Atomistry » Calcium » PDB 2dcj-2dw0 » 2dew
Atomistry »
  Calcium »
    PDB 2dcj-2dw0 »
      2dew »

Calcium in PDB 2dew: Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with Histone H3 N-Terminal Tail Including ARG8

Enzymatic activity of Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with Histone H3 N-Terminal Tail Including ARG8

All present enzymatic activity of Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with Histone H3 N-Terminal Tail Including ARG8:
3.5.3.15;

Protein crystallography data

The structure of Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with Histone H3 N-Terminal Tail Including ARG8, PDB code: 2dew was solved by K.Arita, T.Shimizu, H.Hashimoto, Y.Hidaka, M.Yamada, M.Sato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.34 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 146.268, 60.773, 115.146, 90.00, 124.26, 90.00
R / Rfree (%) 20.2 / 24.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with Histone H3 N-Terminal Tail Including ARG8 (pdb code 2dew). 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 4 in Complex with Histone H3 N-Terminal Tail Including ARG8, PDB code: 2dew:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 2dew

Go back to Calcium Binding Sites List in 2dew
Calcium binding site 1 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with Histone H3 N-Terminal Tail Including ARG8


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 4 in Complex with Histone H3 N-Terminal Tail Including ARG8 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca900

b:40.5
occ:1.00
 O X:PHE407 2.2 46.1 1.0
OE1 X:GLN349 2.3 45.3 1.0
O X:HOH912 2.4 38.7 1.0
O X:HOH928 2.5 42.9 1.0
OE1 X:GLU353 2.5 43.9 1.0
O X:LEU410 2.5 43.0 1.0
OE1 X:GLU411 2.5 47.6 1.0
C X:PHE407 3.4 45.1 1.0
CD X:GLN349 3.5 46.5 1.0
CD X:GLU411 3.5 49.8 1.0
CD X:GLU353 3.6 43.4 1.0
C X:LEU410 3.7 43.0 1.0
OE2 X:GLU353 4.0 44.0 1.0
N X:GLY408 4.2 44.1 1.0
OE2 X:GLU411 4.2 50.7 1.0
O X:HOH1097 4.2 54.6 1.0
CA X:GLY408 4.3 43.5 1.0
NE2 X:GLN349 4.3 44.9 1.0
CB X:PHE407 4.3 46.1 1.0
CG X:GLN349 4.4 44.2 1.0
CA X:PHE407 4.4 45.2 1.0
N X:LEU410 4.4 43.1 1.0
CG X:GLU411 4.5 45.8 1.0
O X:GLN349 4.5 42.5 1.0
CA X:LEU410 4.5 42.9 1.0
CB X:LEU410 4.6 43.1 1.0
CE1 X:HIS644 4.6 41.3 1.0
C X:GLY408 4.7 43.2 1.0
O X:HOH1095 4.7 47.6 1.0
N X:GLU411 4.7 42.2 1.0
CA X:GLU411 4.8 42.1 1.0
CG X:GLU353 4.9 43.5 1.0
O X:GLY408 4.9 43.9 1.0

Calcium binding site 2 out of 5 in 2dew

Go back to Calcium Binding Sites List in 2dew
Calcium binding site 2 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with Histone H3 N-Terminal Tail Including ARG8


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 4 in Complex with Histone H3 N-Terminal Tail Including ARG8 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca901

b:47.8
occ:1.00
 OD2 X:ASP179 2.2 49.4 1.0
OD2 X:ASP165 2.2 45.4 1.0
OD1 X:ASP155 2.4 47.6 1.0
OD1 X:ASP176 2.4 53.3 1.0
OD2 X:ASP157 2.4 49.7 1.0
OD1 X:ASN153 2.4 45.7 1.0
CG X:ASP165 3.3 47.8 1.0
CG X:ASP179 3.3 48.4 1.0
CG X:ASP155 3.4 49.6 1.0
CG X:ASN153 3.4 45.9 1.0
CG X:ASP157 3.6 51.6 1.0
CG X:ASP176 3.6 51.9 1.0
OD2 X:ASP155 3.7 52.1 1.0
ND2 X:ASN153 3.7 45.0 1.0
CA X:CA902 3.7 53.9 1.0
CB X:ASP165 3.7 48.0 1.0
CB X:ASP179 3.9 48.7 1.0
CA X:ASP176 4.2 52.0 1.0
O X:ASP176 4.3 51.0 1.0
CB X:ASP157 4.3 52.3 1.0
OD1 X:ASP179 4.3 45.9 1.0
CB X:ASP176 4.4 52.3 1.0
OD1 X:ASP157 4.4 49.5 1.0
OD1 X:ASP165 4.4 44.5 1.0
OD2 X:ASP176 4.5 51.8 1.0
N X:ASP157 4.6 52.0 1.0
O X:ASP155 4.7 48.1 1.0
CB X:ASP155 4.7 48.8 1.0
C X:ASP176 4.7 51.8 1.0
C X:ASP155 4.8 49.3 1.0
CB X:ASN153 4.8 44.8 1.0
N X:ASP155 5.0 47.7 1.0

Calcium binding site 3 out of 5 in 2dew

Go back to Calcium Binding Sites List in 2dew
Calcium binding site 3 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with Histone H3 N-Terminal Tail Including ARG8


