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Calcium in PDB 4n26: Crystal Structure of Protein Arginine Deiminase 2 (500 Um CA2+)

Enzymatic activity of Crystal Structure of Protein Arginine Deiminase 2 (500 Um CA2+)

All present enzymatic activity of Crystal Structure of Protein Arginine Deiminase 2 (500 Um CA2+):
3.5.3.15;

Protein crystallography data

The structure of Crystal Structure of Protein Arginine Deiminase 2 (500 Um CA2+), PDB code: 4n26 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) 33.99 / 1.94
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 202.278, 51.675, 76.099, 90.00, 105.55, 90.00
R / Rfree (%) 17 / 22.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Protein Arginine Deiminase 2 (500 Um CA2+) (pdb code 4n26). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Protein Arginine Deiminase 2 (500 Um CA2+), PDB code: 4n26:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4n26

Go back to Calcium Binding Sites List in 4n26
Calcium binding site 1 out of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (500 Um 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 (500 Um CA2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca705

b:32.3
occ:1.00
 OD1 A:ASP125 2.1 24.4 1.0
OD1 A:ASP123 2.2 27.2 1.0
O A:VAL129 2.2 23.4 1.0
OE1 A:GLU131 2.3 19.8 1.0
OD1 A:ASP127 2.4 29.0 1.0
O A:HOH1266 2.4 31.1 1.0
CG A:ASP125 3.1 30.9 1.0
CG A:ASP127 3.2 31.7 1.0
CG A:ASP123 3.2 23.3 1.0
CD A:GLU131 3.3 24.1 1.0
OD2 A:ASP125 3.4 32.0 1.0
C A:VAL129 3.4 28.3 1.0
OD2 A:ASP127 3.5 35.8 1.0
CB A:ASP123 3.8 19.2 1.0
CA A:ASP123 3.9 19.2 1.0
OE2 A:GLU131 3.9 22.3 1.0
N A:VAL129 3.9 27.8 1.0
CG1 A:VAL129 3.9 45.6 1.0
N A:GLU131 4.0 22.4 1.0
N A:ASP127 4.1 33.9 1.0
CA A:VAL129 4.2 30.5 1.0
OD2 A:ASP123 4.2 21.1 1.0
CB A:GLU131 4.3 25.6 1.0
N A:ASP125 4.3 22.7 1.0
CB A:ASP127 4.4 36.5 1.0
CB A:ASP125 4.4 27.4 1.0
N A:VAL130 4.4 25.7 1.0
N A:ARG126 4.4 21.2 1.0
CG A:GLU131 4.4 19.6 1.0
C A:ASP123 4.5 25.0 1.0
CA A:VAL130 4.5 22.9 1.0
N A:GLY128 4.6 32.2 1.0
CA A:ASP127 4.6 30.1 1.0
N A:ALA124 4.6 23.0 1.0
C A:ASP125 4.6 26.1 1.0
CA A:ASP125 4.6 24.9 1.0
CB A:VAL129 4.7 44.4 1.0
C A:VAL130 4.7 28.3 1.0
CA A:GLU131 4.8 28.9 1.0
C A:ASP127 4.8 35.5 1.0
C A:GLY128 5.0 32.4 1.0

Calcium binding site 2 out of 5 in 4n26

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Calcium binding site 2 out of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (500 Um 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 (500 Um CA2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca706

b:27.5
occ:1.00
 OD2 A:ASP180 2.2 24.5 1.0
OD1 A:ASP166 2.3 36.3 1.0
OD1 A:ASN154 2.3 26.3 1.0
OD1 A:ASP156 2.4 26.9 1.0
OD1 A:ASP177 2.4 36.8 1.0
OE2 A:GLU158 2.4 35.7 1.0
CG A:ASN154 3.3 35.9 1.0
CG A:ASP156 3.3 36.0 1.0
CD A:GLU158 3.3 38.5 1.0
CG A:ASP166 3.4 41.6 1.0
CG A:ASP180 3.4 32.4 1.0
CG A:GLU158 3.5 33.1 1.0
ND2 A:ASN154 3.5 29.8 1.0
OD2 A:ASP156 3.6 30.8 1.0
CG A:ASP177 3.6 45.6 1.0
CA A:CA707 3.7 30.6 1.0
CB A:ASP166 3.8 36.4 1.0
CB A:ASP180 4.0 28.3 1.0
CA A:ASP177 4.2 32.7 1.0
OD1 A:ASP180 4.4 34.5 1.0
OD2 A:ASP177 4.4 42.2 1.0
O A:ASP177 4.4 31.7 1.0
CB A:ASP177 4.4 43.0 1.0
OD2 A:ASP166 4.5 39.2 1.0
O A:ASP156 4.5 29.2 1.0
OE1 A:GLU158 4.5 32.6 1.0
C A:ASP156 4.5 37.4 1.0
CB A:ASP156 4.6 29.6 1.0
CB A:ASN154 4.7 27.6 1.0
N A:GLU158 4.8 40.8 1.0
N A:ASP156 4.9 27.6 1.0
C A:ASP177 4.9 33.6 1.0
N A:ARG157 4.9 38.1 1.0
CB A:GLU158 4.9 35.2 1.0
CA A:ASP156 4.9 35.1 1.0

