Calcium in PDB 4dl1: Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog
Enzymatic activity of Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog
All present enzymatic activity of Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog:
1.11.2.2;
Protein crystallography data
The structure of Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog, PDB code: 4dl1
was solved by
F.Vajdos,
A.Varghese,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
128.49 /
2.00
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
63.829,
242.636,
151.505,
90.00,
91.19,
90.00
|
|
R / Rfree (%)
|
19 /
24.6
|
Other elements in 4dl1:
The structure of Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog
(pdb code 4dl1). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog, PDB code: 4dl1:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 4dl1
Go back to
Calcium Binding Sites List in 4dl1
Calcium binding site 1 out
of 8 in the Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog
 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 Human Myeloperoxidase with Covalent Thioxanthine Analog within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca610
b:14.8
occ:1.00
|
O
|
A:ASP96
|
2.4
|
12.1
|
1.0
|
|
OG1
|
C:THR168
|
2.4
|
14.5
|
1.0
|
|
OG
|
C:SER174
|
2.4
|
15.2
|
1.0
|
|
O
|
C:PHE170
|
2.4
|
13.8
|
1.0
|
|
OD1
|
C:ASP172
|
2.4
|
13.1
|
1.0
|
|
O
|
C:THR168
|
2.4
|
13.7
|
1.0
|
|
OD1
|
A:ASP96
|
2.5
|
17.4
|
1.0
|
|
C
|
C:THR168
|
3.4
|
15.4
|
1.0
|
|
CG
|
C:ASP172
|
3.4
|
13.6
|
1.0
|
|
C
|
A:ASP96
|
3.5
|
12.5
|
1.0
|
|
CB
|
C:SER174
|
3.5
|
12.7
|
1.0
|
|
C
|
C:PHE170
|
3.6
|
14.9
|
1.0
|
|
CG
|
A:ASP96
|
3.6
|
14.4
|
1.0
|
|
CB
|
C:THR168
|
3.7
|
16.7
|
1.0
|
|
OD2
|
C:ASP172
|
3.8
|
16.6
|
1.0
|
|
N
|
C:PHE170
|
3.9
|
13.3
|
1.0
|
|
CA
|
C:THR168
|
3.9
|
13.7
|
1.0
|
|
C
|
C:SER169
|
4.0
|
14.4
|
1.0
|
|
CA
|
A:ASP96
|
4.1
|
13.1
|
1.0
|
|
N
|
C:THR168
|
4.2
|
14.6
|
1.0
|
|
N
|
C:ASP172
|
4.2
|
15.7
|
1.0
|
|
N
|
C:SER174
|
4.2
|
13.2
|
1.0
|
|
CA
|
C:PHE170
|
4.3
|
15.6
|
1.0
|
|
CB
|
A:ASP96
|
4.3
|
12.3
|
1.0
|
|
N
|
C:SER169
|
4.4
|
15.8
|
1.0
|
|
O
|
C:SER169
|
4.4
|
14.0
|
1.0
|
|
CA
|
C:SER174
|
4.5
|
11.0
|
1.0
|
|
O
|
A:HOH1762
|
4.5
|
8.0
|
