Manganese in PDB 6srg: Crystal Structure of Human Prolidase G448R Variant Expressed in the Presence of Chaperones
Enzymatic activity of Crystal Structure of Human Prolidase G448R Variant Expressed in the Presence of Chaperones
All present enzymatic activity of Crystal Structure of Human Prolidase G448R Variant Expressed in the Presence of Chaperones:
3.4.13.9;
Protein crystallography data
The structure of Crystal Structure of Human Prolidase G448R Variant Expressed in the Presence of Chaperones, PDB code: 6srg
was solved by
E.Wator,
P.Wilk,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
48.13 /
2.56
|
|
Space group
|
C 2 2 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
103.736,
108.184,
210.976,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
20.7 /
23.7
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Crystal Structure of Human Prolidase G448R Variant Expressed in the Presence of Chaperones
(pdb code 6srg). 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 Human Prolidase G448R Variant Expressed in the Presence of Chaperones, PDB code: 6srg:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 6srg
Go back to
Manganese Binding Sites List in 6srg
Manganese binding site 1 out
of 4 in the Crystal Structure of Human Prolidase G448R Variant Expressed in the Presence of Chaperones
 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 Human Prolidase G448R Variant Expressed in the Presence of Chaperones within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn501
b:51.3
occ:1.00
|
OD2
|
A:ASP287
|
2.1
|
50.1
|
1.0
|
|
OE2
|
A:GLU452
|
2.2
|
53.2
|
1.0
|
|
NE2
|
A:HIS370
|
2.3
|
57.3
|
1.0
|
|
OE2
|
A:GLU412
|
2.3
|
48.9
|
1.0
|
|
O
|
A:OH503
|
2.3
|
68.5
|
0.9
|
|
O
|
A:GLY504
|
2.5
|
58.5
|
1.0
|
|
CD
|
A:GLU412
|
3.1
|
50.6
|
1.0
|
|
CG
|
A:ASP287
|
3.1
|
43.2
|
1.0
|
|
H3
|
A:GLY504
|
3.2
|
89.0
|
1.0
|
|
CE1
|
A:HIS370
|
3.2
|
41.8
|
1.0
|
|
HG1
|
A:THR410
|
3.2
|
44.9
|
1.0
|
|
CD
|
A:GLU452
|
3.2
|
50.7
|
1.0
|
|
HG21
|
A:THR410
|
3.2
|
60.4
|
1.0
|
|
CD2
|
A:HIS370
|
3.2
|
35.5
|
1.0
|
|
HO
|
A:OH503
|
3.3
|
82.2
|
0.9
|
|
C
|
A:GLY504
|
3.3
|
73.0
|
1.0
|
|
MN
|
A:MN502
|
3.3
|
65.3
|
0.8
|
|
OE1
|
A:GLU412
|
3.3
|
59.1
|
1.0
|
|
HE1
|
A:HIS370
|
3.4
|
50.1
|
1.0
|
|
HA
|
A:PRO505
|
3.4
|
0.7
|
1.0
|
|
HD2
|
A:HIS370
|
3.4
|
42.6
|
1.0
|
|
OE1
|
A:GLU452
|
3.7
|
