Atomistry » Calcium » PDB 4dg4-4dtj » 4dkt
Atomistry »
  Calcium »
    PDB 4dg4-4dtj »
      4dkt »

Calcium in PDB 4dkt: Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with N-Acetyl-L-Threonyl-L-Alpha-Aspartyl-N5-[(1E)-2- Fluoroethanimidoyl]-L-Ornithinamide

Enzymatic activity of Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with N-Acetyl-L-Threonyl-L-Alpha-Aspartyl-N5-[(1E)-2- Fluoroethanimidoyl]-L-Ornithinamide

All present enzymatic activity of Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with N-Acetyl-L-Threonyl-L-Alpha-Aspartyl-N5-[(1E)-2- Fluoroethanimidoyl]-L-Ornithinamide:
3.5.3.15;

Protein crystallography data

The structure of Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with N-Acetyl-L-Threonyl-L-Alpha-Aspartyl-N5-[(1E)-2- Fluoroethanimidoyl]-L-Ornithinamide, PDB code: 4dkt was solved by J.E.Jones, J.L.Slack, P.Fang, X.Zhang, V.Subramanian, C.P.Causey, S.A.Coonrod, M.Guo, P.R.Thompson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.44 / 2.98
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 147.654, 61.079, 115.382, 90.00, 124.54, 90.00
R / Rfree (%) 19.1 / 23

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with N-Acetyl-L-Threonyl-L-Alpha-Aspartyl-N5-[(1E)-2- Fluoroethanimidoyl]-L-Ornithinamide (pdb code 4dkt). 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-Acetyl-L-Threonyl-L-Alpha-Aspartyl-N5-[(1E)-2- Fluoroethanimidoyl]-L-Ornithinamide, PDB code: 4dkt:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4dkt

Go back to Calcium Binding Sites List in 4dkt
Calcium binding site 1 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with N-Acetyl-L-Threonyl-L-Alpha-Aspartyl-N5-[(1E)-2- Fluoroethanimidoyl]-L-Ornithinamide


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-Acetyl-L-Threonyl-L-Alpha-Aspartyl-N5-[(1E)-2- Fluoroethanimidoyl]-L-Ornithinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:39.4
occ:1.00
 OE1 A:GLN349 2.6 49.4 1.0
OE1 A:GLU353 2.7 33.9 1.0
O A:LEU410 2.8 30.0 1.0
OE1 A:GLU411 2.9 42.9 1.0
O A:PHE407 2.9 32.5 1.0
CD A:GLU411 3.5 45.3 1.0
CD A:GLU353 3.6 38.1 1.0
CD A:GLN349 3.6 49.1 1.0
OE2 A:GLU353 3.8 39.9 1.0
OE2 A:GLU411 3.8 43.7 1.0
NE2 A:GLN349 3.9 42.1 1.0
C A:LEU410 4.0 25.9 1.0
C A:PHE407 4.1 33.2 1.0
CB A:PHE407 4.5 33.4 1.0
CG A:GLU411 4.6 33.4 1.0
O A:GLN349 4.8 49.7 1.0
CA A:LEU410 4.8 22.9 1.0
CA A:PHE407 4.9 31.9 1.0
CA A:GLU411 4.9 25.6 1.0
N A:GLU411 4.9 23.8 1.0
CB A:LEU410 4.9 25.6 1.0
N A:LEU410 4.9 25.3 1.0
CG A:GLN349 4.9 50.9 1.0
CG A:GLU353 4.9 29.8 1.0
N A:GLY408 5.0 32.4 1.0

Calcium binding site 2 out of 5 in 4dkt

Go back to Calcium Binding Sites List in 4dkt
Calcium binding site 2 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with N-Acetyl-L-Threonyl-L-Alpha-Aspartyl-N5-[(1E)-2- Fluoroethanimidoyl]-L-Ornithinamide


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-Acetyl-L-Threonyl-L-Alpha-Aspartyl-N5-[(1E)-2- Fluoroethanimidoyl]-L-Ornithinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:60.2
occ:1.00
 OD2 A:ASP179 2.6 59.0 1.0
OD2 A:ASP157 2.7 66.3 1.0
OD1 A:ASP155 2.7 59.6 1.0
OD2 A:ASP165 2.8 69.6 1.0
OD1 A:ASP176 2.9 61.3 1.0
OD1 A:ASN153 3.3 48.1 1.0
CG A:ASP165 3.4 60.8 1.0
CG A:ASP155 3.6 56.4 1.0
OD2 A:ASP155 3.7 53.9 1.0
CG A:ASP176 3.7 60.4 1.0
CA A:CA703 3.8 64.5 1.0
CG A:ASP179 3.8 55.1 1.0
CG A:ASP157 3.9 65.3 1.0
CB A:ASP165 3.9 58.6 1.0
CG A:ASN153 3.9 54.5 1.0
OD1 A:ASP165 4.1 62.3 1.0
CA A:ASP176 4.4 62.8 1.0
OD2 A:ASP176 4.4 56.5 1.0
CB A:ASP157 4.4 74.9 1.0
CB A:ASP179 4.5 48.0 1.0
ND2 A:ASN153 4.5 48.0 1.0
OE1 A:GLU175 4.6 74.3 1.0
CB A:ASP176 4.6 61.4 1.0
O A:ASP176 4.6 47.2 1.0
N A:ASP157 4.7 72.6 1.0
OD1 A:ASP179 4.8 49.0 1.0
CB A:ASN153 4.8 48.6 1.0
OD1 A:ASP157 4.8 60.9 1.0

Calcium binding site 3 out of 5 in 4dkt

Go back to Calcium Binding Sites List in 4dkt
Calcium binding site 3 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with N-Acetyl-L-Threonyl-L-Alpha-Aspartyl-N5-[(1E)-2- Fluoroethanimidoyl]-L-Ornithinamide


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-Acetyl-L-Threonyl-L-Alpha-Aspartyl-N5-[(1E)-2- Fluoroethanimidoyl]-L-Ornithinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:64.5
occ:1.00
 OD1 A:ASP388 2.6 64.3 1.0
OD2 A:ASP157 2.6 66.3 1.0
OD2 A:ASP179 2.7 59.0 1.0
OD2 A:ASP155 2.8 53.9 1.0
OD1 A:ASP179 2.9 49.0 1.0
OE1 A:GLU175 3.0 74.3 1.0
OE2 A:GLU175 3.0 68.4 1.0
CG A:ASP179 3.2 55.1 1.0
OD1 A:ASP157 3.2 60.9 1.0
CG A:ASP157 3.3 65.3 1.0
CD A:GLU175 3.3 78.0 1.0
CG A:ASP388 3.7 66.3 1.0
CA A:CA702 3.8 60.2 1.0
CG A:ASP155 3.9 56.4 1.0
N A:ASP388 4.0 56.0 1.0
CA A:ASP388 4.1 60.6 1.0
OD1 A:ASP155 4.3 59.6 1.0
CB A:ASP388 4.6 58.7 1.0
OD2 A:ASP388 4.6 74.5 1.0
CB A:ASP179 4.6 48.0 1.0
CE A:LYS362 4.7 44.7 1.0
CB A:ASP157 4.7 74.9 1.0
CG A:GLU175 4.8 84.0 1.0
O A:GLU175 4.9 64.1 1.0
CD1 A:LEU364 4.9 31.6 1.0

Calcium binding site 4 out of 5 in 4dkt

Go back to Calcium Binding Sites List in 4dkt
Calcium binding site 4 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with N-Acetyl-L-Threonyl-L-Alpha-Aspartyl-N5-[(1E)-2- Fluoroethanimidoyl]-L-Ornithinamide


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-Acetyl-L-Threonyl-L-Alpha-Aspartyl-N5-[(1E)-2- Fluoroethanimidoyl]-L-Ornithinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:56.0
occ:1.00
 OD1 A:ASN373 2.5 57.3 1.0
OD2 A:ASP369 2.7 58.9 1.0
O A:SER370 2.7 47.9 1.0
OD1 A:ASP369 2.8 57.0 1.0
OE1 A:GLU351 3.0 56.0 1.0
CG A:ASP369 3.0 55.5 1.0
OE1 A:GLN397 3.7 65.8 1.0
CG A:ASN373 3.7 55.1 1.0
C A:SER370 3.8 48.0 1.0
CD A:GLU351 4.1 60.5 1.0
CB A:LYS377 4.1 69.8 1.0
CA A:LYS377 4.2 72.3 1.0
O A:LYS377 4.2 82.3 1.0
CB A:ASP369 4.3 45.8 1.0
C A:ASP369 4.4 45.8 1.0
N A:SER370 4.5 47.3 1.0
ND2 A:ASN373 4.5 55.9 1.0
CG A:GLU351 4.5 57.5 1.0
O A:ASP369 4.6 47.2 1.0
CD A:GLN397 4.6 65.7 1.0
N A:PRO371 4.6 51.0 1.0
NE2 A:GLN397 4.6 59.2 1.0
CA A:ASN373 4.6 67.7 1.0
N A:ASN373 4.6 63.6 1.0
CA A:PRO371 4.7 59.1 1.0
C A:LYS377 4.7 79.2 1.0
CB A:ASN373 4.7 59.4 1.0
CA A:SER370 4.7 48.2 1.0
OH A:TYR391 4.9 43.7 1.0
C A:PRO371 4.9 59.3 1.0
CA A:ASP369 4.9 42.0 1.0

Calcium binding site 5 out of 5 in 4dkt

Go back to Calcium Binding Sites List in 4dkt
Calcium binding site 5 out of 5 in the Crystal Structure of Human Peptidylarginine Deiminase 4 in Complex with N-Acetyl-L-Threonyl-L-Alpha-Aspartyl-N5-[(1E)-2- Fluoroethanimidoyl]-L-Ornithinamide


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-Acetyl-L-Threonyl-L-Alpha-Aspartyl-N5-[(1E)-2- Fluoroethanimidoyl]-L-Ornithinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca705

b:70.0
occ:1.00
 OD2 A:ASP168 2.7 55.5 1.0
OD2 A:ASP176 3.0 56.5 1.0
O A:GLU170 3.3 74.4 1.0
O A:ASP165 3.3 62.7 1.0
OE1 A:GLU252 3.5 45.1 1.0
CG A:ASP168 3.6 67.2 1.0
CE A:MET180 3.6 42.8 1.0
OD1 A:ASP168 3.7 63.4 1.0
CG A:ASP176 4.0 60.4 1.0
OE2 A:GLU252 4.0 42.3 1.0
CD A:GLU252 4.1 43.8 1.0
C A:ASP165 4.1 61.6 1.0
CB A:ASP165 4.1 58.6 1.0
C A:GLU170 4.2 69.7 1.0
OD1 A:ASN153 4.2 48.1 1.0
OD1 A:ASP176 4.3 61.3 1.0
CA A:VAL171 4.3 62.5 1.0
CZ A:PHE214 4.3 42.1 1.0
CG2 A:VAL171 4.5 57.3 1.0
CE1 A:PHE214 4.5 37.1 1.0
CA A:ASP165 4.6 60.1 1.0
N A:VAL171 4.7 68.8 1.0
OD2 A:ASP165 4.8 69.6 1.0
CG A:ASP165 4.9 60.8 1.0
CB A:VAL171 5.0 60.5 1.0

Reference:

J.E.Jones, J.L.Slack, P.Fang, X.Zhang, V.Subramanian, C.P.Causey, S.A.Coonrod, M.Guo, P.R.Thompson. Synthesis and Screening of A Haloacetamidine Containing Library to Identify PAD4 Selective Inhibitors. Acs Chem.Biol. V. 7 160 2012.
ISSN: ISSN 1554-8929
PubMed: 22004374
DOI: 10.1021/CB200258Q
Page generated: Sat Jul 13 23:30:01 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy