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Platinum in PDB 3ro0: Crystal Structure of Bacillus Amyloliquefaciens Pyroglutamyl Peptidase I and Terpyridine Platinum(II)

Enzymatic activity of Crystal Structure of Bacillus Amyloliquefaciens Pyroglutamyl Peptidase I and Terpyridine Platinum(II)

All present enzymatic activity of Crystal Structure of Bacillus Amyloliquefaciens Pyroglutamyl Peptidase I and Terpyridine Platinum(II):
3.4.19.3;

Protein crystallography data

The structure of Crystal Structure of Bacillus Amyloliquefaciens Pyroglutamyl Peptidase I and Terpyridine Platinum(II), PDB code: 3ro0 was solved by Y.-C.Lo, A.H.-J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 290.320, 45.520, 67.990, 90.00, 91.48, 90.00
R / Rfree (%) 17.9 / 20.5

Platinum Binding Sites:

The binding sites of Platinum atom in the Crystal Structure of Bacillus Amyloliquefaciens Pyroglutamyl Peptidase I and Terpyridine Platinum(II) (pdb code 3ro0). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 5 binding sites of Platinum where determined in the Crystal Structure of Bacillus Amyloliquefaciens Pyroglutamyl Peptidase I and Terpyridine Platinum(II), PDB code: 3ro0:
Jump to Platinum binding site number: 1; 2; 3; 4; 5;

Platinum binding site 1 out of 5 in 3ro0

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Platinum binding site 1 out of 5 in the Crystal Structure of Bacillus Amyloliquefaciens Pyroglutamyl Peptidase I and Terpyridine Platinum(II)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Crystal Structure of Bacillus Amyloliquefaciens Pyroglutamyl Peptidase I and Terpyridine Platinum(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt480

b:32.6
occ:1.00
 PT1 A:TPT480 0.0 32.6 1.0
N2 A:TPT480 2.0 37.2 1.0
N1 A:TPT480 2.0 37.8 1.0
N3 A:TPT480 2.1 39.3 1.0
SG A:CYS144 2.4 14.4 1.0
C5 A:TPT480 2.9 40.3 1.0
C6 A:TPT480 2.9 41.0 1.0
C11 A:TPT480 3.0 40.5 1.0
C10 A:TPT480 3.0 40.2 1.0
C1 A:TPT480 3.0 39.4 1.0
C15 A:TPT480 3.1 42.1 1.0
O A:GLN71 3.6 12.9 1.0
CB A:CYS144 3.7 9.5 1.0
O A:HOH284 4.1 21.2 1.0
CD2 A:PHE142 4.1 13.6 1.0
C4 A:TPT480 4.2 45.4 1.0
O A:HOH910 4.2 52.5 1.0
C7 A:TPT480 4.2 43.1 1.0
N A:CYS144 4.3 10.8 1.0
C2 A:TPT480 4.3 46.0 1.0
C9 A:TPT480 4.3 42.0 1.0
C12 A:TPT480 4.3 43.9 1.0
C14 A:TPT480 4.4 46.8 1.0
NE2 A:HIS168 4.5 15.5 1.0
O A:HOH245 4.5 13.3 1.0
CA A:CYS144 4.6 12.1 1.0
C A:GLN71 4.7 13.5 1.0
C3 A:TPT480 4.8 47.1 1.0
C8 A:TPT480 4.8 44.4 1.0
CB A:PHE142 4.8 11.6 1.0
N A:GLN71 4.9 11.7 1.0
CE2 A:PHE142 4.9 14.8 1.0
C13 A:TPT480 4.9 44.4 1.0
CG A:PHE142 5.0 12.3 1.0

