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Cadmium in PDB 9ibn: Crystal Structure of the Peptidyl-Prolyl Isomerase (Ppiase) From E. Faecium

Enzymatic activity of Crystal Structure of the Peptidyl-Prolyl Isomerase (Ppiase) From E. Faecium

All present enzymatic activity of Crystal Structure of the Peptidyl-Prolyl Isomerase (Ppiase) From E. Faecium:
5.2.1.8;

Protein crystallography data

The structure of Crystal Structure of the Peptidyl-Prolyl Isomerase (Ppiase) From E. Faecium, PDB code: 9ibn was solved by V.Napolitano, E.Kramarska, R.Berisio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.81 / 2.48
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.486, 69.674, 87.413, 90, 102.81, 90
R / Rfree (%) 20.7 / 25

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of the Peptidyl-Prolyl Isomerase (Ppiase) From E. Faecium (pdb code 9ibn). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 15 binding sites of Cadmium where determined in the Crystal Structure of the Peptidyl-Prolyl Isomerase (Ppiase) From E. Faecium, PDB code: 9ibn:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 15 in 9ibn

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Cadmium binding site 1 out of 15 in the Crystal Structure of the Peptidyl-Prolyl Isomerase (Ppiase) From E. Faecium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of the Peptidyl-Prolyl Isomerase (Ppiase) From E. Faecium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd402

b:104.0
occ:1.00
 OE2 A:GLU48 3.0 47.2 1.0
O A:HOH536 3.8 19.9 1.0
OG1 B:THR109 4.1 39.6 1.0
CD A:GLU48 4.2 45.5 1.0
CB B:GLU112 4.9 42.9 1.0
CG A:GLU48 5.0 42.7 1.0

Cadmium binding site 2 out of 15 in 9ibn

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Cadmium binding site 2 out of 15 in the Crystal Structure of the Peptidyl-Prolyl Isomerase (Ppiase) From E. Faecium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of the Peptidyl-Prolyl Isomerase (Ppiase) From E. Faecium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd403

b:75.5
occ:1.00
 O A:HOH513 2.4 15.8 1.0
OD1 A:ASP47 2.4 46.2 1.0
OD2 A:ASP47 2.7 45.0 1.0
CG A:ASP47 2.9 46.0 1.0
O A:HOH538 3.1 35.4 1.0
O A:HOH526 4.3 24.7 1.0
OG A:SER43 4.3 37.2 1.0
CB A:ASP47 4.4 40.8 1.0
CD2 A:TYR46 4.8 38.2 1.0
NZ A:LYS50 4.9 50.4 1.0

Cadmium binding site 3 out of 15 in 9ibn

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Cadmium binding site 3 out of 15 in the Crystal Structure of the Peptidyl-Prolyl Isomerase (Ppiase) From E. Faecium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of the Peptidyl-Prolyl Isomerase (Ppiase) From E. Faecium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd404

b:60.0
occ:1.00
 OD2 A:ASP171 1.9 66.2 1.0
OD1 A:ASP171 2.3 64.1 1.0
CG A:ASP171 2.3 66.6 1.0
O A:HOH525 2.5 3.8 1.0
CB A:ASP171 3.8 69.9 1.0
CB A:SER173 4.1 60.2 1.0
N A:SER173 4.6 60.5 1.0
CA A:ASP171 4.6 71.6 1.0
OG A:SER173 4.7 57.7 1.0
N A:PHE172 4.8 65.0 1.0

Cadmium binding site 4 out of 15 in 9ibn

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Cadmium binding site 4 out of 15 in the Crystal Structure of the Peptidyl-Prolyl Isomerase (Ppiase) From E. Faecium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of the Peptidyl-Prolyl Isomerase (Ppiase) From E. Faecium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd405

b:48.1
occ:1.00
 O A:HIS127 2.9 13.1 1.0
OD2 A:ASP129 3.1 14.1 1.0
N A:ASP129 3.4 14.3 1.0
CG A:ASP129 3.9 14.3 1.0
CB A:ASP129 3.9 15.1 1.0
C A:HIS127 4.0 12.4 1.0
CA A:ASP129 4.1 15.0 1.0
C A:VAL128 4.2 13.7 1.0
O A:ASP129 4.2 16.9 1.0
CA A:VAL128 4.3 12.5 1.0
CE1 A:PHE269 4.5 14.3 1.0
O A:HOH544 4.6 0.5 1.0
N A:VAL128 4.6 12.2 1.0
C A:ASP129 4.6 15.9 1.0
OD1 A:ASP129 5.0 14.1 1.0
CA A:HIS127 5.0 12.1 1.0

Cadmium binding site 5 out of 15 in 9ibn

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Cadmium binding site 5 out of 15 in the Crystal Structure of the Peptidyl-Prolyl Isomerase (Ppiase) From E. Faecium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of the Peptidyl-Prolyl Isomerase (Ppiase) From E. Faecium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd403

b:78.1
occ:1.00
 OD2 B:ASP47 2.6 46.4 1.0
OD1 B:ASP47 2.6 48.6 1.0
CG B:ASP47 2.9 45.9 1.0
CB B:ASP47 4.4 39.4 1.0
OG B:SER43 4.6 30.2 1.0

