Atomistry » Calcium » PDB 3b1u-3biw » 3b1u
Atomistry »
  Calcium »
    PDB 3b1u-3biw »
      3b1u »

Calcium in PDB 3b1u: Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with O-F-Amidine

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

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

Protein crystallography data

The structure of Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with O-F-Amidine, PDB code: 3b1u 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 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 146.422, 60.468, 115.506, 90.00, 124.43, 90.00
R / Rfree (%) 21.9 / 25

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with O-F-Amidine (pdb code 3b1u). 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-F-Amidine, PDB code: 3b1u:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 3b1u

Go back to Calcium Binding Sites List in 3b1u
Calcium binding site 1 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with O-F-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-F-Amidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca900

b:49.9
occ:1.00
 O A:PHE407 2.2 63.0 1.0
OE1 A:GLN349 2.3 62.7 1.0
O A:HOH781 2.3 51.7 1.0
OE1 A:GLU353 2.4 61.5 1.0
O A:LEU410 2.5 59.1 1.0
O A:HOH778 2.6 46.7 1.0
OE1 A:GLU411 2.6 62.8 1.0
C A:PHE407 3.4 63.4 1.0
CD A:GLU353 3.4 61.7 1.0
CD A:GLN349 3.5 64.4 1.0
CD A:GLU411 3.6 62.1 1.0
C A:LEU410 3.6 58.8 1.0
OE2 A:GLU353 3.7 61.8 1.0
OE2 A:GLU411 4.1 63.1 1.0
N A:GLY408 4.2 63.8 1.0
CA A:GLY408 4.2 63.3 1.0
NE2 A:GLN349 4.3 64.5 1.0
N A:LEU410 4.4 59.7 1.0
CA A:LEU410 4.4 58.8 1.0
CB A:PHE407 4.4 63.7 1.0
CG A:GLN349 4.5 65.2 1.0
CA A:PHE407 4.5 63.6 1.0
CG A:GLU411 4.5 60.4 1.0
O A:GLN349 4.6 65.5 1.0
CB A:LEU410 4.6 58.8 1.0
C A:GLY408 4.6 62.3 1.0
N A:GLU411 4.6 58.4 1.0
CE1 A:HIS644 4.7 64.1 1.0
CG A:GLU353 4.8 61.0 1.0
CA A:GLU411 4.8 58.6 1.0
O A:GLY408 4.8 61.8 1.0

Calcium binding site 2 out of 5 in 3b1u

Go back to Calcium Binding Sites List in 3b1u
Calcium binding site 2 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with O-F-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-F-Amidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:54.3
occ:1.00
 O A:SER370 2.2 72.7 1.0
OD1 A:ASN373 2.3 80.6 1.0
OE1 A:GLU351 2.3 71.7 1.0
O A:HOH816 2.3 55.1 1.0
OD1 A:ASP369 2.5 71.1 1.0
O A:HOH789 2.5 47.1 1.0
CG A:ASP369 3.2 71.8 1.0
C A:SER370 3.4 71.4 1.0
OD2 A:ASP369 3.5 73.2 1.0
CD A:GLU351 3.5 71.3 1.0
CG A:ASN373 3.5 82.1 1.0
N A:ASN373 3.9 80.3 1.0
CA A:ASN373 4.0 82.7 1.0
N A:SER370 4.2 69.3 1.0
CG A:GLU351 4.2 71.1 1.0
O A:LYS377 4.2 85.5 1.0
CA A:PRO371 4.3 73.9 1.0
N A:PRO371 4.3 71.9 1.0
CA A:SER370 4.4 69.5 1.0
CB A:ASN373 4.4 83.5 1.0
C A:ASP369 4.4 68.6 1.0
CB A:ASP369 4.5 70.0 1.0
OE2 A:GLU351 4.5 71.4 1.0
ND2 A:ASN373 4.5 82.5 1.0
C A:PRO371 4.5 75.6 1.0
OE1 A:GLN397 4.6 80.1 1.0
O A:GLU351 4.6 66.9 1.0
CA A:LYS377 4.6 86.8 1.0
N A:ARG372 4.7 75.9 1.0
CG A:LYS377 4.7 88.3 1.0
O A:ASP369 4.8 68.4 1.0
CA A:ASP369 4.9 68.6 1.0
C A:LYS377 4.9 87.1 1.0

