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Calcium in PDB 7d8n: Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+

Enzymatic activity of Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+

All present enzymatic activity of Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+:
3.5.3.15;

Protein crystallography data

The structure of Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+, PDB code: 7d8n was solved by K.Funabashi, M.Sawata, M.Unno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.72 / 2.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 178.874, 108.11, 93.56, 90, 118.51, 90
R / Rfree (%) 20.5 / 25.2

Other elements in 7d8n:

The structure of Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+ also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+ (pdb code 7d8n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+, PDB code: 7d8n:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 7d8n

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Calcium binding site 1 out of 10 in the Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:51.0
occ:1.00
 O A:HOH1023 2.3 40.7 1.0
O A:HIS170 2.4 57.8 1.0
OD1 A:ASP168 2.4 53.0 1.0
O A:ASP165 2.4 51.4 1.0
O A:HOH1008 2.5 37.3 1.0
CG A:ASP168 3.3 53.0 1.0
OD2 A:ASP168 3.5 60.2 1.0
C A:ASP165 3.6 49.2 1.0
C A:HIS170 3.6 53.5 1.0
OD2 A:ASP176 4.0 48.6 1.0
CA A:ASP165 4.2 49.0 1.0
CA A:VAL171 4.4 52.3 1.0
N A:VAL171 4.4 53.5 1.0
N A:HIS170 4.4 61.7 1.0
CB A:ASP165 4.5 49.2 1.0
OE2 A:GLU252 4.5 56.2 1.0
N A:HIS172 4.6 52.8 1.0
CA A:HIS170 4.6 61.0 1.0
N A:ASN166 4.6 45.3 1.0
CB A:ASP168 4.7 43.4 1.0
N A:ASP168 4.9 48.7 1.0
CA A:ASN166 4.9 40.8 1.0
O A:ASP168 4.9 45.5 1.0
C A:ASP168 5.0 50.0 1.0
C A:VAL171 5.0 48.9 1.0

Calcium binding site 2 out of 10 in 7d8n

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Calcium binding site 2 out of 10 in the Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:45.2
occ:1.00
 OD2 A:ASP157 2.3 55.3 1.0
OD1 A:ASP388 2.4 51.5 1.0
OD2 A:ASP155 2.4 51.8 1.0
OD1 A:ASP179 2.6 36.9 1.0
O A:HOH1005 2.6 36.8 1.0
OD2 A:ASP179 2.7 36.5 1.0
OD1 A:ASP157 2.7 60.7 1.0
CG A:ASP157 2.9 57.1 1.0
CG A:ASP179 3.0 39.7 1.0
CG A:ASP155 3.4 50.1 1.0
CG A:ASP388 3.6 51.9 1.0
OD1 A:ASP155 3.8 53.3 1.0
CA A:CA904 3.9 41.2 1.0
N A:ASP388 3.9 36.0 1.0
CA A:ASP388 4.0 37.5 1.0
CD2 A:LEU364 4.3 57.2 1.0
O A:GLN175 4.3 55.3 1.0
CB A:ASP157 4.4 57.7 1.0
CD A:LYS362 4.4 53.0 1.0
CB A:ASP388 4.4 41.6 1.0
CB A:ASP179 4.5 41.0 1.0
OD2 A:ASP388 4.5 57.3 1.0
CE A:LYS362 4.7 56.6 1.0
CB A:ASP155 4.7 48.2 1.0
N A:ASP179 5.0 43.1 1.0

