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Calcium in PDB 1cvr: Crystal Structure of the Arg Specific Cysteine Proteinase Gingipain R (Rgpb)

Enzymatic activity of Crystal Structure of the Arg Specific Cysteine Proteinase Gingipain R (Rgpb)

All present enzymatic activity of Crystal Structure of the Arg Specific Cysteine Proteinase Gingipain R (Rgpb):
3.4.22.37;

Protein crystallography data

The structure of Crystal Structure of the Arg Specific Cysteine Proteinase Gingipain R (Rgpb), PDB code: 1cvr was solved by A.Eichinger, H.-G.Beisel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.930, 79.920, 99.820, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 20.7

Other elements in 1cvr:

The structure of Crystal Structure of the Arg Specific Cysteine Proteinase Gingipain R (Rgpb) also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Arg Specific Cysteine Proteinase Gingipain R (Rgpb) (pdb code 1cvr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of the Arg Specific Cysteine Proteinase Gingipain R (Rgpb), PDB code: 1cvr:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1cvr

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Calcium binding site 1 out of 6 in the Crystal Structure of the Arg Specific Cysteine Proteinase Gingipain R (Rgpb)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Arg Specific Cysteine Proteinase Gingipain R (Rgpb) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:9.0
occ:1.00
 OE1 A:GLU161 2.1 20.5 1.0
O A:HOH882 2.1 21.6 1.0
ND1 A:HIS166 2.1 12.1 1.0
OD2 A:ASP292 2.2 17.0 1.0
O A:HOH818 2.2 17.3 1.0
O A:HOH717 2.2 21.0 1.0
CE1 A:HIS166 2.9 15.6 1.0
CD A:GLU161 3.1 23.3 1.0
CG A:ASP292 3.1 16.3 1.0
OD1 A:ASP292 3.3 16.2 1.0
CG A:HIS166 3.3 16.1 1.0
OE2 A:GLU161 3.3 23.2 1.0
CB A:HIS166 3.8 15.3 1.0
CA A:HIS166 4.0 17.5 1.0
NE2 A:HIS166 4.1 12.8 1.0
O A:HOH626 4.1 19.2 1.0
CD2 A:HIS166 4.3 13.1 1.0
O A:HIS166 4.3 16.8 1.0
CG A:GLU161 4.4 21.4 1.0
OD2 A:ASP158 4.5 21.9 1.0
O A:HOH749 4.5 25.6 1.0
CB A:ASP292 4.5 13.9 1.0
C A:HIS166 4.6 16.9 1.0
ND2 A:ASN159 4.6 26.0 1.0
O A:ASP158 4.7 22.0 1.0
CE A:MET288 4.7 13.3 1.0
O A:MET288 4.8 16.9 1.0
CB A:GLU161 4.8 19.8 1.0

Calcium binding site 2 out of 6 in 1cvr

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Calcium binding site 2 out of 6 in the Crystal Structure of the Arg Specific Cysteine Proteinase Gingipain R (Rgpb)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Arg Specific Cysteine Proteinase Gingipain R (Rgpb) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:24.4
occ:1.00
 OD1 A:ASP78 2.3 18.9 1.0
OE2 A:GLU258 2.3 13.9 1.0
O A:HOH690 2.4 26.5 1.0
O A:HOH632 2.4 20.0 1.0
O A:HOH672 2.5 25.4 1.0
OD2 A:ASP78 2.5 18.8 1.0
O A:PHE249 2.6 15.4 1.0
CG A:ASP78 2.8 20.6 1.0
OE1 A:GLU258 2.8 14.2 1.0
CD A:GLU258 2.9 14.9 1.0
C A:PHE249 3.5 14.0 1.0
CA A:PHE249 4.0 14.9 1.0
CB A:PHE249 4.0 14.5 1.0
OG A:SER114 4.2 16.0 1.0
CB A:ASP78 4.3 18.0 1.0
NH2 A:ARG262 4.4 15.2 1.0
CG A:GLU258 4.4 12.9 1.0
OE2 A:GLU116 4.4 29.3 1.0
N A:LEU250 4.7 17.3 1.0
O A:PHE251 4.7 21.7 1.0
CD A:GLU116 4.7 29.0 1.0
CD2 A:PHE249 4.9 15.5 1.0
CA A:PRO254 5.0 19.8 1.0

