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Calcium in PDB 7d56: Structure of the Peptidylarginine Deiminase Type III (PAD3) in Complex with Cl-Amidine

Enzymatic activity of Structure of the Peptidylarginine Deiminase Type III (PAD3) in Complex with Cl-Amidine

All present enzymatic activity of Structure of the Peptidylarginine Deiminase Type III (PAD3) in Complex with Cl-Amidine:
3.5.3.15;

Protein crystallography data

The structure of Structure of the Peptidylarginine Deiminase Type III (PAD3) in Complex with Cl-Amidine, PDB code: 7d56 was solved by K.Funabashi, M.Unno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.36 / 3.18
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 199.577, 115.343, 127.844, 90, 121.38, 90
R / Rfree (%) 24.2 / 29.7

Other elements in 7d56:

The structure of Structure of the Peptidylarginine Deiminase Type III (PAD3) in Complex with Cl-Amidine also contains other interesting chemical elements:

Chlorine (Cl) 12 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Calcium atom in the Structure of the Peptidylarginine Deiminase Type III (PAD3) in Complex with Cl-Amidine (pdb code 7d56). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 15 binding sites of Calcium where determined in the Structure of the Peptidylarginine Deiminase Type III (PAD3) in Complex with Cl-Amidine, PDB code: 7d56:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 15 in 7d56

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Calcium binding site 1 out of 15 in the Structure of the Peptidylarginine Deiminase Type III (PAD3) in Complex with Cl-Amidine


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 Peptidylarginine Deiminase Type III (PAD3) in Complex with Cl-Amidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca702

b:64.7
occ:1.00
 O C:LEU410 2.3 75.1 1.0
OE2 C:GLU411 2.5 69.3 1.0
OE2 C:GLU353 2.7 80.5 1.0
NE2 C:GLN349 2.7 93.0 1.0
O C:PHE407 2.7 101.1 1.0
CD C:GLU411 3.3 71.4 1.0
CD C:GLU353 3.4 72.7 1.0
CD C:GLN349 3.5 91.2 1.0
OE1 C:GLN349 3.5 103.3 1.0
C C:LEU410 3.5 75.4 1.0
OE1 C:GLU353 3.7 76.2 1.0
C C:PHE407 3.8 100.0 1.0
OE1 C:GLU411 4.0 78.5 1.0
CG C:GLU411 4.2 66.7 1.0
O C:GLN349 4.3 84.9 1.0
CA C:LEU410 4.4 66.1 1.0
N C:LEU410 4.5 67.0 1.0
N C:GLU411 4.5 79.0 1.0
CB C:LEU410 4.5 62.6 1.0
CA C:PHE407 4.6 108.0 1.0
CA C:GLU411 4.6 79.6 1.0
CA C:GLY408 4.7 85.2 1.0
O C:GLY408 4.7 76.9 1.0
N C:GLY408 4.7 90.8 1.0
CG C:GLU353 4.7 65.0 1.0
C C:GLY408 4.8 78.5 1.0
CG C:GLN349 4.8 83.0 1.0
CG C:LEU410 4.9 61.0 1.0
CB C:GLU411 5.0 69.8 1.0

Calcium binding site 2 out of 15 in 7d56

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Calcium binding site 2 out of 15 in the Structure of the Peptidylarginine Deiminase Type III (PAD3) in Complex with Cl-Amidine


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 Peptidylarginine Deiminase Type III (PAD3) in Complex with Cl-Amidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca703