Calcium binding site 3 out of 10 in 7d8n

Go back to Calcium Binding Sites List in 7d8n
Calcium binding site 3 out of 10 in the Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:70.2
occ:1.00
 OE1 A:GLU353 2.5 68.3 1.0
O A:HOH1015 2.5 64.7 1.0
OE1 A:GLU411 2.6 78.3 1.0
O A:LEU410 2.7 59.9 1.0
O A:PHE407 2.7 54.6 1.0
CD A:GLU353 3.3 61.6 1.0
OE2 A:GLU353 3.4 68.8 1.0
CD A:GLU411 3.5 75.4 1.0
C A:PHE407 3.9 53.0 1.0
C A:LEU410 3.9 53.2 1.0
O A:GLN349 4.0 62.8 1.0
OE2 A:GLU411 4.0 80.9 1.0
CA A:GLY408 4.6 44.3 1.0
CG A:GLU411 4.6 70.5 1.0
N A:GLY408 4.6 49.8 1.0
CB A:PHE407 4.6 55.8 1.0
CB A:LEU410 4.7 54.0 1.0
CA A:LEU410 4.7 52.1 1.0
CG A:GLU353 4.8 48.9 1.0
CG A:GLN349 4.8 90.1 1.0
N A:LEU410 4.8 51.2 1.0
N A:GLU411 4.8 48.2 1.0
CA A:PHE407 4.9 52.0 1.0
CA A:GLU411 4.9 52.8 1.0

Calcium binding site 4 out of 10 in 7d8n

Go back to Calcium Binding Sites List in 7d8n
Calcium binding site 4 out of 10 in the Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:41.2
occ:1.00
 OD1 A:ASP155 2.3 53.3 1.0
OD1 A:ASP176 2.3 43.5 1.0
OD2 A:ASP179 2.3 36.5 1.0
OD2 A:ASP165 2.3 46.4 1.0
OD1 A:ASN153 2.4 47.0 1.0
OD2 A:ASP157 2.6 55.3 1.0
CG A:ASP155 3.3 50.1 1.0
CG A:ASP157 3.3 57.1 1.0
CG A:ASP165 3.4 49.8 1.0
CG A:ASN153 3.4 44.7 1.0
CG A:ASP176 3.4 50.6 1.0
CG A:ASP179 3.5 39.7 1.0
OD2 A:ASP155 3.6 51.8 1.0
CB A:ASP165 3.7 49.2 1.0
ND2 A:ASN153 3.7 45.1 1.0
CB A:ASP157 3.8 57.7 1.0
CA A:CA902 3.9 45.2 1.0
CA A:ASP176 4.0 63.1 1.0
N A:ASP157 4.1 62.9 1.0
CB A:ASP176 4.2 57.8 1.0
OD1 A:ASP157 4.2 60.7 1.0
OD2 A:ASP176 4.2 48.6 1.0
O A:ASP176 4.3 57.6 1.0
CB A:ASP179 4.3 41.0 1.0
OD1 A:ASP179 4.4 36.9 1.0
N A:ARG156 4.5 61.0 1.0
OD1 A:ASP165 4.5 48.9 1.0
CA A:ASP157 4.6 59.8 1.0
CB A:ASP155 4.6 48.2 1.0
C A:ASP176 4.7 60.5 1.0
N A:ASP155 4.7 39.1 1.0
CB A:ASN153 4.7 40.1 1.0
C A:ASP155 4.8 60.4 1.0
CA A:ASP155 4.9 48.2 1.0
C A:ASN153 5.0 36.3 1.0

Calcium binding site 5 out of 10 in 7d8n

Go back to Calcium Binding Sites List in 7d8n
Calcium binding site 5 out of 10 in the Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:77.4
occ:1.00
 OE1 A:GLU395 2.4 105.3 1.0
O A:ARG372 2.5 80.5 1.0
O A:HOH1044 2.7 45.5 1.0
OE2 A:GLU395 3.1 106.1 1.0
CD A:GLU395 3.1 103.1 1.0
C A:ARG372 3.7 73.8 1.0
CA A:ASN373 4.2 86.1 1.0
N A:ASN373 4.4 78.0 1.0
CG A:GLU395 4.5 94.5 1.0
N A:ARG372 4.5 62.0 1.0
N A:GLY374 4.6 91.9 1.0
CA A:ARG372 4.8 64.2 1.0
OD1 A:ASN373 4.8 107.6 1.0
C A:ASN373 4.9 90.5 1.0
O A:ARG394 5.0 74.3 1.0