1.0
|
|
N
|
A:LEU97
|
4.5
|
12.8
|
1.0
|
|
OD2
|
A:ASP96
|
4.5
|
20.8
|
1.0
|
|
CB
|
C:ASP172
|
4.6
|
15.8
|
1.0
|
|
N
|
C:VAL171
|
4.6
|
17.5
|
1.0
|
|
CA
|
C:SER169
|
4.6
|
14.5
|
1.0
|
|
CA
|
A:LEU97
|
4.7
|
13.6
|
1.0
|
|
CG2
|
C:THR168
|
4.7
|
10.2
|
1.0
|
|
CA
|
C:ASP172
|
4.8
|
15.8
|
1.0
|
|
CA
|
C:VAL171
|
4.8
|
15.7
|
1.0
|
|
CB
|
C:PHE170
|
4.9
|
15.9
|
1.0
|
|
N
|
C:ALA173
|
5.0
|
13.6
|
1.0
|
|
Calcium binding site 2 out
of 8 in 4dl1
Go back to
Calcium Binding Sites List in 4dl1
Calcium binding site 2 out
of 8 in the Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog
 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 Human Myeloperoxidase with Covalent Thioxanthine Analog within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca609
b:16.0
occ:1.00
|
O
|
B:ASP96
|
2.4
|
13.4
|
1.0
|
|
O
|
D:PHE170
|
2.4
|
15.0
|
1.0
|
|
OG
|
D:SER174
|
2.4
|
16.8
|
1.0
|
|
OD1
|
B:ASP96
|
2.4
|
16.7
|
1.0
|
|
O
|
D:THR168
|
2.4
|
13.2
|
1.0
|
|
OG1
|
D:THR168
|
2.4
|
17.0
|
1.0
|
|
OD1
|
D:ASP172
|
2.4
|
14.6
|
1.0
|
|
CB
|
D:SER174
|
3.3
|
16.4
|
1.0
|
|
C
|
D:THR168
|
3.4
|
14.9
|
1.0
|
|
CG
|
D:ASP172
|
3.4
|
15.6
|
1.0
|
|
C
|
B:ASP96
|
3.4
|
15.9
|
1.0
|
|
CG
|
B:ASP96
|
3.5
|
18.3
|
1.0
|
|
C
|
D:PHE170
|
3.6
|
14.6
|
1.0
|
|
CB
|
D:THR168
|
3.7
|
16.0
|
1.0
|
|
OD2
|
D:ASP172
|
3.8
|
15.1
|
1.0
|
|
CA
|
D:THR168
|
4.0
|
14.6
|
1.0
|
|
N
|
D:PHE170
|
4.0
|
15.1
|
1.0
|
|
C
|
D:SER169
|
4.1
|
14.5
|
1.0
|
|
CA
|
B:ASP96
|
4.1
|
14.7
|
1.0
|
|
N
|
D:SER174
|
4.1
|
15.4
|
1.0
|
|
N
|
D:ASP172
|
4.1
|
15.6
|
1.0
|
|
N
|
D:THR168
|
4.2
|
15.7
|
1.0
|
|
CB
|
B:ASP96
|
4.3
|
15.4
|
1.0
|
|
CA
|
D:SER174
|
4.3
|
16.7
|
1.0
|
|
O
|
D:SER169
|
4.3
|
16.7
|
1.0
|
|
CA
|
D:PHE170
|
4.3
|
13.2
|
1.0
|
|
N
|
D:SER169
|
4.4
|
14.5
|
1.0
|
|
O
|
D:HOH702
|
4.4
|
17.1
|
1.0
|
|
OD2
|
B:ASP96
|
4.4
|
22.5
|
1.0
|
|
N
|
B:LEU97
|
4.5
|
15.4
|
1.0
|
|
N
|
D:VAL171
|
4.6
|
15.1
|
1.0
|
|
CA
|
D:SER169
|
4.6
|
14.6
|
1.0
|
|
CB
|
D:ASP172
|
4.7
|
16.9
|
1.0
|
|
CA
|
D:VAL171
|
4.7
|
16.2
|
1.0
|
|
CA
|
B:LEU97
|
4.8
|
15.1
|
1.0
|
|
CG2
|
D:THR168
|
4.8
|
16.8
|
1.0
|
|
CA
|
D:ASP172
|
4.9
|
17.2
|
1.0
|
|
CB
|
D:PHE170
|
4.9
|
12.6
|
1.0
|
|
C
|
D:VAL171
|
5.0
|