Calcium binding site 3 out of 5 in 4n26

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Calcium binding site 3 out of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (500 Um 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 (500 Um CA2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca707

b:30.6
occ:1.00
 OD2 A:ASP156 2.3 30.8 1.0
OD2 A:ASP180 2.4 24.5 1.0
OE2 A:GLU158 2.5 35.7 1.0
O A:HOH948 2.5 31.1 1.0
OD1 A:ASP389 2.5 39.6 1.0
OD1 A:ASP180 2.5 34.5 1.0
O A:HOH1090 2.5 26.8 1.0
CG A:ASP180 2.8 32.4 1.0
CG A:ASP156 3.4 36.0 1.0
CD A:GLU158 3.4 38.5 1.0
CG A:ASP389 3.5 45.6 1.0
OE1 A:GLU158 3.6 32.6 1.0
OD1 A:ASP156 3.7 26.9 1.0
CA A:CA706 3.7 27.5 1.0
N A:ASP389 3.9 36.1 1.0
OD2 A:ASP389 4.2 49.7 1.0
CE A:LYS363 4.2 64.5 1.0
CB A:ASP180 4.3 28.3 1.0
CA A:ASP389 4.3 39.5 1.0
CB A:ASP389 4.5 39.9 1.0
CE2 A:PHE365 4.6 32.9 1.0
CB A:ASP156 4.7 29.6 1.0
O A:GLU176 4.7 33.3 1.0
CD2 A:PHE365 4.8 31.3 1.0
CG A:GLU158 4.8 33.1 1.0
C A:PRO388 4.9 43.0 1.0

Calcium binding site 4 out of 5 in 4n26

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Calcium binding site 4 out of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (500 Um 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 (500 Um CA2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca708

b:32.0
occ:1.00
 O A:HOH1156 2.3 26.8 1.0
O A:ASP166 2.3 31.1 1.0
O A:HOH1013 2.4 28.4 1.0
O A:LYS171 2.4 42.8 1.0
O A:HOH993 2.4 33.4 1.0
OD1 A:ASP169 2.4 38.2 1.0
O A:HOH1182 2.5 35.2 1.0
C A:ASP166 3.4 38.9 1.0
CG A:ASP169 3.5 44.4 1.0
C A:LYS171 3.6 45.9 1.0
OD2 A:ASP169 3.9 46.3 1.0
CA A:ASP166 3.9 34.7 1.0
CB A:ASP166 4.1 36.4 1.0
OD2 A:ASP177 4.2 42.2 1.0
N A:LYS171 4.2 46.4 1.0
O A:HOH1036 4.2 37.6 1.0
O A:ASP169 4.4 38.6 1.0
CA A:LYS171 4.4 43.3 1.0
N A:CYS167 4.5 38.9 1.0
N A:VAL172 4.5 43.5 1.0
C A:ASP169 4.6 39.7 1.0
CA A:VAL172 4.7 49.6 1.0
OE1 A:GLU253 4.7 30.6 1.0
N A:ASP169 4.7 36.7 1.0
CG2 A:VAL172 4.7 44.6 1.0
CB A:ASP169 4.8 42.0 1.0
CA A:CYS167 4.8 39.7 1.0
OE2 A:GLU253 4.9 27.3 1.0
CA A:ASP169 4.9 35.3 1.0

Calcium binding site 5 out of 5 in 4n26

Go back to Calcium Binding Sites List in 4n26
Calcium binding site 5 out of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (500 Um 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 (500 Um CA2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca709

b:32.0
occ:1.00
 O A:PHE408 2.3 20.0 1.0
OE1 A:GLU354 2.4 20.6 1.0
O A:HOH1170 2.4 37.4 1.0
O A:LEU411 2.4 24.4 1.0
O A:HOH860 2.5 29.7 1.0
OE1 A:GLU412 2.6 34.3 1.0
CD A:GLU354 3.4 25.2 1.0
C A:PHE408 3.4 15.8 1.0
CD A:GLU412 3.5 45.4 1.0
C A:LEU411 3.6 19.4 1.0
OE2 A:GLU354 3.7 32.8 1.0
OE2 A:GLU412 4.0 56.8 1.0
CB A:PHE408 4.3 16.3 1.0
N A:GLY409 4.3 18.3 1.0
CA A:LEU411 4.3 15.5 1.0
N A:LEU411 4.3 15.9 1.0
CA A:PHE408 4.4 18.8 1.0
CA A:GLY409 4.4 15.7 1.0
CB A:LEU411 4.4 18.1 1.0
O A:GLN350 4.5 28.9 1.0
CG A:GLU412 4.5 30.9 1.0
O A:HOH1065 4.6 46.4 1.0
N A:GLU412 4.6 17.2 1.0
C A:GLY409 4.7 20.5 1.0
CG A:GLU354 4.7 17.7 1.0
CA A:GLU412 4.8 11.6 1.0
CG A:LEU411 4.9 25.4 1.0
O A:GLY409 5.0 14.7 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 10:42:38 2024

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