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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

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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

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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

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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

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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: Fri Jul 12 09:45:04 2024

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