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Calcium in PDB 7d5r: Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3)

Enzymatic activity of Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3)

All present enzymatic activity of Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3):
3.5.3.15;

Protein crystallography data

The structure of Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3), PDB code: 7d5r was solved by R.Mashimo, M.Akimoto, M.Unno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.07 / 3.15
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 114.536, 114.536, 326.766, 90, 90, 120
R / Rfree (%) 23.3 / 28.1

Other elements in 7d5r:

The structure of Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3) also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3) (pdb code 7d5r). 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 CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3), PDB code: 7d5r:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 7d5r

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Calcium binding site 1 out of 10 in the Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3)


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 CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:82.3
occ:1.00
 OD2 A:ASP179 2.5 68.1 1.0
OD2 A:ASP157 2.5 92.8 1.0
OD1 A:ASP157 2.7 101.3 1.0
OD1 A:ASP179 2.7 80.2 1.0
OD1 A:ASP388 2.9 109.8 1.0
CG A:ASP179 2.9 73.5 1.0
CG A:ASP157 2.9 95.4 1.0
NZ A:LYS362 3.5 90.2 1.0
OD2 A:ASP155 3.7 101.9 1.0
O A:GLN175 3.7 97.5 1.0
CG A:ASP388 4.1 111.3 1.0
CA A:CA704 4.2 77.9 1.0
O A:PRO387 4.3 118.9 1.0
CB A:ASP179 4.3 81.2 1.0
CE A:LYS362 4.4 89.5 1.0
CB A:ASP157 4.4 98.1 1.0
C A:GLN175 4.6 89.8 1.0
CG A:ASP155 4.6 103.4 1.0
CD A:LYS362 4.7 88.3 1.0
N A:ASP179 4.7 99.5 1.0
OD2 A:ASP388 4.8 106.9 1.0
CA A:ASP176 4.9 59.7 1.0
OD1 A:ASP155 4.9 109.5 1.0
C A:PRO387 4.9 112.0 1.0
CB A:GLU178 5.0 89.1 1.0

Calcium binding site 2 out of 10 in 7d5r

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Calcium binding site 2 out of 10 in the Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3)


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 CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:59.5
occ:1.00
 O A:PHE407 2.5 64.2 1.0
O A:LEU410 2.5 76.8 1.0
OE2 A:GLU411 2.5 84.0 1.0
NE2 A:GLN349 2.6 115.6 1.0
OE1 A:GLU353 3.2 69.3 1.0
CD A:GLN349 3.3 109.6 1.0
CD A:GLU411 3.4 77.5 1.0
OE1 A:GLN349 3.4 98.3 1.0
OE2 A:GLU353 3.6 71.9 1.0
CD A:GLU353 3.6 71.6 1.0
C A:PHE407 3.7 76.4 1.0
C A:LEU410 3.7 77.6 1.0
OE1 A:GLU411 3.9 86.2 1.0
CG A:GLU411 4.3 63.6 1.0
CA A:GLY408 4.4 74.5 1.0
O A:GLN349 4.4 88.2 1.0
N A:GLY408 4.4 78.2 1.0
CA A:LEU410 4.4 80.1 1.0
N A:LEU410 4.5 76.1 1.0
CB A:LEU410 4.5 83.4 1.0
CB A:PHE407 4.6 89.3 1.0
N A:GLU411 4.6 74.2 1.0
CG A:GLN349 4.6 108.8 1.0
CA A:PHE407 4.7 91.0 1.0
C A:GLY408 4.7 68.7 1.0
O A:GLY408 4.7 63.3 1.0
CA A:GLU411 4.8 65.6 1.0
CE1 A:HIS645 4.8 67.9 1.0
CG A:GLU353 4.9 79.9 1.0

Calcium binding site 3 out of 10 in 7d5r

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Calcium binding site 3 out of 10 in the Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3)


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 CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:84.5
occ:1.00
 ND2 A:ASN373 2.6 124.3 1.0
O A:SER370 2.7 82.2 1.0
OD2 A:ASP369 2.7 112.7 1.0
CG A:ASP369 2.8 107.1 1.0
OD1 A:ASP369 2.9 110.0 1.0
OE2 A:GLU351 3.2 111.0 1.0
CG A:ASN373 3.5 126.6 1.0
OD1 A:ASN373 3.6 125.6 1.0
C A:SER370 3.8 75.4 1.0
CB A:ASP369 3.8 96.8 1.0
O A:ARG372 3.9 108.5 1.0
OE2 A:GLU395 3.9 132.0 1.0
N A:SER370 4.2 76.7 1.0
C A:ASP369 4.2 84.1 1.0
O A:GLN377 4.2 118.2 1.0
CD A:GLU351 4.4 106.0 1.0
OG1 A:THR393 4.4 116.7 1.0
O A:ASP369 4.5 89.4 1.0
CA A:ASP369 4.6 82.3 1.0
OH A:TYR391 4.6 84.3 1.0
CA A:SER370 4.6 73.5 1.0
N A:PRO371 4.7 82.3 1.0
CA A:PRO371 4.8 89.5 1.0
C A:PRO371 4.9 87.3 1.0
C A:ARG372 4.9 106.7 1.0
CA A:GLN377 4.9 94.7 1.0
CB A:ASN373 4.9 127.3 1.0
CD A:GLU395 5.0 128.5 1.0

Calcium binding site 4 out of 10 in 7d5r

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Calcium binding site 4 out of 10 in the Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3)


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 CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:77.9
occ:1.00
 OD1 A:ASN153 2.4 94.4 1.0
OD2 A:ASP157 2.4 92.8 1.0
OD2 A:ASP165 2.4 100.0 1.0
OD1 A:ASP176 2.7 70.6 1.0
OD1 A:ASP155 2.8 109.5 1.0
OD2 A:ASP179 2.9 68.1 1.0
CG A:ASP165 3.3 103.1 1.0
CG A:ASN153 3.3 102.7 1.0
CB A:ASP165 3.4 98.7 1.0
CG A:ASP176 3.5 58.2 1.0
CG A:ASP157 3.5 95.4 1.0
ND2 A:ASN153 3.5 104.2 1.0
CG A:ASP155 3.7 103.4 1.0
OD2 A:ASP155 4.0 101.9 1.0
CG A:ASP179 4.0 73.5 1.0
CB A:ASP157 4.1 98.1 1.0
CA A:ASP176 4.1 59.7 1.0
CB A:ASP176 4.1 60.9 1.0
OD2 A:ASP176 4.2 75.6 1.0
CA A:CA701 4.2 82.3 1.0
N A:ASP157 4.3 111.9 1.0
O A:ASP155 4.4 111.7 1.0
OD1 A:ASP165 4.5 101.7 1.0
OD1 A:ASP157 4.5 101.3 1.0
O A:ASP176 4.5 88.2 1.0
CB A:ASP179 4.5 81.2 1.0
C A:ASP155 4.7 107.4 1.0
CB A:ASN153 4.7 108.5 1.0
C A:ASP176 4.9 77.9 1.0
CA A:ASP157 4.9 104.7 1.0
O A:ASN153 4.9 98.2 1.0
CB A:ASP155 4.9 97.2 1.0
CA A:ASP165 4.9 95.5 1.0

Calcium binding site 5 out of 10 in 7d5r

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Calcium binding site 5 out of 10 in the Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3)


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 CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca705

b:95.8
occ:1.00
 OD1 A:ASP168 2.5 90.1 1.0
OD2 A:ASP176 2.6 75.6 1.0
OD2 A:ASP168 2.6 85.9 1.0
O A:ASP165 2.9 109.8 1.0
CG A:ASP168 2.9 94.1 1.0
O A:HIS170 3.4 112.6 1.0
CG A:ASP176 3.8 58.2 1.0
C A:ASP165 3.8 109.7 1.0
CB A:ASP165 3.9 98.7 1.0
CA A:ASP165 4.0 95.5 1.0
OD1 A:ASP176 4.4 70.6 1.0
CB A:ASP168 4.4 92.7 1.0
CA A:VAL171 4.4 74.9 1.0
C A:HIS170 4.5 113.0 1.0
OE1 A:GLU252 4.5 93.3 1.0
ND2 A:ASN153 4.6 104.2 1.0
CE A:MET180 4.6 65.1 1.0
CG A:ASP165 4.6 103.1 1.0
OE2 A:GLU252 4.8 107.1 1.0
CB A:ASP176 4.8 60.9 1.0
N A:VAL171 4.9 97.3 1.0
N A:ASN166 5.0 114.9 1.0
O A:ASP168 5.0 77.2 1.0