16.5
|
1.0
|
|
Calcium binding site 3 out
of 8 in 4dl1
Go back to
Calcium Binding Sites List in 4dl1
Calcium binding site 3 out
of 8 in the Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog
 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 Human Myeloperoxidase with Covalent Thioxanthine Analog within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Ca609
b:22.7
occ:1.00
|
O
|
E:ASP96
|
2.4
|
18.2
|
1.0
|
|
OG1
|
G:THR168
|
2.4
|
21.4
|
1.0
|
|
O
|
G:PHE170
|
2.4
|
23.1
|
1.0
|
|
OG
|
G:SER174
|
2.4
|
22.7
|
1.0
|
|
O
|
G:THR168
|
2.4
|
20.7
|
1.0
|
|
OD1
|
E:ASP96
|
2.4
|
27.3
|
1.0
|
|
OD1
|
G:ASP172
|
2.4
|
27.5
|
1.0
|
|
C
|
G:THR168
|
3.3
|
18.8
|
1.0
|
|
CG
|
G:ASP172
|
3.4
|
23.8
|
1.0
|
|
C
|
E:ASP96
|
3.4
|
18.8
|
1.0
|
|
CB
|
G:SER174
|
3.5
|
22.7
|
1.0
|
|
C
|
G:PHE170
|
3.6
|
22.6
|
1.0
|
|
CG
|
E:ASP96
|
3.6
|
24.2
|
1.0
|
|
CB
|
G:THR168
|
3.7
|
22.3
|
1.0
|
|
OD2
|
G:ASP172
|
3.9
|
24.3
|
1.0
|
|
N
|
G:PHE170
|
3.9
|
23.3
|
1.0
|
|
CA
|
G:THR168
|
4.0
|
19.0
|
1.0
|
|
C
|
G:SER169
|
4.0
|
20.9
|
1.0
|
|
CA
|
E:ASP96
|
4.1
|
21.5
|
1.0
|
|
N
|
G:SER174
|
4.1
|
25.1
|
1.0
|
|
N
|
G:ASP172
|
4.2
|
25.1
|
1.0
|
|
O
|
G:SER169
|
4.2
|
21.6
|
1.0
|
|
N
|
G:SER169
|
4.3
|
20.8
|
1.0
|
|
N
|
G:THR168
|
4.3
|
17.1
|
1.0
|
|
CB
|
E:ASP96
|
4.3
|
20.6
|
1.0
|
|
CA
|
G:PHE170
|
4.3
|
21.6
|
1.0
|
|
CA
|
G:SER174
|
4.4
|
24.2
|
1.0
|
|
N
|
E:LEU97
|
4.5
|
19.5
|
1.0
|
|
CA
|
G:SER169
|
4.6
|
20.7
|
1.0
|
|
CB
|
G:ASP172
|
4.6
|
26.0
|
1.0
|
|
OD2
|
E:ASP96
|
4.6
|
27.7
|
1.0
|
|
N
|
G:VAL171
|
4.6
|
24.1
|
1.0
|
|
O
|
G:HOH909
|
4.6
|
9.7
|
1.0
|
|
CA
|
E:LEU97
|
4.7
|
17.1
|
1.0
|
|
CA
|
G:VAL171
|
4.8
|
21.5
|
1.0
|
|
CG2
|
G:THR168
|
4.8
|
15.7
|
1.0
|
|
CA
|
G:ASP172
|
4.8
|
25.4
|
1.0
|
|
N
|
G:ALA173
|
4.9
|
24.6
|
1.0
|
|
CB
|
G:PHE170
|
4.9
|
24.1
|
1.0
|
|
Calcium binding site 4 out
of 8 in 4dl1
Go back to
Calcium Binding Sites List in 4dl1
Calcium binding site 4 out
of 8 in the Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog
 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 Human Myeloperoxidase with Covalent Thioxanthine Analog within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Ca609
b:19.6
occ:1.00
|
O
|
F:ASP96