Platinum binding site 2 out of 5 in 3ro0

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Platinum binding site 2 out of 5 in the Crystal Structure of Bacillus Amyloliquefaciens Pyroglutamyl Peptidase I and Terpyridine Platinum(II)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Crystal Structure of Bacillus Amyloliquefaciens Pyroglutamyl Peptidase I and Terpyridine Platinum(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt481

b:27.2
occ:1.00
 PT1 B:TPT481 0.0 27.2 1.0
N2 B:TPT481 2.0 30.1 1.0
N3 B:TPT481 2.0 31.4 1.0
N1 B:TPT481 2.1 29.3 1.0
SG B:CYS144 2.3 15.2 1.0
C11 B:TPT481 2.9 33.3 1.0
C5 B:TPT481 2.9 33.5 1.0
C10 B:TPT481 3.0 34.1 1.0
C6 B:TPT481 3.0 34.6 1.0
C15 B:TPT481 3.0 32.8 1.0
C1 B:TPT481 3.0 32.9 1.0
CB B:CYS144 3.5 9.5 1.0
O B:GLN71 3.7 14.6 1.0
N B:CYS144 4.1 10.8 1.0
C4 B:TPT481 4.3 38.1 1.0
C12 B:TPT481 4.3 35.8 1.0
CD2 B:PHE142 4.3 15.1 1.0
C9 B:TPT481 4.3 36.7 1.0
C7 B:TPT481 4.3 37.9 1.0
C2 B:TPT481 4.3 39.8 1.0
C14 B:TPT481 4.4 38.6 1.0
O B:HOH337 4.4 24.4 1.0
CA B:CYS144 4.4 10.7 1.0
NE2 B:HIS168 4.4 16.0 1.0
O B:HOH265 4.4 13.3 1.0
C B:GLN71 4.8 14.8 1.0
C3 B:TPT481 4.8 39.8 1.0
C8 B:TPT481 4.8 39.7 1.0
C13 B:TPT481 4.8 35.6 1.0
CB B:PHE142 4.9 12.5 1.0
N B:GLN71 4.9 11.8 1.0

Platinum binding site 3 out of 5 in 3ro0

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Platinum binding site 3 out of 5 in the Crystal Structure of Bacillus Amyloliquefaciens Pyroglutamyl Peptidase I and Terpyridine Platinum(II)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of Crystal Structure of Bacillus Amyloliquefaciens Pyroglutamyl Peptidase I and Terpyridine Platinum(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Pt482

b:27.3
occ:1.00
 PT1 C:TPT482 0.0 27.3 1.0
N2 C:TPT482 2.0 27.3 1.0
N3 C:TPT482 2.0 26.6 1.0
N1 C:TPT482 2.1 28.2 1.0
SG C:CYS144 2.3 13.6 1.0
C11 C:TPT482 2.9 29.8 1.0
C10 C:TPT482 2.9 30.6 1.0
C5 C:TPT482 3.0 31.1 1.0
C6 C:TPT482 3.0 32.5 1.0
C15 C:TPT482 3.0 28.8 1.0
C1 C:TPT482 3.1 32.1 1.0
CB C:CYS144 3.6 8.8 1.0
O C:GLN71 3.6 13.2 1.0
N C:CYS144 4.2 8.8 1.0
C12 C:TPT482 4.3 30.5 1.0
C9 C:TPT482 4.3 32.6 1.0
CD2 C:PHE142 4.3 15.7 1.0
C7 C:TPT482 4.3 35.3 1.0
C4 C:TPT482 4.3 32.6 1.0
C14 C:TPT482 4.4 33.4 1.0
C2 C:TPT482 4.4 36.6 1.0
CA C:CYS144 4.5 8.6 1.0
O C:HOH263 4.5 13.5 1.0
NE2 C:HIS168 4.5 15.8 1.0
O C:HOH304 4.8 25.3 1.0
C C:GLN71 4.8 13.0 1.0
C8 C:TPT482 4.8 34.0 1.0
C13 C:TPT482 4.8 31.3 1.0
N C:GLN71 4.8 10.7 1.0
C3 C:TPT482 4.9 34.4 1.0
CB C:PHE142 5.0 13.2 1.0

Platinum binding site 4 out of 5 in 3ro0

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Platinum binding site 4 out of 5 in the Crystal Structure of Bacillus Amyloliquefaciens Pyroglutamyl Peptidase I and Terpyridine Platinum(II)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of Crystal Structure of Bacillus Amyloliquefaciens Pyroglutamyl Peptidase I and Terpyridine Platinum(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Pt483

