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Cadmium in PDB 6fpc: Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei

Protein crystallography data

The structure of Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei, PDB code: 6fpc was solved by S.D.Weeks, O.I.Klychnikov, P.J.Hensbergen, S.V.Strelkov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 84.90 / 1.75
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 84.900, 84.900, 113.272, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 20.2

Other elements in 6fpc:

The structure of Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Cadmium atom in the Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei (pdb code 6fpc). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 14 binding sites of Cadmium where determined in the Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei, PDB code: 6fpc:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 14 in 6fpc

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Cadmium binding site 1 out of 14 in the Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:25.8
occ:0.51
ZN A:ZN301 0.0 25.9 0.5
OE2 A:GLU181 2.0 23.7 1.0
O A:HOH495 2.1 29.6 1.0
NE2 A:HIS137 2.2 25.7 1.0
NE2 A:HIS141 2.2 25.0 1.0
OH A:TYR174 2.7 23.0 1.0
CD A:GLU181 2.7 21.8 1.0
OE1 A:GLU181 2.7 21.4 1.0
CD2 A:HIS141 3.2 25.8 1.0
CD2 A:HIS137 3.2 26.4 1.0
CE1 A:HIS137 3.2 25.4 1.0
CE1 A:HIS141 3.2 24.8 1.0
CZ A:TYR174 3.6 26.6 1.0
CE1 A:TYR174 4.1 23.8 1.0
OE1 A:GLU138 4.1 32.3 1.0
CG A:GLU181 4.2 19.8 1.0
CG A:HIS137 4.3 25.7 1.0
CG A:HIS141 4.3 24.8 1.0
ND1 A:HIS137 4.3 26.8 1.0
ND1 A:HIS141 4.4 25.3 1.0
O D:ILE81 4.4 24.8 1.0
O A:HOH402 4.5 27.9 1.0
O A:HOH421 4.6 47.3 1.0
CE2 A:TYR174 4.7 24.7 1.0
O A:HOH414 4.7 28.2 1.0
O A:HOH460 4.7 36.8 1.0
CD A:GLU138 4.8 40.0 1.0
CB A:GLU181 4.8 19.1 1.0
O A:HOH520 4.8 38.1 1.0
CA A:GLU181 4.8 19.1 1.0
OE2 A:GLU138 4.9 30.7 1.0
CB A:ALA184 4.9 22.5 1.0

Cadmium binding site 2 out of 14 in 6fpc

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Cadmium binding site 2 out of 14 in the Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:57.9
occ:1.00
O A:HOH525 2.4 53.8 1.0
ND1 A:HIS46 2.4 44.1 1.0
O A:HOH514 2.7 46.7 1.0
CG A:HIS46 3.4 40.7 1.0
CE1 A:HIS46 3.4 43.7 1.0
CB A:HIS46 3.6 36.4 1.0
CD2 A:HIS46 4.5 41.7 1.0
NE2 A:HIS46 4.5 42.6 1.0

Cadmium binding site 3 out of 14 in 6fpc

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Cadmium binding site 3 out of 14 in the Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:34.2
occ:0.17
OE1 A:GLU43 1.9 78.8 1.0
NE2 A:HIS46 2.3 42.6 1.0
O A:HOH419 2.5 38.0 1.0
CE1 A:HIS46 2.8 43.7 1.0
CD A:GLU43 3.0 76.4 1.0
OE2 A:GLU43 3.3 60.5 1.0
O A:HOH423 3.5 50.6 1.0
CD2 A:HIS46 3.6 41.7 1.0
ND1 A:HIS46 4.0 44.1 1.0
CG A:GLU43 4.3 57.8 1.0
CG A:HIS46 4.4 40.7 1.0
O A:TYR44 4.6 32.0 1.0
N A:TYR44 4.8 37.2 1.0
CA A:GLU43 4.9 43.4 1.0

Cadmium binding site 4 out of 14 in 6fpc

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Cadmium binding site 4 out of 14 in the Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd302

b:24.8
occ:0.55
ZN B:ZN301 0.0 24.8 0.5
OE2 B:GLU181 2.1 20.9 1.0
NE2 B:HIS137 2.1 22.2 1.0
NE2 B:HIS141 2.1 24.3 1.0
O C:HOH501 2.3 29.8 1.0
OH B:TYR174 2.7 24.8 1.0
CD B:GLU181 2.8 18.7 1.0
OE1 B:GLU181 2.8 18.6 1.0
CE1 B:HIS137 3.1 22.1 1.0
CD2 B:HIS141 3.1 24.9 1.0
CD2 B:HIS137 3.1 22.7 1.0
CE1 B:HIS141 3.2 23.7 1.0
CZ B:TYR174 3.7 29.8 1.0
CE1 B:TYR174 4.1 24.2 1.0
ND1 B:HIS137 4.2 23.4 1.0
CG B:HIS137 4.3 21.8 1.0
CG B:GLU181 4.3 20.4 1.0
CG B:HIS141 4.3 24.5 1.0
ND1 B:HIS141 4.3 26.2 1.0
O C:ILE81 4.3 24.7 1.0
OE1 B:GLU138 4.3 30.4 1.0
O B:HOH401 4.5 26.4 1.0
O B:HOH429 4.5 30.6 1.0
CE2 B:TYR174 4.7 22.5 1.0
O B:HOH451 4.7 28.6 1.0
O B:HOH528 4.8 36.1 1.0
CB B:ALA184 4.8 20.8 1.0
OE2 B:GLU138 4.8 22.1 1.0
CD B:GLU138 4.8 29.0 1.0
CA B:GLU181 4.8 17.7 1.0
CB B:GLU181 4.9 17.3 1.0
O B:HOH421 4.9 23.4 1.0

Cadmium binding site 5 out of 14 in 6fpc

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Cadmium binding site 5 out of 14 in the Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd303

b:70.9
occ:1.00
NE2 B:HIS46 2.3 42.9 1.0
O B:HOH526 3.1 53.3 1.0
CD2 B:HIS46 3.3 43.4 1.0
CE1 B:HIS46 3.3 42.2 1.0
CG B:HIS46 4.4 41.2 1.0
ND1 B:HIS46 4.4 42.3 1.0
O B:HOH549 4.6 53.5 1.0
OH B:TYR44 4.8 45.0 1.0
CE2 B:TYR44 4.8 33.3 1.0

Cadmium binding site 6 out of 14 in 6fpc

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Cadmium binding site 6 out of 14 in the Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd304

b:64.0
occ:1.00
OD2 B:ASP194 2.6 50.7 1.0
OD1 B:ASP194 2.6 42.4 1.0
CG B:ASP194 2.9 43.1 1.0
O B:HOH541 3.5 56.0 1.0
O B:HOH462 4.3 49.6 1.0
CB B:ASP194 4.5 35.9 1.0

Cadmium binding site 7 out of 14 in 6fpc

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Cadmium binding site 7 out of 14 in the Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd302

b:26.6
occ:0.67
ZN C:ZN301 0.0 26.6 0.3
O C:HOH453 1.9 45.5 1.0
OE1 C:GLU181 2.0 25.9 1.0
NE2 C:HIS137 2.2 25.3 1.0
NE2 C:HIS141 2.3 25.4 1.0
OH C:TYR174 2.6 32.6 1.0
CD C:GLU181 2.9 32.1 1.0
OE2 C:GLU181 3.1 30.5 1.0
CD2 C:HIS137 3.2 25.8 1.0
CE1 C:HIS141 3.2 25.1 1.0
CE1 C:HIS137 3.2 24.9 1.0
CD2 C:HIS141 3.3 26.3 1.0
CZ C:TYR174 3.6 35.3 1.0
OE2 C:GLU138 3.8 44.9 1.0
CE1 C:TYR174 4.3 30.4 1.0
CG C:GLU181 4.3 26.0 1.0
CG C:HIS137 4.3 24.4 1.0
ND1 C:HIS137 4.4 25.8 1.0
ND1 C:HIS141 4.4 26.7 1.0
CG C:HIS141 4.4 25.4 1.0
O C:HOH436 4.5 35.0 1.0
CE2 C:TYR174 4.5 32.2 1.0
CD C:GLU138 4.7 49.2 1.0
CD1 C:LEU103 4.8 38.5 1.0
OE1 C:GLU138 4.9 34.0 1.0
CB C:GLU181 4.9 21.9 1.0
CG C:LEU103 4.9 37.8 1.0
CB C:ALA184 5.0 24.3 1.0
CA C:GLU181 5.0 21.0 1.0