Calcium binding site 6 out of 10 in 7d8n

Go back to Calcium Binding Sites List in 7d8n
Calcium binding site 6 out of 10 in the Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca703

b:54.8
occ:1.00
 O B:ASP165 2.3 48.6 1.0
O B:HIS170 2.4 58.2 1.0
OD1 B:ASP168 2.5 52.7 1.0
CG B:ASP168 3.5 52.8 1.0
C B:ASP165 3.5 45.7 1.0
C B:HIS170 3.6 51.4 1.0
OD2 B:ASP176 3.6 50.7 1.0
OD2 B:ASP168 3.8 58.7 1.0
OE1 B:GLU252 3.9 56.6 1.0
CA B:ASP165 4.3 46.3 1.0
N B:HIS170 4.4 62.0 1.0
CA B:VAL171 4.4 53.2 1.0
N B:VAL171 4.4 52.3 1.0
N B:ASN166 4.5 48.0 1.0
CB B:ASP165 4.5 46.7 1.0
CA B:ASN166 4.6 48.8 1.0
CA B:HIS170 4.6 57.5 1.0
CD B:GLU252 4.8 50.9 1.0
O B:ASP168 4.8 51.1 1.0
OE2 B:GLU252 4.8 50.0 1.0
CB B:ASP168 4.8 50.3 1.0
CG B:ASP176 4.9 48.3 1.0
N B:HIS172 4.9 58.3 1.0
C B:ASP168 4.9 54.7 1.0
N B:ASP168 4.9 57.7 1.0
CZ B:PHE214 4.9 47.4 1.0

Calcium binding site 7 out of 10 in 7d8n

Go back to Calcium Binding Sites List in 7d8n
Calcium binding site 7 out of 10 in the Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca704

b:49.5
occ:1.00
 OD2 B:ASP157 2.3 48.8 1.0
OD2 B:ASP155 2.4 56.1 1.0
OD1 B:ASP388 2.4 50.5 1.0
OD1 B:ASP179 2.6 44.5 1.0
OD2 B:ASP179 2.6 39.2 1.0
OD1 B:ASP157 2.9 48.2 1.0
CG B:ASP179 2.9 46.7 1.0
CG B:ASP157 3.0 47.5 1.0
CG B:ASP155 3.4 55.0 1.0
CG B:ASP388 3.6 55.2 1.0
OD1 B:ASP155 3.9 56.3 1.0
CA B:CA706 3.9 42.0 1.0
N B:ASP388 4.0 43.5 1.0
CA B:ASP388 4.1 45.1 1.0
CD2 B:LEU364 4.1 71.0 1.0
CD B:LYS362 4.2 56.2 1.0
O B:GLN175 4.3 56.3 1.0
CB B:ASP157 4.4 44.6 1.0
CB B:ASP179 4.4 46.6 1.0
CB B:ASP388 4.5 50.4 1.0
OD2 B:ASP388 4.5 57.2 1.0
CB B:ASP155 4.6 53.6 1.0
CE B:LYS362 4.7 62.3 1.0
CD1 B:LEU364 4.7 60.7 1.0
N B:ASP179 5.0 56.4 1.0

Calcium binding site 8 out of 10 in 7d8n

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Calcium binding site 8 out of 10 in the Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca705

b:74.5
occ:1.00
 O B:LEU410 2.5 62.7 1.0
O B:PHE407 2.6 47.0 1.0
O B:HOH810 2.7 35.9 1.0
OE1 B:GLU353 2.8 66.2 1.0
OE1 B:GLU411 2.8 73.5 1.0
O B:HOH828 3.5 52.8 1.0
CD B:GLU411 3.6 77.2 1.0
C B:LEU410 3.7 55.7 1.0
OE2 B:GLU411 3.7 77.3 1.0
C B:PHE407 3.7 49.7 1.0
CD B:GLU353 3.7 61.0 1.0
OE2 B:GLU353 4.0 66.3 1.0
O B:HOH802 4.1 36.9 1.0
CA B:GLY408 4.2 41.4 1.0
O B:HOH859 4.3 63.1 1.0
O B:GLN349 4.3 61.7 1.0
N B:GLY408 4.3 47.0 1.0
CA B:LEU410 4.5 52.4 1.0
N B:LEU410 4.5 52.5 1.0
CB B:LEU410 4.6 53.9 1.0
N B:GLU411 4.6 50.2 1.0
C B:GLY408 4.7 43.1 1.0
CB B:PHE407 4.7 52.7 1.0
CA B:GLU411 4.7 49.8 1.0
CA B:PHE407 4.8 50.0 1.0
CG B:GLU411 4.9 75.2 1.0
O B:GLY408 4.9 44.0 1.0

