Manganese in PDB 6h2q: Crystal Structure of ARG184GLN Mutant of Human Prolidase with Mn Ions and Leupro Ligand
Enzymatic activity of Crystal Structure of ARG184GLN Mutant of Human Prolidase with Mn Ions and Leupro Ligand
All present enzymatic activity of Crystal Structure of ARG184GLN Mutant of Human Prolidase with Mn Ions and Leupro Ligand:
3.4.13.9;
Protein crystallography data
The structure of Crystal Structure of ARG184GLN Mutant of Human Prolidase with Mn Ions and Leupro Ligand, PDB code: 6h2q
was solved by
P.Wilk,
R.Piwowarczyk,
M.S.Weiss,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
46.75 /
1.78
|
|
Space group
|
C 2 2 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
103.559,
106.661,
217.432,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
15.3 /
17.9
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Crystal Structure of ARG184GLN Mutant of Human Prolidase with Mn Ions and Leupro Ligand
(pdb code 6h2q). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the
Crystal Structure of ARG184GLN Mutant of Human Prolidase with Mn Ions and Leupro Ligand, PDB code: 6h2q:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 6h2q
Go back to
Manganese Binding Sites List in 6h2q
Manganese binding site 1 out
of 4 in the Crystal Structure of ARG184GLN Mutant of Human Prolidase with Mn Ions and Leupro Ligand
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Crystal Structure of ARG184GLN Mutant of Human Prolidase with Mn Ions and Leupro Ligand within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn499
b:18.2
occ:1.00
|
OE2
|
A:GLU452
|
2.1
|
18.6
|
1.0
|
|
OE2
|
A:GLU412
|
2.2
|
20.0
|
1.0
|
|
NE2
|
A:HIS370
|
2.2
|
19.5
|
1.0
|
|
OD2
|
A:ASP287
|
2.2
|
18.3
|
1.0
|
|
O
|
A:LEU506
|
2.3
|
34.5
|
1.0
|
|
C
|
A:LEU506
|
2.9
|
34.3
|
1.0
|
|
HG21
|
A:THR410
|
2.9
|
22.6
|
1.0
|
|
OXT
|
A:LEU506
|
3.0
|
34.6
|
1.0
|
|
CD
|
A:GLU412
|
3.0
|
20.0
|
1.0
|
|
HG1
|
A:THR410
|
3.0
|
23.2
|
1.0
|
|
OE1
|
A:GLU412
|
3.1
|
19.3
|
1.0
|
|
CG
|
A:ASP287
|
3.1
|
18.3
|
1.0
