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Calcium in PDB 2dw5: Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with N-Alpha-Benzoyl-N5-(2-Fluoro-1-Iminoethyl)-L-Ornithine Amide

Enzymatic activity of Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with N-Alpha-Benzoyl-N5-(2-Fluoro-1-Iminoethyl)-L-Ornithine Amide

All present enzymatic activity of Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with N-Alpha-Benzoyl-N5-(2-Fluoro-1-Iminoethyl)-L-Ornithine Amide:
3.5.3.15;

Protein crystallography data

The structure of Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with N-Alpha-Benzoyl-N5-(2-Fluoro-1-Iminoethyl)-L-Ornithine Amide, PDB code: 2dw5 was solved by Y.Luo, K.Arita, M.Sato, P.R.Thompson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.70 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 146.259, 60.516, 114.911, 90.00, 124.19, 90.00
R / Rfree (%) 19.8 / 25.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with N-Alpha-Benzoyl-N5-(2-Fluoro-1-Iminoethyl)-L-Ornithine Amide (pdb code 2dw5). 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 N-Alpha-Benzoyl-N5-(2-Fluoro-1-Iminoethyl)-L-Ornithine Amide, PDB code: 2dw5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 2dw5

Go back to Calcium Binding Sites List in 2dw5
Calcium binding site 1 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with N-Alpha-Benzoyl-N5-(2-Fluoro-1-Iminoethyl)-L-Ornithine Amide


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 N-Alpha-Benzoyl-N5-(2-Fluoro-1-Iminoethyl)-L-Ornithine Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca900

b:55.3
occ:1.00
 O A:PHE407 2.3 55.7 1.0
OE1 A:GLN349 2.3 55.5 1.0
O A:LEU410 2.5 52.3 1.0
O A:HOH939 2.5 50.1 1.0
OE1 A:GLU411 2.5 60.8 1.0
O A:HOH918 2.6 55.5 1.0
OE1 A:GLU353 2.6 59.0 1.0
C A:PHE407 3.4 54.9 1.0
CD A:GLU411 3.4 59.8 1.0
CD A:GLN349 3.5 57.2 1.0
CD A:GLU353 3.6 57.9 1.0
C A:LEU410 3.7 51.9 1.0
OE2 A:GLU411 3.9 63.8 1.0
OE2 A:GLU353 3.9 59.2 1.0
N A:GLY408 4.2 55.1 1.0
CA A:GLY408 4.2 54.7 1.0
NE2 A:GLN349 4.4 55.4 1.0
N A:LEU410 4.4 52.7 1.0
CA A:LEU410 4.5 52.3 1.0
CG A:GLN349 4.5 57.9 1.0
CG A:GLU411 4.5 55.6 1.0
CA A:PHE407 4.5 54.6 1.0
CB A:PHE407 4.5 55.1 1.0
O A:GLN349 4.6 59.5 1.0
CB A:LEU410 4.6 52.9 1.0
C A:GLY408 4.6 54.4 1.0
CE1 A:HIS644 4.6 63.3 1.0
N A:GLU411 4.6 51.8 1.0
O A:HOH940 4.8 48.1 1.0
CA A:GLU411 4.8 50.4 1.0
O A:GLY408 4.8 54.6 1.0
CG A:GLU353 4.9 57.3 1.0

Calcium binding site 2 out of 5 in 2dw5

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Calcium binding site 2 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with N-Alpha-Benzoyl-N5-(2-Fluoro-1-Iminoethyl)-L-Ornithine Amide


