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Calcium in PDB 4n2c: Crystal Structure of Protein Arginine Deiminase 2 (F221/222A, 10 Mm CA2+)

Enzymatic activity of Crystal Structure of Protein Arginine Deiminase 2 (F221/222A, 10 Mm CA2+)

All present enzymatic activity of Crystal Structure of Protein Arginine Deiminase 2 (F221/222A, 10 Mm CA2+):
3.5.3.15;

Protein crystallography data

The structure of Crystal Structure of Protein Arginine Deiminase 2 (F221/222A, 10 Mm CA2+), PDB code: 4n2c was solved by D.J.Slade, X.Zhang, P.Fang, C.J.Dreyton, Y.Zhang, M.L.Gross, M.Guo, S.A.Coonrod, P.R.Thompson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.95 / 3.02
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 202.930, 52.180, 75.820, 90.00, 105.21, 90.00
R / Rfree (%) 24.5 / 27.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Protein Arginine Deiminase 2 (F221/222A, 10 Mm CA2+) (pdb code 4n2c). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Protein Arginine Deiminase 2 (F221/222A, 10 Mm CA2+), PDB code: 4n2c:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4n2c

Go back to Calcium Binding Sites List in 4n2c
Calcium binding site 1 out of 6 in the Crystal Structure of Protein Arginine Deiminase 2 (F221/222A, 10 Mm CA2+)


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 Protein Arginine Deiminase 2 (F221/222A, 10 Mm CA2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:46.6
occ:1.00
 OD1 A:ASP180 1.8 48.4 1.0
OD2 A:ASP156 2.6 43.9 1.0
CG A:ASP180 2.7 46.5 1.0
OE2 A:GLU158 3.0 52.1 1.0
OD2 A:ASP180 3.0 47.2 1.0
OD1 A:ASP389 3.2 46.8 1.0
CG A:ASP156 3.7 42.0 1.0
N A:ASP389 3.8 50.4 1.0
CB A:ASP180 4.1 43.4 1.0
CD A:GLU158 4.2 55.3 1.0
CA A:CA702 4.2 43.7 1.0
CG A:ASP389 4.2 49.0 1.0
CA A:ASP389 4.3 47.7 1.0
OD1 A:ASP156 4.3 39.8 1.0
O A:GLU176 4.6 56.7 1.0
CB A:ASP389 4.8 49.9 1.0
OE1 A:GLU158 4.8 59.1 1.0
C A:PRO388 4.9 53.9 1.0
CE2 A:PHE365 4.9 34.4 1.0
CB A:ASP156 4.9 42.5 1.0
O A:HOH803 4.9 42.4 1.0
CD2 A:PHE365 5.0 35.7 1.0

Calcium binding site 2 out of 6 in 4n2c

Go back to Calcium Binding Sites List in 4n2c
Calcium binding site 2 out of 6 in the Crystal Structure of Protein Arginine Deiminase 2 (F221/222A, 10 Mm CA2+)


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 Protein Arginine Deiminase 2 (F221/222A, 10 Mm CA2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:43.7
occ:1.00
 OD1 A:ASP166 2.4 47.3 1.0
OD1 A:ASP156 2.8 39.8 1.0
CG A:ASP166 3.2 47.2 1.0
OD1 A:ASN154 3.3 38.9 1.0
CG A:ASP156 3.3 42.0 1.0
CG A:ASN154 3.3 37.5 1.0
OD2 A:ASP156 3.3 43.9 1.0
CB A:ASP166 3.4 43.4 1.0
ND2 A:ASN154 3.4 38.1 1.0
OD1 A:ASP177 3.4 49.0 1.0
OE2 A:GLU158 3.6 52.1 1.0
OD1 A:ASP180 3.7 48.4 1.0
CG A:GLU158 3.8 54.9 1.0
CG A:ASP177 3.8 51.5 1.0
CD A:GLU158 4.2 55.3 1.0
OD2 A:ASP177 4.2 52.2 1.0
O A:ASP156 4.2 43.9 1.0
CB A:ASN154 4.2 35.4 1.0
CA A:CA701 4.2 46.6 1.0
OD2 A:ASP166 4.2 50.3 1.0
CA A:ASP177 4.3 53.6 1.0
C A:ASP156 4.4 44.7 1.0
CB A:ASP177 4.6 54.3 1.0
CB A:ASP156 4.6 42.5 1.0
O A:ASP177 4.7 47.8 1.0
CG A:ASP180 4.7 46.5 1.0
N A:GLU158 4.7 56.7 1.0
N A:ARG157 4.8 48.4 1.0
CA A:ASP166 4.9 43.0 1.0
CA A:ASP156 4.9 41.8 1.0
CB A:ASP180 4.9 43.4 1.0
CB A:GLU158 5.0 58.9 1.0
N A:ASP156 5.0 38.3 1.0
C A:ASP177 5.0 50.1 1.0