|
2.4
|
21.4
|
1.0
|
|
O
|
H:PHE170
|
2.4
|
17.6
|
1.0
|
|
OD1
|
H:ASP172
|
2.4
|
18.4
|
1.0
|
|
O
|
H:THR168
|
2.4
|
20.7
|
1.0
|
|
OG
|
H:SER174
|
2.4
|
22.3
|
1.0
|
|
OG1
|
H:THR168
|
2.4
|
24.5
|
1.0
|
|
OD1
|
F:ASP96
|
2.4
|
23.2
|
1.0
|
|
CG
|
H:ASP172
|
3.3
|
17.5
|
1.0
|
|
C
|
H:THR168
|
3.3
|
21.4
|
1.0
|
|
C
|
F:ASP96
|
3.4
|
22.9
|
1.0
|
|
CG
|
F:ASP96
|
3.5
|
21.6
|
1.0
|
|
CB
|
H:SER174
|
3.5
|
25.2
|
1.0
|
|
C
|
H:PHE170
|
3.6
|
19.9
|
1.0
|
|
OD2
|
H:ASP172
|
3.6
|
18.4
|
1.0
|
|
CB
|
H:THR168
|
3.7
|
20.5
|
1.0
|
|
N
|
H:PHE170
|
3.9
|
19.6
|
1.0
|
|
CA
|
H:THR168
|
4.0
|
21.0
|
1.0
|
|
C
|
H:SER169
|
4.0
|
20.8
|
1.0
|
|
CA
|
F:ASP96
|
4.1
|
23.2
|
1.0
|
|
N
|
H:ASP172
|
4.1
|
21.8
|
1.0
|
|
N
|
H:SER174
|
4.2
|
25.0
|
1.0
|
|
CB
|
F:ASP96
|
4.2
|
23.5
|
1.0
|
|
N
|
H:THR168
|
4.2
|
19.1
|
1.0
|
|
CA
|
H:PHE170
|
4.3
|
19.0
|
1.0
|
|
N
|
H:SER169
|
4.3
|
20.3
|
1.0
|
|
O
|
H:SER169
|
4.5
|
24.1
|
1.0
|
|
OD2
|
F:ASP96
|
4.5
|
24.6
|
1.0
|
|
CA
|
H:SER174
|
4.5
|
25.6
|
1.0
|
|
N
|
F:LEU97
|
4.5
|
23.2
|
1.0
|
|
CB
|
H:ASP172
|
4.5
|
21.0
|
1.0
|
|
CA
|
H:SER169
|
4.6
|
20.0
|
1.0
|
|
O
|
H:HOH1841
|
4.6
|
7.7
|
1.0
|
|
N
|
H:VAL171
|
4.6
|
19.8
|
1.0
|
|
CA
|
F:LEU97
|
4.7
|
21.6
|
1.0
|
|
CA
|
H:ASP172
|
4.7
|
21.2
|
1.0
|
|
CA
|
H:VAL171
|
4.8
|
19.6
|
1.0
|
|
CG2
|
H:THR168
|
4.8
|
23.1
|
1.0
|
|
CB
|
H:PHE170
|
4.8
|
18.8
|
1.0
|
|
C
|
H:VAL171
|
5.0
|
21.9
|
1.0
|
|
C
|
H:ASP172
|
5.0
|
21.5
|
1.0
|
|
N
|
H:ALA173
|
5.0
|
23.3
|
1.0
|
|
Calcium binding site 5 out
of 8 in 4dl1
Go back to
Calcium Binding Sites List in 4dl1
Calcium binding site 5 out
of 8 in the Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog
 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 Human Myeloperoxidase with Covalent Thioxanthine Analog within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Ca609
b:24.5
occ:1.00
|
O
|
K:THR168
|
2.4
|
23.2
|
1.0
|
|
O
|
I:ASP96
|
2.4
|
19.9
|
1.0
|
|
OD1
|
I:ASP96
|
2.4
|
30.7
|
1.0
|
|
OG
|
K:SER174
|
2.4
|
24.1
|
1.0
|
|
OG1
|
K:THR168
|
2.4
|
24.5
|
1.0
|
|
OD1
|
K:ASP172
|
2.4
|
27.2
|
1.0
|
|
O
|
K:PHE170
|
2.4
|
22.4
|
1.0
|
|
C
|
K:THR168
|
3.3
|
22.6
|
1.0
|
|
CG
|
K:ASP172
|
3.4
|
28.1
|
1.0
|
|
C
|