b:84.7
occ:1.00
 OD2 C:ASP165 2.4 83.6 1.0
OD1 C:ASP176 2.4 102.2 1.0
OD1 C:ASP157 2.5 91.3 1.0
OD2 C:ASP179 2.5 70.4 1.0
OD1 C:ASN153 2.5 76.9 1.0
OD1 C:ASP155 2.9 100.7 1.0
CG C:ASP157 3.3 91.9 1.0
CG C:ASP165 3.4 90.1 1.0
CG C:ASP176 3.4 99.8 1.0
CG C:ASN153 3.5 82.8 1.0
CG C:ASP155 3.6 96.4 1.0
CB C:ASP157 3.6 96.8 1.0
CG C:ASP179 3.7 77.9 1.0
CB C:ASP165 3.7 92.2 1.0
CB C:ASP176 3.8 98.7 1.0
OD2 C:ASP155 3.9 99.0 1.0
ND2 C:ASN153 3.9 88.4 1.0
CA C:ASP176 3.9 103.2 1.0
CA C:CA704 4.0 83.6 1.0
N C:ASP157 4.1 110.2 1.0
OD2 C:ASP157 4.3 91.1 1.0
CB C:ASP179 4.3 94.7 1.0
O C:ASP176 4.3 97.8 1.0
OD2 C:ASP176 4.5 99.4 1.0
O C:ASP155 4.5 96.4 1.0
CA C:ASP157 4.5 104.0 1.0
OD1 C:ASP165 4.5 93.2 1.0
C C:ASP155 4.6 97.2 1.0
C C:ASP176 4.7 100.4 1.0
OD1 C:ASP179 4.7 72.7 1.0
CB C:ASP155 4.8 93.4 1.0
CB C:ASN153 4.9 85.2 1.0

Calcium binding site 3 out of 15 in 7d56

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Calcium binding site 3 out of 15 in the Structure of the Peptidylarginine Deiminase Type III (PAD3) in Complex with Cl-Amidine


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 Peptidylarginine Deiminase Type III (PAD3) in Complex with Cl-Amidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca704

b:83.6
occ:1.00
 OD2 C:ASP179 2.5 70.4 1.0
OD1 C:ASP179 2.5 72.7 1.0
OD2 C:ASP157 2.6 91.1 1.0
OD1 C:ASP157 2.8 91.3 1.0
CG C:ASP179 2.8 77.9 1.0
OD1 C:ASP388 2.9 120.9 1.0
CG C:ASP157 3.0 91.9 1.0
OD2 C:ASP155 3.4 99.0 1.0
O C:PRO387 3.8 138.8 1.0
CA C:CA703 4.0 84.7 1.0
CG C:ASP388 4.1 121.6 1.0
O C:GLN175 4.1 122.6 1.0
CB C:ASP179 4.3 94.7 1.0
CG C:ASP155 4.3 96.4 1.0
CB C:ASP157 4.4 96.8 1.0
C C:PRO387 4.5 137.4 1.0
N C:ASP179 4.7 100.3 1.0
OD1 C:ASP155 4.7 100.7 1.0
OD2 C:ASP388 4.8 121.2 1.0
CA C:ASP388 4.8 127.3 1.0
CA C:ASP176 4.9 103.2 1.0
CA C:ASP179 4.9 98.1 1.0
N C:ASP388 5.0 132.7 1.0

Calcium binding site 4 out of 15 in 7d56

Go back to Calcium Binding Sites List in 7d56
Calcium binding site 4 out of 15 in the Structure of the Peptidylarginine Deiminase Type III (PAD3) in Complex with Cl-Amidine


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 Peptidylarginine Deiminase Type III (PAD3) in Complex with Cl-Amidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca705

b:82.8
occ:1.00
 OD1 C:ASN373 2.3 94.9 1.0
OD2 C:ASP369 2.4 96.5 1.0
O C:SER370 2.5 79.3 1.0
OE2 C:GLU351 2.6 110.9 1.0
OD1 C:ASP369 2.7 95.3 1.0
CG C:ASP369 2.9 93.4 1.0
CG C:ASN373 3.1 97.8 1.0
ND2 C:ASN373 3.6 97.3 1.0
C C:SER370 3.7 76.6 1.0
CD C:GLU351 3.8 109.6 1.0
OE2 C:GLU395 4.2 88.0 1.0
N C:SER370 4.2 74.7 1.0
CB C:ASN373 4.2 101.6 1.0
CB C:ASP369 4.3 85.0 1.0
CA C:GLN377 4.3 94.2 1.0
O C:GLN377 4.5 94.3 1.0
CA C:SER370 4.5 71.3 1.0
O C:ARG372 4.5 98.8 1.0
C C:ASP369 4.5 81.9 1.0
CG C:GLU351 4.6 102.9 1.0
CB C:GLN377 4.6 87.6 1.0
N C:PRO371 4.6 76.1 1.0
CA C:PRO371 4.6 75.9 1.0
CA C:ASN373 4.7 105.5 1.0
OE1 C:GLU351 4.7 112.7 1.0
C C:ARG372 4.9 96.3 1.0
C C:PRO371 4.9 72.4 1.0
C C:GLN377 4.9 103.0 1.0
O C:GLU351 4.9 103.4 1.0
CA C:ASP369 4.9 75.0 1.0
N C:ASN373 4.9 103.3 1.0

