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Calcium in PDB 3b1t: Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with O-Cl-Amidine

Enzymatic activity of Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with O-Cl-Amidine

All present enzymatic activity of Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with O-Cl-Amidine:
3.5.3.15;

Protein crystallography data

The structure of Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with O-Cl-Amidine, PDB code: 3b1t was solved by C.P.Causey, J.E.Jones, J.L.Slack, D.Kamei, L.E.Jones Jr, V.Subramanian, B.Knuckley, P.Ebrahimi, A.A.Chumanevich, Y.Luo, H.Hashimoto, T.Shimizu, M.Sato, L.J.Hofseth, P.R.Thompson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 145.787, 60.853, 114.302, 90.00, 123.99, 90.00
R / Rfree (%) 21.1 / 26.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with O-Cl-Amidine (pdb code 3b1t). 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 O-Cl-Amidine, PDB code: 3b1t:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 3b1t

Go back to Calcium Binding Sites List in 3b1t
Calcium binding site 1 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with O-Cl-Amidine


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 O-Cl-Amidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca900

b:52.0
occ:1.00
 OE1 A:GLN349 2.3 70.9 1.0
O A:PHE407 2.3 61.7 1.0
OE1 A:GLU353 2.4 65.5 1.0
O A:LEU410 2.5 52.5 1.0
O A:HOH756 2.5 63.2 1.0
OE1 A:GLU411 2.7 55.3 1.0
CD A:GLU353 3.4 64.1 1.0
CD A:GLN349 3.5 71.4 1.0
C A:PHE407 3.5 61.4 1.0
C A:LEU410 3.6 51.7 1.0
OE2 A:GLU353 3.8 65.7 1.0
CD A:GLU411 3.8 55.1 1.0
NE2 A:GLN349 4.1 71.6 1.0
CA A:GLY408 4.3 60.7 1.0
N A:GLY408 4.3 61.6 1.0
N A:LEU410 4.4 53.2 1.0
CA A:LEU410 4.4 51.5 1.0
CB A:LEU410 4.5 51.5 1.0
OE2 A:GLU411 4.6 56.9 1.0
CA A:PHE407 4.6 61.9 1.0
CB A:PHE407 4.6 62.9 1.0
O A:GLN349 4.6 72.0 1.0
N A:GLU411 4.6 50.8 1.0
CG A:GLN349 4.6 72.0 1.0
C A:GLY408 4.7 59.0 1.0
CG A:GLU411 4.7 53.4 1.0
CE1 A:HIS644 4.7 76.5 1.0
CG A:GLU353 4.8 63.0 1.0
CA A:GLU411 4.8 50.9 1.0
O A:GLY408 4.9 58.8 1.0
CE A:MET298 5.0 48.6 1.0

Calcium binding site 2 out of 5 in 3b1t

Go back to Calcium Binding Sites List in 3b1t
Calcium binding site 2 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with O-Cl-Amidine


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 O-Cl-Amidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:56.3
occ:1.00
 O A:HOH776 2.3 63.7 1.0
OD1 A:ASN373 2.3 91.3 1.0
O A:SER370 2.3 80.5 1.0
OE1 A:GLU351 2.4 80.2 1.0
OD1 A:ASP369 2.4 78.0 1.0
CG A:ASP369 3.1 78.7 1.0
OD2 A:ASP369 3.1 80.6 1.0
C A:SER370 3.5 79.3 1.0
CG A:ASN373 3.5 92.3 1.0
CD A:GLU351 3.5 79.3 1.0
N A:ASN373 4.1 90.1 1.0
O A:LYS377 4.1 99.5 1.0
CG A:GLU351 4.1 78.4 1.0
CA A:ASN373 4.2 93.0 1.0
N A:SER370 4.2 76.3 1.0
CA A:PRO371 4.3 82.2 1.0
N A:PRO371 4.3 79.5 1.0
C A:ASP369 4.3 74.9 1.0
ND2 A:ASN373 4.4 92.2 1.0
CG A:LYS377 4.4 0.6 1.0
CA A:SER370 4.5 76.8 1.0
CB A:ASN373 4.5 93.9 1.0
CB A:ASP369 4.5 76.5 1.0
OE1 A:GLN397 4.5 85.7 1.0
CA A:LYS377 4.5 0.6 1.0
O A:ASP369 4.5 74.9 1.0
OE2 A:GLU351 4.5 79.4 1.0
C A:PRO371 4.5 84.2 1.0
N A:ARG372 4.7 84.8 1.0
O A:GLU351 4.8 71.0 1.0
C A:LYS377 4.8 0.7 1.0
CB A:LYS377 4.9 0.8 1.0
OG1 A:THR393 4.9 68.6 1.0
CA A:ASP369 4.9 74.0 1.0

Calcium binding site 3 out of 5 in 3b1t

Go back to Calcium Binding Sites List in 3b1t
Calcium binding site 3 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with O-Cl-Amidine