|
|
CD
|
A:GLU452
|
3.1
|
18.6
|
1.0
|
|
CD2
|
A:HIS370
|
3.2
|
19.8
|
1.0
|
|
CE1
|
A:HIS370
|
3.2
|
19.5
|
1.0
|
|
MN
|
A:MN500
|
3.3
|
18.8
|
1.0
|
|
HD2
|
A:HIS370
|
3.3
|
23.8
|
1.0
|
|
HE1
|
A:HIS370
|
3.4
|
23.4
|
1.0
|
|
HA
|
A:PRO507
|
3.4
|
44.3
|
1.0
|
|
OD1
|
A:ASP287
|
3.5
|
18.3
|
1.0
|
|
OE1
|
A:GLU452
|
3.6
|
18.5
|
1.0
|
|
H3
|
A:LEU506
|
3.7
|
41.2
|
1.0
|
|
OG1
|
A:THR410
|
3.8
|
19.3
|
1.0
|
|
CG2
|
A:THR410
|
3.8
|
18.9
|
1.0
|
|
HB
|
A:THR410
|
3.9
|
22.9
|
1.0
|
|
CB
|
A:THR410
|
4.1
|
19.1
|
1.0
|
|
HE2
|
A:HIS377
|
4.1
|
23.7
|
1.0
|
|
CA
|
A:LEU506
|
4.2
|
34.2
|
1.0
|
|
CA
|
A:PRO507
|
4.3
|
36.9
|
1.0
|
|
ND1
|
A:HIS370
|
4.3
|
19.9
|
1.0
|
|
CG
|
A:HIS370
|
4.3
|
20.1
|
1.0
|
|
HG23
|
A:THR410
|
4.3
|
22.6
|
1.0
|
|
CG
|
A:GLU412
|
4.3
|
19.6
|
1.0
|
|
N
|
A:PRO507
|
4.3
|
37.1
|
1.0
|
|
HB3
|
A:ASP287
|
4.4
|
21.9
|
1.0
|
|
N
|
A:LEU506
|
4.4
|
34.3
|
1.0
|
|
HG22
|
A:THR410
|
4.4
|
22.6
|
1.0
|
|
HG22
|
A:VAL376
|
4.4
|
22.8
|
1.0
|
|
CB
|
A:ASP287
|
4.4
|
18.3
|
1.0
|
|
HG3
|
A:GLU452
|
4.4
|
22.6
|
1.0
|
|
CG
|
A:GLU452
|
4.4
|
18.8
|
1.0
|
|
HG2
|
A:GLU412
|
4.5
|
23.5
|
1.0
|
|
HD2
|
A:HIS377
|
4.5
|
23.8
|
1.0
|
|
HB3
|
A:GLU412
|
4.5
|
23.8
|
1.0
|
|
HB2
|
A:LEU506
|
4.7
|
41.2
|
1.0
|
|
HG23
|
A:VAL376
|
4.8
|
22.8
|
1.0
|
|
HB2
|
A:ASP287
|
4.8
|
21.9
|
1.0
|
|
NE2
|
A:HIS377
|
4.8
|
19.8
|
1.0
|
|
HG21
|
A:VAL376
|
4.8
|
22.8
|
1.0
|
|
HA
|
A:LEU506
|
4.8
|
41.0
|
1.0
|
|
H1
|
A:LEU506
|
4.8
|
41.2
|
1.0
|
|
CG2
|
A:VAL376
|
4.9
|
19.0
|
1.0
|
|
HG2
|
A:GLU452
|
4.9
|
22.6
|
1.0
|
|
HB3
|
A:LEU506
|
4.9
|
41.2
|
1.0
|
|
CB
|
A:LEU506
|
4.9
|
34.4
|
1.0
|
|
CB
|
A:GLU412
|
5.0
|
19.8
|
1.0
|
|
H2
|
A:LEU506
|
5.0
|
41.2
|
1.0
|
|
HG3
|
A:GLU412
|
5.0
|
23.5
|
1.0
|
|
Manganese binding site 2 out
of 4 in 6h2q
Go back to
Manganese Binding Sites List in 6h2q
Manganese binding site 2 out
of 4 in the Crystal Structure of ARG184GLN Mutant of Human Prolidase with Mn Ions and Leupro Ligand
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Crystal Structure of ARG184GLN Mutant of Human Prolidase with Mn Ions and Leupro Ligand within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn500
b:18.8
occ:1.00
|
H3
|
A:LEU506
|
1.8
|
41.2
|
1.0
|
|
OD1
|
A:ASP287
|
2.1
|
18.3
|
1.0
|
|
OE1
|
A:GLU452
|
2.1
|
18.5
|
1.0
|
|
O
|
A:LEU506
|
2.3
|
34.5
|
1.0
|
|
OD1
|
A:ASP276
|
2.3
|
18.6
|
1.0
|
|
OD2
|
A:ASP276
|
2.4
|
18.8
|
1.0
|
|
N
|
A:LEU506
|
2.6
|
34.3
|
1.0
|
|
H2
|
A:LEU506
|
2.6
|
41.2
|
1.0
|
|
CG
|
A:ASP276
|
2.6
|
18.8
|
1.0
|
|
CD
|
A:GLU452
|
3.0
|
18.6
|
1.0
|
|
CG
|
A:ASP287
|
3.0
|
18.3
|
1.0
|
|
C
|
A:LEU506
|
3.1
|
34.3
|
1.0
|
|
OE2
|
A:GLU452
|
3.2
|
18.6
|
1.0
|
|
H1
|
A:LEU506
|
3.2
|
41.2
|
1.0
|
|
HG1
|
A:THR289
|
3.3
|
23.6
|
1.0
|
|
OD2
|
A:ASP287
|
3.3
|
18.3
|
1.0
|
|
CA
|
A:LEU506
|
3.3
|
34.2
|
1.0
|
|
MN
|
A:MN499
|
3.3
|
18.2
|
1.0
|
|
HA
|
A:LEU506
|
3.7
|
41.0
|
1.0
|
|
OG1
|
A:THR289
|
3.7
|
19.7
|
1.0
|
|
HH
|
A:TYR241
|
3.8
|
21.8
|
1.0
|
|
OH
|
A:TYR241
|
3.8
|
18.2
|
1.0
|
|
HE
|
A:ARG450
|
4.0
|
23.4
|
1.0
|
|
OE1
|
A:GLU412
|
4.1
|
19.3
|
1.0
|
|
CZ
|
A:TYR241
|
4.1
|
18.0
|
1.0
|
|
CB
|
A:ASP276
|
4.1
|
19.0
|
1.0
|
|
OXT
|
A:LEU506
|
4.2
|
34.6
|
1.0
|
|
HH21
|
A:ARG450
|
4.2
|
23.4
|
1.0
|
|
CG
|
A:GLU452
|
4.4
|
18.8
|
1.0
|
|
CB
|
A:ASP287
|
4.4
|
18.3
|
1.0
|
|
HD12
|
A:ILE244
|
4.5
|
26.4
|
1.0
|
|
CE2
|
A:TYR241
|
4.5
|
18.1
|
1.0
|
|
HE2
|
A:TYR241
|
4.5
|
21.7
|
1.0
|
|
HB2
|
A:ASP276
|
4.5
|
22.8
|
1.0
|
|
HA
|
A:ASP287
|
4.5
|
22.0
|
1.0
|
|
C
|
A:ASP287
|
4.5
|
18.6
|
1.0
|
|
HB3
|
A:ASP276
|
4.6
|
22.8
|
1.0
|
|
HG2
|
A:GLU452
|
4.6
|
22.6
|
1.0
|
|
N
|
A:ILE288
|
4.6
|
18.6
|
1.0
|
|
H
|
A:ILE288
|
4.6
|
22.3
|
1.0
|
|
HB2
|
A:LEU506
|
4.7
|
41.2
|
1.0
|
|
CB
|
A:LEU506
|
4.7
|
34.4
|
1.0
|
|
HD3
|
A:PRO507
|
4.7
|
43.6
|
1.0
|
|
CE1
|
A:TYR241
|
4.7
|
17.9
|
1.0
|
|
HB3
|
A:GLU452
|
4.7
|
22.6
|
1.0
|
|
CA
|
A:ASP287
|
4.8
|
18.3
|
1.0
|
|
NE
|
A:ARG450
|
4.8
|
19.5
|
1.0
|
|
HA
|
A:ASP276
|
4.8
|
22.8
|
1.0
|
|
HB2
|
A:GLU452
|
4.8
|
22.6
|
1.0
|
|
CD
|
A:GLU412
|