50.3
|
1.0
|
|
OD1
|
A:ASP287
|
3.8
|
66.0
|
1.0
|
|
HE2
|
A:HIS377
|
3.8
|
56.4
|
1.0
|
|
N
|
A:GLY504
|
3.8
|
74.2
|
1.0
|
|
H2
|
A:GLY504
|
3.8
|
89.0
|
1.0
|
|
N
|
A:PRO505
|
3.9
|
83.2
|
1.0
|
|
HB3
|
A:ASP287
|
4.0
|
53.9
|
1.0
|
|
OG1
|
A:THR410
|
4.0
|
37.4
|
1.0
|
|
CA
|
A:PRO505
|
4.1
|
95.6
|
1.0
|
|
CA
|
A:GLY504
|
4.1
|
59.5
|
1.0
|
|
CG2
|
A:THR410
|
4.1
|
50.3
|
1.0
|
|
HB
|
A:THR410
|
4.2
|
61.1
|
1.0
|
|
CB
|
A:ASP287
|
4.2
|
45.0
|
1.0
|
|
HD2
|
A:HIS377
|
4.3
|
52.7
|
1.0
|
|
ND1
|
A:HIS370
|
4.3
|
48.9
|
1.0
|
|
CB
|
A:THR410
|
4.4
|
51.0
|
1.0
|
|
CG
|
A:HIS370
|
4.4
|
35.4
|
1.0
|
|
HA2
|
A:GLY504
|
4.4
|
71.4
|
1.0
|
|
HG12
|
A:VAL376
|
4.5
|
59.4
|
1.0
|
|
CG
|
A:GLU412
|
4.5
|
46.8
|
1.0
|
|
HG3
|
A:GLU452
|
4.5
|
57.8
|
1.0
|
|
NE2
|
A:HIS377
|
4.5
|
47.1
|
1.0
|
|
CG
|
A:GLU452
|
4.5
|
48.2
|
1.0
|
|
HG2
|
A:GLU412
|
4.5
|
56.1
|
1.0
|
|
HG13
|
A:VAL376
|
4.6
|
59.4
|
1.0
|
|
H1
|
A:GLY504
|
4.6
|
89.0
|
1.0
|
|
HB2
|
A:ASP287
|
4.6
|
53.9
|
1.0
|
|
HG23
|
A:THR410
|
4.6
|
60.4
|
1.0
|
|
HG22
|
A:THR410
|
4.7
|
60.4
|
1.0
|
|
CD2
|
A:HIS377
|
4.8
|
43.9
|
1.0
|
|
HG11
|
A:VAL376
|
4.8
|
59.4
|
1.0
|
|
CG1
|
A:VAL376
|
4.8
|
49.5
|
1.0
|
|
C
|
A:PRO505
|
4.9
|
90.2
|
1.0
|
|
HB3
|
A:GLU412
|
4.9
|
55.6
|
1.0
|
|
HA3
|
A:GLY504
|
4.9
|
71.4
|
1.0
|
|
Manganese binding site 2 out
of 4 in 6srg
Go back to
Manganese Binding Sites List in 6srg
Manganese binding site 2 out
of 4 in the Crystal Structure of Human Prolidase G448R Variant Expressed in the Presence of Chaperones
 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 Human Prolidase G448R Variant Expressed in the Presence of Chaperones within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn502
b:65.3
occ:0.83
|
O
|
A:OH503
|
1.7
|
68.5
|
0.9
|
|
HO
|
A:OH503
|
1.9
|
82.2
|
0.9
|
|
H2
|
A:GLY504
|
2.0
|
89.0
|
1.0
|
|
OD1
|
A:ASP276
|
2.3
|
62.0
|
1.0
|
|
OD2
|
A:ASP276
|
2.3
|
66.3
|
1.0
|
|
OE1
|
A:GLU452
|
2.4
|
50.3
|
1.0
|
|
OD1
|
A:ASP287
|
2.5
|
66.0
|
1.0
|
|
CG
|
A:ASP276
|
2.6
|
64.8
|
1.0
|
|
N
|
A:GLY504
|
2.7
|
74.2
|
1.0
|
|
H3
|
A:GLY504
|
2.9
|
89.0
|
1.0
|
|
HA2
|
A:GLY504
|
3.0
|
71.4
|
1.0
|
|
CG
|
A:ASP287
|
3.1
|
43.2
|
1.0
|
|
OD2
|
A:ASP287
|
3.1
|
50.1
|
1.0
|
|
HG1
|
A:THR289
|
3.2
|
66.4
|
1.0
|
|
CA
|
A:GLY504
|
3.2
|
59.5
|
1.0
|
|
CD
|
A:GLU452
|
3.3
|
50.7
|
1.0
|
|
MN
|
A:MN501
|
