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Calcium in PDB 2dex: Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with Histone H3 N-Terminal Peptide Including ARG17

Enzymatic activity of Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with Histone H3 N-Terminal Peptide Including ARG17

All present enzymatic activity of Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with Histone H3 N-Terminal Peptide Including ARG17:
3.5.3.15;

Protein crystallography data

The structure of Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with Histone H3 N-Terminal Peptide Including ARG17, PDB code: 2dex 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) 33.13 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 146.072, 60.103, 115.703, 90.00, 124.32, 90.00
R / Rfree (%) 20.3 / 24.7

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 Peptide Including ARG17 (pdb code 2dex). 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 Peptide Including ARG17, PDB code: 2dex:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 2dex

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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 Peptide Including ARG17


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 Peptide Including ARG17 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca900

b:53.2
occ:1.00
 OE1 X:GLN349 2.3 52.4 1.0
O X:PHE407 2.3 57.6 1.0
OE1 X:GLU353 2.4 62.3 1.0
O X:LEU410 2.4 54.8 1.0
O X:HOH934 2.5 56.9 1.0
OE1 X:GLU411 2.5 61.4 1.0
O X:HOH920 2.5 49.5 1.0
CD X:GLU411 3.4 61.2 1.0
CD X:GLN349 3.5 55.9 1.0
C X:PHE407 3.5 57.5 1.0
CD X:GLU353 3.5 61.4 1.0
C X:LEU410 3.6 55.5 1.0
OE2 X:GLU411 3.9 64.3 1.0
OE2 X:GLU353 4.0 63.4 1.0
N X:GLY408 4.3 56.6 1.0
CA X:GLY408 4.3 56.7 1.0
NE2 X:GLN349 4.3 54.1 1.0
N X:LEU410 4.3 56.6 1.0
CA X:LEU410 4.4 56.1 1.0
CG X:GLN349 4.4 55.0 1.0
CG X:GLU411 4.5 56.6 1.0
O X:GLN349 4.5 54.0 1.0
CB X:PHE407 4.5 56.7 1.0
CA X:PHE407 4.5 57.2 1.0
CB X:LEU410 4.6 55.7 1.0
N X:GLU411 4.6 54.4 1.0
C X:GLY408 4.7 56.7 1.0
CE1 X:HIS644 4.7 51.7 1.0
CA X:GLU411 4.8 54.3 1.0
O X:HOH1012 4.8 58.7 1.0
CG X:GLU353 4.8 58.7 1.0
O X:GLY408 4.9 55.9 1.0

Calcium binding site 2 out of 5 in 2dex

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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 Peptide Including ARG17


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 Peptide Including ARG17 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca901

b:61.8
occ:1.00
 OD1 X:ASP176 2.3 67.8 1.0
OD2 X:ASP179 2.3 64.8 1.0
OD2 X:ASP165 2.3 62.8 1.0
OD1 X:ASP155 2.5 61.8 1.0
OD1 X:ASN153 2.5 60.6 1.0
OD2 X:ASP157 2.5 66.4 1.0
CG X:ASP165 3.3 63.1 1.0
CG X:ASP155 3.4 61.6 1.0
CG X:ASP179 3.5 64.7 1.0
CG X:ASN153 3.5 58.2 1.0
CG X:ASP176 3.5 66.4 1.0
CG X:ASP157 3.6 65.9 1.0
CB X:ASP165 3.6 62.2 1.0
OD2 X:ASP155 3.7 63.2 1.0
CA X:CA902 3.8 65.6 1.0
ND2 X:ASN153 3.8 56.4 1.0
CB X:ASP179 4.0 64.5 1.0
CA X:ASP176 4.1 67.0 1.0
CB X:ASP176 4.2 67.0 1.0
O X:ASP176 4.3 66.1 1.0
CB X:ASP157 4.3 66.5 1.0
OD1 X:ASP157 4.4 65.5 1.0
N X:ASP157 4.4 65.4 1.0
OD2 X:ASP176 4.5 64.3 1.0
OD1 X:ASP165 4.5 64.4 1.0
OD1 X:ASP179 4.5 61.5 1.0
O X:ASP155 4.7 59.8 1.0
C X:ASP155 4.7 61.1 1.0
C X:ASP176 4.7 66.9 1.0
CB X:ASP155 4.8 60.8 1.0
CB X:ASN153 4.9 57.5 1.0
N X:ASP155 5.0 59.1 1.0

Calcium binding site 3 out of 5 in 2dex

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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 Peptide Including ARG17


