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Calcium in PDB 4n2i: Crystal Structure of Protein Arginine Deiminase 2 (D177A, 10 Mm CA2+)

Enzymatic activity of Crystal Structure of Protein Arginine Deiminase 2 (D177A, 10 Mm CA2+)

All present enzymatic activity of Crystal Structure of Protein Arginine Deiminase 2 (D177A, 10 Mm CA2+):
3.5.3.15;

Protein crystallography data

The structure of Crystal Structure of Protein Arginine Deiminase 2 (D177A, 10 Mm CA2+), PDB code: 4n2i 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) 48.83 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 203.020, 51.470, 76.130, 90.00, 105.82, 90.00
R / Rfree (%) 17.1 / 21

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Protein Arginine Deiminase 2 (D177A, 10 Mm CA2+) (pdb code 4n2i). 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 (D177A, 10 Mm CA2+), PDB code: 4n2i:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4n2i

Go back to Calcium Binding Sites List in 4n2i
Calcium binding site 1 out of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (D177A, 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 (D177A, 10 Mm CA2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:26.2
occ:1.00
 O A:PHE408 2.3 21.0 1.0
O A:HOH1247 2.3 35.8 1.0
OE1 A:GLU354 2.3 25.7 1.0
O A:LEU411 2.4 23.8 1.0
OE2 A:GLU412 2.5 25.5 1.0
O A:HOH846 2.5 32.2 1.0
OE1 A:GLN350 3.0 28.9 0.4
CD A:GLU354 3.3 32.8 1.0
CD A:GLU412 3.3 28.6 1.0
C A:PHE408 3.5 26.2 1.0
OE2 A:GLU354 3.5 31.4 1.0
C A:LEU411 3.6 22.8 1.0
OE1 A:GLU412 3.8 34.5 1.0
CD A:GLN350 4.1 35.6 0.4
CB A:PHE408 4.3 30.0 1.0
N A:GLY409 4.3 29.6 1.0
CA A:LEU411 4.4 24.2 1.0
N A:LEU411 4.4 22.5 1.0
CG A:GLU412 4.4 28.4 1.0
CA A:PHE408 4.4 25.1 1.0
CB A:LEU411 4.4 23.4 1.0
CA A:GLY409 4.5 23.1 1.0
O A:GLN350 4.5 40.8 1.0
N A:GLU412 4.6 21.3 1.0
NE2 A:GLN350 4.6 26.2 0.4
CG A:GLU354 4.7 22.9 1.0
CA A:GLU412 4.7 23.8 1.0
C A:GLY409 4.8 25.5 1.0
O A:HOH930 4.9 41.5 1.0
O A:HOH1138 4.9 44.0 1.0

Calcium binding site 2 out of 5 in 4n2i

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Calcium binding site 2 out of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (D177A, 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 (D177A, 10 Mm CA2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca705

b:42.1
occ:1.00
 OD2 A:ASP180 2.3 57.0 1.0
OD1 A:ASN154 2.4 49.1 1.0
OD1 A:ASP156 2.4 53.2 1.0
OE2 A:GLU158 2.4 57.6 1.0
OD1 A:ASP166 2.4 98.0 1.0
O A:HOH969 2.5 32.5 1.0
CG A:ASN154 3.3 52.0 1.0
CG A:ASP156 3.3 52.3 1.0
CD A:GLU158 3.4 63.7 1.0
CG A:ASP166 3.5 93.6 1.0
CG A:ASP180 3.5 61.9 1.0
OD2 A:ASP156 3.5 48.3 1.0
ND2 A:ASN154 3.6 49.7 1.0
CA A:CA706 3.6 47.5 1.0
CG A:GLU158 3.7 66.1 1.0
CB A:ASP166 3.9 87.8 1.0
CB A:ASP180 4.1 50.6 1.0
O A:ASP156 4.4 51.4 1.0
OD1 A:ASP180 4.5 62.4 1.0
OD2 A:ASP166 4.5 92.8 1.0
O A:ALA177 4.5 50.6 1.0
C A:ASP156 4.6 51.6 1.0
OE1 A:GLU158 4.6 63.5 1.0
CB A:ASP156 4.6 50.9 1.0
CB A:ASN154 4.7 35.1 1.0
CA A:ALA177 4.8 69.0 1.0
N A:ASP156 4.8 47.3 1.0
CB A:ALA177 4.9 72.4 1.0
CA A:ASP156 4.9 50.8 1.0
N A:GLU158 4.9 67.8 1.0
N A:ARG157 5.0 53.2 1.0

