Chlorine in PDB 5mfa: Crystal Structure of Human Promyeloperoxidase (Prompo)
Enzymatic activity of Crystal Structure of Human Promyeloperoxidase (Prompo)
All present enzymatic activity of Crystal Structure of Human Promyeloperoxidase (Prompo):
1.11.2.2;
Protein crystallography data
The structure of Crystal Structure of Human Promyeloperoxidase (Prompo), PDB code: 5mfa
was solved by
I.Grishkovskaya,
P.G.Furtmueller,
C.Obinger,
K.Djinovic-Carugo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
44.68 /
1.20
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
106.152,
109.151,
83.961,
90.00,
122.66,
90.00
|
R / Rfree (%)
|
12.3 /
14.3
|
Other elements in 5mfa:
The structure of Crystal Structure of Human Promyeloperoxidase (Prompo) also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Crystal Structure of Human Promyeloperoxidase (Prompo)
(pdb code 5mfa). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the
Crystal Structure of Human Promyeloperoxidase (Prompo), PDB code: 5mfa:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
Chlorine binding site 1 out
of 5 in 5mfa
Go back to
Chlorine Binding Sites List in 5mfa
Chlorine binding site 1 out
of 5 in the Crystal Structure of Human Promyeloperoxidase (Prompo)
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Crystal Structure of Human Promyeloperoxidase (Prompo) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl814
b:11.6
occ:1.00
|
H
|
A:TRP198
|
2.4
|
14.4
|
1.0
|
H
|
A:VAL493
|
2.5
|
11.3
|
1.0
|
HA
|
A:ARG197
|
2.8
|
14.8
|
1.0
|
HH2
|
A:TRP602
|
2.9
|
14.6
|
1.0
|
HB3
|
A:ASN492
|
2.9
|
13.6
|
1.0
|
HB
|
A:VAL493
|
3.1
|
12.2
|
1.0
|
O
|
A:HOH1202
|
3.2
|
14.1
|
1.0
|
N
|
A:TRP198
|
3.2
|
12.0
|
1.0
|
HG12
|
A:VAL493
|
3.2
|
13.5
|
1.0
|
N
|
A:VAL493
|
3.3
|
9.4
|
1.0
|
H
|
A:LEU199
|
3.4
|
14.9
|
1.0
|
H
|
A:ASN492
|
3.4
|
12.4
|
1.0
|
HB2
|
A:TRP198
|
3.4
|
15.2
|
1.0
|
HB1
|
A:ALA491
|
3.4
|
13.4
|
1.0
|
HZ2
|
A:TRP602
|
3.5
|
13.8
|
1.0
|
CH2
|
A:TRP602
|
3.7
|
12.2
|
1.0
|
CA
|
A:ARG197
|
3.7
|
12.4
|
1.0
|
CB
|