4.8
|
20.0
|
1.0
|
|
O
|
A:ASP287
|
4.8
|
18.7
|
1.0
|
|
HE1
|
A:TYR241
|
4.9
|
21.5
|
1.0
|
|
N
|
A:PRO507
|
4.9
|
37.1
|
1.0
|
|
HB3
|
A:ASP287
|
4.9
|
21.9
|
1.0
|
|
OE2
|
A:GLU412
|
4.9
|
20.0
|
1.0
|
|
O
|
A:ILE288
|
4.9
|
18.9
|
1.0
|
|
CB
|
A:GLU452
|
4.9
|
18.8
|
1.0
|
|
NH2
|
A:ARG450
|
4.9
|
19.5
|
1.0
|
|
C
|
A:ILE288
|
4.9
|
19.0
|
1.0
|
|
CA
|
A:ASP276
|
5.0
|
19.0
|
1.0
|
|
HB2
|
A:ASP287
|
5.0
|
21.9
|
1.0
|
|
Manganese binding site 3 out
of 4 in 6h2q
Go back to
Manganese Binding Sites List in 6h2q
Manganese binding site 3 out
of 4 in the Crystal Structure of ARG184GLN Mutant of Human Prolidase with Mn Ions and Leupro Ligand
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Crystal Structure of ARG184GLN Mutant of Human Prolidase with Mn Ions and Leupro Ligand within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn499
b:18.1
occ:1.00
|
O
|
B:LEU503
|
2.0
|
28.4
|
1.0
|
|
NE2
|
B:HIS370
|
2.1
|
20.4
|
1.0
|
|
OE2
|
B:GLU452
|
2.2
|
19.3
|
1.0
|
|
OD2
|
B:ASP287
|
2.2
|
20.2
|
1.0
|
|
OE2
|
B:GLU412
|
2.3
|
20.4
|
1.0
|
|
C
|
B:LEU503
|
2.7
|
28.4
|
1.0
|
|
OXT
|
B:LEU503
|
2.8
|
32.3
|
1.0
|
|
HG21
|
B:THR410
|
3.0
|
24.9
|
1.0
|
|
CD
|
B:GLU412
|
3.0
|
20.2
|
1.0
|
|
HG1
|
B:THR410
|
3.0
|
25.3
|
1.0
|
|
CG
|
B:ASP287
|
3.1
|
19.7
|
1.0
|
|
CE1
|
B:HIS370
|
3.1
|
20.6
|
1.0
|
|
CD2
|
B:HIS370
|
3.1
|
20.8
|
1.0
|
|
OE1
|
B:GLU412
|
3.2
|
19.9
|
1.0
|
|
HE1
|
B:HIS370
|
3.3
|
24.7
|
1.0
|
|
CD
|
B:GLU452
|
3.3
|
19.2
|
1.0
|
|
HD2
|
B:HIS370
|
3.3
|
25.0
|
1.0
|
|
MN
|
B:MN500
|
3.3
|
16.6
|
1.0
|
|
OD1
|
B:ASP287
|
3.4
|
19.5
|
1.0
|
|
HA
|
B:PRO504
|
3.4
|
42.5
|
1.0
|
|
OE1
|
B:GLU452
|
3.7
|
19.0
|
1.0
|
|
OG1
|
B:THR410
|
3.8
|
21.1
|
1.0
|
|
CG2
|
B:THR410
|
3.8
|
20.7
|
1.0
|
|
HB
|
B:THR410
|
3.8
|
25.1
|
1.0
|
|
H2
|
B:LEU503
|
4.0
|
33.8
|
1.0
|
|
CA
|
B:LEU503
|
4.0
|
28.2
|
1.0
|
|
CB
|
B:THR410
|
4.1
|
21.0
|
1.0
|
|
HE2
|
B:HIS377
|
4.1
|
24.2
|
1.0
|
|
ND1
|
B:HIS370
|
4.2
|
21.1
|
1.0
|
|
CA
|
B:PRO504
|
4.2
|
35.4
|
1.0
|
|
H3
|
B:LEU503
|