Calcium binding site 3 out of 5 in 3b1u

Go back to Calcium Binding Sites List in 3b1u
Calcium binding site 3 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with O-F-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-F-Amidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:54.5
occ:1.00
 OD2 A:ASP179 2.3 76.0 1.0
OD2 A:ASP176 2.3 81.3 1.0
OD1 A:ASP155 2.4 77.0 1.0
OD1 A:ASN153 2.4 72.9 1.0
OD2 A:ASP157 2.4 85.9 1.0
OD2 A:ASP165 2.5 86.9 1.0
CG A:ASP155 3.3 77.3 1.0
CG A:ASN153 3.4 71.5 1.0
CG A:ASP179 3.5 75.5 1.0
CG A:ASP165 3.5 87.6 1.0
CG A:ASP157 3.5 88.1 1.0
CG A:ASP176 3.5 82.9 1.0
OD2 A:ASP155 3.5 78.8 1.0
ND2 A:ASN153 3.7 72.3 1.0
CA A:CA903 3.8 59.9 1.0
CB A:ASP165 3.9 86.0 1.0
CB A:ASP179 3.9 74.5 1.0
CA A:ASP176 4.1 84.6 1.0
O A:ASP176 4.2 80.6 1.0
CB A:ASP176 4.2 85.0 1.0
CB A:ASP157 4.3 90.2 1.0
OD1 A:ASP157 4.4 88.5 1.0
OD1 A:ASP176 4.5 82.7 1.0
O A:ASP155 4.5 78.8 1.0
N A:ASP157 4.5 88.3 1.0
OD1 A:ASP179 4.5 74.9 1.0
OD1 A:ASP165 4.6 89.3 1.0
C A:ASP155 4.6 78.9 1.0
C A:ASP176 4.7 82.7 1.0
CB A:ASP155 4.7 76.3 1.0
CB A:ASN153 4.8 69.2 1.0
O A:HOH764 4.9 52.3 1.0

Calcium binding site 4 out of 5 in 3b1u

Go back to Calcium Binding Sites List in 3b1u
Calcium binding site 4 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with O-F-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-F-Amidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:59.9
occ:1.00
 OD1 A:ASP388 2.3 82.8 1.0
O A:HOH764 2.3 52.3 1.0
OD2 A:ASP155 2.4 78.8 1.0
OD2 A:ASP179 2.5 76.0 1.0
OD1 A:ASP157 2.6 88.5 1.0
OD2 A:ASP157 2.6 85.9 1.0
OD1 A:ASP179 2.9 74.9 1.0
CG A:ASP157 3.0 88.1 1.0
CG A:ASP179 3.0 75.5 1.0
CG A:ASP388 3.4 83.2 1.0
CG A:ASP155 3.5 77.3 1.0
CA A:CA902 3.8 54.5 1.0
N A:ASP388 3.8 82.8 1.0
OD1 A:ASP155 3.9 77.0 1.0
CA A:ASP388 3.9 80.5 1.0
CB A:ASP388 4.3 81.8 1.0
OD2 A:ASP388 4.3 86.0 1.0
CB A:ASP179 4.5 74.5 1.0
CB A:ASP157 4.5 90.2 1.0
O A:GLU175 4.6 86.3 1.0
CB A:ASP155 4.8 76.3 1.0

Calcium binding site 5 out of 5 in 3b1u

Go back to Calcium Binding Sites List in 3b1u
Calcium binding site 5 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with O-F-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-F-Amidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:55.0
occ:1.00
 O A:GLU170 2.3 89.2 1.0
O A:HOH753 2.3 54.5 1.0
O A:ASP165 2.3 85.9 1.0
OD2 A:ASP168 2.4 88.9 1.0
O A:HOH788 2.4 46.8 1.0
C A:ASP165 3.4 85.1 1.0
C A:GLU170 3.5 90.2 1.0
CG A:ASP168 3.5 91.3 1.0
OD1 A:ASP168 3.9 93.7 1.0
CA A:ASP165 4.1 86.5 1.0
OD1 A:ASP176 4.1 82.7 1.0
N A:GLU170 4.2 89.8 1.0
O A:ASP168 4.2 85.8 1.0
CB A:ASP165 4.3 86.0 1.0
N A:VAL171 4.4 90.5 1.0
N A:CYS166 4.4 83.0 1.0
CA A:VAL171 4.4 90.4 1.0
CA A:GLU170 4.4 91.2 1.0
C A:ASP168 4.6 87.8 1.0
OE1 A:GLU252 4.7 70.9 1.0
CA A:CYS166 4.7 81.7 1.0
OE2 A:GLU252 4.7 70.8 1.0
N A:LEU172 4.8 93.6 1.0
CB A:ASP168 4.8 91.6 1.0
CZ A:PHE214 4.8 77.9 1.0
N A:ASP168 4.9 87.7 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: Tue Jul 8 11:01:27 2025

Last articles

Mg in 7BNR
Mg in 7BNK
Mg in 7BMC
Mg in 7BM9
Mg in 7BM8
Mg in 7BM6
Mg in 7BL4
Mg in 7BL6
Mg in 7BL5
Mg in 7BJT
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy