Calcium in PDB 8smk: HPAD4 Bound to Activating Fab HA362

Enzymatic activity of HPAD4 Bound to Activating Fab HA362

All present enzymatic activity of HPAD4 Bound to Activating Fab HA362:
3.5.3.15;

Calcium Binding Sites:

The binding sites of Calcium atom in the HPAD4 Bound to Activating Fab HA362 (pdb code 8smk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the HPAD4 Bound to Activating Fab HA362, PDB code: 8smk:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 8smk

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Calcium binding site 1 out of 8 in the HPAD4 Bound to Activating Fab HA362


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of HPAD4 Bound to Activating Fab HA362 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:97.1
occ:1.00
 OE2 A:GLU353 2.1 94.4 1.0
OE2 A:GLU411 2.2 78.5 1.0
O A:LEU410 2.2 78.8 1.0
O A:PHE407 2.4 97.2 1.0
CD A:GLU411 2.9 78.5 1.0
CD A:GLU353 3.3 94.4 1.0
C A:LEU410 3.3 78.8 1.0
C A:PHE407 3.5 97.2 1.0
OE1 A:GLU411 3.5 78.5 1.0
CG A:GLU411 3.9 78.5 1.0
OE1 A:GLU353 4.0 94.4 1.0
N A:LEU410 4.1 78.8 1.0
CA A:LEU410 4.2 78.8 1.0
N A:GLU411 4.2 78.5 1.0
OE2 A:GLU351 4.3 123.3 1.0
CG A:GLU353 4.3 94.4 1.0
N A:GLY408 4.4 98.3 1.0
CA A:GLU411 4.4 78.5 1.0
CA A:GLY408 4.4 98.3 1.0
CB A:PHE407 4.4 97.2 1.0
CA A:PHE407 4.5 97.2 1.0
C A:GLY408 4.6 98.3 1.0
CB A:LEU410 4.6 78.8 1.0
CB A:GLU411 4.7 78.5 1.0
O A:GLY408 4.7 98.3 1.0

Calcium binding site 2 out of 8 in 8smk

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Calcium binding site 2 out of 8 in the HPAD4 Bound to Activating Fab HA362


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of HPAD4 Bound to Activating Fab HA362 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:93.0
occ:1.00
 OD2 A:ASP157 2.1 96.4 1.0
OD1 A:ASP155 2.1 91.8 1.0
OD1 A:ASP176 2.1 92.2 1.0
OD2 A:ASP165 2.1 94.9 1.0
OD1 A:ASN153 2.5 81.7 1.0
CG A:ASP155 3.0 91.8 1.0
CG A:ASP165 3.1 94.9 1.0
OD2 A:ASP155 3.2 91.8 1.0
CG A:ASP157 3.3 96.4 1.0
CG A:ASP176 3.3 92.2 1.0
OD2 A:ASP179 3.3 85.8 1.0
CB A:ASP165 3.4 94.9 1.0
CG A:ASN153 3.5 81.7 1.0
ND2 A:ASN153 3.8 81.7 1.0
CA A:CA703 3.9 92.9 1.0
CB A:ASP157 3.9 96.4 1.0
OD2 A:ASP176 4.1 92.2 1.0
OD1 A:ASP165 4.2 94.9 1.0
CB A:ASP176 4.2 92.2 1.0
N A:ASP157 4.2 96.4 1.0
CG A:ASP179 4.2 85.8 1.0
OD1 A:ASP157 4.2 96.4 1.0
O A:ASP155 4.2 91.8 1.0
C A:ASP155 4.3 91.8 1.0
CA A:ASP176 4.3 92.2 1.0
CB A:ASP155 4.3 91.8 1.0
CB A:ASP179 4.4 85.8 1.0
O A:ASP176 4.7 92.2 1.0
N A:ARG156 4.7 102.7 1.0
CA A:ASP155 4.7 91.8 1.0
CA A:ASP157 4.7 96.4 1.0
N A:ASP155 4.8 91.8 1.0
CB A:ASN153 4.8 81.7 1.0
O A:PRO387 4.9 98.0 1.0
CA A:ASP165 5.0 94.9 1.0

Calcium binding site 3 out of 8 in 8smk

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Calcium binding site 3 out of 8 in the HPAD4 Bound to Activating Fab HA362


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of HPAD4 Bound to Activating Fab HA362 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:92.9
occ:1.00
 OD2 A:ASP155 2.1 91.8 1.0
OD2 A:ASP179 2.2 85.8 1.0
OD1 A:ASP388 2.2 95.5 1.0
OD1 A:ASP157 2.2 96.4 1.0
O A:PRO387 2.3 98.0 1.0
OD2 A:ASP157 2.5 96.4 1.0
CG A:ASP157 2.7 96.4 1.0
CG A:ASP179 3.1 85.8 1.0
CG A:ASP155 3.1 91.8 1.0
CG A:ASP388 3.4 95.5 1.0
OD1 A:ASP179 3.4 85.8 1.0
C A:PRO387 3.5 98.0 1.0
OD1 A:ASP155 3.8 91.8 1.0
CA A:CA702 3.9 93.0 1.0
CA A:ASP388 4.0 95.5 1.0
N A:ASP388 4.1 95.5 1.0
CB A:ASP155 4.1 91.8 1.0
CB A:ASP157 4.2 96.4 1.0
OD2 A:ASP388 4.2 95.5 1.0
CB A:ASP388 4.3 95.5 1.0
CB A:ASP179 4.5 85.8 1.0
CA A:PRO387 4.6 98.0 1.0
O A:GLU175 4.7 97.8 1.0
CE A:LYS362 4.7 81.1 1.0
CA A:ASP157 4.8 96.4 1.0
CD1 A:LEU364 5.0 74.8 1.0

Calcium binding site 4 out of 8 in 8smk

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Calcium binding site 4 out of 8 in the HPAD4 Bound to Activating Fab HA362


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of HPAD4 Bound to Activating Fab HA362 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:102.9
occ:1.00
 OD1 A:ASP168 2.1 97.0 1.0
O A:ASP165 2.3 94.9 1.0
O A:GLU170 2.4 100.2 1.0
CG A:ASP168 2.9 97.0 1.0
OD2 A:ASP168 3.1 97.0 1.0
C A:ASP165 3.4 94.9 1.0
C A:GLU170 3.6 100.2 1.0
CA A:ASP165 4.0 94.9 1.0
N A:GLU170 4.0 100.2 1.0
O A:ASP168 4.0 97.0 1.0
CB A:ASP168 4.3 97.0 1.0
C A:ASP168 4.3 97.0 1.0
CA A:GLU170 4.4 100.2 1.0
CB A:ASP165 4.4 94.9 1.0
N A:CYS166 4.5 92.7 1.0
N A:VAL171 4.6 91.6 1.0
OD2 A:ASP176 4.6 92.2 1.0
CA A:ASP168 4.6 97.0 1.0
N A:ASP168 4.6 97.0 1.0
CA A:VAL171 4.8 91.6 1.0
CA A:CYS166 4.8 92.7 1.0
N A:ASP169 4.9 94.4 1.0
OE2 A:GLU252 5.0 79.3 1.0

Calcium binding site 5 out of 8 in 8smk

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Calcium binding site 5 out of 8 in the HPAD4 Bound to Activating Fab HA362


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of HPAD4 Bound to Activating Fab HA362 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca701

b:96.9
occ:1.00
 OE2 D:GLU353 2.1 94.4 1.0
OE2 D:GLU411 2.2 79.1 1.0
O D:LEU410 2.2 79.2 1.0
O D:PHE407 2.4 97.5 1.0
CD D:GLU411 2.9 79.1 1.0
CD D:GLU353 3.3 94.4 1.0
C D:LEU410 3.3 79.2 1.0
C D:PHE407 3.5 97.5 1.0
OE1 D:GLU411 3.5 79.1 1.0
CG D:GLU411 3.9 79.1 1.0
OE1 D:GLU353 4.0 94.4 1.0
N D:LEU410 4.1 79.2 1.0
CA D:LEU410 4.2 79.2 1.0
N D:GLU411 4.2 79.1 1.0
OE2 D:GLU351 4.3 123.8 1.0
CG D:GLU353 4.3 94.4 1.0
N D:GLY408 4.4 98.3 1.0
CA D:GLU411 4.4 79.1 1.0
CA D:GLY408 4.4 98.3 1.0
CB D:PHE407 4.4 97.5 1.0
CA D:PHE407 4.5 97.5 1.0
C D:GLY408 4.6 98.3 1.0
CB D:LEU410 4.6 79.2 1.0
CB D:GLU411 4.7 79.1 1.0
O D:GLY408 4.7 98.3 1.0

Calcium binding site 6 out of 8 in 8smk

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Calcium binding site 6 out of 8 in the HPAD4 Bound to Activating Fab HA362


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of HPAD4 Bound to Activating Fab HA362 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca702

