Mercury in PDB 1nu6: Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp-IV)
Enzymatic activity of Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp-IV)
All present enzymatic activity of Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp-IV):
3.4.14.5;
Protein crystallography data
The structure of Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp-IV), PDB code: 1nu6
was solved by
M.Hennig,
M.Stihle,
R.Thoma,
A.Ruf,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
12.00 /
2.10
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
65.496,
68.240,
419.289,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.5 /
26.6
|
Mercury Binding Sites:
The binding sites of Mercury atom in the Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp-IV)
(pdb code 1nu6). This binding sites where shown within
5.0 Angstroms radius around Mercury atom.
In total 6 binding sites of Mercury where determined in the
Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp-IV), PDB code: 1nu6:
Jump to Mercury binding site number:
1;
2;
3;
4;
5;
6;
Mercury binding site 1 out
of 6 in 1nu6
Go back to
Mercury Binding Sites List in 1nu6
Mercury binding site 1 out
of 6 in the Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp-IV)
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 1 of Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp-IV) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg1301
b:65.7
occ:1.00
|
HG
|
A:HG1302
|
2.4
|
0.5
|
1.0
|
SG
|
A:CYS301
|
2.7
|
21.4
|
1.0
|
CD2
|
A:TYR299
|
3.1
|
21.8
|
1.0
|
CG
|
A:TYR299
|
3.4
|
24.6
|
1.0
|
CD1
|
A:LEU316
|
3.4
|
27.3
|
1.0
|
CE2
|
A:TYR299
|
3.6
|
27.9
|
1.0
|
CG1
|
A:VAL665
|
3.6
|
23.3
|
1.0
|
CB
|
A:TYR299
|
3.8
|
27.2
|
1.0
|
CG2
|
A:VAL207
|
3.8
|
26.2
|
1.0
|
CG1
|
A:VAL207
|
3.8
|
24.8
|
1.0
|
CD1
|
A:TYR299
|
4.0
|
25.2
|
1.0
|
CZ
|
A:TYR299
|
4.3
|
23.9
|
1.0
|
OE1
|
A:GLN320
|
4.4
|
33.0
|
1.0
|
CB
|
A:VAL207
|
4.4
|
27.6
|
1.0
|
CE1
|
A:TYR299
|
4.4
|
23.5
|
1.0
|
CD
|
A:GLN320
|
4.5
|
34.2
|
1.0
|
NE2
|
A:GLN320
|
4.5
|
30.8
|
1.0
|
CB
|
A:CYS301
|
4.6
|
30.2
|
1.0
|
CG2
|
A:VAL665
|
4.7
|
26.4
|
1.0
|
CG
|
A:LEU316
|
4.7
|
29.6
|
1.0
|
CB
|
A:LEU316
|
4.8
|
27.6
|
1.0
|
CB
|
A:VAL665
|
4.8
|
25.2
|
1.0
|
CA
|
A:VAL207
|
5.0
|
26.9
|
1.0
|
|
Mercury binding site 2 out
of 6 in 1nu6
Go back to
Mercury Binding Sites List in 1nu6
Mercury binding site 2 out
of 6 in the Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp-IV)
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 2 of Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp-IV) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg1302
b:0.5
occ:1.00
|
SG
|
A:CYS301
|
2.0
|
21.4
|
1.0
|
HG
|
A:HG1301
|
2.4
|
65.7
|
1.0
|
CG1
|
A:VAL207
|
3.5
|
24.8
|
1.0
|
CB
|
A:CYS301
|
3.6
|
30.2
|
1.0
|
CB
|
A:ARG358
|
3.7
|
36.2
|
1.0
|
CD1
|
A:LEU316
|
3.8
|
27.3
|
1.0
|
CD
|
A:PRO359
|
4.1
|
34.4
|
1.0
|
NH1
|
A:ARG358
|
4.2
|
56.1
|
1.0
|
CB
|
A:VAL207
|
4.3
|