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 N-Alpha-Benzoyl-N5-(2-Fluoro-1-Iminoethyl)-L-Ornithine Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:61.2
occ:1.00
 OD2 A:ASP179 2.3 60.1 1.0
OD2 A:ASP165 2.3 62.2 1.0
OD1 A:ASP155 2.3 60.1 1.0
OD2 A:ASP176 2.4 59.1 1.0
OD1 A:ASN153 2.4 57.6 1.0
OD2 A:ASP157 2.5 65.9 1.0
CG A:ASP155 3.3 60.2 1.0
CG A:ASP165 3.4 63.5 1.0
CG A:ASN153 3.4 55.8 1.0
CG A:ASP179 3.5 57.1 1.0
CG A:ASP176 3.6 61.8 1.0
CG A:ASP157 3.6 66.5 1.0
OD2 A:ASP155 3.7 62.9 1.0
ND2 A:ASN153 3.7 56.1 1.0
CB A:ASP165 3.8 64.2 1.0
CA A:CA902 3.9 72.2 1.0
CB A:ASP179 4.0 57.5 1.0
CA A:ASP176 4.1 61.3 1.0
O A:ASP176 4.2 59.8 1.0
CB A:ASP176 4.3 61.5 1.0
CB A:ASP157 4.4 67.2 1.0
OD1 A:ASP157 4.4 64.4 1.0
OD1 A:ASP165 4.4 58.8 1.0
O A:ASP155 4.5 59.2 1.0
OD1 A:ASP179 4.5 55.7 1.0
OD1 A:ASP176 4.6 62.5 1.0
C A:ASP155 4.6 60.1 1.0
N A:ASP157 4.6 66.0 1.0
C A:ASP176 4.7 60.7 1.0
CB A:ASP155 4.7 59.1 1.0
CB A:ASN153 4.9 53.1 1.0
O A:ASN153 4.9 55.0 1.0

Calcium binding site 3 out of 5 in 2dw5

Go back to Calcium Binding Sites List in 2dw5
Calcium binding site 3 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with N-Alpha-Benzoyl-N5-(2-Fluoro-1-Iminoethyl)-L-Ornithine Amide


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 N-Alpha-Benzoyl-N5-(2-Fluoro-1-Iminoethyl)-L-Ornithine Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:72.2
occ:1.00
 OD1 A:ASP388 2.3 70.2 1.0
OD2 A:ASP179 2.5 60.1 1.0
OD2 A:ASP155 2.7 62.9 1.0
OD1 A:ASP179 2.7 55.7 1.0
OD2 A:ASP157 2.8 65.9 1.0
OD1 A:ASP157 2.8 64.4 1.0
CG A:ASP179 2.9 57.1 1.0
CG A:ASP157 3.1 66.5 1.0
CG A:ASP388 3.4 66.0 1.0
CG A:ASP155 3.7 60.2 1.0
CA A:CA901 3.9 61.2 1.0
OD1 A:ASP155 3.9 60.1 1.0
OD2 A:ASP388 4.0 68.2 1.0
N A:ASP388 4.2 65.4 1.0
CA A:ASP388 4.2 64.7 1.0
CE A:LYS362 4.3 58.1 1.0
CB A:ASP179 4.4 57.5 1.0
CB A:ASP388 4.4 64.9 1.0
O A:GLU175 4.5 63.4 1.0
CB A:ASP157 4.6 67.2 1.0
NZ A:LYS362 4.7 58.1 1.0
CB A:ASP155 5.0 59.1 1.0
N A:ASP179 5.0 57.7 1.0

Calcium binding site 4 out of 5 in 2dw5

Go back to Calcium Binding Sites List in 2dw5
Calcium binding site 4 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with N-Alpha-Benzoyl-N5-(2-Fluoro-1-Iminoethyl)-L-Ornithine Amide


