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Calcium in PDB 1wc5: Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Alpha,Beta-Methylene-Atp in Presence of Bicarbonate

Enzymatic activity of Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Alpha,Beta-Methylene-Atp in Presence of Bicarbonate

All present enzymatic activity of Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Alpha,Beta-Methylene-Atp in Presence of Bicarbonate:
4.6.1.1;

Protein crystallography data

The structure of Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Alpha,Beta-Methylene-Atp in Presence of Bicarbonate, PDB code: 1wc5 was solved by C.Steegborn, T.N.Litvin, L.R.Levin, J.Buck, H.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.99 / 2.3
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.303, 71.193, 106.733, 90.00, 95.81, 90.00
R / Rfree (%) 20.2 / 26.2

Other elements in 1wc5:

The structure of Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Alpha,Beta-Methylene-Atp in Presence of Bicarbonate also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Alpha,Beta-Methylene-Atp in Presence of Bicarbonate (pdb code 1wc5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Alpha,Beta-Methylene-Atp in Presence of Bicarbonate, PDB code: 1wc5:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1wc5

Go back to Calcium Binding Sites List in 1wc5
Calcium binding site 1 out of 4 in the Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Alpha,Beta-Methylene-Atp in Presence of Bicarbonate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Alpha,Beta-Methylene-Atp in Presence of Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2100

b:32.6
occ:1.00
 OD2 A:ASP1061 2.2 37.0 1.0
O3G A:APC1500 2.4 39.7 1.0
O1A A:APC1500 2.5 45.0 1.0
O A:ILE1018 2.5 31.7 1.0
O2B A:APC1500 2.5 39.2 1.0
OD2 A:ASP1017 2.6 43.6 1.0
OD1 A:ASP1017 2.9 46.9 1.0
CG A:ASP1017 3.0 41.4 1.0
CG A:ASP1061 3.0 37.2 1.0
OD1 A:ASP1061 3.1 41.1 1.0
PA A:APC1500 3.4 46.0 1.0
PB A:APC1500 3.4 39.3 1.0
C3A A:APC1500 3.6 43.7 1.0
PG A:APC1500 3.6 42.1 1.0
O2A A:APC1500 3.7 43.7 1.0
C A:ILE1018 3.7 33.3 1.0
O3B A:APC1500 3.7 40.4 1.0
N A:ILE1018 3.9 34.7 1.0
MG A:MG2000 4.0 42.3 1.0
CB A:ASP1017 4.3 39.0 1.0
CA A:ILE1018 4.3 33.9 1.0
C A:ASP1017 4.4 36.1 1.0
O1G A:APC1500 4.4 42.4 1.0
CB A:PHE1021 4.4 41.1 1.0
CB A:ASP1061 4.5 33.4 1.0
CB A:ILE1018 4.7 35.1 1.0
CA A:ASP1017 4.7 35.9 1.0
N A:VAL1019 4.8 32.5 1.0
O2G A:APC1500 4.8 43.8 1.0
O1B A:APC1500 4.8 43.5 1.0
N A:PHE1021 4.8 39.7 1.0
O5' A:APC1500 4.8 43.6 1.0

Calcium binding site 2 out of 4 in 1wc5

Go back to Calcium Binding Sites List in 1wc5
Calcium binding site 2 out of 4 in the Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Alpha,Beta-Methylene-Atp in Presence of Bicarbonate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Alpha,Beta-Methylene-Atp in Presence of Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2100

b:29.9
occ:1.00
 OD2 B:ASP1061 2.2 23.6 1.0
O2B B:APC1500 2.3 20.6 1.0
O B:ILE1018 2.4 24.7 1.0
O2G B:APC1500 2.4 23.4 1.0
OD2 B:ASP1017 2.5 37.2 1.0
O1A B:APC1500 2.6 35.1 1.0
OD1 B:ASP1017 2.7 40.6 1.0
CG B:ASP1017 2.9 34.1 1.0
CG B:ASP1061 3.2 27.1 1.0
PB B:APC1500 3.5 25.5 1.0
PA B:APC1500 3.5 35.9 1.0
C B:ILE1018 3.5 25.6 1.0
OD1 B:ASP1061 3.5 33.0 1.0
O2A B:APC1500 3.5 34.2 1.0
PG B:APC1500 3.6 23.8 1.0
N B:ILE1018 3.9 25.1 1.0
O3B B:APC1500 3.9 25.2 1.0
C3A B:APC1500 4.1 31.3 1.0
O3G B:APC1500 4.2 25.8 1.0
CA B:ILE1018 4.2 24.2 1.0
MG B:MG2000 4.3 27.8 1.0
CB B:ASP1017 4.3 30.5 1.0
C B:ASP1017 4.5 27.2 1.0
CB B:PHE1021 4.5 30.8 1.0
CB B:ASP1061 4.5 25.2 1.0
CB B:ILE1018 4.6 23.1 1.0
N B:VAL1019 4.6 26.4 1.0
N B:PHE1021 4.6 31.0 1.0
N B:GLY1020 4.8 29.7 1.0
O1B B:APC1500 4.8 30.9 1.0
O1G B:APC1500 4.9 25.1 1.0
CA B:ASP1017 4.9 27.9 1.0
CA B:VAL1019 4.9 27.9 1.0
NH1 B:ARG1117 4.9 34.7 1.0