3.3
|
51.3
|
1.0
|
|
OE2
|
A:GLU452
|
3.4
|
53.2
|
1.0
|
|
H1
|
A:GLY504
|
3.4
|
89.0
|
1.0
|
|
OG1
|
A:THR289
|
3.5
|
55.3
|
1.0
|
|
OH
|
A:TYR241
|
3.6
|
77.9
|
1.0
|
|
C
|
A:GLY504
|
3.6
|
73.0
|
1.0
|
|
HE2
|
A:TYR241
|
3.9
|
0.2
|
1.0
|
|
HE
|
A:ARG450
|
3.9
|
62.0
|
1.0
|
|
O
|
A:GLY504
|
3.9
|
58.5
|
1.0
|
|
HH21
|
A:ARG450
|
4.0
|
53.3
|
1.0
|
|
HH
|
A:TYR241
|
4.0
|
93.4
|
1.0
|
|
CZ
|
A:TYR241
|
4.0
|
75.2
|
1.0
|
|
CB
|
A:ASP276
|
4.1
|
74.6
|
1.0
|
|
OE1
|
A:GLU412
|
4.1
|
59.1
|
1.0
|
|
CE2
|
A:TYR241
|
4.1
|
91.1
|
1.0
|
|
HA3
|
A:GLY504
|
4.2
|
71.4
|
1.0
|
|
HD3
|
A:PRO505
|
4.2
|
83.1
|
1.0
|
|
N
|
A:PRO505
|
4.3
|
83.2
|
1.0
|
|
HD12
|
A:ILE244
|
4.3
|
0.8
|
1.0
|
|
HB2
|
A:ASP276
|
4.4
|
89.5
|
1.0
|
|
CB
|
A:ASP287
|
4.5
|
45.0
|
1.0
|
|
HB3
|
A:ASP276
|
4.6
|
89.5
|
1.0
|
|
NE
|
A:ARG450
|
4.7
|
51.7
|
1.0
|
|
CG
|
A:GLU452
|
4.7
|
48.2
|
1.0
|
|
CD
|
A:PRO505
|
4.7
|
69.3
|
1.0
|
|
HA
|
A:ASP276
|
4.7
|
65.0
|
1.0
|
|
NH2
|
A:ARG450
|
4.7
|
44.5
|
1.0
|
|
OE2
|
A:GLU412
|
4.8
|
48.9
|
1.0
|
|
CD
|
A:GLU412
|
4.8
|
50.6
|
1.0
|
|
HB2
|
A:GLU452
|
4.8
|
58.5
|
1.0
|
|
HA
|
A:ASP287
|
4.8
|
55.2
|
1.0
|
|
HB3
|
A:GLU452
|
4.8
|
58.5
|
1.0
|
|
HD13
|
A:ILE244
|
4.8
|
0.8
|
1.0
|
|
HB3
|
A:ASP287
|
4.9
|
53.9
|
1.0
|
|
CA
|
A:ASP276
|
4.9
|
54.2
|
1.0
|
|
O
|
A:ILE288
|
4.9
|
43.6
|
1.0
|
|
C
|
A:ASP287
|
4.9
|
40.9
|
1.0
|
|
H
|
A:ILE288
|
4.9
|
61.5
|
1.0
|
|
N
|
A:ILE288
|
4.9
|
51.2
|
1.0
|
|
CE1
|
A:TYR241
|
4.9
|
75.5
|
1.0
|
|
CB
|
A:THR289
|
4.9
|
37.3
|
1.0
|
|
CD1
|
A:ILE244
|
5.0
|
94.9
|
1.0
|
|
Manganese binding site 3 out
of 4 in 6srg
Go back to
Manganese Binding Sites List in 6srg
Manganese binding site 3 out
of 4 in the Crystal Structure of Human Prolidase G448R Variant Expressed in the Presence of Chaperones
 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 Human Prolidase G448R Variant Expressed in the Presence of Chaperones within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn501
b:49.7
occ:1.00
|
OD2
|
B:ASP287
|
2.2
|
49.7
|
1.0
|
|
O
|
B:OH503
|
2.2
|
68.6
|
1.0
|
|
OE2
|
B:GLU452
|
2.3
|
44.0
|
1.0
|
|
OE2
|
B:GLU412
|
2.3
|
52.1
|
1.0
|
|
NE2
|
B:HIS370
|
2.3
|
41.0
|
1.0
|
|
O
|
B:GLY504
|
2.5
|
49.7
|
1.0
|
|
H3
|
B:GLY504
|
3.0
|
0.7
|
1.0
|
|
CG
|
B:ASP287
|
3.1
|
48.5
|
1.0
|
|
CD
|
B:GLU412
|
3.2
|
56.3
|
1.0
|
|
HO
|
B:OH503
|
3.2
|
