Manganese in PDB 6qsc: Crystal Structure of ARG470HIS Mutant of Human Prolidase with Mn Ions and Glypro Ligand
Enzymatic activity of Crystal Structure of ARG470HIS Mutant of Human Prolidase with Mn Ions and Glypro Ligand
All present enzymatic activity of Crystal Structure of ARG470HIS Mutant of Human Prolidase with Mn Ions and Glypro Ligand:
3.4.13.9;
Protein crystallography data
The structure of Crystal Structure of ARG470HIS Mutant of Human Prolidase with Mn Ions and Glypro Ligand, PDB code: 6qsc
was solved by
P.Wilk,
E.Wator,
M.S.Weiss,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
48.35 /
1.57
|
|
Space group
|
C 2 2 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
103.541,
108.714,
211.548,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
14.7 /
16.7
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Crystal Structure of ARG470HIS Mutant of Human Prolidase with Mn Ions and Glypro Ligand
(pdb code 6qsc). 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 ARG470HIS Mutant of Human Prolidase with Mn Ions and Glypro Ligand, PDB code: 6qsc:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 6qsc
Go back to
Manganese Binding Sites List in 6qsc
Manganese binding site 1 out
of 4 in the Crystal Structure of ARG470HIS Mutant of Human Prolidase with Mn Ions and Glypro 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 ARG470HIS Mutant of Human Prolidase with Mn Ions and Glypro Ligand within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn499
b:24.6
occ:0.58
|
OE2
|
A:GLU412
|
2.2
|
21.0
|
1.0
|
|
NE2
|
A:HIS370
|
2.3
|
17.8
|
1.0
|
|
OD2
|
A:ASP287
|
2.3
|
25.7
|
1.0
|
|
O1
|
A:MH2500
|
2.4
|
30.2
|
0.8
|
|
OE2
|
A:GLU452
|
2.6
|
22.7
|
1.0
|
|
O
|
A:GLY506
|
2.6
|
21.8
|
1.0
|
|
H2
|
A:GLY506
|
3.0
|
32.8
|
1.0
|
|
CG
|
A:ASP287
|
3.1
|
22.5
|
1.0
|
|
CD
|
A:GLU412
|
3.1
|
27.8
|
1.0
|
|
HG21
|
A:THR410
|
3.1
|
22.9
|
1.0
|
|
HG1
|
A:THR410
|
3.2
|
23.0
|
1.0
|
|
CD2
|
A:HIS370
|
3.2
|
19.8
|
1.0
|
|
MN
|
A:MH2500
|
3.2
|
95.0
|
0.8
|
|
CE1
|
A:HIS370
|
3.2
|
20.7
|
1.0
|
|
C
|
A:GLY506
|
3.3
|
21.8
|
1.0
|
|
HA
|
A:PRO507
|
3.3
|
26.1
|
1.0
|
|
HD2
|
A:HIS370
|
3.3
|
23.7
|
1.0
|
|
OE1
|
A:GLU412
|
3.4
|
31.6
|
1.0
|
|
HE1
|
A:HIS370
|
3.4
|
24.9
|
1.0
|
|
OD1
|
A:ASP287
|
3.5
|
26.0
|
1.0
|
|
CD
|
A:GLU452
|
3.6
|
25.5