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 N-Alpha-Benzoyl-N5-(2-Fluoro-1-Iminoethyl)-L-Ornithine Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:65.1
occ:1.00
 O A:SER370 2.3 60.9 1.0
OD1 A:ASN373 2.3 64.7 1.0
OD1 A:ASP369 2.3 62.9 1.0
O A:HOH1035 2.5 56.5 1.0
OE1 A:GLU351 2.5 63.0 1.0
CG A:ASP369 3.1 59.9 1.0
OD2 A:ASP369 3.4 59.3 1.0
C A:SER370 3.4 61.1 1.0
CG A:ASN373 3.6 64.5 1.0
CD A:GLU351 3.7 62.5 1.0
N A:ASN373 4.0 63.9 1.0
N A:SER370 4.1 59.1 1.0
CA A:ASN373 4.1 64.3 1.0
N A:PRO371 4.2 61.9 1.0
O A:LYS377 4.2 65.8 1.0
CA A:PRO371 4.3 62.4 1.0
OE2 A:GLU351 4.3 67.3 1.0
C A:ASP369 4.3 58.7 1.0
CA A:SER370 4.4 60.3 1.0
ND2 A:ASN373 4.4 62.5 1.0
C A:PRO371 4.4 62.9 1.0
CB A:ASP369 4.5 58.4 1.0
CB A:ASN373 4.5 63.8 1.0
O A:GLU351 4.5 58.6 1.0
CA A:LYS377 4.5 65.5 1.0
OE1 A:GLN397 4.6 70.2 1.0
O A:ASP369 4.6 59.5 1.0
N A:ARG372 4.7 64.1 1.0
CG A:GLU351 4.8 62.3 1.0
CA A:ASP369 4.8 57.8 1.0
C A:LYS377 4.9 65.5 1.0
O A:PRO371 4.9 62.3 1.0
CB A:GLU351 4.9 60.0 1.0
CB A:LYS377 5.0 65.7 1.0
CG A:LYS377 5.0 69.0 0.0

Calcium binding site 5 out of 5 in 2dw5

Go back to Calcium Binding Sites List in 2dw5
Calcium binding site 5 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with N-Alpha-Benzoyl-N5-(2-Fluoro-1-Iminoethyl)-L-Ornithine Amide


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 N-Alpha-Benzoyl-N5-(2-Fluoro-1-Iminoethyl)-L-Ornithine Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:67.1
occ:1.00
 O A:HOH1031 2.3 66.2 1.0
O A:ASP165 2.3 64.7 1.0
O A:GLU170 2.3 67.2 1.0
OD2 A:ASP168 2.3 67.5 1.0
O A:HOH1036 2.7 61.5 1.0
CG A:ASP168 3.4 68.1 1.0
C A:ASP165 3.4 65.1 1.0
C A:GLU170 3.5 67.6 1.0
OD1 A:ASP168 3.7 70.2 1.0
N A:GLU170 4.0 68.3 1.0
O A:ASP168 4.0 68.3 1.0
OD1 A:ASP176 4.1 62.5 1.0
CA A:ASP165 4.2 64.7 1.0
CA A:GLU170 4.3 68.1 1.0
CB A:ASP165 4.3 64.2 1.0
N A:CYS166 4.3 65.1 1.0
C A:ASP168 4.4 68.5 1.0
N A:VAL171 4.4 67.1 1.0
CA A:CYS166 4.5 65.2 1.0
CA A:VAL171 4.6 67.1 1.0
OE2 A:GLU252 4.6 55.3 1.0
OE1 A:GLU252 4.7 57.8 1.0
CB A:ASP168 4.7 67.7 1.0
N A:ASP168 4.7 67.7 1.0
CZ A:PHE214 4.8 56.0 1.0
N A:LEU172 4.8 67.1 1.0
CA A:ASP168 4.9 67.9 1.0
CB A:GLU170 4.9 68.2 1.0

Reference:

Y.Luo, K.Arita, M.Bhatia, B.Knuckley, Y.H.Lee, M.R.Stallcup, M.Sato, P.R.Thompson. Inhibitors and Inactivators of Protein Arginine Deiminase 4: Functional and Structural Characterization Biochemistry V. 45 11727 2006.
ISSN: ISSN 0006-2960
PubMed: 17002273
DOI: 10.1021/BI061180D
Page generated: Fri Jul 12 10:00:14 2024

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