Calcium binding site 5 out of 15 in 7d56

Go back to Calcium Binding Sites List in 7d56
Calcium binding site 5 out of 15 in the Structure of the Peptidylarginine Deiminase Type III (PAD3) in Complex with Cl-Amidine


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 Peptidylarginine Deiminase Type III (PAD3) in Complex with Cl-Amidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca706

b:85.8
occ:1.00
 OD2 C:ASP168 2.5 79.2 1.0
OD1 C:ASP168 2.6 89.3 1.0
CG C:ASP168 2.9 86.7 1.0
OD2 C:ASP176 3.1 99.4 1.0
O C:ASP165 3.2 102.2 1.0
O C:HIS170 3.3 96.0 1.0
CG C:ASP176 4.0 99.8 1.0
CA C:VAL171 4.2 87.0 1.0
C C:ASP165 4.2 108.3 1.0
CB C:ASP168 4.4 91.7 1.0
C C:HIS170 4.4 97.9 1.0
OE2 C:GLU252 4.4 102.4 1.0
CB C:ASP165 4.4 92.2 1.0
CA C:ASP165 4.5 107.4 1.0
OD1 C:ASP176 4.6 102.2 1.0
OE1 C:GLU252 4.6 100.3 1.0
O C:ASP168 4.7 99.0 1.0
CE C:MET180 4.7 65.0 1.0
CG1 C:VAL171 4.7 82.4 1.0
CG2 C:VAL171 4.7 88.0 1.0
CB C:VAL171 4.8 84.7 1.0
N C:VAL171 4.8 92.1 1.0
ND2 C:ASN153 4.9 88.4 1.0
CG C:ASP165 4.9 90.1 1.0
N C:HIS172 4.9 96.8 1.0
CD C:GLU252 4.9 98.1 1.0
CB C:ASP176 5.0 98.7 1.0

Calcium binding site 6 out of 15 in 7d56

Go back to Calcium Binding Sites List in 7d56
Calcium binding site 6 out of 15 in the Structure of the Peptidylarginine Deiminase Type III (PAD3) in Complex with Cl-Amidine


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 Peptidylarginine Deiminase Type III (PAD3) in Complex with Cl-Amidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:60.7
occ:1.00
 O B:LEU410 2.4 64.8 1.0
OE2 B:GLU411 2.4 77.9 1.0
O B:PHE407 2.5 86.1 1.0
NE2 B:GLN349 2.6 96.9 1.0
OE2 B:GLU353 2.6 81.3 1.0
CD B:GLU411 3.3 77.1 1.0
OE1 B:GLN349 3.3 93.6 1.0
CD B:GLN349 3.3 90.8 1.0
CD B:GLU353 3.4 75.1 1.0
C B:LEU410 3.6 68.3 1.0
OE1 B:GLU353 3.6 76.0 1.0
C B:PHE407 3.7 85.5 1.0
OE1 B:GLU411 4.0 83.2 1.0
CG B:GLU411 4.1 71.0 1.0
CA B:GLY408 4.2 76.2 1.0
O B:GLN349 4.4 89.3 1.0
N B:GLY408 4.4 78.1 1.0
O B:GLY408 4.4 76.9 1.0
CA B:LEU410 4.4 66.3 1.0
N B:LEU410 4.4 70.9 1.0
N B:GLU411 4.5 70.8 1.0
C B:GLY408 4.5 77.3 1.0
CA B:GLU411 4.5 75.1 1.0
CB B:LEU410 4.7 62.8 1.0
CG B:GLN349 4.7 83.2 1.0
CG B:GLU353 4.7 72.1 1.0
CA B:PHE407 4.8 91.6 1.0
CB B:PHE407 4.9 88.4 1.0
CB B:GLU411 4.9 71.3 1.0