I:ASP96
|
3.4
|
17.9
|
1.0
|
|
CB
|
K:SER174
|
3.5
|
23.1
|
1.0
|
|
CG
|
I:ASP96
|
3.5
|
28.6
|
1.0
|
|
C
|
K:PHE170
|
3.6
|
24.9
|
1.0
|
|
CB
|
K:THR168
|
3.6
|
20.8
|
1.0
|
|
OD2
|
K:ASP172
|
3.8
|
26.9
|
1.0
|
|
CA
|
K:THR168
|
3.9
|
21.0
|
1.0
|
|
N
|
K:PHE170
|
3.9
|
24.7
|
1.0
|
|
CA
|
I:ASP96
|
4.0
|
20.7
|
1.0
|
|
C
|
K:SER169
|
4.1
|
22.6
|
1.0
|
|
N
|
K:THR168
|
4.2
|
19.7
|
1.0
|
|
N
|
K:SER174
|
4.2
|
21.1
|
1.0
|
|
N
|
K:ASP172
|
4.2
|
26.8
|
1.0
|
|
CB
|
I:ASP96
|
4.2
|
20.1
|
1.0
|
|
N
|
K:SER169
|
4.3
|
23.6
|
1.0
|
|
CA
|
K:PHE170
|
4.4
|
22.5
|
1.0
|
|
O
|
I:HOH1766
|
4.4
|
6.0
|
1.0
|
|
OD2
|
I:ASP96
|
4.4
|
23.8
|
1.0
|
|
O
|
K:SER169
|
4.4
|
23.1
|
1.0
|
|
CA
|
K:SER174
|
4.5
|
23.5
|
1.0
|
|
N
|
I:LEU97
|
4.5
|
15.0
|
1.0
|
|
CA
|
K:SER169
|
4.6
|
24.0
|
1.0
|
|
N
|
K:VAL171
|
4.7
|
25.9
|
1.0
|
|
CB
|
K:ASP172
|
4.7
|
27.3
|
1.0
|
|
CG2
|
K:THR168
|
4.8
|
17.5
|
1.0
|
|
CA
|
I:LEU97
|
4.8
|
16.9
|
1.0
|
|
CA
|
K:VAL171
|
4.8
|
25.9
|
1.0
|
|
CA
|
K:ASP172
|
4.9
|
26.3
|
1.0
|
|
Calcium binding site 6 out
of 8 in 4dl1
Go back to
Calcium Binding Sites List in 4dl1
Calcium binding site 6 out
of 8 in the Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog
 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 Human Myeloperoxidase with Covalent Thioxanthine Analog within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Ca609
b:20.6
occ:1.00
|
O
|
J:ASP96
|
2.4
|
23.3
|
1.0
|
|
O
|
L:PHE170
|
2.4
|
20.9
|
1.0
|
|
OD1
|
J:ASP96
|
2.4
|
21.9
|
1.0
|
|
O
|
L:THR168
|
2.4
|
20.0
|
1.0
|
|
OG1
|
L:THR168
|
2.4
|
22.4
|
1.0
|
|
OG
|
L:SER174
|
2.4
|
24.1
|
1.0
|
|
OD1
|
L:ASP172
|
2.4
|
17.3
|
1.0
|
|
C
|
L:THR168
|
3.3
|
19.8
|
1.0
|
|
C
|
J:ASP96
|
3.4
|
21.6
|
1.0
|
|
CG
|
L:ASP172
|
3.4
|
18.9
|
1.0
|
|
CB
|
L:SER174
|
3.4
|
21.9
|
1.0
|
|
C
|
L:PHE170
|
3.6
|
19.2
|
1.0
|
|
CG
|
J:ASP96
|
3.6
|
22.2
|
1.0
|
|
CB
|
L:THR168
|
3.7
|
17.4
|
1.0
|
|
N
|
L:PHE170
|
3.8
|
20.2
|
1.0
|
|
OD2
|
L:ASP172
|
3.8
|
16.6
|
1.0
|
|
CA
|
L:THR168
|
3.9
|
19.6
|
1.0
|
|
CA
|
J:ASP96
|
4.1
|
21.4
|
1.0
|
|
C
|
L:SER169
|
4.1
|
19.0
|
1.0
|
|
N
|
L:ASP172
|
4.1
|
19.3
|
1.0
|
|
N
|
L:SER174
|
4.1
|
22.1
|
1.0
|
|
N
|
L:THR168
|
4.2
|
17.3
|
1.0
|
|
CA