Calcium binding site 6 out of 10 in 7d5r

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Calcium binding site 6 out of 10 in the Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3)


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 CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca902

b:99.0
occ:1.00
 OD1 B:ASP157 2.5 117.4 1.0
OD2 B:ASP179 2.5 73.3 1.0
OD1 B:ASP388 2.6 125.5 1.0
OD1 B:ASP179 2.6 101.4 1.0
OD2 B:ASP157 2.8 103.8 1.0
CG B:ASP179 2.8 93.4 1.0
CG B:ASP157 2.9 108.1 1.0
NZ B:LYS362 3.4 136.0 1.0
CE B:LYS362 3.7 124.8 1.0
CG B:ASP388 3.8 120.1 1.0
OD2 B:ASP155 3.9 105.6 1.0
O B:GLN175 4.2 101.1 1.0
CB B:ASP157 4.2 100.2 1.0
CB B:ASP179 4.2 97.1 1.0
O B:PRO387 4.4 130.9 1.0
OD2 B:ASP388 4.5 122.3 1.0
N B:ASP179 4.6 83.2 1.0
O B:ASP176 4.8 100.6 1.0
CB B:ASP388 4.8 112.7 1.0
CA B:ASP388 4.8 111.7 1.0
CA B:ASP179 4.9 87.5 1.0
CG B:ASP155 4.9 105.7 1.0
CB B:GLU178 5.0 96.7 1.0
C B:PRO387 5.0 122.9 1.0

Calcium binding site 7 out of 10 in 7d5r

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Calcium binding site 7 out of 10 in the Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3)


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 CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca903

b:54.8
occ:1.00
 O B:LEU410 2.4 62.4 1.0
O B:PHE407 2.5 68.7 1.0
NE2 B:GLN349 2.5 113.8 1.0
OE2 B:GLU411 2.6 75.9 1.0
OE1 B:GLU353 3.2 76.4 1.0
CD B:GLN349 3.2 107.2 1.0
OE1 B:GLN349 3.4 99.6 1.0
CD B:GLU411 3.4 62.8 1.0
C B:LEU410 3.6 69.1 1.0
CD B:GLU353 3.6 71.5 1.0
OE2 B:GLU353 3.6 72.0 1.0
C B:PHE407 3.7 75.9 1.0
OE1 B:GLU411 4.0 71.5 1.0
O B:GLN349 4.3 89.8 1.0
CA B:LEU410 4.3 75.8 1.0
N B:LEU410 4.3 74.6 1.0
CA B:GLY408 4.4 81.3 1.0
CG B:GLU411 4.4 46.4 1.0
CB B:LEU410 4.4 74.5 1.0
N B:GLY408 4.5 74.9 1.0
O B:GLY408 4.6 77.7 1.0
CG B:GLN349 4.6 103.2 1.0
C B:GLY408 4.6 76.8 1.0
N B:GLU411 4.6 62.7 1.0
CA B:PHE407 4.7 99.4 1.0
CB B:PHE407 4.8 99.8 1.0
CG B:GLU353 4.8 73.4 1.0
CA B:GLU411 4.8 52.0 1.0
CB B:GLU353 4.9 81.2 1.0
CE1 B:HIS645 5.0 80.0 1.0

Calcium binding site 8 out of 10 in 7d5r

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Calcium binding site 8 out of 10 in the Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3)


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 CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca904

b:81.5
occ:1.00
 ND2 B:ASN373 2.6 120.3 1.0
O B:SER370 2.6 70.0 1.0
OD2 B:ASP369 2.7 105.5 1.0
CG B:ASP369 2.8 103.5 1.0
OD1 B:ASP369 2.8 101.7 1.0
OE2 B:GLU351 3.1 109.1 1.0
CG B:ASN373 3.5 124.1 1.0
OD1 B:ASN373 3.7 118.1 1.0
O B:ARG372 3.8 114.7 1.0
C B:SER370 3.8 67.0 1.0
CB B:ASP369 3.8 97.0 1.0
OE2 B:GLU395 3.9 136.7 1.0
N B:SER370 4.1 73.0 1.0
C B:ASP369 4.2 83.1 1.0
CD B:GLU351 4.3 103.4 1.0
O B:GLN377 4.3 125.7 1.0
O B:ASP369 4.5 90.0 1.0
CA B:ASP369 4.5 81.6 1.0
OG1 B:THR393 4.5 113.3 1.0
CA B:SER370 4.6 70.4 1.0
OH B:TYR391 4.6 79.8 1.0
N B:PRO371 4.7 76.4 1.0
CA B:GLN377 4.7 106.4 1.0
C B:ARG372 4.8 109.9 1.0
CA B:PRO371 4.8 89.1 1.0
C B:PRO371 4.9 89.5 1.0
CB B:ASN373 4.9 132.8 1.0
CD B:GLU395 4.9 136.0 1.0
O B:GLU351 5.0 82.2 1.0