4.2
|
33.8
|
1.0
|
|
CG
|
B:HIS370
|
4.2
|
21.2
|
1.0
|
|
N
|
B:LEU503
|
4.3
|
28.2
|
1.0
|
|
N
|
B:PRO504
|
4.3
|
35.9
|
1.0
|
|
HB3
|
B:ASP287
|
4.3
|
23.8
|
1.0
|
|
HG22
|
B:VAL376
|
4.3
|
23.5
|
1.0
|
|
CB
|
B:ASP287
|
4.3
|
19.8
|
1.0
|
|
HB3
|
B:LEU503
|
4.4
|
38.2
|
1.0
|
|
CG
|
B:GLU412
|
4.4
|
20.6
|
1.0
|
|
HG23
|
B:THR410
|
4.4
|
24.9
|
1.0
|
|
HG22
|
B:THR410
|
4.4
|
24.9
|
1.0
|
|
HD2
|
B:HIS377
|
4.5
|
24.5
|
1.0
|
|
HG3
|
B:GLU452
|
4.5
|
23.3
|
1.0
|
|
HG2
|
B:GLU412
|
4.5
|
24.7
|
1.0
|
|
CG
|
B:GLU452
|
4.5
|
19.4
|
1.0
|
|
HB3
|
B:GLU412
|
4.7
|
25.4
|
1.0
|
|
HA
|
B:LEU503
|
4.7
|
33.8
|
1.0
|
|
HB2
|
B:ASP287
|
4.8
|
23.8
|
1.0
|
|
CB
|
B:LEU503
|
4.8
|
31.8
|
1.0
|
|
NE2
|
B:HIS377
|
4.8
|
20.1
|
1.0
|
|
HG23
|
B:VAL376
|
4.8
|
23.5
|
1.0
|
|
CG2
|
B:VAL376
|
4.9
|
19.6
|
1.0
|
|
HG21
|
B:VAL376
|
4.9
|
23.5
|
1.0
|
|
C
|
B:PRO504
|
4.9
|
35.3
|
1.0
|
|
CD2
|
B:HIS377
|
5.0
|
20.4
|
1.0
|
|
HD1
|
B:HIS370
|
5.0
|
25.3
|
1.0
|
|
HG2
|
B:GLU452
|
5.0
|
23.3
|
1.0
|
|
Manganese binding site 4 out
of 4 in 6h2q
Go back to
Manganese Binding Sites List in 6h2q
Manganese binding site 4 out
of 4 in the Crystal Structure of ARG184GLN Mutant of Human Prolidase with Mn Ions and Leupro Ligand
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Crystal Structure of ARG184GLN Mutant of Human Prolidase with Mn Ions and Leupro Ligand within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn500
b:16.6
occ:1.00
|
H2
|
B:LEU503
|
1.6
|
33.8
|
1.0
|
|
OD1
|
B:ASP287
|
2.1
|
19.5
|
1.0
|
|
OD2
|
B:ASP276
|
2.1
|
19.3
|
1.0
|
|
O
|
B:LEU503
|
2.2
|
28.4
|
1.0
|
|
OE1
|
B:GLU452
|
2.2
|
19.0
|
1.0
|
|
OD1
|
B:ASP276
|
2.3
|
19.2
|
1.0
|
|
N
|
B:LEU503
|
2.4
|
28.2
|
1.0
|
|
CG
|
B:ASP276
|
2.6
|
19.2
|
1.0
|
|
H3
|
B:LEU503
|
2.7
|
33.8
|
1.0
|
|
CD
|
B:GLU452
|
3.0
|
19.2
|
1.0
|
|
C
|
B:LEU503
|
3.0
|
28.4
|
1.0
|
|
H1
|
B:LEU503
|
3.0
|
33.8
|
1.0
|
|
CG
|
B:ASP287
|
3.1
|
19.7
|
1.0
|
|
OE2
|
B:GLU452
|
3.1
|
19.3
|
1.0
|
|
CA
|
B:LEU503
|
3.2
|
28.2
|
1.0
|
|
HG1
|
B:THR289