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 Peptide Including ARG17 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca902

b:65.6
occ:1.00
 OD1 X:ASP388 2.3 65.6 1.0
O X:HOH1045 2.4 59.5 1.0
OD2 X:ASP179 2.4 64.8 1.0
OD2 X:ASP155 2.5 63.2 1.0
OD2 X:ASP157 2.6 66.4 1.0
OD1 X:ASP179 2.7 61.5 1.0
OD1 X:ASP157 2.7 65.5 1.0
CG X:ASP179 2.9 64.7 1.0
CG X:ASP157 3.0 65.9 1.0
CG X:ASP388 3.4 63.2 1.0
CG X:ASP155 3.5 61.6 1.0
CA X:CA901 3.8 61.8 1.0
OD1 X:ASP155 3.9 61.8 1.0
N X:ASP388 4.0 61.6 1.0
OD2 X:ASP388 4.1 67.5 1.0
CA X:ASP388 4.1 61.3 1.0
CB X:ASP388 4.4 61.6 1.0
CB X:ASP179 4.4 64.5 1.0
O X:GLU175 4.4 67.9 1.0
CE X:LYS362 4.4 64.2 1.0
CB X:ASP157 4.5 66.5 1.0
CB X:ASP155 4.9 60.8 1.0
NZ X:LYS362 5.0 63.7 1.0

Calcium binding site 4 out of 5 in 2dex

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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 Peptide Including ARG17


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 Peptide Including ARG17 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca903

b:62.0
occ:1.00
 OD1 X:ASN373 2.2 64.4 1.0
O X:SER370 2.3 57.3 1.0
OE1 X:GLU351 2.3 56.7 1.0
OD1 X:ASP369 2.5 52.9 1.0
O X:HOH1096 2.5 64.0 1.0
CG X:ASP369 3.3 56.8 1.0
CG X:ASN373 3.4 63.7 1.0
C X:SER370 3.4 58.3 1.0
CD X:GLU351 3.5 56.0 1.0
OD2 X:ASP369 3.7 57.9 1.0
N X:ASN373 3.9 62.6 1.0
CA X:ASN373 4.1 62.8 1.0
CG X:GLU351 4.1 55.6 1.0
CA X:PRO371 4.2 60.0 1.0
N X:PRO371 4.2 59.0 1.0
N X:SER370 4.3 57.6 1.0
ND2 X:ASN373 4.3 62.9 1.0
C X:ASP369 4.3 57.0 1.0
CB X:ASN373 4.3 63.0 1.0
O X:LYS377 4.3 62.5 1.0
C X:PRO371 4.4 60.8 1.0
OE1 X:GLN397 4.4 64.7 1.0
CA X:SER370 4.4 58.0 1.0
OE2 X:GLU351 4.5 55.1 1.0
CB X:ASP369 4.6 56.4 1.0
O X:ASP369 4.6 57.5 1.0
N X:ARG372 4.6 62.2 1.0
CG X:LYS377 4.7 64.5 1.0
O X:GLU351 4.7 55.9 1.0
CA X:LYS377 4.7 63.3 1.0
O X:PRO371 4.8 61.3 1.0
CA X:ASP369 4.9 56.0 1.0

Calcium binding site 5 out of 5 in 2dex

Go back to Calcium Binding Sites List in 2dex
Calcium binding site 5 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with Histone H3 N-Terminal Peptide Including ARG17


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 Peptide Including ARG17 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca904

b:62.5
occ:1.00
 OD1 X:ASP168 2.2 67.6 1.0
O X:HOH951 2.3 53.5 1.0
O X:GLU170 2.3 67.1 1.0
O X:HOH958 2.4 50.5 1.0
O X:ASP165 2.4 62.1 1.0
CG X:ASP168 3.3 67.4 1.0
C X:GLU170 3.5 66.8 1.0
C X:ASP165 3.5 62.4 1.0
OD2 X:ASP168 3.6 67.1 1.0
O X:ASP168 4.1 67.2 1.0
N X:GLU170 4.1 67.1 1.0
OD2 X:ASP176 4.2 64.3 1.0
CA X:ASP165 4.2 62.6 1.0
CA X:GLU170 4.4 66.9 1.0
N X:VAL171 4.4 67.0 1.0
CB X:ASP165 4.4 62.2 1.0
OE1 X:GLU252 4.5 55.1 1.0
N X:CYS166 4.5 62.5 1.0
C X:ASP168 4.5 67.2 1.0
CA X:VAL171 4.5 67.1 1.0
CB X:ASP168 4.6 67.1 1.0
CA X:CYS166 4.6 62.7 1.0
OE2 X:GLU252 4.7 55.3 1.0
N X:ASP168 4.7 67.2 1.0
CA X:ASP168 4.9 67.2 1.0
N X:LEU172 4.9 67.9 1.0
CZ X:PHE214 4.9 62.2 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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