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 4 in Complex with Histone H3 N-Terminal Tail Including ARG8 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca902

b:53.9
occ:1.00
 O X:HOH1020 2.3 45.6 1.0
OD1 X:ASP388 2.4 55.0 1.0
OD2 X:ASP179 2.4 49.4 1.0
OD2 X:ASP157 2.6 49.7 1.0
OD2 X:ASP155 2.6 52.1 1.0
OD1 X:ASP157 2.7 49.5 1.0
OD1 X:ASP179 2.8 45.9 1.0
CG X:ASP179 2.9 48.4 1.0
CG X:ASP157 3.0 51.6 1.0
CG X:ASP388 3.4 52.0 1.0
CG X:ASP155 3.6 49.6 1.0
CA X:CA901 3.7 47.8 1.0
OD1 X:ASP155 3.9 47.6 1.0
N X:ASP388 4.0 50.1 1.0
CA X:ASP388 4.1 49.9 1.0
OD2 X:ASP388 4.1 55.4 1.0
CB X:ASP388 4.3 50.4 1.0
CE X:LYS362 4.4 48.9 1.0
CB X:ASP179 4.4 48.7 1.0
O X:HOH1046 4.4 48.6 1.0
O X:GLU175 4.5 52.3 1.0
CB X:ASP157 4.5 52.3 1.0
NZ X:LYS362 4.9 48.9 1.0
CB X:ASP155 4.9 48.8 1.0

Calcium binding site 4 out of 5 in 2dew

Go back to Calcium Binding Sites List in 2dew
Calcium binding site 4 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with Histone H3 N-Terminal Tail Including ARG8


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 4 in Complex with Histone H3 N-Terminal Tail Including ARG8 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca903

b:51.0
occ:1.00
 O X:SER370 2.2 45.9 1.0
OD1 X:ASN373 2.2 53.1 1.0
OD1 X:ASP369 2.3 39.2 1.0
O X:HOH1055 2.3 52.8 1.0
OE1 X:GLU351 2.4 47.4 1.0
CG X:ASP369 3.2 43.7 1.0
C X:SER370 3.4 47.0 1.0
CG X:ASN373 3.5 50.7 1.0
OD2 X:ASP369 3.5 41.7 1.0
CD X:GLU351 3.5 46.3 1.0
N X:ASN373 3.9 48.8 1.0
CG X:GLU351 4.0 43.2 1.0
N X:SER370 4.1 46.8 1.0
CA X:ASN373 4.1 49.0 1.0
N X:PRO371 4.2 47.0 1.0
CA X:PRO371 4.2 47.6 1.0
C X:ASP369 4.3 46.6 1.0
CA X:SER370 4.3 46.4 1.0
OE1 X:GLN397 4.3 49.6 1.0
ND2 X:ASN373 4.4 51.3 1.0
O X:LYS377 4.4 49.5 1.0
CB X:ASN373 4.4 48.8 1.0
CB X:ASP369 4.4 45.6 1.0
C X:PRO371 4.5 48.2 1.0
OE2 X:GLU351 4.6 47.1 1.0
CA X:LYS377 4.6 50.7 1.0
O X:GLU351 4.7 43.1 1.0
O X:ASP369 4.7 46.8 1.0
N X:ARG372 4.7 48.8 1.0
CA X:ASP369 4.8 45.5 1.0
CB X:LYS377 4.9 50.9 1.0
O X:PRO371 5.0 48.5 1.0
C X:LYS377 5.0 50.6 1.0

Calcium binding site 5 out of 5 in 2dew

Go back to Calcium Binding Sites List in 2dew
Calcium binding site 5 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with Histone H3 N-Terminal Tail Including ARG8


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 4 in Complex with Histone H3 N-Terminal Tail Including ARG8 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca904

b:44.8
occ:1.00
 O X:GLU170 2.3 54.5 1.0
O X:HOH991 2.3 39.8 1.0
O X:HOH1007 2.3 42.8 1.0
OD1 X:ASP168 2.4 49.5 1.0
O X:ASP165 2.4 47.6 1.0
CG X:ASP168 3.4 53.1 1.0
C X:GLU170 3.5 54.4 1.0
C X:ASP165 3.5 48.7 1.0
OD2 X:ASP168 3.7 51.5 1.0
OD2 X:ASP176 4.1 51.8 1.0
N X:GLU170 4.1 55.3 1.0
CA X:ASP165 4.2 48.4 1.0
CD2 X:LEU172 4.3 56.5 1.0
O X:ASP168 4.3 55.0 1.0
CA X:GLU170 4.4 55.0 1.0
N X:VAL171 4.4 54.0 1.0
CB X:ASP165 4.4 48.0 1.0
CA X:VAL171 4.5 53.6 1.0
N X:CYS166 4.5 49.4 1.0
OE2 X:GLU252 4.6 43.4 1.0
OE1 X:GLU252 4.6 44.1 1.0
C X:ASP168 4.6 54.7 1.0
CA X:CYS166 4.7 50.2 1.0
CB X:ASP168 4.8 53.9 1.0
O X:HOH1044 4.8 62.4 1.0
N X:ASP168 4.8 54.1 1.0
CZ X:PHE214 4.9 46.7 1.0
N X:LEU172 4.9 54.2 1.0

Reference:

K.Arita, T.Shimizu, H.Hashimoto, Y.Hidaka, M.Yamada, M.Sato. Structural Basis For Histone N-Terminal Recognition By Human Peptidylarginine Deiminase 4 Proc.Natl.Acad.Sci.Usa V. 103 5291 2006.
ISSN: ISSN 0027-8424
PubMed: 16567635
DOI: 10.1073/PNAS.0509639103
Page generated: Sat Dec 12 03:35:00 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy