Atomistry » Calcium » PDB 1w7x-1wws » 1wd9
Atomistry »
  Calcium »
    PDB 1w7x-1wws »
      1wd9 »

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

Go back to Calcium Binding Sites List in 1wd9
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

Go back to Calcium Binding Sites List in 1wd9
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

Go back to Calcium Binding Sites List in 1wd9
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

Go back to Calcium Binding Sites List in 1wd9
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

Go back to Calcium Binding Sites List in 1wd9
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: Tue Jul 8 03:12:43 2025

Last articles

Mg in 6M34
Mg in 6M2Z
Mg in 6M0X
Mg in 6M2Y
Mg in 6M1B
Mg in 6M0E
Mg in 6M0V
Mg in 6LZZ
Mg in 6M0D
Mg in 6LZQ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy