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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

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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: Tue Jul 8 19:29:21 2025

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