|
3.3
|
23.7
|
1.0
|
|
MN
|
B:MN499
|
3.3
|
18.1
|
1.0
|
|
OD2
|
B:ASP287
|
3.4
|
20.2
|
1.0
|
|
HA
|
B:LEU503
|
3.6
|
33.8
|
1.0
|
|
OG1
|
B:THR289
|
3.7
|
19.8
|
1.0
|
|
HH
|
B:TYR241
|
3.8
|
22.9
|
1.0
|
|
OH
|
B:TYR241
|
3.8
|
19.1
|
1.0
|
|
HE
|
B:ARG450
|
4.0
|
23.0
|
1.0
|
|
CB
|
B:ASP276
|
4.1
|
19.2
|
1.0
|
|
OXT
|
B:LEU503
|
4.1
|
32.3
|
1.0
|
|
CZ
|
B:TYR241
|
4.1
|
18.9
|
1.0
|
|
OE1
|
B:GLU412
|
4.2
|
19.9
|
1.0
|
|
HH21
|
B:ARG450
|
4.3
|
22.7
|
1.0
|
|
CG
|
B:GLU452
|
4.4
|
19.4
|
1.0
|
|
HB2
|
B:ASP276
|
4.4
|
23.1
|
1.0
|
|
CB
|
B:ASP287
|
4.4
|
19.8
|
1.0
|
|
HB3
|
B:ASP276
|
4.5
|
23.1
|
1.0
|
|
HD12
|
B:ILE244
|
4.5
|
29.9
|
1.0
|
|
HE2
|
B:TYR241
|
4.5
|
23.9
|
1.0
|
|
CE2
|
B:TYR241
|
4.5
|
19.9
|
1.0
|
|
CB
|
B:LEU503
|
4.5
|
31.8
|
1.0
|
|
HA
|
B:ASP287
|
4.5
|
23.8
|
1.0
|
|
HB2
|
B:LEU503
|
4.5
|
38.2
|
1.0
|
|
C
|
B:ASP287
|
4.6
|
20.0
|
1.0
|
|
HG2
|
B:GLU452
|
4.7
|
23.3
|
1.0
|
|
H
|
B:ILE288
|
4.7
|
23.8
|
1.0
|
|
N
|
B:ILE288
|
4.7
|
19.8
|
1.0
|
|
N
|
B:PRO504
|
4.7
|
35.9
|
1.0
|
|
HD3
|
B:PRO504
|
4.7
|
42.5
|
1.0
|
|
CE1
|
B:TYR241
|
4.7
|
19.0
|
1.0
|
|
NE
|
B:ARG450
|
4.8
|
19.2
|
1.0
|
|
CA
|
B:ASP287
|
4.8
|
19.8
|
1.0
|
|
HA
|
B:ASP276
|
4.8
|
23.2
|
1.0
|
|
HB3
|
B:GLU452
|
4.8
|
23.3
|
1.0
|
|
HB3
|
B:LEU503
|
4.8
|
38.2
|
1.0
|
|
CD
|
B:GLU412
|
4.8
|
20.2
|
1.0
|
|
HB2
|
B:GLU452
|
4.9
|
23.3
|
1.0
|
|
HE1
|
B:TYR241
|
4.9
|
22.8
|
1.0
|
|
OE2
|
B:GLU412
|
4.9
|
20.4
|
1.0
|
|
CA
|
B:ASP276
|
4.9
|
19.3
|
1.0
|
|
HB3
|
B:ASP287
|
4.9
|
23.8
|
1.0
|
|
O
|
B:ILE288
|
4.9
|
19.7
|
1.0
|
|
O
|
B:ASP287
|
4.9
|
20.2
|
1.0
|
|
NH2
|
B:ARG450
|
5.0
|
18.9
|
1.0
|
|
C
|
B:ILE288
|
5.0
|
19.9
|
1.0
|
|
CB
|
B:GLU452
|
5.0
|
19.4
|
1.0
|
|
HB2
|
B:ASP287
|
5.0
|
23.8
|
1.0
|
|
Reference:
P.Wilk,
M.Uehlein,
R.Piwowarczyk,
H.Dobbek,
U.Mueller,
M.S.Weiss.
Structural Basis For Prolidase Deficiency Disease Mechanisms. Febs J. V. 285 3422 2018.
ISSN: ISSN 1742-4658
PubMed: 30066404
DOI: 10.1111/FEBS.14620
Page generated: Sun Oct 6 04:47:52 2024
|
