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Magnesium in PDB 1wc6: Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Rp-Atpalphas in Presence of Bicarbonate

Enzymatic activity of Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Rp-Atpalphas in Presence of Bicarbonate

All present enzymatic activity of Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Rp-Atpalphas in Presence of Bicarbonate:
4.6.1.1;

Protein crystallography data

The structure of Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Rp-Atpalphas in Presence of Bicarbonate, PDB code: 1wc6 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 / 2.51
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 51.148, 73.965, 266.861, 90.00, 90.00, 90.00
R / Rfree (%) 24.1 / 29.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Rp-Atpalphas in Presence of Bicarbonate (pdb code 1wc6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Rp-Atpalphas in Presence of Bicarbonate, PDB code: 1wc6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1wc6

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Magnesium binding site 1 out of 6 in the Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Rp-Atpalphas 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 Rp-Atpalphas in Presence of Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2201

b:17.4
occ:1.00
 OD1 A:ASP1017 2.1 28.4 1.0
O2A A:TAT2200 2.4 38.9 1.0
O3' A:TAT2200 2.8 34.0 1.0
CG A:ASP1017 2.8 27.0 1.0
OD2 A:ASP1017 3.0 29.4 1.0
C3' A:TAT2200 3.1 30.4 1.0
MG A:MG2202 3.3 7.8 1.0
OD1 A:ASP1061 3.4 24.9 1.0
PA A:TAT2200 3.7 41.4 1.0
O A:VAL1059 3.7 15.0 1.0
CB A:ALA1062 3.7 19.6 1.0
C2' A:TAT2200 4.2 29.5 1.0
CB A:ASP1017 4.2 25.4 1.0
C5' A:TAT2200 4.2 35.3 1.0
O5' A:TAT2200 4.2 38.1 1.0
C4' A:TAT2200 4.2 32.2 1.0
S1G A:TAT2200 4.4 41.2 1.0
NH2 A:ARG1117 4.4 39.0 1.0
CG A:ASP1061 4.4 24.0 1.0
N A:ALA1062 4.6 18.6 1.0
OD2 A:ASP1061 4.7 26.0 1.0
O3G A:TAT2200 4.7 41.7 1.0
CA A:ALA1062 4.8 17.6 1.0
CG1 A:VAL1059 4.8 14.4 1.0
C A:VAL1059 4.9 15.6 1.0

Magnesium binding site 2 out of 6 in 1wc6

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Magnesium binding site 2 out of 6 in the Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Rp-Atpalphas 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 Rp-Atpalphas in Presence of Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2202

b:7.8
occ:1.00
 OD2 A:ASP1017 2.0 29.4 1.0
OD2 A:ASP1061 2.1 26.0 1.0
O3G A:TAT2200 2.1 41.7 1.0
O2B A:TAT2200 2.3 41.4 1.0
O2A A:TAT2200 2.5 38.9 1.0
OD1 A:ASP1061 2.6 24.9 1.0
CG A:ASP1017 2.6 27.0 1.0
CG A:ASP1061 2.6 24.0 1.0
O A:ILE1018 2.8 15.9 1.0
OD1 A:ASP1017 2.9 28.4 1.0
MG A:MG2201 3.3 17.4 1.0
PB A:TAT2200 3.3 41.7 1.0
PG A:TAT2200 3.3 41.7 1.0
PA A:TAT2200 3.4 41.4 1.0
NH2 A:ARG1117 3.5 39.0 1.0
O3B A:TAT2200 3.6 40.0 1.0
O3A A:TAT2200 3.8 41.7 1.0
N A:ILE1018 3.8 21.0 1.0
CB A:ASP1017 3.9 25.4 1.0
S1G A:TAT2200 3.9 41.2 1.0
C A:ILE1018 3.9 16.9 1.0
O2G A:TAT2200 4.1 42.6 1.0
CB A:ASP1061 4.1 22.3 1.0
C A:ASP1017 4.3 21.8 1.0
CA A:ILE1018 4.4 17.9 1.0
CB A:PHE1021 4.4 28.3 1.0
CA A:ASP1017 4.4 23.5 1.0
O1A A:TAT2200 4.4 42.0 1.0
O1B A:TAT2200 4.6 39.9 1.0
CZ A:ARG1117 4.7 37.6 1.0
CB A:ILE1018 4.8 16.1 1.0
N A:PHE1021 4.8 27.1 1.0
O5' A:TAT2200 4.9 38.1 1.0
N A:VAL1019 5.0 17.1 1.0
C A:ASP1061 5.0 18.0 1.0

