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Calcium in PDB 4ief: Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains

Enzymatic activity of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains

All present enzymatic activity of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains:
3.4.22.37;

Protein crystallography data

The structure of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains, PDB code: 4ief was solved by I.De Diego, F.T.Veillard, T.Guevara, B.Potempa, M.Sztukowska, J.Potempa, F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.67 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 84.420, 133.140, 109.830, 90.00, 90.52, 90.00
R / Rfree (%) 18.9 / 22.5

Other elements in 4ief:

The structure of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Barium (Ba) 4 atoms
Chlorine (Cl) 1 atom
Sodium (Na) 3 atoms

Calcium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Calcium atom in the Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains (pdb code 4ief). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 14 binding sites of Calcium where determined in the Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains, PDB code: 4ief:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 14 in 4ief

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Calcium binding site 1 out of 14 in the Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:28.0
occ:1.00
 O B:TYR334 2.3 32.0 1.0
O B:VAL329 2.4 38.3 1.0
OD2 B:ASP332 2.4 33.7 1.0
O A:ILE159 2.5 32.6 1.0
OE2 B:GLU336 2.6 35.1 1.0
O B:HOH831 2.6 26.9 1.0
OE1 B:GLU336 2.6 38.1 1.0
CD B:GLU336 2.9 48.5 1.0
CG B:ASP332 3.4 35.4 1.0
C B:TYR334 3.4 31.8 1.0
C B:VAL329 3.5 39.4 1.0
OD1 B:ASP332 3.7 34.1 1.0
C A:ILE159 3.7 34.4 1.0
CB B:TYR334 4.1 30.3 1.0
CA B:TYR334 4.1 29.1 1.0
N B:TYR334 4.2 30.5 1.0
N B:VAL329 4.3 36.2 1.0
O B:GLY330 4.3 37.4 1.0
CA B:VAL329 4.4 36.4 1.0
CG B:GLU336 4.4 37.8 1.0
N B:GLY330 4.5 36.3 1.0
N B:ASN335 4.5 27.3 1.0
O B:ASP332 4.6 38.5 1.0
CA A:ILE159 4.6 30.4 1.0
N A:LEU160 4.7 32.2 1.0
CA B:GLY330 4.7 36.4 1.0
N A:ILE159 4.7 30.0 1.0
CB B:ASP332 4.7 35.7 1.0
CA A:LEU160 4.7 32.2 1.0
CB A:ILE159 4.8 34.7 1.0
C B:GLY330 4.8 39.3 1.0
N B:ILE328 4.8 34.8 1.0
C B:ASP332 4.9 38.5 1.0
CB B:VAL329 4.9 40.4 1.0
CA B:ASN335 4.9 26.1 1.0
CA B:GLN327 4.9 29.3 1.0
C B:ASN335 4.9 30.8 1.0
N B:GLU336 4.9 27.9 1.0
N A:ARG161 5.0 34.6 1.0

Calcium binding site 2 out of 14 in 4ief

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Calcium binding site 2 out of 14 in the Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca703

b:26.0
occ:1.00
 OE2 B:GLU487 2.3 28.7 1.0
O B:HOH845 2.4 32.0 1.0
O B:PHE478 2.4 24.0 1.0
OD1 B:ASP307 2.5 27.4 1.0
O B:HOH846 2.5 26.0 1.0
OD2 B:ASP307 2.5 28.1 1.0
O B:HOH847 2.5 20.2 1.0
OE1 B:GLU487 2.7 31.4 1.0
CD B:GLU487 2.8 37.3 1.0
CG B:ASP307 2.8 27.9 1.0
C B:PHE478 3.4 24.8 1.0
CA B:PHE478 3.9 21.5 1.0
O B:HOH964 4.1 38.5 1.0
CB B:PHE478 4.1 22.4 1.0
NH2 B:ARG491 4.2 16.9 1.0
CG B:GLU487 4.3 23.1 1.0
CB B:ASP307 4.3 21.9 1.0
OG B:SER343 4.4 26.5 1.0
O B:TYR480 4.4 30.0 1.0
OE1 B:GLU345 4.4 29.0 1.0
N B:LEU479 4.6 21.6 1.0
CD2 B:HIS308 4.7 32.1 1.0
CA B:PRO483 4.7 26.4 1.0
CD B:GLU345 4.9 47.0 1.0
CD2 B:PHE478 4.9 25.8 1.0
O B:VAL482 5.0 27.8 1.0
CZ B:ARG491 5.0 32.2 1.0