27.6
|
1.0
|
CA
|
A:VAL207
|
4.4
|
26.9
|
1.0
|
CA
|
A:ARG358
|
4.4
|
36.5
|
1.0
|
CG2
|
A:VAL207
|
4.5
|
26.2
|
1.0
|
CA
|
A:CYS301
|
4.5
|
30.0
|
1.0
|
O
|
A:VAL207
|
4.5
|
27.8
|
1.0
|
O
|
A:PHE357
|
4.7
|
35.0
|
1.0
|
CG1
|
A:VAL665
|
4.8
|
23.3
|
1.0
|
O
|
A:GLU206
|
4.9
|
26.3
|
1.0
|
C
|
A:VAL207
|
4.9
|
27.1
|
1.0
|
CG
|
A:LEU316
|
5.0
|
29.6
|
1.0
|
|
Mercury binding site 3 out
of 6 in 1nu6
Go back to
Mercury Binding Sites List in 1nu6
Mercury binding site 3 out
of 6 in the Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp-IV)
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 3 of Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp-IV) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg1303
b:59.7
occ:1.00
|
SG
|
A:CYS551
|
2.2
|
33.8
|
1.0
|
OH
|
A:TYR670
|
2.5
|
30.3
|
1.0
|
O
|
A:ARG356
|
2.6
|
33.0
|
1.0
|
CB
|
A:CYS551
|
3.1
|
27.8
|
1.0
|
O
|
A:PRO550
|
3.2
|
22.8
|
1.0
|
CE1
|
A:PHE357
|
3.2
|
38.7
|
1.0
|
CD1
|
A:PHE357
|
3.2
|
38.3
|
1.0
|
CZ
|
A:TYR670
|
3.3
|
26.8
|
1.0
|
CE1
|
A:TYR670
|
3.3
|
28.0
|
1.0
|
C
|
A:ARG356
|
3.4
|
33.8
|
1.0
|
C
|
A:PRO550
|
3.6
|
24.9
|
1.0
|
CB
|
A:PRO550
|
3.8
|
26.0
|
1.0
|
CZ
|
A:PHE357
|
3.9
|
41.2
|
1.0
|
CG
|
A:PHE357
|
3.9
|
38.1
|
1.0
|
NE1
|
A:TRP353
|
4.0
|
26.6
|
1.0
|
N
|
A:CYS551
|
4.1
|
26.4
|
1.0
|
CZ2
|
A:TRP353
|
4.1
|
23.3
|
1.0
|
N
|
A:PHE357
|
4.1
|
34.1
|
1.0
|
CA
|
A:PHE357
|
4.2
|
35.5
|
1.0
|
CA
|
A:CYS551
|
4.3
|
27.8
|
1.0
|
CE2
|
A:TRP353
|
4.3
|
24.1
|
1.0
|
CA
|
A:ARG356
|
4.4
|
33.3
|
1.0
|
CA
|
A:PRO550
|
4.4
|
25.1
|
1.0
|
CE2
|
A:PHE357
|
4.5
|
42.6
|
1.0
|
CD2
|
A:PHE357
|
4.5
|
41.0
|
1.0
|
NE
|
A:ARG669
|
4.5
|
38.4
|
1.0
|
CE2
|
A:TYR670
|
4.6
|
27.4
|
1.0
|
CD1
|
A:TYR670
|
4.6
|
30.9
|
1.0
|
NH2
|
A:ARG669
|
4.7
|
35.8
|
1.0
|
CB
|
A:PHE357
|
4.7
|
35.9
|
1.0
|
CG
|
A:PRO550
|
4.9
|
25.3
|
1.0
|
|
Mercury binding site 4 out
of 6 in 1nu6
Go back to
Mercury Binding Sites List in 1nu6
Mercury binding site 4 out
of 6 in the Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp-IV)
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 4 of Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp-IV) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Hg2301
b:65.4
occ:1.00
|
HG
|
B:HG2302
|
2.7
|
0.1
|
1.0
|
SG
|
B:CYS301
|
2.8
|
27.6
|
1.0
|
CD2
|
B:TYR299
|
3.2
|
24.8
|
1.0
|
CG
|
B:TYR299
|
3.4
|
26.0
|
1.0
|
CD2
|
B:LEU316
|
3.5
|
34.1
|
1.0
|
CG1
|
B:VAL665
|
3.6
|
24.5
|
1.0
|
CB
|
B:TYR299
|
3.7
|
27.8
|
1.0
|
CG2
|
B:VAL207
|
3.8
|
27.5
|
1.0
|
CE2
|
B:TYR299
|
3.8
|
25.1
|
1.0
|
CG1
|
B:VAL207
|
3.8
|
27.3
|
1.0
|
CD1
|
B:TYR299
|
4.1
|
25.7
|
1.0
|
CB
|
B:VAL207
|
4.4
|
28.0
|
1.0
|
CZ
|
B:TYR299
|
4.4
|
25.1
|
1.0
|
OE1
|
B:GLN320
|
4.6
|
33.3
|
1.0
|
CE1
|
B:TYR299
|
4.6
|
27.5
|
1.0
|
CG
|
B:LEU316
|
4.6
|
33.1
|
1.0
|
CD
|
B:GLN320
|
4.6
|
37.1
|
1.0
|
CG2
|
B:VAL665
|
4.7
|
24.5
|
1.0
|
CB
|
B:CYS301
|
4.7
|
31.3
|
1.0
|
NE2
|
B:GLN320
|
4.7
|
37.0
|
1.0
|
CB
|