82.3
|
1.0
|
|
C
|
B:GLY504
|
3.2
|
80.8
|
1.0
|
|
MN
|
B:MN502
|
3.3
|
57.4
|
0.9
|
|
HG1
|
B:THR410
|
3.3
|
58.1
|
1.0
|
|
CD
|
B:GLU452
|
3.3
|
47.8
|
1.0
|
|
CD2
|
B:HIS370
|
3.3
|
42.3
|
1.0
|
|
HG21
|
B:THR410
|
3.3
|
72.3
|
1.0
|
|
CE1
|
B:HIS370
|
3.3
|
51.7
|
1.0
|
|
HD2
|
B:HIS370
|
3.4
|
50.7
|
1.0
|
|
OE1
|
B:GLU412
|
3.4
|
58.6
|
1.0
|
|
HE1
|
B:HIS370
|
3.5
|
62.0
|
1.0
|
|
HA
|
B:PRO505
|
3.6
|
0.1
|
1.0
|
|
OE1
|
B:GLU452
|
3.6
|
52.0
|
1.0
|
|
OD1
|
B:ASP287
|
3.7
|
45.2
|
1.0
|
|
N
|
B:GLY504
|
3.7
|
84.0
|
1.0
|
|
HE2
|
B:HIS377
|
3.8
|
74.5
|
1.0
|
|
H2
|
B:GLY504
|
3.9
|
0.7
|
1.0
|
|
N
|
B:PRO505
|
4.0
|
77.2
|
1.0
|
|
CA
|
B:GLY504
|
4.0
|
81.2
|
1.0
|
|
HB3
|
B:ASP287
|
4.1
|
64.4
|
1.0
|
|
OG1
|
B:THR410
|
4.1
|
48.4
|
1.0
|
|
CG2
|
B:THR410
|
4.2
|
60.3
|
1.0
|
|
CA
|
B:PRO505
|
4.2
|
88.5
|
1.0
|
|
CB
|
B:ASP287
|
4.2
|
53.7
|
1.0
|
|
HB
|
B:THR410
|
4.2
|
59.3
|
1.0
|
|
HD2
|
B:HIS377
|
4.3
|
62.6
|
1.0
|
|
HA2
|
B:GLY504
|
4.3
|
97.5
|
1.0
|
|
CB
|
B:THR410
|
4.4
|
49.4
|
1.0
|
|
H1
|
B:GLY504
|
4.4
|
0.7
|
1.0
|
|
ND1
|
B:HIS370
|
4.4
|
43.9
|
1.0
|
|
CG
|
B:HIS370
|
4.4
|
44.0
|
1.0
|
|
NE2
|
B:HIS377
|
4.5
|
62.1
|
1.0
|
|
HG12
|
B:VAL376
|
4.5
|
82.6
|
1.0
|
|
CG
|
B:GLU412
|
4.5
|
52.8
|
1.0
|
|
HG3
|
B:GLU452
|
4.6
|
62.4
|
1.0
|
|
CG
|
B:GLU452
|
4.6
|
52.1
|
1.0
|
|
HG2
|
B:GLU412
|
4.6
|
63.3
|
1.0
|
|
HB2
|
B:ASP287
|
4.6
|
64.4
|
1.0
|
|
HG23
|
B:THR410
|
4.7
|
72.3
|
1.0
|
|
HG13
|
B:VAL376
|
4.7
|
82.6
|
1.0
|
|
HG11
|
B:VAL376
|
4.7
|
82.6
|
1.0
|
|
C
|
B:PRO505
|
4.8
|
99.2
|
1.0
|
|
HG22
|
B:THR410
|
4.8
|
72.3
|
1.0
|
|
CD2
|
B:HIS377
|
4.8
|
52.2
|
1.0
|
|
HA3
|
B:GLY504
|
4.8
|
97.5
|
1.0
|
|
CG1
|
B:VAL376
|
4.8
|
68.9
|
1.0
|
|
HB3
|
B:GLU412
|
4.9
|
55.5
|
1.0
|
|
Manganese binding site 4 out
of 4 in 6srg
Go back to
Manganese Binding Sites List in 6srg
Manganese binding site 4 out
of 4 in the Crystal Structure of Human Prolidase G448R Variant Expressed in the Presence of Chaperones
 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 Human Prolidase G448R Variant Expressed in the Presence of Chaperones within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn502
b:57.4
occ:0.91
|
O
|
B:OH503
|
1.8
|
68.6
|
1.0
|
|
H2
|
B:GLY504
|
2.0
|
0.7
|
1.0
|
|
HO
|
B:OH503
|
2.0
|
82.3
|
1.0
|
|
OD1
|
B:ASP276
|
2.3
|
55.4
|
1.0
|
|
OD1
|
B:ASP287
|