Calcium binding site 3 out of 14 in 4ief

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Calcium binding site 3 out of 14 in the Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca704

b:51.9
occ:1.00
 O D:HOH917 2.4 29.6 1.0
OD2 B:ASP613 2.5 49.0 1.0
OE2 B:GLU639 2.5 53.4 1.0
OE1 B:GLU639 2.6 63.2 1.0
OD1 B:ASP613 2.7 40.3 1.0
O D:HOH816 2.8 37.9 1.0
CD B:GLU639 2.9 62.6 1.0
CG B:ASP613 2.9 40.4 1.0
NH1 D:ARG362 4.1 42.8 1.0
O D:HOH815 4.1 24.2 1.0
O D:HOH817 4.3 49.1 1.0
CG B:GLU639 4.3 49.9 1.0
CB B:ASP613 4.4 34.2 1.0
OD2 D:ASP255 4.8 66.2 1.0
OD2 B:ASP614 4.8 44.2 1.0
NH2 D:ARG362 4.9 39.0 1.0
CZ D:ARG362 5.0 55.5 1.0

Calcium binding site 4 out of 14 in 4ief

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Calcium binding site 4 out of 14 in the Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca705

b:44.7
occ:1.00
 OD1 B:ASP614 2.3 40.4 1.0
OD1 D:ASP614 2.5 41.5 1.0
O B:HOH813 3.0 38.6 1.0
CG B:ASP614 3.5 40.0 1.0
CG D:ASP614 3.7 40.4 1.0
OG1 D:THR643 4.1 33.8 1.0
CA D:ASP614 4.1 31.1 1.0
CA B:ASP614 4.1 31.7 1.0
OG1 B:THR643 4.2 30.8 1.0
N B:ASP614 4.3 31.8 1.0
N D:ASP614 4.3 31.6 1.0
CB B:ASP614 4.4 34.4 1.0
CB D:ASP614 4.4 33.5 1.0
OD2 B:ASP614 4.4 44.2 1.0
OD2 D:ASP614 4.6 46.6 1.0
O B:HOH811 4.8 28.8 1.0
O D:HOH820 4.9 28.5 1.0

Calcium binding site 5 out of 14 in 4ief

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Calcium binding site 5 out of 14 in the Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca702

b:28.2
occ:1.00
 OD1 D:ASP307 2.4 27.6 1.0
OE2 D:GLU487 2.4 27.4 1.0
O D:PHE478 2.4 28.3 1.0
OD2 D:ASP307 2.4 26.6 1.0
O D:HOH898 2.5 39.5 1.0
O D:HOH832 2.6 28.8 1.0
O D:HOH833 2.7 24.0 1.0
CG D:ASP307 2.7 27.5 1.0
OE1 D:GLU487 2.8 31.1 1.0
CD D:GLU487 2.9 31.9 1.0
C D:PHE478 3.4 28.5 1.0
CA D:PHE478 3.9 23.4 1.0
CB D:PHE478 4.1 23.5 1.0
CB D:ASP307 4.2 26.3 1.0
O D:TYR480 4.3 32.3 1.0
NH2 D:ARG491 4.4 17.2 1.0
CG D:GLU487 4.4 28.3 1.0
OG D:SER343 4.5 33.7 1.0
N D:LEU479 4.6 25.9 1.0
OE2 D:GLU345 4.6 41.9 1.0
CA D:PRO483 4.8 27.3 1.0
CD D:GLU345 4.9 51.6 1.0
O D:VAL482 4.9 31.2 1.0
CD2 D:PHE478 4.9 25.0 1.0

