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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

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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

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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: Sat Jul 13 08:08:34 2024

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