Calcium binding site 3 out of 5 in 4n2i

Go back to Calcium Binding Sites List in 4n2i
Calcium binding site 3 out of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (D177A, 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 (D177A, 10 Mm CA2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca706

b:47.5
occ:1.00
 OD2 A:ASP180 2.3 57.0 1.0
OD2 A:ASP156 2.4 48.3 1.0
O A:HOH1235 2.5 46.4 1.0
OD1 A:ASP389 2.5 81.0 1.0
OE2 A:GLU158 2.5 57.6 1.0
OD1 A:ASP180 2.7 62.4 1.0
CG A:ASP180 2.8 61.9 1.0
CG A:ASP156 3.5 52.3 1.0
CD A:GLU158 3.5 63.7 1.0
CA A:CA705 3.6 42.1 1.0
CG A:ASP389 3.6 82.1 1.0
OE1 A:GLU158 3.8 63.5 1.0
OD1 A:ASP156 3.8 53.2 1.0
N A:ASP389 3.9 72.4 1.0
CA A:ASP389 4.3 68.5 1.0
CB A:ASP180 4.3 50.6 1.0
OD2 A:ASP389 4.4 87.5 1.0
NZ A:LYS363 4.5 58.9 1.0
CB A:ASP389 4.6 75.8 1.0
CB A:ASP156 4.8 50.9 1.0
CE A:LYS363 4.8 68.0 1.0
CE2 A:PHE365 4.8 46.5 1.0
CG A:GLU158 4.9 66.1 1.0
C A:PRO388 4.9 69.5 1.0
O A:HOH969 5.0 32.5 1.0

Calcium binding site 4 out of 5 in 4n2i

Go back to Calcium Binding Sites List in 4n2i
Calcium binding site 4 out of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (D177A, 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 (D177A, 10 Mm CA2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca707

b:70.4
occ:1.00
 O A:LYS171 2.3 76.6 1.0
O A:HOH1058 2.4 46.0 1.0
OD1 A:ASP169 2.4 67.0 1.0
O A:ASP166 2.4 80.6 1.0
C A:ASP166 3.5 82.8 1.0
C A:LYS171 3.5 73.3 1.0
CG A:ASP169 3.5 75.2 1.0
O A:ASP169 3.8 72.0 1.0
N A:LYS171 3.9 80.2 1.0
CA A:ASP166 4.0 84.7 1.0
OD2 A:ASP169 4.0 80.2 1.0
CB A:ASP166 4.2 87.8 1.0
CA A:LYS171 4.2 77.6 1.0
C A:ASP169 4.3 75.1 1.0
N A:VAL172 4.6 69.3 1.0
N A:CYS167 4.6 83.0 1.0
CB A:LYS171 4.7 77.9 1.0
C A:GLU170 4.7 75.2 1.0
CB A:ASP169 4.8 76.9 1.0
OE1 A:GLU253 4.8 37.5 1.0
N A:ASP169 4.8 78.6 1.0
CA A:ASP169 4.8 76.7 1.0
CA A:VAL172 4.9 70.7 1.0
CG2 A:VAL172 4.9 67.6 1.0
N A:GLU170 4.9 73.9 1.0
OE2 A:GLU253 4.9 43.1 1.0
OD2 A:ASP166 4.9 92.8 1.0
CA A:CYS167 5.0 79.5 1.0

Calcium binding site 5 out of 5 in 4n2i

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Calcium binding site 5 out of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (D177A, 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 (D177A, 10 Mm CA2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca711

b:33.4
occ:1.00
 OD1 A:ASP125 2.2 35.5 1.0
OD1 A:ASP123 2.2 29.4 1.0
O A:VAL129 2.2 33.3 1.0
OE1 A:GLU131 2.3 27.1 1.0
OD1 A:ASP127 2.3 32.7 1.0
O A:HOH1253 2.3 37.0 1.0
CG A:ASP125 3.2 38.8 1.0
CG A:ASP123 3.2 31.1 1.0
CG A:ASP127 3.2 36.1 1.0
CD A:GLU131 3.3 32.0 1.0
C A:VAL129 3.4 37.1 1.0
OD2 A:ASP125 3.6 36.2 1.0
OD2 A:ASP127 3.7 43.6 1.0
CB A:ASP123 3.8 22.7 1.0
CA A:ASP123 3.9 24.0 1.0
N A:VAL129 3.9 35.0 1.0
OE2 A:GLU131 3.9 28.4 1.0
N A:ASP127 4.0 37.3 1.0
N A:GLU131 4.1 28.6 1.0
CA A:VAL129 4.1 38.1 1.0
OD2 A:ASP123 4.2 27.6 1.0
CB A:GLU131 4.3 29.5 1.0
CB A:ASP127 4.3 36.9 1.0
N A:ASP125 4.3 25.8 1.0
N A:ARG126 4.3 26.4 1.0
CG A:GLU131 4.4 20.9 1.0
N A:VAL130 4.4 35.5 1.0
C A:ASP123 4.4 32.1 1.0
CB A:ASP125 4.5 33.5 1.0
CB A:VAL129 4.5 45.3 1.0
CA A:ASP127 4.5 37.7 1.0
N A:GLY128 4.5 37.6 1.0
CA A:VAL130 4.6 34.4 1.0
C A:ASP125 4.6 29.9 1.0
CA A:ASP125 4.6 30.4 1.0
N A:ALA124 4.6 25.2 1.0
C A:ASP127 4.7 43.2 1.0
C A:VAL130 4.7 36.7 1.0
CA A:GLU131 4.8 35.2 1.0
O A:ASP123 5.0 23.8 1.0
C A:GLY128 5.0 42.2 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 10:46:36 2024

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