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 O-Cl-Amidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:63.6
occ:1.00
 OD2 A:ASP176 2.3 95.7 1.0
OD2 A:ASP179 2.3 86.6 1.0
OD2 A:ASP157 2.3 0.8 1.0
OD2 A:ASP165 2.3 0.4 1.0
OD1 A:ASP155 2.4 89.8 1.0
OD1 A:ASN153 2.4 78.0 1.0
CG A:ASP155 3.3 90.4 1.0
CG A:ASP179 3.4 83.7 1.0
OD2 A:ASP155 3.5 92.4 1.0
CG A:ASN153 3.5 76.0 1.0
CG A:ASP165 3.5 0.6 1.0
CG A:ASP157 3.5 0.6 1.0
CG A:ASP176 3.5 97.6 1.0
CA A:CA903 3.7 65.6 1.0
CB A:ASP179 3.8 81.6 1.0
ND2 A:ASN153 3.9 77.6 1.0
CB A:ASP165 4.1 0.6 1.0
CA A:ASP176 4.2 99.3 1.0
O A:ASP176 4.3 93.7 1.0
CB A:ASP157 4.3 0.5 1.0
CB A:ASP176 4.3 0.0 1.0
OD1 A:ASP157 4.4 0.8 1.0
OD1 A:ASP179 4.4 83.4 1.0
OD1 A:ASP176 4.5 97.1 1.0
OD1 A:ASP165 4.5 0.1 1.0
O A:ASP155 4.7 91.8 1.0
CB A:ASP155 4.7 89.0 1.0
N A:ASP157 4.7 0.1 1.0
C A:ASP176 4.8 96.6 1.0
C A:ASP155 4.8 92.5 1.0
CB A:ASN153 4.9 73.3 1.0
O A:HOH757 5.0 78.4 1.0

Calcium binding site 4 out of 5 in 3b1t

Go back to Calcium Binding Sites List in 3b1t
Calcium binding site 4 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with O-Cl-Amidine


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 O-Cl-Amidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:65.6
occ:1.00
 OD1 A:ASP388 2.3 94.2 1.0
OD2 A:ASP155 2.4 92.4 1.0
OD2 A:ASP179 2.4 86.6 1.0
OD2 A:ASP157 2.4 0.8 1.0
OD1 A:ASP157 2.4 0.8 1.0
O A:HOH757 2.6 78.4 1.0
CG A:ASP157 2.8 0.6 1.0
CG A:ASP179 3.1 83.7 1.0
OD1 A:ASP179 3.1 83.4 1.0
CG A:ASP155 3.4 90.4 1.0
CG A:ASP388 3.6 94.8 1.0
CA A:CA902 3.7 63.6 1.0
OD1 A:ASP155 3.8 89.8 1.0
N A:ASP388 3.8 95.0 1.0
CA A:ASP388 4.0 91.9 1.0
CB A:ASP157 4.3 0.5 1.0
CB A:ASP388 4.4 93.5 1.0
OD2 A:ASP388 4.5 96.6 1.0
CB A:ASP179 4.5 81.6 1.0
CB A:ASP155 4.7 89.0 1.0
O A:GLU175 4.8 0.4 1.0

Calcium binding site 5 out of 5 in 3b1t

Go back to Calcium Binding Sites List in 3b1t
Calcium binding site 5 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with O-Cl-Amidine


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 O-Cl-Amidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:67.0
occ:1.00
 O A:ASP165 2.3 0.3 1.0
O A:GLU170 2.3 0.1 1.0
OD2 A:ASP168 2.4 0.5 1.0
C A:ASP165 3.3 0.5 1.0
O A:ASP168 3.4 0.3 1.0
C A:GLU170 3.5 0.8 1.0
CG A:ASP168 3.6 0.2 1.0
N A:GLU170 4.0 0.9 1.0
OD1 A:ASP168 4.1 0.2 1.0
C A:ASP168 4.1 0.7 1.0
CA A:ASP165 4.1 0.6 1.0
N A:CYS166 4.3 0.3 1.0
OD1 A:ASP176 4.3 97.1 1.0
CA A:GLU170 4.3 1.0 1.0
CB A:ASP165 4.4 0.6 1.0
CA A:CYS166 4.4 0.9 1.0
N A:VAL171 4.5 0.3 1.0
N A:ASP168 4.6 0.7 1.0
CA A:ASP168 4.7 0.1 1.0
CB A:ASP168 4.7 0.9 1.0
CA A:VAL171 4.8 0.5 1.0
OE1 A:GLU252 4.8 66.3 1.0
OE2 A:GLU252 4.8 65.2 1.0
CZ A:PHE214 4.9 73.2 1.0
NH1 A:ARG212 4.9 67.6 1.0
N A:ASP169 5.0 0.7 1.0
C A:CYS166 5.0 0.8 1.0
CB A:GLU170 5.0 0.7 1.0

Reference:

C.P.Causey, J.E.Jones, J.L.Slack, D.Kamei, L.E.Jones Jr, V.Subramanian, B.Knuckley, P.Ebrahimi, A.A.Chumanevich, Y.Luo, H.Hashimoto, M.Sato, L.J.Hofseth, P.R.Thompson. The Development of N-Alpha-(2-Carboxyl)Benzoyl-N(5)-(2-Fluoro-1-Iminoethyl)-L- Ornithine Amide (O-F-Amidine) and N-Alpha-(2-Carboxyl)Benzoyl-N(5)-(2-Chloro-1-Iminoethyl)-L- Ornithine Amide (O-Cl-Amidine) As Second Generation Protein Arginine Deiminase (Pad) Inhibitors J.Med.Chem. V. 54 6919 2011.
ISSN: ISSN 0022-2623
PubMed: 21882827
DOI: 10.1021/JM2008985
Page generated: Sat Jul 13 08:07:08 2024

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