|
1.0
|
|
N
|
A:GLY506
|
3.8
|
27.4
|
1.0
|
|
HE2
|
A:HIS377
|
3.9
|
24.5
|
1.0
|
|
OE1
|
A:GLU452
|
3.9
|
29.4
|
1.0
|
|
N
|
A:PRO507
|
4.0
|
22.0
|
1.0
|
|
OG1
|
A:THR410
|
4.0
|
19.1
|
1.0
|
|
CG2
|
A:THR410
|
4.0
|
19.1
|
1.0
|
|
CA
|
A:GLY506
|
4.0
|
27.2
|
1.0
|
|
HB3
|
A:ASP287
|
4.0
|
21.7
|
1.0
|
|
CA
|
A:PRO507
|
4.1
|
21.8
|
1.0
|
|
HB
|
A:THR410
|
4.1
|
22.6
|
1.0
|
|
H1
|
A:GLY506
|
4.1
|
32.8
|
1.0
|
|
CB
|
A:ASP287
|
4.2
|
18.0
|
1.0
|
|
HA2
|
A:GLY506
|
4.2
|
32.6
|
1.0
|
|
CB
|
A:THR410
|
4.3
|
18.8
|
1.0
|
|
HG22
|
A:VAL376
|
4.3
|
30.5
|
1.0
|
|
ND1
|
A:HIS370
|
4.4
|
17.5
|
1.0
|
|
CG
|
A:HIS370
|
4.4
|
17.7
|
1.0
|
|
HD2
|
A:HIS377
|
4.4
|
20.9
|
1.0
|
|
CG
|
A:GLU412
|
4.4
|
18.6
|
1.0
|
|
H3
|
A:GLY506
|
4.5
|
32.8
|
1.0
|
|
HG23
|
A:THR410
|
4.5
|
22.9
|
1.0
|
|
HG2
|
A:GLU412
|
4.5
|
22.4
|
1.0
|
|
HB2
|
A:ASP287
|
4.5
|
21.7
|
1.0
|
|
NE2
|
A:HIS377
|
4.6
|
20.4
|
1.0
|
|
HG22
|
A:THR410
|
4.6
|
22.9
|
1.0
|
|
HB3
|
A:GLU412
|
4.8
|
22.1
|
1.0
|
|
C
|
A:PRO507
|
4.8
|
23.5
|
1.0
|
|
CD2
|
A:HIS377
|
4.8
|
17.4
|
1.0
|
|
HG3
|
A:GLU452
|
4.9
|
24.3
|
1.0
|
|
CG
|
A:GLU452
|
4.9
|
20.3
|
1.0
|
|
HA3
|
A:GLY506
|
4.9
|
32.6
|
1.0
|
|
HD3
|
A:PRO507
|
4.9
|
35.6
|
1.0
|
|
HG21
|
A:VAL376
|
5.0
|
30.5
|
1.0
|
|
CG2
|
A:VAL376
|
5.0
|
25.4
|
1.0
|
|
Manganese binding site 2 out
of 4 in 6qsc
Go back to
Manganese Binding Sites List in 6qsc
Manganese binding site 2 out
of 4 in the Crystal Structure of ARG470HIS Mutant of Human Prolidase with Mn Ions and Glypro 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 ARG470HIS Mutant of Human Prolidase with Mn Ions and Glypro Ligand within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn500
b:95.0
occ:0.77
|
MN
|
A:MH2500
|
0.0
|
95.0
|
0.8
|
|
O1
|
A:MH2500
|
2.0
|
30.2
|
0.8
|
|
OD1
|
A:ASP276
|
2.1
|
21.9
|
1.0
|
|
OD1
|
A:ASP287
|
2.2
|
26.0
|
1.0
|
|
H1
|
A:GLY506
|
2.2
|
32.8
|
1.0
|
|
OD2
|
A:ASP276
|
2.3
|
19.4
|
1.0
|
|
HA2
|
A:GLY506
|
2.4
|
32.6
|
1.0
|
|
CG
|
A:ASP276
|
2.5
|
19.8
|
1.0
|
|
H2
|
A:GLY506
|
2.6
|
32.8
|
1.0
|
|
N
|
A:GLY506
|
2.7
|
27.4
|
1.0
|
|
OE1
|
A:GLU452
|
2.9
|
29.4
|
1.0
|
|
CG
|
A:ASP287
|
2.9
|
22.5
|
1.0
|
|
CA
|
A:GLY506
|
2.9
|
27.2
|
1.0
|
|
OD2
|
A:ASP287
|
2.9
|
25.7
|
1.0
|
|
MN
|
A:MN499
|
3.2
|
24.6
|
0.6
|
|
C
|
A:GLY506
|
3.4
|
21.8
