.0
CA A:ASP388 4.0 44.8 1.0
N A:ASP388 4.0 44.9 1.0
CB A:ASP388 4.4 45.0 1.0
CB A:ASP179 4.4 44.2 1.0
CE A:LYS362 4.5 48.6 1.0
CB A:ASP157 4.5 48.0 1.0
O A:GLU175 4.6 48.9 1.0
CB A:ASP155 4.8 42.7 1.0
NZ A:LYS362 4.8 48.3 1.0

Calcium binding site 4 out of 5 in 1wda

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Calcium binding site 4 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with Benzoyl-L-Arginine Amide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with Benzoyl-L-Arginine Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:50.6
occ:1.00
 O A:SER370 2.3 41.6 1.0
OD1 A:ASP369 2.3 40.8 1.0
OD1 A:ASN373 2.5 40.3 1.0
OE1 A:GLU351 2.5 38.4 1.0
O A:HOH1065 2.6 41.7 1.0
CG A:ASP369 3.1 40.8 1.0
OD2 A:ASP369 3.3 41.9 1.0
C A:SER370 3.5 41.5 1.0
CD A:GLU351 3.7 38.1 1.0
CG A:ASN373 3.7 42.4 1.0
N A:ASN373 4.1 41.7 1.0
N A:SER370 4.1 41.0 1.0
C A:ASP369 4.2 40.7 1.0
OE2 A:GLU351 4.2 42.6 1.0
O A:LYS377 4.3 43.9 1.0
CA A:ASN373 4.3 41.9 1.0
CA A:PRO371 4.3 42.4 1.0
N A:PRO371 4.3 41.5 1.0
CB A:ASP369 4.4 39.5 1.0
CA A:SER370 4.4 41.5 1.0
O A:GLU351 4.4 36.1 1.0
C A:PRO371 4.5 42.6 1.0
O A:ASP369 4.5 41.4 1.0
CB A:ASN373 4.6 41.2 1.0
ND2 A:ASN373 4.6 42.2 1.0
OE1 A:GLN397 4.7 50.7 1.0
CA A:ASP369 4.7 39.9 1.0
N A:ARG372 4.7 43.5 1.0
CA A:LYS377 4.7 44.1 1.0
CG A:GLU351 4.8 38.7 1.0
O A:PRO371 4.9 43.0 1.0
CG A:LYS377 4.9 58.6 0.0
C A:LYS377 5.0 44.1 1.0

Calcium binding site 5 out of 5 in 1wda

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Calcium binding site 5 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with Benzoyl-L-Arginine Amide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with Benzoyl-L-Arginine Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:47.2
occ:1.00
 O A:HOH1059 2.2 35.5 1.0
O A:GLU170 2.3 48.2 1.0
O A:HOH1066 2.3 38.5 1.0
O A:ASP165 2.3 44.9 1.0
OD1 A:ASP168 2.5 48.8 1.0
C A:GLU170 3.4 48.4 1.0
C A:ASP165 3.5 45.5 1.0
CG A:ASP168 3.6 48.8 1.0
OD2 A:ASP168 3.9 48.3 1.0
N A:GLU170 4.1 48.8 1.0
CA A:ASP165 4.2 45.3 1.0
O A:ASP168 4.2 48.7 1.0
OD2 A:ASP176 4.3 45.0 1.0
CB A:ASP165 4.3 45.0 1.0
N A:VAL171 4.3 48.2 1.0
CA A:GLU170 4.4 48.5 1.0
N A:CYS166 4.4 45.3 1.0
CA A:VAL171 4.5 48.1 1.0
C A:ASP168 4.5 49.2 1.0
OE2 A:GLU252 4.6 39.3 1.0
CA A:CYS166 4.6 45.8 1.0
OE1 A:GLU252 4.6 40.0 1.0
N A:ASP168 4.8 49.2 1.0
CB A:ASP168 4.8 48.9 1.0
CZ A:PHE214 4.9 45.4 1.0
N A:LEU172 4.9 48.9 1.0
CA A:ASP168 4.9 49.2 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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