Calcium binding site 6 out of 14 in 4ief

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Calcium binding site 6 out of 14 in the Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca703

b:23.4
occ:1.00
 O D:TYR334 2.3 24.9 1.0
OE2 D:GLU336 2.4 25.5 1.0
O D:VAL329 2.4 28.0 1.0
O D:HOH834 2.4 21.6 1.0
OD2 D:ASP332 2.4 27.9 1.0
O C:ILE159 2.5 26.8 1.0
OE1 D:GLU336 2.7 32.2 1.0
CD D:GLU336 2.9 36.3 1.0
CG D:ASP332 3.4 26.9 1.0
C D:TYR334 3.4 24.3 1.0
C D:VAL329 3.6 29.7 1.0
OD1 D:ASP332 3.7 25.7 1.0
C C:ILE159 3.7 27.5 1.0
CB D:TYR334 3.9 20.9 1.0
CA D:TYR334 4.0 19.7 1.0
N D:TYR334 4.2 20.8 1.0
N D:VAL329 4.3 26.5 1.0
CG D:GLU336 4.4 26.5 1.0
CA D:VAL329 4.4 27.1 1.0
N D:GLY330 4.5 27.3 1.0
N D:ASN335 4.6 19.9 1.0
O D:GLY330 4.6 30.0 1.0
N C:LEU160 4.6 24.7 1.0
CA C:ILE159 4.6 24.0 1.0
CA C:LEU160 4.6 24.8 1.0
O D:ASP332 4.7 27.3 1.0
CA D:GLY330 4.7 27.3 1.0
N C:ILE159 4.7 24.1 1.0
O D:HOH911 4.7 37.3 1.0
CB D:ASP332 4.8 26.9 1.0
CB D:VAL329 4.8 31.7 1.0
CB C:ILE159 4.8 27.1 1.0
C D:ASN335 4.9 24.6 1.0
N D:GLU336 4.9 22.3 1.0
CA D:ASN335 5.0 19.7 1.0
N C:ARG161 5.0 27.3 1.0
C D:GLY330 5.0 31.3 1.0
C D:ASP332 5.0 27.4 1.0
N D:ILE328 5.0 24.8 1.0

Calcium binding site 7 out of 14 in 4ief

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Calcium binding site 7 out of 14 in the Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca704

b:42.3
occ:1.00
 O D:HOH899 2.2 34.8 1.0
O B:HOH815 2.3 39.4 1.0
OD2 D:ASP613 2.5 44.0 1.0
OE2 D:GLU639 2.5 54.7 1.0
OE1 D:GLU639 2.6 61.5 1.0
OD1 D:ASP613 2.7 40.1 1.0
O B:HOH947 2.8 32.2 1.0
CD D:GLU639 2.9 64.9 1.0
CG D:ASP613 2.9 39.8 1.0
CG D:GLU639 4.3 46.4 1.0
NH1 B:ARG362 4.4 33.0 1.0
CB D:ASP613 4.5 33.9 1.0
O D:HOH896 4.5 36.5 1.0
OD2 B:ASP255 4.7 59.6 1.0
OD2 D:ASP614 4.8 46.6 1.0

Calcium binding site 8 out of 14 in 4ief

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Calcium binding site 8 out of 14 in the Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca702