Calcium binding site 9 out of 10 in 7d5r

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Calcium binding site 9 out of 10 in the Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3)


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 CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca905

b:78.2
occ:1.00
 OD2 B:ASP157 2.4 103.8 1.0
OD1 B:ASP176 2.5 61.5 1.0
OD2 B:ASP165 2.6 144.8 1.0
OD1 B:ASN153 2.6 86.0 1.0
CG B:ASP165 2.9 146.4 1.0
CB B:ASP165 2.9 132.4 1.0
OD1 B:ASP155 3.2 108.3 1.0
CG B:ASP176 3.2 62.2 1.0
ND2 B:ASN153 3.3 92.7 1.0
CG B:ASN153 3.3 89.8 1.0
CG B:ASP157 3.4 108.1 1.0
CB B:ASP157 3.6 100.2 1.0
OD2 B:ASP176 3.7 66.2 1.0
OD1 B:ASP165 3.8 157.9 1.0
N B:ASP157 3.8 114.0 1.0
OD2 B:ASP179 3.8 73.3 1.0
CG B:ASP155 4.1 105.7 1.0
O B:ASP155 4.2 110.7 1.0
CB B:ASP176 4.3 64.6 1.0
CA B:ASP157 4.4 106.9 1.0
CA B:ASP165 4.4 126.5 1.0
OD1 B:ASP157 4.5 117.4 1.0
OD2 B:ASP155 4.5 105.6 1.0
C B:ASP155 4.6 108.3 1.0
CA B:ASP176 4.6 73.1 1.0
O B:ASN153 4.8 107.4 1.0
CB B:ASN153 4.8 91.9 1.0
C B:ARG156 4.9 106.5 1.0
O B:ASP176 4.9 100.6 1.0
C B:ASP165 4.9 124.1 1.0
CG B:ASP179 4.9 93.4 1.0
CA B:ARG156 5.0 102.9 1.0
N B:ARG156 5.0 96.5 1.0

Calcium binding site 10 out of 10 in 7d5r

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Calcium binding site 10 out of 10 in the Structure of the CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3)


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 CA2+-Bound C646A Mutant of Peptidylarginine Deiminase Type III (PAD3) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca906

b:88.4
occ:1.00
 OD1 B:ASP168 2.5 77.9 1.0
OD2 B:ASP168 2.7 71.4 1.0
OD2 B:ASP176 2.8 66.2 1.0
CG B:ASP168 3.0 85.3 1.0
O B:ASP165 3.1 110.1 1.0
O B:HIS170 3.1 110.3 1.0
OD1 B:ASP165 3.2 157.9 1.0
CA B:VAL171 4.0 74.3 1.0
CG B:ASP165 4.0 146.4 1.0
CG B:ASP176 4.0 62.2 1.0
C B:ASP165 4.1 124.1 1.0
C B:HIS170 4.2 105.0 1.0
CB B:ASP165 4.3 132.4 1.0
CA B:ASP165 4.3 126.5 1.0
CB B:ASP168 4.5 84.5 1.0
CG1 B:VAL171 4.5 76.7 1.0
N B:HIS172 4.5 97.4 1.0
N B:VAL171 4.6 86.0 1.0
OE1 B:GLU252 4.7 99.4 1.0
CB B:VAL171 4.7 58.8 1.0
OD1 B:ASP176 4.7 61.5 1.0
CE B:MET180 4.7 66.7 1.0
C B:VAL171 4.8 88.9 1.0
ND2 B:ASN153 4.9 92.7 1.0
O B:ASP168 4.9 66.2 1.0
OE2 B:GLU252 4.9 104.9 1.0
CG2 B:VAL171 4.9 57.4 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 23:56:02 2024

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