Magnesium binding site 3 out of 6 in 1wc6

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Magnesium binding site 3 out of 6 in the Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Rp-Atpalphas 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 Rp-Atpalphas in Presence of Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2200

b:43.6
occ:1.00
 O2A B:TAT2199 1.9 44.2 1.0
OD1 B:ASP1061 2.6 22.8 1.0
OD1 B:ASP1017 2.7 30.9 1.0
OD2 B:ASP1017 2.7 29.2 1.0
MG B:MG2201 2.8 8.3 1.0
CG B:ASP1017 3.0 27.8 1.0
PA B:TAT2199 3.1 44.7 1.0
C3' B:TAT2199 3.5 31.6 1.0
O B:VAL1059 3.5 16.2 1.0
O3' B:TAT2199 3.6 33.8 1.0
O5' B:TAT2199 3.6 40.7 1.0
CG B:ASP1061 3.6 23.6 1.0
S1G B:TAT2199 3.8 45.2 1.0
O B:HOH2035 3.8 44.6 1.0
C5' B:TAT2199 3.9 36.3 1.0
OD2 B:ASP1061 4.0 26.3 1.0
CB B:ALA1062 4.0 15.7 1.0
C4' B:TAT2199 4.3 33.9 1.0
O3G B:TAT2199 4.3 46.7 1.0
N B:ALA1062 4.4 19.5 1.0
O3A B:TAT2199 4.5 42.2 1.0
CB B:ASP1017 4.5 24.9 1.0
N B:ASP1061 4.5 20.0 1.0
O2B B:TAT2199 4.6 42.0 1.0
C2' B:TAT2199 4.7 30.1 1.0
NH2 B:ARG1117 4.7 30.8 1.0
O B:HOH2021 4.7 19.6 1.0
O3B B:TAT2199 4.7 44.6 1.0
C B:VAL1059 4.8 15.9 1.0
CA B:ALA1062 4.8 18.2 1.0
PB B:TAT2199 4.9 41.4 1.0
CB B:ASP1061 4.9 21.9 1.0
C B:ASP1061 5.0 20.7 1.0

Magnesium binding site 4 out of 6 in 1wc6

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Magnesium binding site 4 out of 6 in the Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Rp-Atpalphas 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 Rp-Atpalphas in Presence of Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2201

b:8.3
occ:1.00
 OD2 B:ASP1017 1.9 29.2 1.0
OD2 B:ASP1061 2.0 26.3 1.0
O3G B:TAT2199 2.1 46.7 1.0
O2A B:TAT2199 2.4 44.2 1.0
CG B:ASP1017 2.5 27.8 1.0
OD1 B:ASP1061 2.7 22.8 1.0
CG B:ASP1061 2.7 23.6 1.0
O B:ILE1018 2.7 16.2 1.0
O2B B:TAT2199 2.7 42.0 1.0
MG B:MG2200 2.8 43.6 1.0
OD1 B:ASP1017 2.8 30.9 1.0
PG B:TAT2199 3.3 46.4 1.0
NH2 B:ARG1117 3.4 30.8 1.0
O3B B:TAT2199 3.5 44.6 1.0
PB B:TAT2199 3.6 41.4 1.0
PA B:TAT2199 3.6 44.7 1.0
N B:ILE1018 3.7 22.2 1.0
CB B:ASP1017 3.7 24.9 1.0
C B:ILE1018 3.7 19.8 1.0
O3A B:TAT2199 4.1 42.2 1.0
C B:ASP1017 4.1 23.9 1.0
CB B:ASP1061 4.2 21.9 1.0
O1A B:TAT2199 4.2 45.8 1.0
S1G B:TAT2199 4.2 45.2 1.0
CA B:ILE1018 4.3 20.4 1.0
CA B:ASP1017 4.3 23.6 1.0
O2G B:TAT2199 4.4 46.9 1.0
CB B:PHE1021 4.5 31.9 1.0
CZ B:ARG1117 4.6 31.9 1.0
O B:HOH2035 4.7 44.6 1.0
CB B:ILE1018 4.7 21.6 1.0
N B:VAL1019 4.9 20.5 1.0
N B:PHE1021 4.9 30.1 1.0
O1B B:TAT2199 4.9 41.9 1.0
O5' B:TAT2199 4.9 40.7 1.0
C B:ASP1061 5.0 20.7 1.0
O B:ASP1017 5.0 24.1 1.0