Calcium binding site 7 out of 15 in 7d56

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Calcium binding site 7 out of 15 in the Structure of the Peptidylarginine Deiminase Type III (PAD3) in Complex with Cl-Amidine


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 Peptidylarginine Deiminase Type III (PAD3) in Complex with Cl-Amidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca703

b:77.3
occ:1.00
 OD1 B:ASP176 2.4 94.7 1.0
OD2 B:ASP165 2.4 79.4 1.0
OD1 B:ASP157 2.5 85.4 1.0
OD2 B:ASP179 2.5 66.0 1.0
OD1 B:ASN153 2.5 95.8 1.0
OD1 B:ASP155 2.8 104.2 1.0
CG B:ASP176 3.4 92.0 1.0
CG B:ASP157 3.4 86.2 1.0
CG B:ASP165 3.5 87.7 1.0
CG B:ASN153 3.5 97.2 1.0
CG B:ASP155 3.6 101.5 1.0
CG B:ASP179 3.7 76.6 1.0
CB B:ASP176 3.8 91.2 1.0
CB B:ASP165 3.8 94.4 1.0
OD2 B:ASP155 3.8 103.8 1.0
CB B:ASP157 3.9 95.9 1.0
ND2 B:ASN153 3.9 99.6 1.0
CA B:ASP176 4.0 96.5 1.0
N B:ASP157 4.1 111.7 1.0
CA B:CA704 4.1 87.7 1.0
CB B:ASP179 4.3 85.0 1.0
O B:ASP155 4.4 107.1 1.0
OD2 B:ASP157 4.4 82.6 1.0
OD2 B:ASP176 4.4 91.9 1.0
O B:ASP176 4.4 91.0 1.0
C B:ASP155 4.5 105.5 1.0
OD1 B:ASP165 4.6 87.0 1.0
CA B:ASP157 4.7 109.7 1.0
OD1 B:ASP179 4.7 75.8 1.0
CB B:ASP155 4.7 100.3 1.0
C B:ASP176 4.8 93.5 1.0
CB B:ASN153 4.9 95.7 1.0
N B:ARG156 4.9 107.6 1.0
N B:ASP155 5.0 102.7 1.0
CA B:ASP155 5.0 102.3 1.0

Calcium binding site 8 out of 15 in 7d56

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Calcium binding site 8 out of 15 in the Structure of the Peptidylarginine Deiminase Type III (PAD3) in Complex with Cl-Amidine


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 Peptidylarginine Deiminase Type III (PAD3) in Complex with Cl-Amidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca704

b:87.7
occ:1.00
 OD1 B:ASP179 2.4 75.8 1.0
OD2 B:ASP157 2.4 82.6 1.0
OD2 B:ASP179 2.5 66.0 1.0
OD1 B:ASP157 2.7 85.4 1.0
CG B:ASP179 2.8 76.6 1.0
OD1 B:ASP388 2.8 112.1 1.0
CG B:ASP157 2.9 86.2 1.0
OD2 B:ASP155 3.5 103.8 1.0
O B:PRO387 4.0 115.0 1.0
CG B:ASP388 4.0 111.3 1.0
CA B:CA703 4.1 77.3 1.0
O B:GLN175 4.2 121.7 1.0
CB B:ASP179 4.2 85.0 1.0
CB B:ASP157 4.3 95.9 1.0
CG B:ASP155 4.5 101.5 1.0
N B:ASP179 4.7 100.2 1.0
OD2 B:ASP388 4.7 112.9 1.0
C B:PRO387 4.7 115.3 1.0
OD1 B:ASP155 4.8 104.2 1.0
CA B:ASP388 4.9 113.5 1.0
CA B:ASP179 4.9 90.1 1.0
CA B:ASP176 5.0 96.5 1.0