|
1.0
|
|
HG1
|
A:THR289
|
3.5
|
25.0
|
1.0
|
|
HH
|
A:TYR241
|
3.5
|
24.0
|
1.0
|
|
H3
|
A:GLY506
|
3.5
|
32.8
|
1.0
|
|
OH
|
A:TYR241
|
3.6
|
20.0
|
1.0
|
|
CD
|
A:GLU452
|
3.6
|
25.5
|
1.0
|
|
OE2
|
A:GLU452
|
3.7
|
22.7
|
1.0
|
|
HD3
|
A:PRO507
|
3.8
|
35.6
|
1.0
|
|
HA3
|
A:GLY506
|
3.8
|
32.6
|
1.0
|
|
O
|
A:GLY506
|
3.8
|
21.8
|
1.0
|
|
OG1
|
A:THR289
|
3.8
|
20.8
|
1.0
|
|
CB
|
A:ASP276
|
4.0
|
19.2
|
1.0
|
|
CZ
|
A:TYR241
|
4.0
|
20.1
|
1.0
|
|
HE
|
A:ARG450
|
4.1
|
22.1
|
1.0
|
|
HE2
|
A:TYR241
|
4.2
|
24.1
|
1.0
|
|
N
|
A:PRO507
|
4.2
|
22.0
|
1.0
|
|
HD12
|
A:ILE244
|
4.2
|
24.9
|
1.0
|
|
OE1
|
A:GLU412
|
4.2
|
31.6
|
1.0
|
|
HH21
|
A:ARG450
|
4.2
|
26.2
|
1.0
|
|
CE2
|
A:TYR241
|
4.3
|
20.0
|
1.0
|
|
CB
|
A:ASP287
|
4.3
|
18.0
|
1.0
|
|
HB2
|
A:ASP276
|
4.3
|
23.1
|
1.0
|
|
HB3
|
A:ASP276
|
4.4
|
23.1
|
1.0
|
|
CD
|
A:PRO507
|
4.4
|
29.6
|
1.0
|
|
HA
|
A:ASP276
|
4.5
|
19.7
|
1.0
|
|
HA
|
A:ASP287
|
4.7
|
19.1
|
1.0
|
|
OE2
|
A:GLU412
|
4.7
|
21.0
|
1.0
|
|
CA
|
A:ASP276
|
4.7
|
16.4
|
1.0
|
|
CE1
|
A:TYR241
|
4.7
|
19.3
|
1.0
|
|
HB3
|
A:ASP287
|
4.7
|
21.7
|
1.0
|
|
CD
|
A:GLU412
|
4.8
|
27.8
|
1.0
|
|
NE
|
A:ARG450
|
4.8
|
18.4
|
1.0
|
|
HB2
|
A:ASP287
|
4.8
|
21.7
|
1.0
|
|
HA
|
A:PRO507
|
4.9
|
26.1
|
1.0
|
|
CA
|
A:ASP287
|
4.9
|
15.9
|
1.0
|
|
C
|
A:ASP287
|
4.9
|
16.6
|
1.0
|
|
H
|
A:ILE288
|
4.9
|
22.3
|
1.0
|
|
O
|
A:ILE288
|
4.9
|
18.5
|
1.0
|
|
HE1
|
A:TYR241
|
4.9
|
23.1
|
1.0
|
|
C
|
A:ASP276
|
4.9
|
20.2
|
1.0
|
|
N
|
A:ILE288
|
5.0
|
18.6
|
1.0
|
|
CD1
|
A:ILE244
|
5.0
|
20.7
|
1.0
|
|
NH2
|
A:ARG450
|
5.0
|
21.8
|
1.0
|
|
Manganese binding site 3 out
of 4 in 6qsc
Go back to
Manganese Binding Sites List in 6qsc
Manganese binding site 3 out
of 4 in the Crystal Structure of ARG470HIS Mutant of Human Prolidase with Mn Ions and Glypro 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 ARG470HIS Mutant of Human Prolidase with Mn Ions and Glypro Ligand within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn499
b:26.3
occ:0.63
|
OD2
|
B:ASP287
|
2.2
|
23.7
|
1.0
|
|
OE2
|
B:GLU412
|
2.3
|
21.8
|
1.0
|
|
O1
|
B:MH2500
|
2.3
|
25.5
|
0.8
|
|
NE2
|
B:HIS370
|
2.3
|
19.8
|
1.0
|
|
OE2
|
B:GLU452
|
2.5
|
23.4
|
1.0
|
|
O
|
B:GLY509
|
2.6
|
23.6
|
1.0
|
|
CG
|
B:ASP287
|
3.1
|
25.4
|
1.0
|
|
H2
|
B:GLY509
|
3.1
|
36.6
|
