Calcium in PDB 4n2b: Crystal Structure of Protein Arginine Deiminase 2 (10 Mm CA2+)
Enzymatic activity of Crystal Structure of Protein Arginine Deiminase 2 (10 Mm CA2+)
All present enzymatic activity of Crystal Structure of Protein Arginine Deiminase 2 (10 Mm CA2+):
3.5.3.15;
Protein crystallography data
The structure of Crystal Structure of Protein Arginine Deiminase 2 (10 Mm CA2+), PDB code: 4n2b
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)
|
40.39 /
1.69
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
202.665,
51.549,
76.217,
90.00,
105.76,
90.00
|
R / Rfree (%)
|
16.8 /
20
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Protein Arginine Deiminase 2 (10 Mm CA2+)
(pdb code 4n2b). 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 (10 Mm CA2+), PDB code: 4n2b:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
Calcium binding site 1 out
of 5 in 4n2b
Go back to
Calcium Binding Sites List in 4n2b
Calcium binding site 1 out
of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (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 (10 Mm CA2+) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca704
b:21.1
occ:1.00
|
OD1
|
A:ASP123
|
2.2
|
16.1
|
1.0
|
OD1
|
A:ASP125
|
2.2
|
21.8
|
1.0
|
O
|
A:VAL129
|
2.2
|
21.4
|
1.0
|
OD1
|
A:ASP127
|
2.3
|
25.3
|
1.0
|
OE1
|
A:GLU131
|
2.3
|
16.8
|
1.0
|
O
|
A:HOH954
|
2.3
|
25.5
|
1.0
|
CG
|
A:ASP127
|
3.2
|
28.3
|
1.0
|
CG
|
A:ASP125
|
3.2
|
24.4
|
1.0
|
CG
|
A:ASP123
|
3.2
|
19.1
|
1.0
|
CD
|
A:GLU131
|
3.4
|
19.1
|
1.0
|
C
|
A:VAL129
|
3.4
|
24.2
|
1.0
|
OD2
|
A:ASP125
|
3.6
|
28.3
|
1.0
|
OD2
|
A:ASP127
|
3.6
|
29.4
|
1.0
|
CB
|
A:ASP123
|
3.9
|
15.6
|
1.0
|
N
|
A:VAL129
|
3.9
|
28.9
|
1.0
|
CA
|
A:ASP123
|
3.9
|
12.9
|
1.0
|
OE2
|
A:GLU131
|
4.0
|
17.5
|
1.0
|
N
|
A:ASP127
|
4.1
|
23.2
|
1.0
|
N
|
A:GLU131
|
4.1
|
16.0
|
1.0
|
CA
|
A:VAL129
|
4.1
|
25.4
|
1.0
|
OD2
|
A:ASP123
|
4.2
|
20.7
|
1.0
|
CB
|
A:GLU131
|
4.3
|
21.3
|
1.0
|
CB
|
A:ASP127
|
4.4
|
25.7
|
1.0
|
N
|
A:ARG126
|
4.4
|
15.4
|
0.8
|
CB
|
A:VAL129
|
4.4
|
29.9
|
1.0
|
N
|
A:ARG126
|
4.4
|
17.0
|
0.2
|
N
|
A:ASP125
|
4.4
|
14.6
|
1.0
|
N
|
A:VAL130
|
4.4
|
26.2
|
1.0
|
CG
|
A:GLU131
|
4.4
|
18.0
|
1.0
|
CB
|
A:ASP125
|
4.5
|
19.4
|
1.0
|
C
|
A:ASP123
|
4.5
|
13.1
|
1.0
|
CA
|
A:VAL130
|
4.5
|
25.7
|
1.0
|
CA
|
A:ASP127
|
4.6
|
28.4
|
1.0
|
N
|
A:GLY128
|
4.6
|
27.3
|
1.0
|
C
|
A:ASP125
|
4.6
|
17.6
|
1.0
|
CA
|
A:ASP125
|
4.7
|
17.9
|
1.0
|
N
|
A:ALA124
|
4.7
|
11.3
|
1.0
|
C
|
A:VAL130
|
4.7
|
22.9
|
1.0
|
CA
|
A:GLU131
|
4.8
|
18.5
|
1.0
|
C
|
A:ASP127
|
4.8
|
34.6
|
1.0
|
|
Calcium binding site 2 out
of 5 in 4n2b
Go back to
Calcium Binding Sites List in 4n2b
Calcium binding site 2 out