Magnesium binding site 5 out of 6 in 1wc6

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Magnesium binding site 5 out of 6 in the Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Rp-Atpalphas in Presence of Bicarbonate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Rp-Atpalphas in Presence of Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2201

b:36.9
occ:1.00
 OD1 C:ASP1017 2.7 35.9 1.0
OD2 C:ASP1017 2.8 37.4 1.0
OD1 C:ASP1061 2.8 29.7 1.0
O C:VAL1059 2.9 16.4 1.0
O2A C:TAT2200 2.9 45.3 1.0
CG C:ASP1017 3.0 35.8 1.0
MG C:MG2202 3.2 21.7 1.0
CB C:ALA1062 3.2 22.5 1.0
C3' C:TAT2200 3.4 28.8 1.0
O3' C:TAT2200 3.5 29.6 1.0
N C:ALA1062 3.8 22.5 1.0
O C:HOH2025 3.8 35.0 1.0
CG C:ASP1061 3.9 26.8 1.0
CA C:ALA1062 4.1 22.2 1.0
C C:VAL1059 4.1 14.4 1.0
PA C:TAT2200 4.1 47.1 1.0
C2' C:TAT2200 4.2 28.0 1.0
N C:ASP1061 4.3 19.7 1.0
CB C:ASP1017 4.3 33.0 1.0
CG1 C:VAL1059 4.4 13.1 1.0
OD2 C:ASP1061 4.4 26.4 1.0
S1G C:TAT2200 4.5 43.8 1.0
O5' C:TAT2200 4.6 41.8 1.0
C4' C:TAT2200 4.6 32.0 1.0
CB C:VAL1059 4.6 13.3 1.0
C C:ASP1061 4.7 23.1 1.0
C5' C:TAT2200 4.7 36.5 1.0
CA C:GLY1060 4.9 16.4 1.0
CA C:ASP1061 5.0 22.1 1.0

Magnesium binding site 6 out of 6 in 1wc6

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Magnesium binding site 6 out of 6 in the Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Rp-Atpalphas in Presence of Bicarbonate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Soluble Adenylyl Cyclase Cyac From S. Platensis in Complex with Rp-Atpalphas in Presence of Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2202

b:21.7
occ:1.00
 OD2 C:ASP1017 1.8 37.4 1.0
OD2 C:ASP1061 2.0 26.4 1.0
OD1 C:ASP1061 2.3 29.7 1.0
O2A C:TAT2200 2.3 45.3 1.0
CG C:ASP1061 2.4 26.8 1.0
O3G C:TAT2200 2.4 57.0 1.0
O2B C:TAT2200 2.5 49.9 1.0
CG C:ASP1017 2.6 35.8 1.0
OD1 C:ASP1017 2.9 35.9 1.0
O C:ILE1018 3.0 31.7 1.0
MG C:MG2201 3.2 36.9 1.0
PA C:TAT2200 3.5 47.1 1.0
PB C:TAT2200 3.5 50.7 1.0
PG C:TAT2200 3.6 58.0 1.0
O3B C:TAT2200 3.7 53.9 1.0
O C:HOH2025 3.8 35.0 1.0
N C:ILE1018 3.8 32.5 1.0
NH2 C:ARG1117 3.8 35.4 1.0
CB C:ASP1017 3.9 33.0 1.0
CB C:ASP1061 3.9 24.1 1.0
S1G C:TAT2200 3.9 43.8 1.0
O3A C:TAT2200 4.0 47.5 1.0
C C:ILE1018 4.0 33.0 1.0
C C:ASP1017 4.3 31.6 1.0
CB C:PHE1021 4.4 46.4 1.0
CA C:ASP1017 4.4 31.4 1.0
CA C:ILE1018 4.4 32.5 1.0
O2G C:TAT2200 4.4 58.4 1.0
O1A C:TAT2200 4.7 57.1 1.0
C C:ASP1061 4.7 23.1 1.0
N C:ALA1062 4.7 22.5 1.0
CA C:ASP1061 4.7 22.1 1.0
CB C:ILE1018 4.8 32.4 1.0
O5' C:TAT2200 4.8 41.8 1.0
N C:ASP1061 4.8 19.7 1.0
O1B C:TAT2200 4.8 49.8 1.0
CZ C:ARG1117 4.9 35.1 1.0
N C:PHE1021 5.0 46.4 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 17:13:48 2024

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