1.0
|
|
CD
|
B:GLU412
|
3.1
|
28.9
|
1.0
|
|
HG21
|
B:THR410
|
3.1
|
22.9
|
1.0
|
|
MN
|
B:MH2500
|
3.2
|
90.5
|
0.8
|
|
HG1
|
B:THR410
|
3.2
|
25.0
|
1.0
|
|
CD2
|
B:HIS370
|
3.2
|
21.4
|
1.0
|
|
CE1
|
B:HIS370
|
3.3
|
21.6
|
1.0
|
|
C
|
B:GLY509
|
3.3
|
23.1
|
1.0
|
|
HA
|
B:PRO510
|
3.3
|
29.2
|
1.0
|
|
OE1
|
B:GLU412
|
3.4
|
28.1
|
1.0
|
|
HD2
|
B:HIS370
|
3.4
|
25.7
|
1.0
|
|
CD
|
B:GLU452
|
3.4
|
25.6
|
1.0
|
|
HE1
|
B:HIS370
|
3.5
|
25.9
|
1.0
|
|
OD1
|
B:ASP287
|
3.5
|
26.7
|
1.0
|
|
OE1
|
B:GLU452
|
3.7
|
28.9
|
1.0
|
|
N
|
B:GLY509
|
3.8
|
30.5
|
1.0
|
|
HE2
|
B:HIS377
|
3.9
|
25.5
|
1.0
|
|
N
|
B:PRO510
|
3.9
|
23.1
|
1.0
|
|
OG1
|
B:THR410
|
4.0
|
20.8
|
1.0
|
|
HB3
|
B:ASP287
|
4.0
|
26.3
|
1.0
|
|
CG2
|
B:THR410
|
4.0
|
19.0
|
1.0
|
|
H1
|
B:GLY509
|
4.0
|
36.6
|
1.0
|
|
CA
|
B:PRO510
|
4.1
|
24.3
|
1.0
|
|
CA
|
B:GLY509
|
4.1
|
30.2
|
1.0
|
|
HB
|
B:THR410
|
4.1
|
24.7
|
1.0
|
|
CB
|
B:ASP287
|
4.1
|
21.9
|
1.0
|
|
HA2
|
B:GLY509
|
4.3
|
36.2
|
1.0
|
|
CB
|
B:THR410
|
4.3
|
20.6
|
1.0
|
|
ND1
|
B:HIS370
|
4.4
|
18.5
|
1.0
|
|
CG
|
B:HIS370
|
4.4
|
18.6
|
1.0
|
|
HG22
|
B:VAL376
|
4.4
|
26.4
|
1.0
|
|
HD2
|
B:HIS377
|
4.4
|
24.6
|
1.0
|
|
HG23
|
B:THR410
|
4.5
|
22.9
|
1.0
|
|
HB2
|
B:ASP287
|
4.5
|
26.3
|
1.0
|
|
CG
|
B:GLU412
|
4.5
|
23.8
|
1.0
|
|
H3
|
B:GLY509
|
4.6
|
36.6
|
1.0
|
|
NE2
|
B:HIS377
|
4.6
|
21.3
|
1.0
|
|
HG2
|
B:GLU412
|
4.6
|
28.5
|
1.0
|
|
HG22
|
B:THR410
|
4.6
|
22.9
|
1.0
|
|
CG
|
B:GLU452
|
4.7
|
22.2
|
1.0
|
|
HG3
|
B:GLU452
|
4.8
|
26.7
|
1.0
|
|
HB3
|
B:GLU412
|
4.8
|
25.1
|
1.0
|
|
C
|
B:PRO510
|
4.8
|
28.3
|
1.0
|
|
CD2
|
B:HIS377
|
4.9
|
20.5
|
1.0
|
|
HA3
|
B:GLY509
|
4.9
|
36.2
|
1.0
|
|
HD3
|
B:PRO510
|
5.0
|
31.9
|
1.0
|
|
Manganese binding site 4 out
of 4 in 6qsc
Go back to
Manganese Binding Sites List in 6qsc
Manganese binding site 4 out
of 4 in the Crystal Structure of ARG470HIS Mutant of Human Prolidase with Mn Ions and Glypro 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 ARG470HIS Mutant of Human Prolidase with Mn Ions and Glypro Ligand within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn500
b:90.5
occ:0.80
|
MN
|
B:MH2500
|
0.0
|
90.5
|
0.8
|
|
O1
|
B:MH2500
|
2.0
|
25.5
|
0.8
|
|
OD1
|
B:ASP276
|
2.1
|
25.4
|
1.0
|
|
OD1
|
B:ASP287
|
2.2
|
26.7
|
1.0
|
|
OD2
|
B:ASP276
|
2.3
|