Calcium binding site 3 out of 6 in 4n2c

Go back to Calcium Binding Sites List in 4n2c
Calcium binding site 3 out of 6 in the Crystal Structure of Protein Arginine Deiminase 2 (F221/222A, 10 Mm CA2+)


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 Protein Arginine Deiminase 2 (F221/222A, 10 Mm CA2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:44.3
occ:1.00
 OD1 A:ASP169 2.3 46.9 1.0
O A:LYS171 2.5 50.8 1.0
O A:ASP166 2.5 40.5 1.0
CG A:ASP169 3.5 49.4 1.0
C A:ASP166 3.5 40.0 1.0
C A:LYS171 3.6 51.9 1.0
O A:HOH834 3.8 40.9 1.0
OD2 A:ASP169 3.9 52.0 1.0
CA A:ASP166 4.0 43.0 1.0
O A:ASP169 4.0 41.0 1.0
CB A:ASP166 4.1 43.4 1.0
OD2 A:ASP177 4.1 52.2 1.0
CG2 A:VAL172 4.1 45.1 1.0
CA A:VAL172 4.3 52.6 1.0
OE2 A:GLU253 4.3 44.9 1.0
N A:VAL172 4.4 52.4 1.0
N A:LYS171 4.4 49.9 1.0
OE1 A:GLU253 4.5 43.9 1.0
C A:ASP169 4.5 43.4 1.0
CA A:LYS171 4.6 53.1 1.0
N A:CYS167 4.7 37.1 1.0
OD2 A:ASP166 4.7 50.3 1.0
CB A:ASP169 4.7 48.7 1.0
N A:ASP169 4.7 42.7 1.0
CD A:GLU253 4.8 42.7 1.0
CG A:ASP166 4.8 47.2 1.0
CA A:ASP169 4.9 44.7 1.0
CB A:VAL172 4.9 49.3 1.0
CZ A:PHE215 4.9 38.8 1.0

Calcium binding site 4 out of 6 in 4n2c

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Calcium binding site 4 out of 6 in the Crystal Structure of Protein Arginine Deiminase 2 (F221/222A, 10 Mm CA2+)


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 Protein Arginine Deiminase 2 (F221/222A, 10 Mm CA2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:22.3
occ:1.00
 O A:PHE408 2.1 25.6 1.0
O A:LEU411 2.4 26.4 1.0
OE1 A:GLN350 2.4 31.3 1.0
OE1 A:GLU354 2.8 22.1 1.0
OE2 A:GLU412 3.0 32.7 1.0
C A:PHE408 3.3 25.7 1.0
CD A:GLU412 3.6 31.9 1.0
C A:LEU411 3.6 25.1 1.0
CD A:GLN350 3.6 33.3 1.0
CD A:GLU354 3.9 22.1 1.0
OE1 A:GLU412 4.0 33.1 1.0
N A:GLY409 4.1 26.0 1.0
CA A:GLY409 4.1 22.5 1.0
OE2 A:GLU354 4.3 22.6 1.0
CB A:PHE408 4.4 27.3 1.0
CA A:PHE408 4.4 26.1 1.0
NE2 A:HIS646 4.4 39.2 1.0
CG A:GLN350 4.4 33.9 1.0
CG A:GLU412 4.4 29.3 1.0
N A:LEU411 4.4 17.8 1.0
CA A:LEU411 4.4 17.2 1.0
N A:GLU412 4.5 24.4 1.0
C A:GLY409 4.6 27.3 1.0
NE2 A:GLN350 4.6 35.3 1.0
CA A:GLU412 4.6 25.4 1.0
CB A:LEU411 4.7 26.7 1.0
O A:GLN350 4.8 33.5 1.0
CD2 A:HIS646 4.9 40.0 1.0
O A:HOH822 4.9 40.3 1.0
O A:GLY409 4.9 19.8 1.0

Calcium binding site 5 out of 6 in 4n2c

Go back to Calcium Binding Sites List in 4n2c
Calcium binding site 5 out of 6 in the Crystal Structure of Protein Arginine Deiminase 2 (F221/222A, 10 Mm CA2+)