Calcium binding site 3 out of 6 in 1cvr

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Calcium binding site 3 out of 6 in the Crystal Structure of the Arg Specific Cysteine Proteinase Gingipain R (Rgpb)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Arg Specific Cysteine Proteinase Gingipain R (Rgpb) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:18.0
occ:1.00
 O A:HOH819 2.3 14.7 1.0
O A:VAL100 2.3 21.6 1.0
O A:HOH716 2.3 24.1 1.0
O A:TYR105 2.3 18.9 1.0
OD2 A:ASP103 2.4 22.1 1.0
OE2 A:GLU107 2.5 18.8 1.0
OE1 A:GLU107 2.7 19.9 1.0
CD A:GLU107 2.9 16.8 1.0
CG A:ASP103 3.4 19.5 1.0
C A:TYR105 3.5 18.5 1.0
C A:VAL100 3.5 22.5 1.0
OD1 A:ASP103 3.6 22.5 1.0
N A:VAL100 4.1 20.9 1.0
N A:TYR105 4.1 18.5 1.0
CB A:TYR105 4.1 19.6 1.0
CA A:TYR105 4.2 18.6 1.0
CA A:VAL100 4.3 22.2 1.0
O A:HOH739 4.3 28.2 1.0
O A:ASP103 4.4 19.5 1.0
CG A:GLU107 4.4 18.9 1.0
N A:ASN106 4.6 16.3 1.0
N A:GLY101 4.6 18.9 1.0
C A:ASN106 4.6 14.6 1.0
O A:HOH654 4.7 23.9 1.0
CA A:GLY101 4.7 19.1 1.0
C A:ASP103 4.7 19.1 1.0
N A:ILE99 4.7 20.2 1.0
CB A:ASP103 4.7 18.6 1.0
CA A:ASN106 4.8 15.5 1.0
N A:GLU107 4.8 12.7 1.0
CB A:VAL100 4.8 25.8 1.0
N A:ASP103 4.9 19.1 1.0
O A:ASN106 4.9 13.7 1.0

Calcium binding site 4 out of 6 in 1cvr

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Calcium binding site 4 out of 6 in the Crystal Structure of the Arg Specific Cysteine Proteinase Gingipain R (Rgpb)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Arg Specific Cysteine Proteinase Gingipain R (Rgpb) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:14.0
occ:1.00
 OE2 A:GLU296 2.0 24.7 1.0
OE1 A:GLU293 2.1 19.7 1.0
CE1 A:HIS302 2.1 25.3 1.0
O A:HOH619 2.2 26.9 1.0
CD A:GLU293 2.8 20.3 1.0
NE2 A:HIS302 2.9 28.1 1.0
OE2 A:GLU293 2.9 19.3 1.0
CD A:GLU296 3.0 25.9 1.0
ND1 A:HIS302 3.3 27.0 1.0
CB A:GLU296 3.8 20.6 1.0
OE1 A:GLU296 3.8 32.2 1.0
CG A:GLU296 4.0 23.5 1.0
NH2 A:ARG289 4.1 27.8 1.0
CD2 A:HIS302 4.2 26.6 1.0
CG A:GLU293 4.3 15.1 1.0
CG A:HIS302 4.3 27.7 1.0
NH1 A:ARG289 4.6 24.9 1.0
CA A:GLU293 4.8 13.4 1.0
CB A:GLU293 4.8 11.3 1.0
CZ A:ARG289 4.8 27.8 1.0

Calcium binding site 5 out of 6 in 1cvr

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Calcium binding site 5 out of 6 in the Crystal Structure of the Arg Specific Cysteine Proteinase Gingipain R (Rgpb)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Arg Specific Cysteine Proteinase Gingipain R (Rgpb) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:20.8
occ:1.00
 ND1 A:HIS221 2.0 26.2 1.0
O A:HOH677 2.4 37.6 1.0
CE1 A:HIS221 2.7 26.7 1.0
CG A:HIS221 3.1 23.9 1.0
CB A:HIS221 3.7 20.9 1.0
NE2 A:HIS221 3.8 27.5 1.0
CD2 A:HIS221 4.0 26.7 1.0
CA A:HIS221 4.4 18.3 1.0
O A:GLY218 4.8 17.8 1.0

Calcium binding site 6 out of 6 in 1cvr

Go back to Calcium Binding Sites List in 1cvr
Calcium binding site 6 out of 6 in the Crystal Structure of the Arg Specific Cysteine Proteinase Gingipain R (Rgpb)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Arg Specific Cysteine Proteinase Gingipain R (Rgpb) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca508

b:28.2
occ:1.00
 OE1 A:GLU119 2.1 41.2 1.0
O A:HOH922 2.3 37.2 1.0
O A:HOH712 2.5 34.9 1.0
OE2 A:GLU119 2.5 34.5 1.0
CD A:GLU119 2.6 36.3 1.0
CG A:GLU119 4.0 31.6 1.0
CB A:GLU119 4.9 24.4 1.0

Reference:

A.Eichinger, H.G.Beisel, U.Jacob, R.Huber, F.J.Medrano, A.Banbula, J.Potempa, J.Travis, W.Bode. Crystal Structure of Gingipain R: An Arg-Specific Bacterial Cysteine Proteinase with A Caspase-Like Fold. Embo J. V. 18 5453 1999.
ISSN: ISSN 0261-4189
PubMed: 10523290
DOI: 10.1093/EMBOJ/18.20.5453
Page generated: Mon Jul 7 14:12:05 2025

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