Cadmium binding site 6 out of 15 in 9ibn

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Cadmium binding site 6 out of 15 in the Crystal Structure of the Peptidyl-Prolyl Isomerase (Ppiase) From E. Faecium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of the Peptidyl-Prolyl Isomerase (Ppiase) From E. Faecium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd404

b:101.9
occ:1.00
 OE2 B:GLU48 3.5 40.8 1.0
CG A:GLU112 4.6 39.6 1.0
CD B:GLU48 4.7 39.8 1.0

Cadmium binding site 7 out of 15 in 9ibn

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Cadmium binding site 7 out of 15 in the Crystal Structure of the Peptidyl-Prolyl Isomerase (Ppiase) From E. Faecium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of the Peptidyl-Prolyl Isomerase (Ppiase) From E. Faecium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd405

b:57.6
occ:1.00
 OE1 B:GLU112 3.3 59.0 1.0
O B:HOH532 3.4 19.0 1.0
CD B:GLU112 4.2 63.4 1.0
OE2 B:GLU112 4.3 65.2 1.0

Cadmium binding site 8 out of 15 in 9ibn

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Cadmium binding site 8 out of 15 in the Crystal Structure of the Peptidyl-Prolyl Isomerase (Ppiase) From E. Faecium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of the Peptidyl-Prolyl Isomerase (Ppiase) From E. Faecium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd406

b:60.0
occ:1.00
 OD2 B:ASP78 2.4 50.4 1.0
OD1 B:ASP82 2.8 41.8 1.0
OD1 B:ASP78 2.9 42.2 1.0
OD2 B:ASP82 3.0 43.7 1.0
CG B:ASP78 3.0 43.7 1.0
CG B:ASP82 3.2 42.5 1.0
CB B:ASP78 4.5 39.1 1.0
CE B:LYS111 4.6 36.2 1.0
O B:ASP78 4.7 32.0 1.0
CB B:ASP82 4.7 40.9 1.0
NZ B:LYS111 4.9 38.9 1.0

Cadmium binding site 9 out of 15 in 9ibn

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Cadmium binding site 9 out of 15 in the Crystal Structure of the Peptidyl-Prolyl Isomerase (Ppiase) From E. Faecium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of the Peptidyl-Prolyl Isomerase (Ppiase) From E. Faecium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd407

b:21.4
occ:1.00
 OE2 B:GLU276 2.0 26.3 1.0
ND1 B:HIS127 2.5 13.1 1.0
CD B:GLU276 3.1 26.4 1.0
CE1 B:HIS127 3.3 12.9 1.0
CG B:HIS127 3.6 12.4 1.0
OE1 B:GLU276 3.6 30.7 1.0
CD B:CD408 3.8 19.2 1.0
CB B:HIS127 3.9 12.6 1.0
CG B:GLU276 4.4 22.6 1.0
NE2 B:HIS127 4.5 12.1 1.0
CD2 B:HIS127 4.6 12.0 1.0
CA B:HIS127 4.7 13.1 1.0
O B:HOH527 4.7 14.2 1.0
CE B:LYS272 4.8 19.6 1.0
O B:HIS127 4.8 14.0 1.0

Cadmium binding site 10 out of 15 in 9ibn

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Cadmium binding site 10 out of 15 in the Crystal Structure of the Peptidyl-Prolyl Isomerase (Ppiase) From E. Faecium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of the Peptidyl-Prolyl Isomerase (Ppiase) From E. Faecium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd408

b:19.2
occ:1.00
 OD2 B:ASP129 2.4 15.5 1.0
O B:HIS127 2.6 14.0 1.0
C B:HIS127 3.4 13.4 1.0
CG B:ASP129 3.6 15.8 1.0
CD B:CD409 3.7 20.2 1.0
CD B:CD407 3.8 21.4 1.0
CA B:HIS127 3.8 13.1 1.0
O B:HOH512 3.9 25.4 1.0
CB B:HIS127 4.1 12.6 1.0
N B:ASP129 4.3 15.1 1.0
CB B:ASP129 4.3 16.1 1.0
N B:VAL128 4.3 13.1 1.0
OD1 B:ASP129 4.4 15.8 1.0
C B:VAL128 4.5 14.6 1.0
CA B:VAL128 4.6 13.4 1.0
ND1 B:HIS127 4.8 13.1 1.0
CG B:HIS127 4.9 12.4 1.0
CA B:ASP129 5.0 15.8 1.0

Reference:

V.Napolitano, E.Kramarska, O.Ghilardi, F.Romero-Saavedra, P.Del Vecchio, F.Squeglia, J.Huebner, R.Berisio. Crystal Structure and Biophysical Characterisation of the Enterococcal Foldase Ppic, A Cross-Opsonic Antigen Against Gram-Positive Nosocomial Pathogens. Febs J. 2025.
ISSN: ISSN 1742-464X
PubMed: 40589145
DOI: 10.1111/FEBS.70160
Page generated: Mon Aug 4 19:10:24 2025

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