of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (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 (10 Mm CA2+) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca705
b:13.0
occ:1.00
|
OD2
|
A:ASP166
|
2.2
|
17.3
|
1.0
|
OD2
|
A:ASP180
|
2.2
|
13.7
|
1.0
|
OD1
|
A:ASP156
|
2.3
|
12.2
|
1.0
|
OD1
|
A:ASN154
|
2.3
|
10.8
|
1.0
|
OD1
|
A:ASP177
|
2.3
|
13.0
|
1.0
|
OE2
|
A:GLU158
|
2.5
|
16.0
|
1.0
|
CG
|
A:ASP156
|
3.3
|
15.2
|
1.0
|
CG
|
A:ASN154
|
3.3
|
10.9
|
1.0
|
CG
|
A:ASP166
|
3.3
|
18.4
|
1.0
|
CG
|
A:ASP180
|
3.4
|
14.7
|
1.0
|
CD
|
A:GLU158
|
3.5
|
22.1
|
1.0
|
OD2
|
A:ASP156
|
3.5
|
15.2
|
1.0
|
CG
|
A:ASP177
|
3.5
|
16.1
|
1.0
|
ND2
|
A:ASN154
|
3.6
|
15.1
|
1.0
|
CA
|
A:CA709
|
3.7
|
14.8
|
1.0
|
CG
|
A:GLU158
|
3.7
|
16.8
|
1.0
|
CB
|
A:ASP166
|
3.8
|
16.1
|
1.0
|
CB
|
A:ASP180
|
4.0
|
12.8
|
1.0
|
CA
|
A:ASP177
|
4.3
|
15.1
|
1.0
|
OD2
|
A:ASP177
|
4.4
|
18.0
|
1.0
|
OD1
|
A:ASP166
|
4.4
|
15.8
|
1.0
|
CB
|
A:ASP177
|
4.4
|
17.3
|
1.0
|
OD1
|
A:ASP180
|
4.4
|
14.8
|
1.0
|
O
|
A:ASP177
|
4.5
|
14.6
|
1.0
|
O
|
A:ASP156
|
4.6
|
14.2
|
1.0
|
C
|
A:ASP156
|
4.6
|
14.5
|
1.0
|
CB
|
A:ASP156
|
4.6
|
13.1
|
1.0
|
OE1
|
A:GLU158
|
4.6
|
21.9
|
1.0
|
CB
|
A:ASN154
|
4.7
|
11.5
|
1.0
|
N
|
A:ASP156
|
4.8
|
12.1
|
1.0
|
N
|
A:GLU158
|
4.9
|
16.9
|
1.0
|
C
|
A:ASP177
|
4.9
|
15.7
|
1.0
|
CA
|
A:ASP156
|
4.9
|
13.0
|
1.0
|
N
|
A:ARG157
|
4.9
|
16.0
|
1.0
|
|
Calcium binding site 3 out
of 5 in 4n2b
Go back to
Calcium Binding Sites List in 4n2b
Calcium binding site 3 out
of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (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 (10 Mm CA2+) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca706
b:14.2
occ:1.00
|
O
|
A:LYS171
|
2.3
|
17.6
|
1.0
|
O
|
A:ASP166
|
2.3
|
15.1
|
1.0
|
OD1
|
A:ASP169
|
2.3
|
17.1
|
1.0
|
O
|
A:HOH886
|
2.4
|
16.0
|
1.0
|
O
|
A:HOH844
|
2.4
|
18.1
|
1.0
|
O
|
A:HOH826
|
2.4
|
13.8
|
1.0
|
O
|
A:HOH900
|
2.5
|
18.2
|
1.0
|
C
|
A:ASP166
|
3.4
|
15.4
|
1.0
|
CG
|
A:ASP169
|
3.4
|
20.5
|
1.0
|
C
|
A:LYS171
|
3.5
|
20.9
|
1.0
|
OD2
|
A:ASP169
|
3.8
|
22.4
|
1.0
|
CA
|
A:ASP166
|
4.0
|
18.6
|
1.0
|
N
|
A:LYS171
|
4.2
|
16.6
|
1.0
|
CB
|
A:ASP166
|
4.2
|
16.1
|
1.0
|
OD2
|
A:ASP177
|
4.2
|
18.0
|
1.0
|
O
|
A:HOH989
|
4.4
|
23.5
|
1.0
|
O
|
A:ASP169
|
4.4
|
16.4
|
1.0
|
CA
|
A:LYS171
|
4.4
|
20.0
|
1.0
|
N
|
A:CYS167
|
4.4
|
17.4
|
1.0
|
N
|
A:VAL172
|
4.5
|
18.5
|
1.0
|
OE1
|
A:GLU253
|
4.6
|
16.6
|
1.0
|
O
|
A:HOH1128
|
4.6
|
34.8
|
1.0
|
C
|
A:ASP169
|
4.6
|
17.4
|
1.0
|
CA
|
A:VAL172
|
4.6
|
18.6
|
1.0
|
CB
|
A:ASP169
|
4.7
|
20.9
|
1.0
|
OE2
|
A:GLU253
|
4.7
|
12.8
|
1.0
|
CA
|
A:CYS167
|
4.7
|
17.7
|
1.0
|
N
|
A:ASP169
|
4.7
|
18.4
|
1.0
|
CG2
|
A:VAL172
|
4.8
|
15.9
|
1.0
|
CA
|
A:ASP169
|
4.9
|
20.8
|
1.0
|
|
Calcium binding site 4 out
of 5 in 4n2b
Go back to
Calcium Binding Sites List in 4n2b