B:VAL665
|
4.8
|
25.2
|
1.0
|
CB
|
B:LEU316
|
4.8
|
30.4
|
1.0
|
|
Mercury binding site 5 out
of 6 in 1nu6
Go back to
Mercury Binding Sites List in 1nu6
Mercury binding site 5 out
of 6 in the Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp-IV)
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 5 of Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp-IV) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Hg2302
b:0.1
occ:1.00
|
SG
|
B:CYS301
|
1.6
|
27.6
|
1.0
|
HG
|
B:HG2301
|
2.7
|
65.4
|
1.0
|
CB
|
B:CYS301
|
3.0
|
31.3
|
1.0
|
CG1
|
B:VAL207
|
3.4
|
27.3
|
1.0
|
CD2
|
B:LEU316
|
3.7
|
34.1
|
1.0
|
CD
|
B:PRO359
|
3.8
|
33.3
|
1.0
|
CB
|
B:ARG358
|
3.9
|
35.3
|
1.0
|
CA
|
B:CYS301
|
4.0
|
31.1
|
1.0
|
CB
|
B:VAL207
|
4.4
|
28.0
|
1.0
|
CA
|
B:ARG358
|
4.5
|
35.4
|
1.0
|
CA
|
B:VAL207
|
4.6
|
27.6
|
1.0
|
CG2
|
B:VAL207
|
4.7
|
27.5
|
1.0
|
O
|
B:VAL207
|
4.8
|
25.9
|
1.0
|
CG
|
B:PRO359
|
4.8
|
33.5
|
1.0
|
CB
|
B:LEU316
|
4.9
|
30.4
|
1.0
|
N
|
B:PRO359
|
4.9
|
33.0
|
1.0
|
CG
|
B:LEU316
|
5.0
|
33.1
|
1.0
|
O
|
B:CYS301
|
5.0
|
35.2
|
1.0
|
O
|
B:PHE357
|
5.0
|
34.1
|
1.0
|
|
Mercury binding site 6 out
of 6 in 1nu6
Go back to
Mercury Binding Sites List in 1nu6
Mercury binding site 6 out
of 6 in the Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp-IV)
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 6 of Crystal Structure of Human Dipeptidyl Peptidase IV (Dpp-IV) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Hg2303
b:63.8
occ:1.00
|
SG
|
B:CYS551
|
2.1
|
36.9
|
1.0
|
OH
|
B:TYR670
|
2.4
|
28.9
|
1.0
|
O
|
B:ARG356
|
2.9
|
35.2
|
1.0
|
CB
|
B:CYS551
|
3.2
|
30.1
|
1.0
|
CZ
|
B:TYR670
|
3.2
|
27.3
|
1.0
|
O
|
B:PRO550
|
3.2
|
26.9
|
1.0
|
CE1
|
B:PHE357
|
3.2
|
37.8
|
1.0
|
CE1
|
B:TYR670
|
3.3
|
29.8
|
1.0
|
CD1
|
B:PHE357
|
3.3
|
35.5
|
1.0
|
C
|
B:ARG356
|
3.6
|
34.4
|
1.0
|
C
|
B:PRO550
|
3.7
|
28.4
|
1.0
|
CB
|
B:PRO550
|
3.8
|
28.9
|
1.0
|
CZ
|
B:PHE357
|
3.9
|
37.6
|
1.0
|
CG
|
B:PHE357
|
4.0
|
37.5
|
1.0
|
NE1
|
B:TRP353
|
4.2
|
26.8
|
1.0
|
N
|
B:PHE357
|
4.2
|
35.3
|
1.0
|
N
|
B:CYS551
|
4.2
|
28.4
|
1.0
|
CZ2
|
B:TRP353
|
4.2
|
24.6
|
1.0
|
CA
|
B:PHE357
|
4.2
|
35.5
|
1.0
|
CA
|
B:CYS551
|
4.3
|
29.9
|
1.0
|
CA
|
B:ARG356
|
4.4
|
34.6
|
1.0
|
CA
|
B:PRO550
|
4.4
|
28.2
|
1.0
|
CE2
|
B:TRP353
|
4.4
|
25.3
|
1.0
|
CE2
|
B:PHE357
|
4.4
|
41.2
|
1.0
|
CD2
|
B:PHE357
|
4.5
|
40.0
|
1.0
|
CE2
|
B:TYR670
|
4.5
|
27.0
|
1.0
|
CD1
|
B:TYR670
|
4.6
|
31.3
|
1.0
|
NH2
|
B:ARG669
|
4.6
|
32.4
|
1.0
|
NE
|
B:ARG669
|
4.6
|
32.4
|
1.0
|
CB
|
B:PHE357
|
4.7
|
35.5
|
1.0
|
CG
|
B:PRO550
|
4.9
|
29.5
|
1.0
|
CB
|
B:ARG356
|
5.0
|
34.6
|
1.0
|
|
Reference:
R.Thoma,
B.Loeffler,
M.Stihle,
W.Huber,
A.Ruf,
M.Hennig.
Structural Basis of Proline-Specific Exopeptidase Activity As Observed in Human Dipeptidyl Peptidase-IV. Structure V. 11 947 2003.
ISSN: ISSN 0969-2126
PubMed: 12906826
DOI: 10.1016/S0969-2126(03)00160-6
Page generated: Sun Aug 11 00:40:18 2024
|