|
L:PHE170
|
4.2
|
19.2
|
1.0
|
|
CB
|
J:ASP96
|
4.3
|
22.2
|
1.0
|
|
N
|
L:SER169
|
4.4
|
18.6
|
1.0
|
|
CA
|
L:SER174
|
4.4
|
20.9
|
1.0
|
|
N
|
J:LEU97
|
4.4
|
21.0
|
1.0
|
|
O
|
L:SER169
|
4.5
|
19.9
|
1.0
|
|
O
|
L:HOH915
|
4.5
|
10.7
|
1.0
|
|
OD2
|
J:ASP96
|
4.6
|
20.2
|
1.0
|
|
CB
|
L:ASP172
|
4.6
|
20.4
|
1.0
|
|
N
|
L:VAL171
|
4.6
|
18.1
|
1.0
|
|
CA
|
L:SER169
|
4.7
|
19.4
|
1.0
|
|
CA
|
J:LEU97
|
4.7
|
20.3
|
1.0
|
|
CG2
|
L:THR168
|
4.7
|
20.6
|
1.0
|
|
CA
|
L:ASP172
|
4.8
|
20.0
|
1.0
|
|
CA
|
L:VAL171
|
4.8
|
18.1
|
1.0
|
|
N
|
L:ALA173
|
4.9
|
19.6
|
1.0
|
|
CB
|
L:PHE170
|
4.9
|
18.3
|
1.0
|
|
C
|
L:ASP172
|
5.0
|
20.3
|
1.0
|
|
Calcium binding site 7 out
of 8 in 4dl1
Go back to
Calcium Binding Sites List in 4dl1
Calcium binding site 7 out
of 8 in the Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:Ca609
b:21.4
occ:1.00
|
O
|
M:ASP96
|
2.4
|
22.1
|
1.0
|
|
O
|
O:PHE170
|
2.4
|
17.6
|
1.0
|
|
OG1
|
O:THR168
|
2.4
|
21.2
|
1.0
|
|
OG
|
O:SER174
|
2.4
|
19.5
|
1.0
|
|
O
|
O:THR168
|
2.4
|
20.4
|
1.0
|
|
OD1
|
M:ASP96
|
2.4
|
25.5
|
1.0
|
|
OD1
|
O:ASP172
|
2.4
|
14.6
|
1.0
|
|
C
|
O:THR168
|
3.3
|
21.3
|
1.0
|
|
CG
|
O:ASP172
|
3.4
|
18.4
|
1.0
|
|
C
|
M:ASP96
|
3.5
|
24.5
|
1.0
|
|
CB
|
O:SER174
|
3.5
|
19.8
|
1.0
|
|
CG
|
M:ASP96
|
3.5
|
26.4
|
1.0
|
|
C
|
O:PHE170
|
3.6
|
19.2
|
1.0
|
|
CB
|
O:THR168
|
3.6
|
21.3
|
1.0
|
|
OD2
|
O:ASP172
|
3.8
|
25.0
|
1.0
|
|
CA
|
O:THR168
|
3.9
|
20.2
|
1.0
|
|
N
|
O:PHE170
|
4.0
|
19.9
|
1.0
|
|
C
|
O:SER169
|
4.1
|
20.0
|
1.0
|
|
N
|
O:ASP172
|
4.1
|
19.1
|
1.0
|
|
CA
|
M:ASP96
|
4.1
|
23.4
|
1.0
|
|
N
|
O:THR168
|
4.2
|
20.5
|
1.0
|
|
O
|
O:SER169
|
4.2
|
20.2
|
1.0
|
|
N
|
O:SER174
|
4.2
|
19.5
|
1.0
|
|
CB
|
M:ASP96
|
4.3
|
23.5
|
1.0
|
|
N
|
O:SER169
|
4.3
|
20.7
|
1.0
|
|
CA
|
O:PHE170
|
4.3
|
21.6
|
1.0
|
|
OD2
|
M:ASP96
|
4.4
|
21.8
|
1.0
|
|
CA
|
O:SER174
|
4.5
|
18.9
|
1.0
|
|
N
|
M:LEU97
|
4.5
|
22.0
|
1.0
|
|
CB
|
O:ASP172
|
4.6
|
20.6
|
1.0
|
|
N
|
O:VAL171
|
4.6
|
21.4
|
1.0
|
|
CA
|
O:SER169
|
4.6
|
20.1
|
1.0
|
|
O
|
M:HOH1754
|
4.6
|
12.8
|
1.0
|
|
CA
|
M:LEU97
|
4.7
|
21.1
|
1.0
|
|
CA
|
O:VAL171
|
4.7
|
20.5
|
1.0
|
|
CA
|
O:ASP172
|
4.8
|
18.6
|
1.0
|
|
CG2
|
O:THR168
|
4.8
|