Calcium binding site 9 out of 15 in 7d56

Go back to Calcium Binding Sites List in 7d56
Calcium binding site 9 out of 15 in the Structure of the Peptidylarginine Deiminase Type III (PAD3) in Complex with Cl-Amidine


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 Peptidylarginine Deiminase Type III (PAD3) in Complex with Cl-Amidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca705

b:84.8
occ:1.00
 OD1 B:ASN373 2.3 102.2 1.0
OD2 B:ASP369 2.4 96.3 1.0
O B:SER370 2.4 78.8 1.0
OE2 B:GLU351 2.6 99.0 1.0
OD1 B:ASP369 2.7 93.6 1.0
CG B:ASP369 2.8 92.0 1.0
CG B:ASN373 3.2 103.4 1.0
C B:SER370 3.7 78.5 1.0
ND2 B:ASN373 3.8 103.4 1.0
CD B:GLU351 3.8 97.7 1.0
N B:SER370 4.2 80.8 1.0
CB B:ASP369 4.2 82.2 1.0
CB B:ASN373 4.3 102.7 1.0
O B:ARG372 4.3 99.0 1.0
OE2 B:GLU395 4.3 102.0 1.0
CA B:GLN377 4.4 97.8 1.0
C B:ASP369 4.5 82.6 1.0
CA B:SER370 4.5 78.3 1.0
O B:GLN377 4.5 103.8 1.0
CB B:GLN377 4.6 95.0 1.0
CA B:ASN373 4.6 99.0 1.0
N B:PRO371 4.6 76.2 1.0
CG B:GLU351 4.6 88.7 1.0
CA B:PRO371 4.6 79.6 1.0
C B:ARG372 4.7 89.5 1.0
OE1 B:GLU351 4.7 102.8 1.0
CA B:ASP369 4.8 77.1 1.0
C B:PRO371 4.9 73.3 1.0
O B:GLU351 4.9 88.8 1.0
N B:ASN373 4.9 94.1 1.0
O B:ASP369 4.9 89.4 1.0
OG1 B:THR393 4.9 81.2 1.0
N B:ARG372 5.0 66.4 1.0
C B:GLN377 5.0 104.1 1.0

Calcium binding site 10 out of 15 in 7d56

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Calcium binding site 10 out of 15 in the Structure of the Peptidylarginine Deiminase Type III (PAD3) in Complex with Cl-Amidine


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 Peptidylarginine Deiminase Type III (PAD3) in Complex with Cl-Amidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca706

b:94.3
occ:1.00
 OD1 B:ASP168 2.5 81.2 1.0
OD2 B:ASP168 2.5 76.0 1.0
CG B:ASP168 2.9 81.0 1.0
O B:ASP165 3.1 111.9 1.0
O B:HIS170 3.2 104.2 1.0
OD2 B:ASP176 3.3 91.9 1.0
C B:ASP165 4.1 115.1 1.0
OE2 B:GLU252 4.2 95.0 1.0
CA B:VAL171 4.2 88.5 1.0
CG B:ASP176 4.3 92.0 1.0
CA B:ASP165 4.3 108.9 1.0
C B:HIS170 4.3 107.0 1.0
CB B:ASP168 4.4 81.7 1.0
CB B:ASP165 4.4 94.4 1.0
OE1 B:GLU252 4.5 92.8 1.0
O B:ASP168 4.6 85.2 1.0
CE B:MET180 4.6 66.5 1.0
CG2 B:VAL171 4.7 79.8 1.0
ND2 B:ASN153 4.7 99.6 1.0
CG1 B:VAL171 4.7 69.2 1.0
CD B:GLU252 4.7 91.0 1.0
N B:VAL171 4.8 99.4 1.0
CB B:VAL171 4.8 76.8 1.0
CG B:ASP165 4.8 87.7 1.0
OD1 B:ASP176 4.8 94.7 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: Thu Jul 18 23:55:34 2024

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