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 Protein Arginine Deiminase 2 (F221/222A, 10 Mm CA2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca705

b:37.7
occ:1.00
 O A:SER371 2.3 35.1 1.0
OD2 A:ASP374 2.7 53.5 1.0
OE2 A:GLU352 2.7 38.1 1.0
OD1 A:ASP370 2.7 43.9 1.0
OD2 A:ASP370 3.0 46.3 1.0
CG A:ASP370 3.1 44.2 1.0
C A:SER371 3.5 32.4 1.0
CG A:ASP374 3.9 54.1 1.0
CD A:GLU352 3.9 38.8 1.0
N A:ASP374 4.1 50.1 1.0
CA A:ASP374 4.1 53.8 1.0
OE2 A:GLU396 4.1 44.4 1.0
N A:SER371 4.1 29.7 1.0
CB A:LYS378 4.2 55.3 1.0
CA A:LYS378 4.3 55.8 1.0
CA A:SER371 4.4 29.1 1.0
C A:ASP370 4.4 29.5 1.0
CB A:ASP370 4.4 42.0 1.0
O A:LYS378 4.4 55.5 1.0
N A:PRO372 4.5 32.6 1.0
CG A:GLU352 4.6 39.6 1.0
CB A:ASP374 4.6 54.9 1.0
CA A:PRO372 4.7 35.6 1.0
O A:ASP370 4.7 28.3 1.0
C A:PRO372 4.7 39.3 1.0
CG2 A:THR394 4.8 31.6 1.0
OD1 A:ASP374 4.8 54.4 1.0
OE1 A:GLU352 4.9 38.9 1.0
C A:LYS378 4.9 57.4 1.0
N A:ARG373 4.9 40.5 1.0
CA A:ASP370 4.9 30.9 1.0

Calcium binding site 6 out of 6 in 4n2c

Go back to Calcium Binding Sites List in 4n2c
Calcium binding site 6 out of 6 in the Crystal Structure of Protein Arginine Deiminase 2 (F221/222A, 10 Mm CA2+)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Protein Arginine Deiminase 2 (F221/222A, 10 Mm CA2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca706

b:36.3
occ:1.00
 OE2 A:GLU131 1.4 34.4 1.0
OD2 A:ASP125 2.2 39.4 1.0
OD1 A:ASP123 2.3 33.5 1.0
O A:VAL129 2.5 39.4 1.0
CD A:GLU131 2.5 30.4 1.0
OD1 A:ASP127 2.7 44.8 1.0
CG A:ASP125 3.0 38.8 1.0
OE1 A:GLU131 3.1 27.4 1.0
CG A:ASP127 3.2 45.2 1.0
OD1 A:ASP125 3.2 39.6 1.0
CG A:ASP123 3.3 32.4 1.0
OD2 A:ASP127 3.3 46.1 1.0
C A:VAL129 3.6 40.7 1.0
CG A:GLU131 3.9 29.9 1.0
CB A:ASP123 3.9 27.6 1.0
N A:ASP127 4.0 37.2 1.0
N A:GLU131 4.1 32.7 1.0
CA A:ASP123 4.1 28.1 1.0
CB A:GLU131 4.2 33.0 1.0
OD2 A:ASP123 4.2 32.3 1.0
N A:VAL129 4.2 42.9 1.0
N A:ASP125 4.2 28.1 1.0
CG2 A:VAL129 4.2 45.4 1.0
N A:ARG126 4.3 31.3 1.0
CB A:ASP125 4.3 30.5 1.0
CB A:ASP127 4.4 44.8 1.0
CA A:VAL129 4.5 43.4 1.0
N A:VAL130 4.5 39.8 1.0
CA A:ASP125 4.6 30.6 1.0
CA A:VAL130 4.6 36.3 1.0
CA A:ASP127 4.6 41.6 1.0
C A:ASP125 4.6 32.3 1.0
N A:GLY128 4.6 40.6 1.0
C A:ASP123 4.7 26.4 1.0
N A:ALA124 4.7 25.9 1.0
C A:VAL130 4.7 33.8 1.0
CA A:GLU131 4.8 34.0 1.0
C A:ASP127 5.0 42.9 1.0

Reference:

D.J.Slade, P.Fang, C.J.Dreyton, Y.Zhang, J.Furhmann, D.Rempel, B.D.Bax, S.A.Coonrod, H.D.Lewis, M.Guo, M.L.Gross, P.R.Thompson. Protein Arginine Deiminase 2 Binds Calcium in An Ordered Fashion: Implications For Inhibitor Design. Acs Chem.Biol. 2015.
ISSN: ESSN 1554-8937
PubMed: 25621824
DOI: 10.1021/CB500933J
Page generated: Sun Jul 14 10:45:38 2024

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