A:ASN492
|
3.7
|
11.4
|
1.0
|
N
|
A:ASN492
|
3.7
|
10.3
|
1.0
|
CB
|
A:VAL493
|
3.8
|
10.2
|
1.0
|
HD22
|
A:LEU596
|
3.8
|
15.1
|
1.0
|
HG2
|
A:ARG197
|
3.8
|
21.8
|
1.0
|
HB2
|
A:ASN492
|
3.9
|
13.6
|
1.0
|
CG1
|
A:VAL493
|
3.9
|
11.2
|
1.0
|
C
|
A:ARG197
|
3.9
|
12.5
|
1.0
|
CZ2
|
A:TRP602
|
3.9
|
11.5
|
1.0
|
CA
|
A:ASN492
|
4.0
|
10.3
|
1.0
|
O
|
A:VAL196
|
4.0
|
12.0
|
1.0
|
HB3
|
A:ARG197
|
4.1
|
18.5
|
1.0
|
C
|
A:ASN492
|
4.1
|
9.8
|
1.0
|
HD21
|
A:LEU596
|
4.1
|
15.1
|
1.0
|
CA
|
A:VAL493
|
4.1
|
9.6
|
1.0
|
HG11
|
A:VAL493
|
4.1
|
13.5
|
1.0
|
N
|
A:LEU199
|
4.1
|
12.4
|
1.0
|
CA
|
A:TRP198
|
4.1
|
12.4
|
1.0
|
CB
|
A:TRP198
|
4.1
|
12.7
|
1.0
|
HD23
|
A:LEU596
|
4.2
|
15.1
|
1.0
|
CD2
|
A:LEU596
|
4.2
|
12.5
|
1.0
|
HH11
|
A:ARG197
|
4.2
|
16.9
|
1.0
|
CB
|
A:ARG197
|
4.3
|
15.4
|
1.0
|
CB
|
A:ALA491
|
4.4
|
11.2
|
1.0
|
HA
|
A:VAL493
|
4.5
|
11.5
|
1.0
|
CG
|
A:ARG197
|
4.5
|
18.1
|
1.0
|
C
|
A:ALA491
|
4.5
|
9.7
|
1.0
|
HD3
|
A:ARG197
|
4.5
|
22.4
|
1.0
|
O
|
A:LEU199
|
4.5
|
13.9
|
1.0
|
C
|
A:TRP198
|
4.6
|
13.2
|
1.0
|
N
|
A:ARG197
|
4.7
|
12.2
|
1.0
|
HA
|
A:ALA491
|
4.7
|
12.1
|
1.0
|
HG13
|
A:VAL493
|
4.7
|
13.5
|
1.0
|
CG
|
A:TRP198
|
4.8
|
12.4
|
1.0
|
HB2
|
A:LEU199
|
4.8
|
16.4
|
1.0
|
HB3
|
A:ALA491
|
4.8
|
13.4
|
1.0
|
C
|
A:VAL196
|
4.8
|
11.4
|
1.0
|
CZ3
|
A:TRP602
|
4.8
|
11.4
|
1.0
|
CA
|
A:ALA491
|
4.8
|
10.1
|
1.0
|
HB3
|
A:TRP198
|
4.9
|
15.2
|
1.0
|
CG
|
A:ASN492
|
4.9
|
11.3
|
1.0
|
NH1
|
A:ARG197
|
4.9
|
14.1
|
1.0
|
HB2
|
A:ALA491
|
4.9
|
13.4
|
1.0
|
HA
|
A:TRP198
|
5.0
|
14.8
|
1.0
|
HA
|
A:ASN492
|
5.0
|
12.4
|
1.0
|
HZ3
|
A:TRP602
|
5.0
|
13.7
|
1.0
|
|
Chlorine binding site 2 out
of 5 in 5mfa
Go back to
Chlorine Binding Sites List in 5mfa
Chlorine binding site 2 out
of 5 in the Crystal Structure of Human Promyeloperoxidase (Prompo)
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Crystal Structure of Human Promyeloperoxidase (Prompo) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl815
b:38.1
occ:1.00
|
HD21
|
A:ASN623
|
2.4
|
20.9
|
1.0
|
HB3
|
A:ASN561
|
2.8
|
19.8
|
1.0
|
O
|
A:HOH925
|
3.0
|
41.5
|
1.0
|
HD3
|
A:LYS625
|
3.2
|
36.5
|
1.0
|
ND2
|
A:ASN623
|
3.3
|
17.5
|
1.0
|
O
|
A:HOH1433
|
3.4
|
42.6
|
1.0
|
CB
|
A:ASN561
|
3.8
|
16.5
|
1.0
|
HB3
|
A:LYS625
|
3.8
|
26.7
|
1.0
|
HD22
|
A:ASN623
|
3.8
|
20.9
|
1.0
|
OD1
|
A:ASN623
|
4.0
|
17.8
|
1.0
|
CG
|
A:ASN623
|
4.1
|
17.2
|
1.0
|
O
|
A:HOH1327
|
4.1
|
46.0
|
1.0
|
CD
|
A:LYS625
|
4.1
|
30.4
|
1.0
|
HB2
|
A:LEU626
|
4.2
|
18.5
|
1.0
|
HB2
|
A:GLN560
|
4.2
|
16.2
|
1.0
|
O
|
A:HOH1387
|
4.3
|
50.5
|
1.0
|
HB2
|
A:ASN561
|
4.3
|
19.8
|
1.0
|
CG
|
A:ASN561
|
4.3
|
18.6
|
1.0
|
HB3
|
A:GLN560
|
4.3
|
16.2
|
1.0
|
HG2
|
A:LYS625
|
4.4
|
31.4
|
1.0
|
HZ1
|
A:LYS629
|
4.4
|
34.9
|
0.5
|
HD22
|
A:ASN561
|
4.4
|
26.7
|
1.0
|
N
|
A:ASN561
|
4.4
|
13.3
|
1.0
|
HE2
|
A:LYS625
|
4.5
|
41.0
|
1.0
|
CA
|
A:ASN561
|
4.5
|
14.0
|
1.0
|
ND2
|
A:ASN561
|
4.6
|
22.3
|
1.0
|
H
|
A:ASN561
|
4.6
|
15.9
|
1.0
|
HZ3
|
A:LYS629
|
4.6
|
34.9
|
0.5
|
C
|
A:GLN560
|
4.6
|
13.6
|
1.0
|
HA
|
A:ASN561
|
4.6
|
16.8
|
1.0
|
CB
|
A:LYS625
|
4.6
|
22.2
|
1.0
|
CG
|
A:LYS625
|
4.6
|
26.2
|
1.0
|
H
|
A:LEU626
|
4.6
|
20.1
|
1.0
|
HD2
|
A:LYS625
|
4.7
|
36.5
|
1.0
|
CB
|
A:GLN560
|
4.7
|
13.5
|
1.0
|
HZ3
|
A:LYS625
|
4.7
|
44.1
|
1.0
|
O
|
A:GLN560
|
4.7
|
14.9
|
1.0
|
CE
|
A:LYS625
|
4.9
|
34.2
|
1.0
|
NZ
|
A:LYS629
|
4.9
|
29.1
|
0.5
|
OD1
|
A:ASN561
|
4.9
|
19.1
|
1.0
|
N
|
A:LEU626
|
5.0
|
16.8
|
1.0
|
|
Chlorine binding site 3 out
of 5 in 5mfa
Go back to
Chlorine Binding Sites List in 5mfa
Chlorine binding site 3 out
of 5 in the Crystal Structure of Human Promyeloperoxidase (Prompo)
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Crystal Structure of Human Promyeloperoxidase (Prompo) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl816
b:25.8
occ:0.78
|
HH22
|
A:ARG327
|
2.3
|
21.4
|
0.6
|
HH12
|
A:ARG327
|
2.5
|
19.5
|
0.4
|
HH22
|
A:ARG327
|
2.7
|
21.2
|
0.4
|
HA
|
A:PRO290
|
2.8
|
27.7
|
1.0
|
NH2
|
A:ARG327
|
2.9
|
17.9
|
0.6
|
HD3
|
A:ARG314
|
3.0
|
18.7
|
1.0
|
HH12
|
A:ARG327
|
3.1
|
22.4
|
0.6
|
HB2
|
A:ARG314
|
3.2
|
16.6
|
1.0
|
NH1
|
A:ARG327
|
3.3
|
16.2
|
0.4
|
O
|
A:HOH1358
|
3.3
|
21.9
|
1.0
|
HB3
|
A:PRO289
|
3.3
|
34.1
|
1.0
|
HH21
|
A:ARG327
|
3.4
|
21.4
|
0.6
|
NH2
|
A:ARG327
|
3.4
|
17.7
|
0.4
|
HB3
|
A:PRO290
|
3.5
|
29.4
|
1.0
|
NH1
|
A:ARG327
|
3.6
|
18.7
|
0.6
|
CZ
|
A:ARG327
|
3.7
|
17.6
|
0.6
|
CA
|
A:PRO290
|
3.7
|
23.1
|
1.0
|
O
|
A:HOH1333
|
3.8
|
32.1
|
1.0
|
CZ
|
A:ARG327
|
3.8
|
17.3
|
0.4
|
CB
|
A:PRO290
|
3.9
|
24.5
|
1.0
|
CD
|
A:ARG314
|
3.9
|
15.6
|
1.0
|
HH11
|
A:ARG327
|
3.9
|
19.5
|
0.4
|
CB
|
A:ARG314
|
4.0
|
13.8
|
1.0
|
HB3
|
A:ARG314
|
4.0
|
16.6
|
1.0
|
HB2
|
A:PRO290
|
4.0
|
29.4
|
1.0
|
O
|
A:HOH1302
|
4.1
|
34.5
|
1.0
|
HH11
|
A:ARG314
|
4.1
|
17.9
|
1.0
|
HH21
|
A:ARG327
|
4.2
|
21.2
|
0.4
|
HD3
|
A:PRO317
|
4.2
|
21.4
|
1.0
|
HA
|
A:PRO289
|
4.2
|
31.6
|
1.0
|
CB
|
A:PRO289
|
4.3
|
28.4
|
1.0
|
CG
|
A:ARG314
|
4.3
|
15.2
|
1.0
|
HG3
|
A:ARG314
|
4.4
|
18.3
|
1.0
|
HH11
|
A:ARG327
|
4.4
|
22.4
|
0.6
|
HD2
|
A:ARG314
|
4.5
|
18.7
|
1.0
|
C
|
A:PRO290
|
4.6
|
20.3
|
1.0
|
O
|
A:PRO290
|
4.6
|
22.3
|
1.0
|
O
|
A:HOH1479
|
4.6
|
31.8
|
1.0
|
NH1
|
A:ARG314
|
4.6
|
14.9
|
1.0
|
NE
|
A:ARG314
|
4.6
|
14.8
|
1.0
|
CA
|
A:PRO289
|
4.7
|
26.3
|
1.0
|
N
|
A:PRO290
|
4.7
|
25.1
|
1.0
|
HB2
|
A:PRO289
|
4.7
|
34.1
|
1.0
|
NE
|
A:ARG327
|
4.9
|
17.9
|
0.6
|
HG3
|
A:PRO317
|
4.9
|
23.6
|
1.0
|
HG3
|
A:PRO289
|
4.9
|
34.0
|
1.0
|
CZ
|
A:ARG314
|
4.9
|
14.3
|
1.0
|
|
Chlorine binding site 4 out
of 5 in 5mfa
Go back to
Chlorine Binding Sites List in 5mfa
Chlorine binding site 4 out
of 5 in the Crystal Structure of Human Promyeloperoxidase (Prompo)
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Crystal Structure of Human Promyeloperoxidase (Prompo) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl817
b:22.3
occ:0.89
|
H
|
A:GLN367
|
2.5
|
24.2
|
1.0
|
H
|
A:PHE379
|
2.5
|
18.5
|
1.0
|
HA
|
A:ASN366
|
2.8
|
20.3
|
1.0
|
HA
|
A:PRO378
|
3.1
|
18.7
|
1.0
|
N
|
A:GLN367
|
3.3
|
20.2
|
1.0
|
N
|
A:PHE379
|
3.4
|
15.4
|
1.0
|
HB2
|
A:PHE379
|
3.5
|
21.0
|
1.0
|
HB3
|
A:PRO378
|
3.6
|
19.8
|
1.0
|
HB2
|
A:GLN367
|
3.6
|
29.7
|
1.0
|
HD2
|
A:PHE379
|
3.7
|
20.7
|
1.0
|
CA
|
A:ASN366
|
3.7
|
16.9
|
1.0
|
CG
|
A:ASN366
|
3.8
|
17.5
|
1.0
|
CA
|
A:PRO378
|
3.8
|
15.6
|
1.0
|
ND2
|
A:ASN366
|
3.8
|
17.3
|
1.0
|
HG2
|
A:GLN367
|
3.9
|
32.0
|
1.0
|
OD1
|
A:ASN366
|
3.9
|
18.5
|
1.0
|
HD21
|
A:ASN366
|
3.9
|
20.8
|
1.0
|
O
|
A:HOH1185
|
4.0
|
31.9
|
1.0
|
C
|
A:ASN366
|
4.0
|
18.7
|
1.0
|
H
|
A:ARG368
|
4.1
|
27.1
|
1.0
|
C
|
A:PRO378
|
4.1
|
14.8
|
1.0
|
CD2
|
A:PHE379
|
4.1
|
17.3
|
1.0
|
HD22
|
A:ASN366
|
4.1
|
20.8
|
1.0
|
CB
|
A:PRO378
|
4.2
|
16.5
|
1.0
|
CB
|
A:PHE379
|
4.2
|
17.5
|
1.0
|
CB
|
A:GLN367
|
4.3
|
24.8
|
1.0
|
CA
|
A:GLN367
|
4.3
|
22.2
|
1.0
|
CB
|
A:ASN366
|
4.3
|
17.2
|
1.0
|
CA
|
A:PHE379
|
4.4
|
16.5
|
1.0
|
CG
|
A:PHE379
|
4.4
|
17.0
|
1.0
|
CG
|
A:GLN367
|
4.5
|
26.7
|
1.0
|
O
|
A:VAL365
|
4.5
|
18.7
|
1.0
|
HB2
|
A:PRO378
|
4.5
|
19.8
|
1.0
|
HG3
|
A:ARG368
|
4.6
|
35.1
|
1.0
|
N
|
A:ARG368
|
4.7
|
22.6
|
1.0
|
HD3
|
A:ARG368
|
4.7
|
38.7
|
1.0
|
N
|
A:ASN366
|
4.7
|
16.5
|
1.0
|
HG3
|
A:GLN367
|
4.8
|
32.0
|
1.0
|
HB2
|
A:ASN366
|
4.8
|
20.6
|
1.0
|
O
|
A:PHE379
|
4.8
|
17.7
|
1.0
|
HB2
|
A:ARG368
|
4.8
|
30.6
|
1.0
|
C
|
A:GLN367
|
5.0
|
23.1
|
1.0
|
CE2
|
A:PHE379
|
5.0
|
17.6
|
1.0
|
|
Chlorine binding site 5 out
of 5 in 5mfa
Go back to
Chlorine Binding Sites List in 5mfa
Chlorine binding site 5 out
of 5 in the Crystal Structure of Human Promyeloperoxidase (Prompo)
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Crystal Structure of Human Promyeloperoxidase (Prompo) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl818
b:20.8
occ:1.00
|
HE
|
A:ARG548
|
2.4
|
20.7
|
1.0
|
H
|
A:THR710
|
2.5
|
23.1
|
1.0
|
HH21
|
A:ARG548
|
2.6
|
21.9
|
1.0
|
HA
|
A:ILE709
|
2.9
|
20.9
|
1.0
|
HG23
|
A:ILE709
|
2.9
|
21.0
|
1.0
|
O
|
A:HOH949
|
2.9
|
42.5
|
1.0
|
H
|
A:THR711
|
3.0
|
22.8
|
1.0
|
O
|
A:HOH950
|
3.2
|
40.1
|
1.0
|
NE
|
A:ARG548
|
3.2
|
17.2
|
1.0
|
HE1
|
A:TYR516
|
3.3
|
19.2
|
1.0
|