2.3
|
45.2
|
1.0
|
|
OD2
|
B:ASP276
|
2.4
|
56.0
|
1.0
|
|
OE1
|
B:GLU452
|
2.4
|
52.0
|
1.0
|
|
N
|
B:GLY504
|
2.6
|
84.0
|
1.0
|
|
H3
|
B:GLY504
|
2.6
|
0.7
|
1.0
|
|
CG
|
B:ASP276
|
2.6
|
52.2
|
1.0
|
|
HA2
|
B:GLY504
|
2.9
|
97.5
|
1.0
|
|
CG
|
B:ASP287
|
3.0
|
48.5
|
1.0
|
|
OD2
|
B:ASP287
|
3.1
|
49.7
|
1.0
|
|
CA
|
B:GLY504
|
3.2
|
81.2
|
1.0
|
|
CD
|
B:GLU452
|
3.2
|
47.8
|
1.0
|
|
MN
|
B:MN501
|
3.3
|
49.7
|
1.0
|
|
H1
|
B:GLY504
|
3.3
|
0.7
|
1.0
|
|
OE2
|
B:GLU452
|
3.4
|
44.0
|
1.0
|
|
HH
|
B:TYR241
|
3.5
|
82.6
|
1.0
|
|
HG1
|
B:THR289
|
3.5
|
72.3
|
1.0
|
|
OG1
|
B:THR289
|
3.6
|
60.3
|
1.0
|
|
C
|
B:GLY504
|
3.7
|
80.8
|
1.0
|
|
OH
|
B:TYR241
|
3.7
|
68.8
|
1.0
|
|
HE2
|
B:TYR241
|
3.9
|
0.8
|
1.0
|
|
O
|
B:GLY504
|
3.9
|
49.7
|
1.0
|
|
CZ
|
B:TYR241
|
4.0
|
85.7
|
1.0
|
|
HH21
|
B:ARG450
|
4.0
|
78.2
|
1.0
|
|
HD3
|
B:PRO505
|
4.1
|
0.8
|
1.0
|
|
HA3
|
B:GLY504
|
4.1
|
97.5
|
1.0
|
|
CE2
|
B:TYR241
|
4.1
|
0.1
|
1.0
|
|
CB
|
B:ASP276
|
4.1
|
50.9
|
1.0
|
|
HE
|
B:ARG450
|
4.1
|
70.7
|
1.0
|
|
OE1
|
B:GLU412
|
4.2
|
58.6
|
1.0
|
|
N
|
B:PRO505
|
4.4
|
77.2
|
1.0
|
|
HB2
|
B:ASP276
|
4.4
|
61.1
|
1.0
|
|
CB
|
B:ASP287
|
4.5
|
53.7
|
1.0
|
|
HB3
|
B:ASP276
|
4.6
|
61.1
|
1.0
|
|
HD12
|
B:ILE244
|
4.6
|
0.1
|
1.0
|
|
CG
|
B:GLU452
|
4.6
|
52.1
|
1.0
|
|
CD
|
B:PRO505
|
4.7
|
97.3
|
1.0
|
|
HA
|
B:ASP276
|
4.7
|
59.1
|
1.0
|
|
HA
|
B:ASP287
|
4.8
|
71.7
|
1.0
|
|
OE2
|
B:GLU412
|
4.8
|
52.1
|
1.0
|
|
NH2
|
B:ARG450
|
4.8
|
65.2
|
1.0
|
|
HB3
|
B:ASP287
|
4.8
|
64.4
|
1.0
|
|
C
|
B:ASP287
|
4.8
|
49.0
|
1.0
|
|
NE
|
B:ARG450
|
4.8
|
59.0
|
1.0
|
|
CE1
|
B:TYR241
|
4.8
|
84.5
|
1.0
|
|
HD13
|
B:ILE244
|
4.8
|
0.1
|
1.0
|
|
HB3
|
B:GLU452
|
4.9
|
60.5
|
1.0
|
|
CA
|
B:ASP276
|
4.9
|
49.3
|
1.0
|
|
CD
|
B:GLU412
|
4.9
|
56.3
|
1.0
|
|
N
|
B:ILE288
|
4.9
|
47.4
|
1.0
|
|
HB2
|
B:GLU452
|
4.9
|
60.5
|
1.0
|
|
O
|
B:ILE288
|
4.9
|
39.7
|
1.0
|
|
CA
|
B:ASP287
|
4.9
|
59.8
|
1.0
|
|
H
|
B:ILE288
|
4.9
|
56.9
|
1.0
|
|
CD2
|
B:TYR241
|
5.0
|
0.2
|
1.0
|
|
HG2
|
B:GLU452
|
5.0
|
62.4
|
1.0
|
|
Reference:
E.Wator,
M.Rutkiewicz,
M.S.Weiss,
P.Wilk.
Co-Expression with Chaperones Can Affect Protein 3D-Structure As Exemplified By Loss-of-Function Variants of Human Prolidase. Febs Lett. 2020.
ISSN: ISSN 0014-5793
PubMed: 32598484
DOI: 10.1002/1873-3468.13877
Page generated: Sun Oct 6 07:09:03 2024
|