Calcium binding site 9 out of 10 in 7d8n

Go back to Calcium Binding Sites List in 7d8n
Calcium binding site 9 out of 10 in the Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca706

b:42.0
occ:1.00
 OD1 B:ASP155 2.3 56.3 1.0
OD2 B:ASP179 2.4 39.2 1.0
OD1 B:ASN153 2.4 48.5 1.0
OD2 B:ASP165 2.4 41.3 1.0
OD1 B:ASP176 2.5 43.7 1.0
OD2 B:ASP157 2.6 48.8 1.0
CG B:ASP155 3.2 55.0 1.0
CG B:ASP157 3.3 47.5 1.0
CG B:ASN153 3.4 44.8 1.0
CG B:ASP165 3.4 45.5 1.0
OD2 B:ASP155 3.4 56.1 1.0
CG B:ASP176 3.5 48.3 1.0
CG B:ASP179 3.5 46.7 1.0
CB B:ASP165 3.7 46.7 1.0
ND2 B:ASN153 3.7 46.9 1.0
CB B:ASP157 3.8 44.6 1.0
CA B:CA704 3.9 49.5 1.0
CA B:ASP176 4.0 59.6 1.0
N B:ASP157 4.1 55.5 1.0
CB B:ASP176 4.2 53.4 1.0
OD1 B:ASP157 4.2 48.2 1.0
CB B:ASP179 4.3 46.6 1.0
O B:ASP176 4.3 65.9 1.0
OD2 B:ASP176 4.4 50.7 1.0
OD1 B:ASP179 4.5 44.5 1.0
N B:ARG156 4.5 53.9 1.0
OD1 B:ASP165 4.6 41.0 1.0
CA B:ASP157 4.6 49.8 1.0
CB B:ASP155 4.6 53.6 1.0
C B:ASP176 4.7 62.3 1.0
CB B:ASN153 4.8 41.2 1.0
N B:ASP155 4.8 45.8 1.0
C B:ASP155 4.9 62.5 1.0
CA B:ASP155 5.0 53.8 1.0
N B:ASP176 5.0 59.3 1.0

Calcium binding site 10 out of 10 in 7d8n

Go back to Calcium Binding Sites List in 7d8n
Calcium binding site 10 out of 10 in the Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of the Inactive Form of Wild-Type Peptidylarginine Deiminase Type III (PAD3) Crystallized Under the Condition with High Concentrations of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca707

b:99.6
occ:1.00
 O B:ARG372 2.4 95.9 1.0
O B:HOH842 2.6 44.3 1.0
OE2 B:GLU395 2.7 97.7 1.0
OE1 B:GLU395 3.2 96.9 1.0
CD B:GLU395 3.3 93.5 1.0
C B:ARG372 3.5 91.3 1.0
N B:ARG372 4.2 68.6 1.0
CA B:ASN373 4.3 108.8 1.0
N B:ASN373 4.3 102.2 1.0
CA B:ARG372 4.5 76.9 1.0
N B:GLY374 4.6 108.2 1.0
CG B:GLU395 4.8 82.0 1.0
O B:ARG394 4.8 61.2 1.0
C B:ASN373 4.9 106.6 1.0

Reference:

K.Funabashi, M.Sawata, A.Nagai, M.Akimoto, R.Mashimo, H.Takahara, K.Kizawa, P.R.Thompson, K.Ite, K.Kitanishi, M.Unno. Structures of Human Peptidylarginine Deiminase Type III Provide Insights Into Substrate Recognition and Inhibitor Design. Arch.Biochem.Biophys. 08911 2021.
ISSN: ESSN 1096-0384
PubMed: 33971157
DOI: 10.1016/J.ABB.2021.108911
Page generated: Wed Jul 9 21:31:17 2025

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