b:93.8
occ:1.00
 OD2 D:ASP157 2.1 96.0 1.0
OD1 D:ASP155 2.1 91.5 1.0
OD1 D:ASP176 2.1 91.9 1.0
OD2 D:ASP165 2.1 94.8 1.0
OD1 D:ASN153 2.5 81.8 1.0
CG D:ASP155 3.0 91.5 1.0
CG D:ASP165 3.1 94.8 1.0
OD2 D:ASP155 3.2 91.5 1.0
CG D:ASP157 3.3 96.0 1.0
CG D:ASP176 3.3 91.9 1.0
OD2 D:ASP179 3.3 85.3 1.0
CB D:ASP165 3.4 94.8 1.0
CG D:ASN153 3.5 81.8 1.0
ND2 D:ASN153 3.8 81.8 1.0
CA D:CA703 3.9 92.8 1.0
CB D:ASP157 3.9 96.0 1.0
OD2 D:ASP176 4.1 91.9 1.0
OD1 D:ASP165 4.2 94.8 1.0
CB D:ASP176 4.2 91.9 1.0
N D:ASP157 4.2 96.0 1.0
CG D:ASP179 4.2 85.3 1.0
OD1 D:ASP157 4.2 96.0 1.0
O D:ASP155 4.2 91.5 1.0
C D:ASP155 4.3 91.5 1.0
CA D:ASP176 4.3 91.9 1.0
CB D:ASP155 4.3 91.5 1.0
CB D:ASP179 4.4 85.3 1.0
O D:ASP176 4.7 91.9 1.0
N D:ARG156 4.7 102.4 1.0
CA D:ASP155 4.7 91.5 1.0
CA D:ASP157 4.7 96.0 1.0
N D:ASP155 4.8 91.5 1.0
CB D:ASN153 4.8 81.8 1.0
O D:PRO387 4.9 97.3 1.0
CA D:ASP165 5.0 94.8 1.0

Calcium binding site 7 out of 8 in 8smk

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Calcium binding site 7 out of 8 in the HPAD4 Bound to Activating Fab HA362


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of HPAD4 Bound to Activating Fab HA362 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca703

b:92.8
occ:1.00
 OD2 D:ASP155 2.1 91.5 1.0
OD2 D:ASP179 2.2 85.3 1.0
OD1 D:ASP388 2.2 95.4 1.0
OD1 D:ASP157 2.2 96.0 1.0
O D:PRO387 2.3 97.3 1.0
OD2 D:ASP157 2.5 96.0 1.0
CG D:ASP157 2.7 96.0 1.0
CG D:ASP179 3.1 85.3 1.0
CG D:ASP155 3.1 91.5 1.0
CG D:ASP388 3.4 95.4 1.0
OD1 D:ASP179 3.4 85.3 1.0
C D:PRO387 3.5 97.3 1.0
OD1 D:ASP155 3.8 91.5 1.0
CA D:CA702 3.9 93.8 1.0
CA D:ASP388 4.0 95.4 1.0
N D:ASP388 4.1 95.4 1.0
CB D:ASP155 4.1 91.5 1.0
CB D:ASP157 4.2 96.0 1.0
OD2 D:ASP388 4.2 95.4 1.0
CB D:ASP388 4.3 95.4 1.0
CB D:ASP179 4.5 85.3 1.0
CA D:PRO387 4.6 97.3 1.0
O D:GLU175 4.7 97.7 1.0
CE D:LYS362 4.7 81.8 1.0
CA D:ASP157 4.8 96.0 1.0
CD1 D:LEU364 5.0 74.8 1.0

Calcium binding site 8 out of 8 in 8smk

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Calcium binding site 8 out of 8 in the HPAD4 Bound to Activating Fab HA362


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of HPAD4 Bound to Activating Fab HA362 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca704

b:101.6
occ:1.00
 OD1 D:ASP168 2.1 96.8 1.0
O D:ASP165 2.3 94.8 1.0
O D:GLU170 2.4 98.8 1.0
CG D:ASP168 2.9 96.8 1.0
OD2 D:ASP168 3.1 96.8 1.0
C D:ASP165 3.4 94.8 1.0
C D:GLU170 3.6 98.8 1.0
CA D:ASP165 4.0 94.8 1.0
N D:GLU170 4.0 98.8 1.0
O D:ASP168 4.0 96.8 1.0
CB D:ASP168 4.3 96.8 1.0
C D:ASP168 4.3 96.8 1.0
CA D:GLU170 4.4 98.8 1.0
CB D:ASP165 4.4 94.8 1.0
N D:CYS166 4.5 92.4 1.0
N D:VAL171 4.6 90.8 1.0
OD2 D:ASP176 4.6 91.9 1.0
CA D:ASP168 4.6 96.8 1.0
N D:ASP168 4.6 96.8 1.0
CA D:VAL171 4.8 90.8 1.0
CA D:CYS166 4.8 92.4 1.0
N D:ASP169 4.9 94.3 1.0
OE2 D:GLU252 5.0 79.6 1.0

Reference:

X.Zhou, S.Kong, A.Maker, S.G.Remesh, K.K.Leung, K.A.Verba, J.A.Wells. Antibody Discovery Identifies Regulatory Mechanisms of Protein Arginine Deiminase 4. Nat.Chem.Biol. 2024.
ISSN: ESSN 1552-4469
PubMed: 38308046
DOI: 10.1038/S41589-023-01535-8
Page generated: Fri Jul 19 11:34:19 2024

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