20.9
|
1.0
|
|
OE1
|
B:GLU452
|
2.4
|
28.9
|
1.0
|
|
CG
|
B:ASP276
|
2.5
|
21.1
|
1.0
|
|
H1
|
B:GLY509
|
2.5
|
36.6
|
1.0
|
|
HA2
|
B:GLY509
|
2.8
|
36.2
|
1.0
|
|
CG
|
B:ASP287
|
2.9
|
25.4
|
1.0
|
|
H2
|
B:GLY509
|
3.0
|
36.6
|
1.0
|
|
N
|
B:GLY509
|
3.0
|
30.5
|
1.0
|
|
OD2
|
B:ASP287
|
3.1
|
23.7
|
1.0
|
|
HG1
|
B:THR289
|
3.1
|
26.0
|
1.0
|
|
MN
|
B:MN499
|
3.2
|
26.3
|
0.6
|
|
CD
|
B:GLU452
|
3.2
|
25.6
|
1.0
|
|
CA
|
B:GLY509
|
3.3
|
30.2
|
1.0
|
|
OE2
|
B:GLU452
|
3.4
|
23.4
|
1.0
|
|
OG1
|
B:THR289
|
3.5
|
21.7
|
1.0
|
|
HH
|
B:TYR241
|
3.7
|
25.7
|
1.0
|
|
C
|
B:GLY509
|
3.7
|
23.1
|
1.0
|
|
OH
|
B:TYR241
|
3.8
|
21.4
|
1.0
|
|
H3
|
B:GLY509
|
3.8
|
36.6
|
1.0
|
|
HD3
|
B:PRO510
|
3.9
|
31.9
|
1.0
|
|
HE
|
B:ARG450
|
3.9
|
26.7
|
1.0
|
|
CB
|
B:ASP276
|
3.9
|
17.5
|
1.0
|
|
O
|
B:GLY509
|
3.9
|
23.6
|
1.0
|
|
OE1
|
B:GLU412
|
4.1
|
28.1
|
1.0
|
|
HH21
|
B:ARG450
|
4.1
|
30.7
|
1.0
|
|
HA3
|
B:GLY509
|
4.2
|
36.2
|
1.0
|
|
N
|
B:PRO510
|
4.2
|
23.1
|
1.0
|
|
CZ
|
B:TYR241
|
4.3
|
20.8
|
1.0
|
|
HB2
|
B:ASP276
|
4.3
|
21.0
|
1.0
|
|
CB
|
B:ASP287
|
4.4
|
21.9
|
1.0
|
|
HD12
|
B:ILE244
|
4.4
|
27.7
|
1.0
|
|
HB3
|
B:ASP276
|
4.4
|
21.0
|
1.0
|
|
HE2
|
B:TYR241
|
4.4
|
27.7
|
1.0
|
|
HA
|
B:ASP276
|
4.5
|
21.0
|
1.0
|
|
CD
|
B:PRO510
|
4.5
|
26.6
|
1.0
|
|
CE2
|
B:TYR241
|
4.6
|
23.1
|
1.0
|
|
OE2
|
B:GLU412
|
4.6
|
21.8
|
1.0
|
|
NE
|
B:ARG450
|
4.6
|
22.2
|
1.0
|
|
CG
|
B:GLU452
|
4.6
|
22.2
|
1.0
|
|
CD
|
B:GLU412
|
4.7
|
28.9
|
1.0
|
|
HA
|
B:ASP287
|
4.7
|
22.5
|
1.0
|
|
CA
|
B:ASP276
|
4.7
|
17.5
|
1.0
|
|
HB3
|
B:ASP287
|
4.7
|
26.3
|
1.0
|
|
C
|
B:ASP287
|
4.8
|
18.3
|
1.0
|
|
HB2
|
B:GLU452
|
4.8
|
25.0
|
1.0
|
|
HB3
|
B:GLU452
|
4.8
|
25.0
|
1.0
|
|
HG3
|
B:PRO510
|
4.8
|
35.4
|
1.0
|
|
O
|
B:ILE288
|
4.8
|
18.5
|
1.0
|
|
N
|
B:ILE288
|
4.8
|
17.5
|
1.0
|
|
H
|
B:ILE288
|
4.8
|
21.1
|
1.0
|
|
NH2
|
B:ARG450
|
4.8
|
25.6
|
1.0
|
|
CA
|
B:ASP287
|
4.9
|
18.8
|
1.0
|
|
HA
|
B:PRO510
|
4.9
|
29.2
|
1.0
|
|
CB
|
B:THR289
|
4.9
|
20.6
|
1.0
|
|
C
|
B:ILE288
|
4.9
|
19.2
|
1.0
|
|
HB2
|
B:ASP287
|
5.0
|
26.3
|
1.0
|
|
CE1
|
B:TYR241
|
5.0
|
19.1
|
1.0
|
|
Reference:
P.Wilk,
E.Wator,
M.S.Weiss.
Crystal Structure of ARG470HIS Mutant of Human Prolidase with Mn Ions and Glypro Ligand To Be Published.
Page generated: Sun Oct 6 06:06:27 2024
|
