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Calcium in PDB 2dey: Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with Histone H4 N-Terminal Tail Including ARG3

Enzymatic activity of Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with Histone H4 N-Terminal Tail Including ARG3

All present enzymatic activity of Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with Histone H4 N-Terminal Tail Including ARG3:
3.5.3.15;

Protein crystallography data

The structure of Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with Histone H4 N-Terminal Tail Including ARG3, PDB code: 2dey 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) 33.57 / 2.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 146.192, 60.611, 115.203, 90.00, 124.18, 90.00
R / Rfree (%) 19.9 / 24.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with Histone H4 N-Terminal Tail Including ARG3 (pdb code 2dey). 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 H4 N-Terminal Tail Including ARG3, PDB code: 2dey:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 2dey

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Calcium binding site 1 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with Histone H4 N-Terminal Tail Including ARG3


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 H4 N-Terminal Tail Including ARG3 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca900

b:48.9
occ:1.00
 O X:PHE407 2.2 51.7 1.0
OE1 X:GLN349 2.3 50.6 1.0
O X:HOH928 2.4 48.2 1.0
O X:HOH1034 2.4 40.8 1.0
OE1 X:GLU353 2.5 54.1 1.0
O X:LEU410 2.5 48.5 1.0
OE1 X:GLU411 2.6 54.1 1.0
CD X:GLN349 3.4 49.6 1.0
C X:PHE407 3.4 50.8 1.0
CD X:GLU411 3.5 54.6 1.0
CD X:GLU353 3.6 53.5 1.0
C X:LEU410 3.7 48.0 1.0
OE2 X:GLU411 4.0 58.2 1.0
OE2 X:GLU353 4.0 54.9 1.0
CA X:GLY408 4.1 50.7 1.0
N X:GLY408 4.1 50.5 1.0
NE2 X:GLN349 4.2 46.5 1.0
N X:LEU410 4.4 49.8 1.0
CG X:GLN349 4.4 49.0 1.0
CA X:LEU410 4.4 49.2 1.0
O X:GLN349 4.4 50.1 1.0
CG X:GLU411 4.5 50.9 1.0
CB X:PHE407 4.5 50.1 1.0
CA X:PHE407 4.5 50.0 1.0
C X:GLY408 4.6 51.2 1.0
N X:GLU411 4.6 47.3 1.0
CB X:LEU410 4.6 49.9 1.0
CE1 X:HIS644 4.8 52.6 1.0
CG X:GLU353 4.8 49.5 1.0
CA X:GLU411 4.9 47.3 1.0
O X:GLY408 4.9 51.1 1.0

Calcium binding site 2 out of 5 in 2dey

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Calcium binding site 2 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with Histone H4 N-Terminal Tail Including ARG3


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 H4 N-Terminal Tail Including ARG3 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca901

b:56.4
occ:1.00
 OD2 X:ASP165 2.3 63.5 1.0
OD1 X:ASP176 2.3 53.9 1.0
OD2 X:ASP179 2.3 56.0 1.0
OD1 X:ASN153 2.4 55.0 1.0
OD1 X:ASP155 2.5 57.2 1.0
OD2 X:ASP157 2.7 60.2 1.0
CG X:ASP165 3.3 62.2 1.0
CG X:ASN153 3.4 51.9 1.0
CG X:ASP179 3.5 57.0 1.0
CG X:ASP155 3.5 57.5 1.0
CG X:ASP176 3.5 58.3 1.0
CB X:ASP165 3.5 61.5 1.0
CG X:ASP157 3.7 59.7 1.0
ND2 X:ASN153 3.7 47.5 1.0
OD2 X:ASP155 3.8 58.7 1.0
CA X:CA902 3.9 65.7 1.0
CB X:ASP179 4.1 57.3 1.0
CA X:ASP176 4.2 59.2 1.0
CB X:ASP176 4.2 59.1 1.0
O X:ASP176 4.4 58.3 1.0
CB X:ASP157 4.4 60.4 1.0
OD1 X:ASP165 4.4 62.6 1.0
OD2 X:ASP176 4.5 54.8 1.0
N X:ASP157 4.5 59.9 1.0
OD1 X:ASP179 4.5 56.1 1.0
OD1 X:ASP157 4.6 58.8 1.0
O X:ASP155 4.6 56.8 1.0
C X:ASP155 4.6 57.5 1.0
C X:ASP176 4.8 59.1 1.0
CB X:ASN153 4.8 51.9 1.0
CB X:ASP155 4.8 57.0 1.0
N X:ARG156 4.9 58.6 1.0
O X:HOH1024 4.9 53.5 1.0

Calcium binding site 3 out of 5 in 2dey

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Calcium binding site 3 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with Histone H4 N-Terminal Tail Including ARG3