19.1
|
1.0
|
|
C
|
O:VAL171
|
4.9
|
20.6
|
1.0
|
|
CB
|
O:PHE170
|
4.9
|
20.8
|
1.0
|
|
N
|
O:ALA173
|
4.9
|
17.9
|
1.0
|
|
C
|
O:ASP172
|
5.0
|
20.0
|
1.0
|
|
Calcium binding site 8 out
of 8 in 4dl1
Go back to
Calcium Binding Sites List in 4dl1
Calcium binding site 8 out
of 8 in the Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Ca601
b:19.8
occ:1.00
|
O
|
N:ASP96
|
2.4
|
18.9
|
1.0
|
|
O
|
P:PHE170
|
2.4
|
19.0
|
1.0
|
|
O
|
P:THR168
|
2.4
|
18.7
|
1.0
|
|
OG1
|
P:THR168
|
2.4
|
20.6
|
1.0
|
|
OD1
|
P:ASP172
|
2.4
|
16.9
|
1.0
|
|
OG
|
P:SER174
|
2.4
|
19.4
|
1.0
|
|
OD1
|
N:ASP96
|
2.5
|
22.1
|
1.0
|
|
C
|
P:THR168
|
3.3
|
19.4
|
1.0
|
|
CB
|
P:SER174
|
3.4
|
16.9
|
1.0
|
|
CG
|
P:ASP172
|
3.4
|
18.0
|
1.0
|
|
C
|
N:ASP96
|
3.4
|
19.8
|
1.0
|
|
CG
|
N:ASP96
|
3.6
|
22.9
|
1.0
|
|
C
|
P:PHE170
|
3.6
|
17.4
|
1.0
|
|
CB
|
P:THR168
|
3.7
|
20.1
|
1.0
|
|
OD2
|
P:ASP172
|
3.8
|
20.8
|
1.0
|
|
CA
|
P:THR168
|
3.9
|
19.6
|
1.0
|
|
N
|
P:PHE170
|
4.0
|
18.9
|
1.0
|
|
CA
|
N:ASP96
|
4.0
|
20.1
|
1.0
|
|
C
|
P:SER169
|
4.1
|
18.5
|
1.0
|
|
N
|
P:SER174
|
4.1
|
17.2
|
1.0
|
|
N
|
P:THR168
|
4.2
|
21.1
|
1.0
|
|
N
|
P:ASP172
|
4.2
|
19.7
|
1.0
|
|
CB
|
N:ASP96
|
4.2
|
21.9
|
1.0
|
|
N
|
P:SER169
|
4.3
|
18.5
|
1.0
|
|
CA
|
P:PHE170
|
4.3
|
18.4
|
1.0
|
|
CA
|
P:SER174
|
4.3
|
17.1
|
1.0
|
|
O
|
P:SER169
|
4.4
|
17.4
|
1.0
|
|
N
|
N:LEU97
|
4.5
|
20.5
|
1.0
|
|
O
|
P:HOH856
|
4.6
|
2.9
|
1.0
|
|
OD2
|
N:ASP96
|
4.6
|
21.8
|
1.0
|
|
CA
|
P:SER169
|
4.6
|
18.0
|
1.0
|
|
N
|
P:VAL171
|
4.6
|
16.4
|
1.0
|
|
CB
|
P:ASP172
|
4.7
|
20.8
|
1.0
|
|
CA
|
N:LEU97
|
4.8
|
19.7
|
1.0
|
|
CG2
|
P:THR168
|
4.8
|
16.9
|
1.0
|
|
CA
|
P:VAL171
|
4.8
|
18.1
|
1.0
|
|
CA
|
P:ASP172
|
4.9
|
20.5
|
1.0
|
|
CB
|
P:PHE170
|
5.0
|
16.7
|
1.0
|
|
Reference:
K.F.Geoghegan,
A.H.Varghese,
X.Feng,
A.J.Bessire,
J.J.Conboy,
R.B.Ruggeri,
K.Ahn,
S.N.Spath,
S.V.Filippov,
S.J.Conrad,
P.A.Carpino,
C.R.Guimaraes,
F.F.Vajdos.
Deconstruction of Activity-Dependent Covalent Modification of Heme in Human Neutrophil Myeloperoxidase By Multistage Mass Spectrometry (Ms(4)). Biochemistry V. 51 2065 2012.
ISSN: ISSN 0006-2960
PubMed: 22352991
DOI: 10.1021/BI201872J
Page generated: Tue Jul 8 19:29:31 2025
|