b:29.7
occ:1.00
 PT1 D:TPT483 0.0 29.7 1.0
N2 D:TPT483 2.0 32.7 1.0
N3 D:TPT483 2.1 31.4 1.0
N1 D:TPT483 2.1 31.3 1.0
SG D:CYS144 2.3 17.7 1.0
C11 D:TPT483 2.9 33.8 1.0
C10 D:TPT483 2.9 34.8 1.0
C5 D:TPT483 3.0 33.4 1.0
C6 D:TPT483 3.0 35.7 1.0
C15 D:TPT483 3.0 33.0 1.0
C1 D:TPT483 3.0 32.3 1.0
CB D:CYS144 3.5 11.9 1.0
O D:GLN71 3.7 13.6 1.0
N D:CYS144 4.1 12.2 1.0
CD2 D:PHE142 4.3 16.5 1.0
C12 D:TPT483 4.3 36.5 1.0
C9 D:TPT483 4.3 36.4 1.0
O D:HOH454 4.3 31.6 1.0
C4 D:TPT483 4.3 34.4 1.0
C7 D:TPT483 4.3 38.4 1.0
C2 D:TPT483 4.3 37.7 1.0
C14 D:TPT483 4.4 38.8 1.0
CA D:CYS144 4.4 12.0 1.0
NE2 D:HIS168 4.4 18.4 1.0
O D:HOH244 4.5 13.4 1.0
C D:GLN71 4.8 15.8 1.0
C8 D:TPT483 4.8 38.3 1.0
C13 D:TPT483 4.8 35.3 1.0
C3 D:TPT483 4.8 34.2 1.0
N D:GLN71 4.8 13.0 1.0
CB D:PHE142 4.9 14.5 1.0

Platinum binding site 5 out of 5 in 3ro0

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Platinum binding site 5 out of 5 in the Crystal Structure of Bacillus Amyloliquefaciens Pyroglutamyl Peptidase I and Terpyridine Platinum(II)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of Crystal Structure of Bacillus Amyloliquefaciens Pyroglutamyl Peptidase I and Terpyridine Platinum(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Pt484

b:51.0
occ:1.00
 PT1 D:TPT484 0.0 51.0 1.0
N2 D:TPT484 2.0 53.4 1.0
N3 D:TPT484 2.1 50.8 1.0
N1 D:TPT484 2.1 51.3 1.0
ND1 D:HIS161 2.6 40.9 1.0
CE1 D:HIS161 3.0 41.4 1.0
C11 D:TPT484 3.0 51.4 1.0
C10 D:TPT484 3.0 52.9 1.0
C5 D:TPT484 3.0 52.9 1.0
C6 D:TPT484 3.0 53.7 1.0
C1 D:TPT484 3.1 50.4 1.0
C15 D:TPT484 3.1 50.4 1.0
CG D:PRO160 3.3 32.3 1.0
CD D:PRO160 3.3 31.6 1.0
CG D:HIS161 3.8 40.1 1.0
N D:PRO160 3.9 29.7 1.0
O D:HOH881 3.9 49.1 1.0
N D:HIS161 4.0 29.5 1.0
NE2 D:HIS161 4.1 42.3 1.0
C9 D:TPT484 4.4 55.2 1.0
C12 D:TPT484 4.4 52.6 1.0
C7 D:TPT484 4.4 57.5 1.0
C4 D:TPT484 4.4 52.7 1.0
CB D:PRO160 4.4 30.6 1.0
C2 D:TPT484 4.4 56.1 1.0
CA D:PRO160 4.4 30.1 1.0
CB D:HIS161 4.5 35.9 1.0
C14 D:TPT484 4.5 53.5 1.0
CD2 D:HIS161 4.6 39.8 1.0
C D:HIS159 4.6 30.3 1.0
C D:PRO160 4.7 29.0 1.0
CA D:HIS159 4.7 30.6 1.0
CA D:HIS161 4.8 31.8 1.0
C8 D:TPT484 4.9 54.7 1.0
C13 D:TPT484 4.9 50.8 1.0
C3 D:TPT484 5.0 52.2 1.0

Reference:

Y.-C.Lo, W.-C.Su, T.-P.Ko, N.-C.Wang, A.H.-J.Wang. Terpyridine Platinum(II) Complexes Inhibit Cysteine Proteases By Binding to Active-Site Cysteine. J.Biomol.Struct.Dyn. V. 29 267 2011.
ISSN: ESSN 1538-0254
PubMed: 21875148
DOI: 10.1080/073911011010524993
Page generated: Thu Oct 10 10:48:42 2024

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