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 H4 N-Terminal Tail Including ARG3 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca902

b:65.7
occ:1.00
 O X:HOH1024 2.2 53.5 1.0
OD1 X:ASP388 2.3 60.2 1.0
OD2 X:ASP179 2.5 56.0 1.0
OD2 X:ASP157 2.6 60.2 1.0
OD2 X:ASP155 2.6 58.7 1.0
OD1 X:ASP179 2.7 56.1 1.0
OD1 X:ASP157 2.9 58.8 1.0
CG X:ASP179 2.9 57.0 1.0
CG X:ASP157 3.1 59.7 1.0
CG X:ASP388 3.5 60.2 1.0
CG X:ASP155 3.6 57.5 1.0
CA X:CA901 3.9 56.4 1.0
OD1 X:ASP155 3.9 57.2 1.0
N X:ASP388 4.0 59.0 1.0
CA X:ASP388 4.1 58.6 1.0
CE X:LYS362 4.2 60.9 1.0
OD2 X:ASP388 4.3 61.1 1.0
CB X:ASP388 4.4 58.9 1.0
CB X:ASP179 4.4 57.3 1.0
O X:GLU175 4.6 60.7 1.0
CB X:ASP157 4.6 60.4 1.0
NZ X:LYS362 4.7 62.0 1.0
CB X:ASP155 5.0 57.0 1.0

Calcium binding site 4 out of 5 in 2dey

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Calcium binding site 4 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with Histone H4 N-Terminal Tail Including ARG3


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 H4 N-Terminal Tail Including ARG3 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca903

b:52.9
occ:1.00
 O X:SER370 2.3 48.5 1.0
O X:HOH1040 2.4 53.8 1.0
OD1 X:ASN373 2.5 53.2 1.0
OD1 X:ASP369 2.5 46.2 1.0
OE1 X:GLU351 2.5 52.5 1.0
O X:HOH1058 2.6 59.1 1.0
CG X:ASP369 3.3 50.4 1.0
C X:SER370 3.5 50.0 1.0
CG X:ASN373 3.5 53.1 1.0
OD2 X:ASP369 3.6 45.7 1.0
CD X:GLU351 3.6 49.2 1.0
N X:ASN373 3.7 52.3 1.0
CA X:ASN373 3.9 53.0 1.0
OE2 X:GLU351 3.9 52.9 1.0
CA X:PRO371 4.1 50.9 1.0
N X:PRO371 4.2 50.2 1.0
C X:PRO371 4.2 51.5 1.0
CB X:ASN373 4.4 52.5 1.0
OE1 X:GLN397 4.4 57.7 1.0
O X:LYS377 4.4 58.0 1.0
CA X:LYS377 4.4 58.0 1.0
ND2 X:ASN373 4.5 53.0 1.0
C X:ASP369 4.5 51.4 1.0
N X:SER370 4.5 51.1 1.0
N X:ARG372 4.5 52.1 1.0
CB X:LYS377 4.6 58.4 1.0
O X:ASP369 4.6 51.3 1.0
CA X:SER370 4.6 50.4 1.0
O X:PRO371 4.7 50.5 1.0
CB X:ASP369 4.7 50.5 1.0
O X:GLU351 4.9 49.2 1.0
CG X:GLU351 4.9 49.5 1.0
C X:ARG372 4.9 52.2 1.0
C X:LYS377 4.9 58.2 1.0

Calcium binding site 5 out of 5 in 2dey

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Calcium binding site 5 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with Histone H4 N-Terminal Tail Including ARG3


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 H4 N-Terminal Tail Including ARG3 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca904

b:58.4
occ:1.00
 OD1 X:ASP168 2.3 63.0 1.0
O X:GLU170 2.3 59.9 1.0
O X:ASP165 2.4 61.4 1.0
O X:HOH1028 2.4 50.8 1.0
O X:HOH1017 2.4 45.7 1.0
CG X:ASP168 3.4 62.8 1.0
C X:ASP165 3.5 61.8 1.0
C X:GLU170 3.5 59.9 1.0
OD2 X:ASP168 3.8 63.4 1.0
O X:ASP168 4.1 63.0 1.0
N X:GLU170 4.2 61.0 1.0
OD2 X:ASP176 4.2 54.8 1.0
CA X:ASP165 4.3 61.6 1.0
CA X:GLU170 4.4 60.3 1.0
N X:VAL171 4.4 59.5 1.0
N X:CYS166 4.4 61.5 1.0
OE2 X:GLU252 4.4 47.8 1.0
CA X:VAL171 4.5 59.4 1.0
C X:ASP168 4.5 62.6 1.0
CB X:ASP165 4.5 61.5 1.0
OE1 X:GLU252 4.5 50.1 1.0
CA X:CYS166 4.6 61.6 1.0
N X:ASP168 4.6 62.6 1.0
CB X:ASP168 4.7 62.6 1.0
CA X:ASP168 4.8 62.7 1.0
CZ X:PHE214 4.9 53.8 1.0
N X:LEU172 4.9 59.9 1.0
CD X:GLU252 4.9 50.8 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 09:46:00 2024

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