N
|
A:THR710
|
3.3
|
19.3
|
1.0
|
NH2
|
A:ARG548
|
3.3
|
18.3
|
1.0
|
HB
|
A:THR711
|
3.7
|
26.8
|
1.0
|
HA
|
A:ASN514
|
3.7
|
25.4
|
1.0
|
CA
|
A:ILE709
|
3.7
|
17.4
|
1.0
|
CG2
|
A:ILE709
|
3.7
|
17.5
|
1.0
|
N
|
A:THR711
|
3.7
|
19.0
|
1.0
|
CZ
|
A:ARG548
|
3.8
|
17.4
|
1.0
|
HG12
|
A:ILE709
|
3.9
|
18.9
|
1.0
|
HG1
|
A:THR710
|
3.9
|
27.2
|
1.0
|
O
|
A:HOH947
|
3.9
|
28.4
|
1.0
|
HG22
|
A:ILE709
|
4.0
|
21.0
|
1.0
|
C
|
A:ILE709
|
4.0
|
18.4
|
1.0
|
CE1
|
A:TYR516
|
4.0
|
16.0
|
1.0
|
HB2
|
A:ASN514
|
4.0
|
27.8
|
1.0
|
HH22
|
A:ARG548
|
4.1
|
21.9
|
1.0
|
OG1
|
A:THR710
|
4.1
|
22.6
|
1.0
|
CB
|
A:ILE709
|
4.2
|
16.0
|
1.0
|
O
|
A:THR711
|
4.3
|
17.4
|
1.0
|
HD3
|
A:ARG548
|
4.3
|
19.6
|
1.0
|
CA
|
A:THR710
|
4.3
|
20.0
|
1.0
|
CD
|
A:ARG548
|
4.4
|
16.4
|
1.0
|
HD1
|
A:TYR516
|
4.4
|
19.9
|
1.0
|
HH
|
A:TYR516
|
4.4
|
19.3
|
1.0
|
O
|
A:ASN514
|
4.4
|
22.7
|
1.0
|
HG1
|
A:THR711
|
4.4
|
30.8
|
1.0
|
CB
|
A:THR711
|
4.4
|
22.4
|
1.0
|
HG21
|
A:ILE709
|
4.4
|
21.0
|
1.0
|
C
|
A:THR710
|
4.5
|
19.5
|
1.0
|
CA
|
A:ASN514
|
4.5
|
21.2
|
1.0
|
CG1
|
A:ILE709
|
4.5
|
15.8
|
1.0
|
O
|
A:GLY708
|
4.6
|
21.3
|
1.0
|
CD1
|
A:TYR516
|
4.6
|
16.5
|
1.0
|
CA
|
A:THR711
|
4.6
|
19.3
|
1.0
|
CB
|
A:ASN514
|
4.6
|
23.1
|
1.0
|
HG2
|
A:ARG548
|
4.7
|
18.5
|
1.0
|
HB3
|
A:ASN514
|
4.8
|
27.8
|
1.0
|
C
|
A:ASN514
|
4.8
|
21.3
|
1.0
|
CB
|
A:THR710
|
4.8
|
21.4
|
1.0
|
N
|
A:ILE709
|
4.9
|
17.9
|
1.0
|
OG1
|
A:THR711
|
4.9
|
25.6
|
1.0
|
CZ
|
A:TYR516
|
4.9
|
15.6
|
1.0
|
C
|
A:THR711
|
4.9
|
17.3
|
1.0
|
HG13
|
A:ILE709
|
5.0
|
18.9
|
1.0
|
OH
|
A:TYR516
|
5.0
|
16.1
|
1.0
|
|
Reference:
I.Grishkovskaya,
M.Paumann-Page,
R.Tscheliessnig,
J.Stampler,
S.Hofbauer,
M.Soudi,
B.Sevcnikar,
C.Oostenbrink,
P.G.Furtmuller,
K.Djinovic-Carugo,
W.M.Nauseef,
C.Obinger.
Structure of Human Promyeloperoxidase (Prompo) and the Role of the Propeptide in Processing and Maturation. J. Biol. Chem. V. 292 8244 2017.
ISSN: ESSN 1083-351X
PubMed: 28348079
DOI: 10.1074/JBC.M117.775031
Page generated: Fri Jul 26 12:38:29 2024
|