Calcium binding site 4 out
of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (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 (10 Mm CA2+) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca707
b:10.2
occ:1.00
|
O
|
A:PHE408
|
2.3
|
8.9
|
1.0
|
OE1
|
A:GLU354
|
2.3
|
12.0
|
1.0
|
O
|
A:HOH952
|
2.3
|
18.4
|
1.0
|
O
|
A:LEU411
|
2.4
|
9.1
|
1.0
|
OE2
|
A:GLU412
|
2.5
|
13.4
|
1.0
|
O
|
A:HOH819
|
2.5
|
12.2
|
1.0
|
OE1
|
A:GLN350
|
2.6
|
10.8
|
0.5
|
CD
|
A:GLU412
|
3.3
|
14.2
|
1.0
|
CD
|
A:GLU354
|
3.4
|
14.9
|
1.0
|
C
|
A:PHE408
|
3.4
|
11.3
|
1.0
|
C
|
A:LEU411
|
3.6
|
9.2
|
1.0
|
CD
|
A:GLN350
|
3.7
|
24.5
|
0.5
|
OE2
|
A:GLU354
|
3.7
|
15.8
|
1.0
|
OE1
|
A:GLU412
|
3.8
|
21.3
|
1.0
|
NE2
|
A:GLN350
|
4.2
|
14.5
|
0.5
|
O
|
A:HOH1257
|
4.2
|
32.4
|
1.0
|
N
|
A:GLY409
|
4.3
|
9.5
|
1.0
|
CB
|
A:PHE408
|
4.3
|
6.8
|
1.0
|
CG
|
A:GLU412
|
4.4
|
13.9
|
1.0
|
CA
|
A:GLY409
|
4.4
|
6.6
|
1.0
|
N
|
A:LEU411
|
4.4
|
8.5
|
1.0
|
CA
|
A:LEU411
|
4.4
|
9.5
|
1.0
|
CA
|
A:PHE408
|
4.4
|
9.2
|
1.0
|
CB
|
A:LEU411
|
4.5
|
9.3
|
1.0
|
O
|
A:GLN350
|
4.5
|
19.4
|
1.0
|
N
|
A:GLU412
|
4.6
|
6.9
|
1.0
|
O
|
A:HOH1084
|
4.6
|
27.0
|
1.0
|
O
|
A:HOH1125
|
4.7
|
35.5
|
1.0
|
CA
|
A:GLU412
|
4.7
|
6.1
|
1.0
|
C
|
A:GLY409
|
4.7
|
7.3
|
1.0
|
CG
|
A:GLU354
|
4.7
|
9.2
|
1.0
|
CG
|
A:GLN350
|
4.9
|
21.7
|
0.5
|
|
Calcium binding site 5 out
of 5 in 4n2b
Go back to
Calcium Binding Sites List in 4n2b
Calcium binding site 5 out
of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (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 (10 Mm CA2+) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca709
b:14.8
occ:1.00
|
OD2
|
A:ASP156
|
2.3
|
15.2
|
1.0
|
OD1
|
A:ASP389
|
2.3
|
17.9
|
1.0
|
OD2
|
A:ASP180
|
2.4
|
13.7
|
1.0
|
O
|
A:HOH850
|
2.4
|
12.2
|
1.0
|
O
|
A:HOH857
|
2.5
|
13.8
|
1.0
|
OE2
|
A:GLU158
|
2.5
|
16.0
|
1.0
|
OD1
|
A:ASP180
|
2.6
|
14.8
|
1.0
|
CG
|
A:ASP180
|
2.8
|
14.7
|
1.0
|
CG
|
A:ASP156
|
3.4
|
15.2
|
1.0
|
CD
|
A:GLU158
|
3.5
|
22.1
|
1.0
|
CG
|
A:ASP389
|
3.5
|
25.9
|
1.0
|
OE1
|
A:GLU158
|
3.7
|
21.9
|
1.0
|
CA
|
A:CA705
|
3.7
|
13.0
|
1.0
|
NZ
|
A:LYS363
|
3.7
|
25.5
|
1.0
|
OD1
|
A:ASP156
|
3.7
|
12.2
|
1.0
|
N
|
A:ASP389
|
3.9
|
16.5
|
1.0
|
OD2
|
A:ASP389
|
4.2
|
26.9
|
1.0
|
CA
|
A:ASP389
|
4.2
|
13.7
|
1.0
|
CB
|
A:ASP180
|
4.3
|
12.8
|
1.0
|
CB
|
A:ASP389
|
4.5
|
11.8
|
1.0
|
O
|
A:HOH1531
|
4.5
|
36.0
|
1.0
|
CE2
|
A:PHE365
|
4.6
|
14.2
|
1.0
|
O
|
A:GLU176
|
4.6
|
18.0
|
1.0
|
CB
|
A:ASP156
|
4.7
|
13.1
|
1.0
|
O
|
A:HOH1223
|
4.8
|
28.3
|
1.0
|
CD2
|
A:PHE365
|
4.8
|
13.2
|
1.0
|
CG
|
A:GLU158
|
4.8
|
16.8
|
1.0
|
C
|
A:PRO388
|
4.9
|
20.2
|
1.0
|
CE
|
A:LYS363
|
4.9
|
30.6
|
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
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