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Magnesium 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:

Calcium (Ca) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1wc5

Go back to Magnesium Binding Sites List in 1wc5
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg2000

b:42.3
occ:1.00
 O A:HOH2010 2.6 49.1 1.0
OD2 A:ASP1017 2.6 43.6 1.0
O3G A:APC1500 2.8 39.7 1.0
O2A A:APC1500 2.8 43.7 1.0
O2G A:APC1500 3.0 43.8 1.0
PG A:APC1500 3.3 42.1 1.0
CG A:ASP1017 3.7 41.4 1.0
O3B A:APC1500 3.9 40.4 1.0
O1A A:APC1500 3.9 45.0 1.0
CA A:CA2100 4.0 32.6 1.0
PA A:APC1500 4.0 46.0 1.0
OD1 A:ASP1017 4.4 46.9 1.0
NH1 A:ARG1117 4.5 42.3 1.0
OE1 A:GLN1152 4.7 31.0 1.0
CB A:ASP1017 4.7 39.0 1.0
O1G A:APC1500 4.7 42.4 1.0
NE2 A:GLN1152 4.8 33.8 1.0
PB A:APC1500 5.0 39.3 1.0

Magnesium binding site 2 out of 4 in 1wc5

Go back to Magnesium Binding Sites List in 1wc5
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg2000

b:27.8
occ:1.00
 O2G B:APC1500 2.7 23.4 1.0
O2A B:APC1500 2.7 34.2 1.0
O1G B:APC1500 3.0 25.1 1.0
OD2 B:ASP1017 3.3 37.2 1.0
PG B:APC1500 3.4 23.8 1.0
O3B B:APC1500 4.1 25.2 1.0
PA B:APC1500 4.2 35.9 1.0
CA B:CA2100 4.3 29.9 1.0
NH1 B:ARG1117 4.3 34.7 1.0
CG B:ASP1017 4.4 34.1 1.0
O1A B:APC1500 4.6 35.1 1.0
NE2 B:GLN1152 4.6 29.8 1.0
O3G B:APC1500 4.7 25.8 1.0
NZ C:LYS1184 4.7 56.5 1.0
CB B:GLU1153 4.9 25.0 1.0
OE1 B:GLN1152 4.9 29.3 1.0
CZ B:ARG1117 5.0 36.6 1.0

Magnesium binding site 3 out of 4 in 1wc5

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg2000

b:18.1
occ:1.00
 O2A C:APC1500 2.2 25.9 1.0
O C:HOH2022 2.2 19.7 1.0
O3G C:APC1500 2.5 26.5 1.0
O1G C:APC1500 2.9 25.7 1.0
PG C:APC1500 3.2 24.2 1.0
OD1 C:ASP1017 3.4 40.5 1.0
PA C:APC1500 3.5 30.6 1.0
O C:HOH2028 3.7 40.8 1.0
O1A C:APC1500 3.7 31.2 1.0
O3B C:APC1500 4.0 23.6 1.0
NZ B:LYS1184 4.2 46.7 1.0
CA C:CA2100 4.3 24.1 1.0
O C:HOH2018 4.5 19.1 1.0
O2G C:APC1500 4.5 27.5 1.0
CG C:ASP1017 4.5 38.5 1.0
O5' C:APC1500 4.6 28.8 1.0
C3A C:APC1500 4.7 27.9 1.0
PB C:APC1500 4.8 28.0 1.0
OE2 C:GLU1153 4.9 42.1 1.0
NH1 B:ARG1150 4.9 32.9 1.0
NE2 C:GLN1152 4.9 32.6 1.0
OD2 C:ASP1017 4.9 44.1 1.0
O2B C:APC1500 5.0 28.6 1.0

Magnesium binding site 4 out of 4 in 1wc5

Go back to Magnesium Binding Sites List in 1wc5
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg2000

b:40.9
occ:1.00
 O2A D:APC1500 2.2 42.2 1.0
O3G D:APC1500 2.5 38.2 1.0
OD2 D:ASP1017 2.8 31.7 1.0
O2G D:APC1500 2.9 37.8 1.0
PG D:APC1500 3.2 35.9 1.0
PA D:APC1500 3.7 44.4 1.0
CA D:CA2100 3.9 32.6 1.0
CG D:ASP1017 4.0 33.1 1.0
O1A D:APC1500 4.3 47.3 1.0
O1G D:APC1500 4.3 40.0 1.0
O3B D:APC1500 4.4 39.5 1.0
OE2 D:GLU1153 4.5 47.7 1.0
C3A D:APC1500 4.6 43.5 1.0
OD1 D:ASP1017 4.6 35.7 1.0
O5' D:APC1500 4.7 41.9 1.0
O2B D:APC1500 4.8 38.9 1.0
O D:HOH2013 4.8 40.4 1.0
PB D:APC1500 4.8 39.5 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: Tue Aug 13 17:13:46 2024

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