Calcium binding site 3 out of 4 in 1wc5

Go back to Calcium Binding Sites List in 1wc5
Calcium binding site 3 out of 4 in the Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Alpha,Beta-Methylene-Atp in Presence of Bicarbonate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Alpha,Beta-Methylene-Atp in Presence of Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2100

b:24.1
occ:1.00
 O1A C:APC1500 2.1 31.2 1.0
O2B C:APC1500 2.2 28.6 1.0
O1G C:APC1500 2.3 25.7 1.0
OD2 C:ASP1017 2.3 44.1 1.0
O C:ILE1018 2.4 18.6 1.0
OD2 C:ASP1061 2.5 25.7 1.0
CG C:ASP1017 3.1 38.5 1.0
CG C:ASP1061 3.2 28.2 1.0
OD1 C:ASP1061 3.3 32.2 1.0
OD1 C:ASP1017 3.3 40.5 1.0
PA C:APC1500 3.3 30.6 1.0
PB C:APC1500 3.4 28.0 1.0
C C:ILE1018 3.6 22.5 1.0
PG C:APC1500 3.6 24.2 1.0
C3A C:APC1500 3.8 27.9 1.0
O2A C:APC1500 3.9 25.9 1.0
O3B C:APC1500 3.9 23.6 1.0
N C:ILE1018 4.1 28.0 1.0
O C:HOH2018 4.1 19.1 1.0
CA C:ILE1018 4.3 24.8 1.0
MG C:MG2000 4.3 18.1 1.0
O2G C:APC1500 4.4 27.5 1.0
CB C:PHE1021 4.5 27.9 1.0
CB C:ASP1017 4.5 36.6 1.0
C C:ASP1017 4.5 30.5 1.0
N C:PHE1021 4.6 27.3 1.0
O5' C:APC1500 4.6 28.8 1.0
CB C:ILE1018 4.6 24.7 1.0
N C:VAL1019 4.6 22.0 1.0
O1B C:APC1500 4.6 27.0 1.0
CB C:ASP1061 4.7 25.1 1.0
O3G C:APC1500 4.7 26.5 1.0
N C:GLY1020 4.7 23.1 1.0
CA C:VAL1019 4.9 21.8 1.0
CA C:ASP1017 5.0 31.0 1.0

Calcium binding site 4 out of 4 in 1wc5

Go back to Calcium Binding Sites List in 1wc5
Calcium binding site 4 out of 4 in the Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Alpha,Beta-Methylene-Atp in Presence of Bicarbonate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Alpha,Beta-Methylene-Atp in Presence of Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2100

b:32.6
occ:1.00
 O2B D:APC1500 2.2 38.9 1.0
O3G D:APC1500 2.4 38.2 1.0
O D:ILE1018 2.4 30.9 1.0
OD1 D:ASP1017 2.4 35.7 1.0
OD2 D:ASP1061 2.6 35.9 1.0
O1A D:APC1500 2.6 47.3 1.0
OD1 D:ASP1061 2.9 37.5 1.0
OD2 D:ASP1017 3.0 31.7 1.0
CG D:ASP1017 3.1 33.1 1.0
CG D:ASP1061 3.1 34.6 1.0
O2A D:APC1500 3.5 42.2 1.0
PA D:APC1500 3.5 44.4 1.0
PB D:APC1500 3.5 39.5 1.0
C D:ILE1018 3.6 31.0 1.0
PG D:APC1500 3.7 35.9 1.0
MG D:MG2000 3.9 40.9 1.0
N D:ILE1018 4.1 30.8 1.0
O3B D:APC1500 4.1 39.5 1.0
C3A D:APC1500 4.1 43.5 1.0
CA D:ILE1018 4.3 31.2 1.0
O1G D:APC1500 4.4 40.0 1.0
CB D:ASP1017 4.5 31.4 1.0
CB D:PHE1021 4.5 50.5 1.0
C D:ASP1017 4.6 31.0 1.0
CB D:ASP1061 4.6 32.5 1.0
N D:VAL1019 4.6 32.2 1.0
O1B D:APC1500 4.7 41.6 1.0
CB D:ILE1018 4.7 30.8 1.0
N D:PHE1021 4.8 48.0 1.0
CA D:VAL1019 4.8 33.1 1.0
O2G D:APC1500 4.9 37.8 1.0
O5' D:APC1500 4.9 41.9 1.0
N D:GLY1020 4.9 38.1 1.0
CA D:ASP1017 5.0 30.3 1.0

Reference:

C.Steegborn, T.N.Litvin, L.R.Levin, J.Buck, H.Wu. Bicarbonate Activation of Adenylyl Cyclase Via Promotion of Catalytic Active Site Closure and Metal Recruitment Nat.Struct.Mol.Biol. V. 12 32 2005.
ISSN: ISSN 1545-9993
PubMed: 15619637
DOI: 10.1038/NSMB880
Page generated: Fri Jul 12 07:09:48 2024

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