b:32.1
occ:1.00
 OD2 F:ASP332 2.3 38.0 1.0
O F:TYR334 2.3 35.1 1.0
O F:VAL329 2.4 41.0 1.0
O F:HOH817 2.5 36.4 1.0
O E:ILE159 2.5 36.0 1.0
OE2 F:GLU336 2.6 33.5 1.0
OE1 F:GLU336 2.7 30.9 1.0
CD F:GLU336 3.0 45.3 1.0
CG F:ASP332 3.3 37.8 1.0
C F:TYR334 3.5 34.1 1.0
C F:VAL329 3.6 41.3 1.0
OD1 F:ASP332 3.6 38.3 1.0
C E:ILE159 3.7 37.6 1.0
CB F:TYR334 4.0 29.7 1.0
CA F:TYR334 4.1 29.2 1.0
N F:TYR334 4.1 30.3 1.0
N F:VAL329 4.3 36.8 1.0
O F:GLY330 4.4 39.0 1.0
CA F:VAL329 4.4 37.6 1.0
CG F:GLU336 4.5 35.4 1.0
N F:GLY330 4.5 38.0 1.0
O F:ASP332 4.5 34.3 1.0
N F:ASN335 4.6 29.7 1.0
CA E:ILE159 4.6 33.2 1.0
CB F:ASP332 4.6 33.9 1.0
CA F:GLY330 4.7 37.7 1.0
N E:LEU160 4.7 35.5 1.0
N E:ILE159 4.7 32.8 1.0
CB E:ILE159 4.8 37.4 1.0
C F:ASP332 4.8 36.0 1.0
CA E:LEU160 4.8 35.1 1.0
C F:GLY330 4.8 40.6 1.0
CB F:VAL329 4.9 41.6 1.0
N F:ILE328 5.0 37.0 1.0
CA F:ASN335 5.0 28.7 1.0

Calcium binding site 9 out of 14 in 4ief

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Calcium binding site 9 out of 14 in the Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca703

b:36.4
occ:1.00
 O F:PHE478 2.4 35.2 1.0
OD1 F:ASP307 2.4 31.0 1.0
OE2 F:GLU487 2.4 28.9 1.0
OD2 F:ASP307 2.4 28.5 1.0
O F:HOH837 2.5 29.4 1.0
O F:HOH836 2.6 43.2 1.0
OE1 F:GLU487 2.7 29.8 1.0
CG F:ASP307 2.7 30.1 1.0
CD F:GLU487 2.9 42.0 1.0
C F:PHE478 3.4 34.9 1.0
CA F:PHE478 3.9 28.8 1.0
CB F:PHE478 4.0 29.2 1.0
NH2 F:ARG491 4.2 28.4 1.0
CB F:ASP307 4.3 26.2 1.0
CG F:GLU487 4.4 31.0 1.0
OG F:SER343 4.4 36.8 1.0
O F:TYR480 4.5 39.6 1.0
OE2 F:GLU345 4.5 51.6 1.0
N F:LEU479 4.5 32.5 1.0
CA F:PRO483 4.8 34.0 1.0
CD2 F:PHE478 4.8 31.4 1.0
CD F:GLU345 4.9 61.9 1.0
CG F:PHE478 5.0 29.4 1.0
O F:VAL482 5.0 39.3 1.0

Calcium binding site 10 out of 14 in 4ief

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Calcium binding site 10 out of 14 in the Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca704

b:54.7
occ:1.00
 OD2 F:ASP613 2.5 44.3 1.0
OE2 F:GLU639 2.5 62.6 1.0
OE1 F:GLU639 2.6 44.9 1.0
OD1 F:ASP613 2.7 40.9 1.0
CD F:GLU639 2.8 62.8 1.0
CG F:ASP613 2.9 39.5 1.0
NH1 H:ARG362 4.2 29.6 1.0
CG F:GLU639 4.3 46.5 1.0
OD2 H:ASP255 4.3 58.4 1.0
CB F:ASP613 4.4 32.4 1.0
O F:HOH916 4.7 37.1 1.0
CG H:ASP255 4.7 49.4 1.0
O F:HOH829 4.8 46.4 1.0
OD2 F:ASP614 4.8 51.0 1.0
O F:HOH929 4.9 32.7 1.0

Reference:

I.De Diego, F.T.Veillard, T.Guevara, B.Potempa, M.Sztukowska, J.Potempa, F.X.Gomis-Ruth. Porphyromonas Gingivalis Virulence Factor Gingipain Rgpb Shows A Unique Zymogenic Mechanism For Cysteine Peptidases. J.Biol.Chem. V. 288 14287 2013.
ISSN: ISSN 0021-9258
PubMed: 23558682
DOI: 10.1074/JBC.M112.444927
Page generated: Tue Jul 8 22:54:08 2025

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