Atomistry » Calcium » PDB 1ck6-1cxi » 1cvr
Atomistry »
  Calcium »
    PDB 1ck6-1cxi »
      1cvr »

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

Go back to Calcium Binding Sites List in 1cvr
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

Go back to Calcium Binding Sites List in 1cvr
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

Go back to Calcium Binding Sites List in 1cvr
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

Go back to Calcium Binding Sites List in 1cvr
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

Go back to Calcium Binding Sites List in 1cvr
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: Thu Jul 11 07:13:25 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy