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Calcium in PDB 2xts: Crystal Structure of the Sulfane Dehydrogenase Soxcd From Paracoccus Pantotrophus

Enzymatic activity of Crystal Structure of the Sulfane Dehydrogenase Soxcd From Paracoccus Pantotrophus

All present enzymatic activity of Crystal Structure of the Sulfane Dehydrogenase Soxcd From Paracoccus Pantotrophus:
1.8.2.1;

Protein crystallography data

The structure of Crystal Structure of the Sulfane Dehydrogenase Soxcd From Paracoccus Pantotrophus, PDB code: 2xts was solved by U.Zander, A.Faust, B.U.Klink, D.De Sanctis, S.Panjikar, A.Quentmeier, F.Bardischewski, C.G.Friedrich, A.J.Scheidig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.01 / 1.33
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 122.970, 122.970, 76.390, 90.00, 90.00, 120.00
R / Rfree (%) 10.699 / 11.11

Other elements in 2xts:

The structure of Crystal Structure of the Sulfane Dehydrogenase Soxcd From Paracoccus Pantotrophus also contains other interesting chemical elements:

Molybdenum (Mo) 2 atoms
Cobalt (Co) 2 atoms
Iron (Fe) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Sulfane Dehydrogenase Soxcd From Paracoccus Pantotrophus (pdb code 2xts). 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 Sulfane Dehydrogenase Soxcd From Paracoccus Pantotrophus, PDB code: 2xts:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2xts

Go back to Calcium Binding Sites List in 2xts
Calcium binding site 1 out of 6 in the Crystal Structure of the Sulfane Dehydrogenase Soxcd From Paracoccus Pantotrophus


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 Sulfane Dehydrogenase Soxcd From Paracoccus Pantotrophus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1228

b:5.7
occ:0.75
 OD1 B:ASP68 4.6 20.7 1.0
O B:ASP68 4.7 13.2 1.0
CG B:ASP68 5.0 16.9 1.0

Calcium binding site 2 out of 6 in 2xts

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Calcium binding site 2 out of 6 in the Crystal Structure of the Sulfane Dehydrogenase Soxcd From Paracoccus Pantotrophus


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 Sulfane Dehydrogenase Soxcd From Paracoccus Pantotrophus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1229

b:5.6
occ:0.75
 O A:HOH2127 2.3 19.5 1.0
O A:HOH2066 2.3 33.7 1.0
O B:GLY214 2.3 14.1 1.0
O A:HOH2129 2.5 27.1 1.0
O B:HOH2156 2.7 29.7 1.0
C B:GLY214 3.5 13.2 1.0
CA B:GLY214 4.4 14.2 1.0
O B:HOH2147 4.4 18.5 1.0
OD1 B:ASN206 4.4 16.6 1.0
OE1 A:GLU174 4.4 12.5 1.0
N B:ARG215 4.4 12.0 1.0
CA B:ARG215 4.5 11.3 1.0
CD B:GLU210 4.8 22.9 1.0
C B:ARG215 4.8 11.4 1.0
O B:HOH2146 4.8 14.8 1.0
CG B:GLU210 4.9 17.5 1.0
OE1 B:GLU210 4.9 27.8 1.0
CD B:PRO216 4.9 10.9 1.0

Calcium binding site 3 out of 6 in 2xts

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Calcium binding site 3 out of 6 in the Crystal Structure of the Sulfane Dehydrogenase Soxcd From Paracoccus Pantotrophus


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 Sulfane Dehydrogenase Soxcd From Paracoccus Pantotrophus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1229

b:4.3
occ:0.50
 O D:HOH2029 2.2 23.1 1.0
OD1 D:ASP68 4.5 20.5 1.0
O D:ASP68 4.8 12.8 1.0
CG D:ASP68 5.0 16.5 1.0

Calcium binding site 4 out of 6 in 2xts

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Calcium binding site 4 out of 6 in the Crystal Structure of the Sulfane Dehydrogenase Soxcd From Paracoccus Pantotrophus


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 Sulfane Dehydrogenase Soxcd From Paracoccus Pantotrophus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1230

b:4.9
occ:0.60
 OE2 D:GLU36 2.3 19.5 1.0
O D:HOH2004 2.5 26.9 1.0
CD D:GLU36 3.3 15.8 1.0
CG D:GLU36 3.6 13.9 1.0
O D:HOH2006 4.2 25.4 1.0
OE1 D:GLU36 4.4 16.8 1.0

Calcium binding site 5 out of 6 in 2xts

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Calcium binding site 5 out of 6 in the Crystal Structure of the Sulfane Dehydrogenase Soxcd From Paracoccus Pantotrophus


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 Sulfane Dehydrogenase Soxcd From Paracoccus Pantotrophus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1231

b:5.5
occ:0.50
 O D:THR128 2.2 12.8 1.0
O D:HOH2088 2.4 33.2 1.0
O D:HOH2095 2.5 21.4 1.0
O D:HOH2097 2.6 28.5 1.0
C D:THR128 3.4 10.6 1.0
OD2 D:ASP133 4.2 14.8 1.0
CA D:THR128 4.3 10.4 1.0
CB D:THR128 4.3 10.8 1.0
N D:LEU129 4.4 10.2 1.0
CA D:LEU129 4.4 10.2 1.0
N D:SER130 4.9 10.1 1.0

Calcium binding site 6 out of 6 in 2xts

Go back to Calcium Binding Sites List in 2xts
Calcium binding site 6 out of 6 in the Crystal Structure of the Sulfane Dehydrogenase Soxcd From Paracoccus Pantotrophus


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 Sulfane Dehydrogenase Soxcd From Paracoccus Pantotrophus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1232

b:5.6
occ:0.75
 O C:HOH2120 2.2 21.5 1.0
O D:GLY214 2.4 13.5 1.0
O C:HOH2122 2.5 26.7 1.0
O D:HOH2156 2.6 27.7 1.0
C D:GLY214 3.6 13.0 1.0
OE1 C:GLU174 4.4 12.2 1.0
OD1 D:ASN206 4.4 17.6 1.0
CA D:GLY214 4.4 13.6 1.0
O D:HOH2151 4.5 20.9 1.0
N D:ARG215 4.5 12.2 1.0
CA D:ARG215 4.5 11.6 1.0
OE1 D:GLU210 4.6 24.6 1.0
C D:ARG215 4.8 11.0 1.0
O D:HOH2150 4.8 14.8 1.0
CD D:PRO216 5.0 10.6 1.0

Reference:

U.Zander, A.Faust, B.U.Klink, D.De Sanctis, S.Panjikar, A.Quentmeier, F.Bardischewsky, C.G.Friedrich, A.J.Scheidig. Structural Basis For the Oxidation of Protein- Bound Sulfur By the Sulfur Cycle Molybdohemo- Enzyme Sulfane Dehydrogenase Soxcd. J.Biol.Chem. V. 286 8349 2011.
ISSN: ISSN 0021-9258
PubMed: 21147779
DOI: 10.1074/JBC.M110.193631
Page generated: Fri Jul 12 19:15:37 2024

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