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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

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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

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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

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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

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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

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