Cadmium binding site 8 out of 14 in 6fpc

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Cadmium binding site 8 out of 14 in the Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd303

b:75.1
occ:1.00
OE2 C:GLU57 2.4 43.3 1.0
O C:HOH474 2.5 48.8 1.0
OE1 C:GLN54 2.5 51.2 1.0
OE1 C:GLU29 2.7 82.1 1.0
OE2 C:GLU29 2.8 75.7 1.0
CD C:GLU29 3.0 82.8 1.0
CD C:GLU57 3.1 54.9 1.0
OE1 C:GLU57 3.1 49.3 1.0
CD C:GLN54 3.6 57.2 1.0
N C:GLU29 4.1 53.9 1.0
NE2 C:GLN54 4.1 51.2 1.0
CG C:GLU29 4.4 65.2 1.0
CG C:GLU57 4.6 33.5 1.0
O C:HOH433 4.8 31.8 1.0
CG C:GLN54 4.9 31.4 1.0

Cadmium binding site 9 out of 14 in 6fpc

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Cadmium binding site 9 out of 14 in the Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd304

b:47.5
occ:0.49
NE2 C:HIS46 2.4 38.4 0.8
CE1 C:HIS46 2.5 35.1 0.2
NE2 C:HIS46 2.7 35.0 0.2
CE1 C:HIS46 3.3 37.6 0.8
CD2 C:HIS46 3.4 38.3 0.8
ND1 C:HIS46 3.7 35.4 0.2
CD2 C:HIS46 4.0 34.8 0.2
ND1 C:HIS46 4.4 37.4 0.8
CG C:HIS46 4.5 33.1 0.2
CG C:HIS46 4.5 35.6 0.8
OH C:TYR44 4.5 34.1 1.0
CE2 C:TYR44 4.6 28.3 1.0
CZ C:TYR44 4.8 33.2 1.0

Cadmium binding site 10 out of 14 in 6fpc

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Cadmium binding site 10 out of 14 in the Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Structure of the Pro-Pro Endopeptidase (Ppep-2) From Paenibacillus Alvei within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd305

b:72.2
occ:0.43
O C:HOH503 2.2 42.9 1.0
ND1 C:HIS46 2.6 35.4 0.2
O C:HOH419 2.6 43.8 1.0
CD2 C:HIS46 3.0 38.3 0.8
CE1 C:HIS46 3.4 35.1 0.2
CG C:HIS46 3.7 33.1 0.2
CG C:HIS46 3.8 35.6 0.8
CB C:HIS46 4.0 31.1 0.8
CB C:HIS46 4.0 29.2 0.2
O C:HOH467 4.1 39.8 1.0
NE2 C:HIS46 4.1 38.4 0.8
NE2 C:HIS46 4.6 35.0 0.2
OH C:TYR44 4.6 34.1 1.0
CD2 C:HIS46 4.7 34.8 0.2

Reference:

O.I.Klychnikov, T.M.Shamorkina, S.D.Weeks, H.C.Van Leeuwen, J.Corver, J.W.Drijfhout, P.A.Van Veelen, N.N.Sluchanko, S.V.Strelkov, P.J.Hensbergen. Discovery of A New Pro-Pro Endopeptidase, Ppep-2, Provides Mechanistic Insights Into the Differences in Substrate Specificity Within the Ppep Family. J. Biol. Chem. V. 293 11154 2018.
ISSN: ESSN 1083-351X
PubMed: 29794027
DOI: 10.1074/JBC.RA118.003244
Page generated: Sat Dec 12 08:28:22 2020

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