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Magnesium in PDB 4wp9: Crystal Structure of Adenylyl Cyclase MA1120 From Mycobacterium Avium Bound to 2'5'-Dd-3'-Atp, Calcium and Magnesium Ion

Enzymatic activity of Crystal Structure of Adenylyl Cyclase MA1120 From Mycobacterium Avium Bound to 2'5'-Dd-3'-Atp, Calcium and Magnesium Ion

All present enzymatic activity of Crystal Structure of Adenylyl Cyclase MA1120 From Mycobacterium Avium Bound to 2'5'-Dd-3'-Atp, Calcium and Magnesium Ion:
4.6.1.1;

Protein crystallography data

The structure of Crystal Structure of Adenylyl Cyclase MA1120 From Mycobacterium Avium Bound to 2'5'-Dd-3'-Atp, Calcium and Magnesium Ion, PDB code: 4wp9 was solved by N.G.Bharambe, D.V.Barathy, K.Suguna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.95 / 1.38
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.470, 56.090, 55.770, 90.00, 110.72, 90.00
R / Rfree (%) 23.1 / 26.4

Other elements in 4wp9:

The structure of Crystal Structure of Adenylyl Cyclase MA1120 From Mycobacterium Avium Bound to 2'5'-Dd-3'-Atp, Calcium and Magnesium Ion also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Adenylyl Cyclase MA1120 From Mycobacterium Avium Bound to 2'5'-Dd-3'-Atp, Calcium and Magnesium Ion (pdb code 4wp9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Adenylyl Cyclase MA1120 From Mycobacterium Avium Bound to 2'5'-Dd-3'-Atp, Calcium and Magnesium Ion, PDB code: 4wp9:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4wp9

Go back to Magnesium Binding Sites List in 4wp9
Magnesium binding site 1 out of 3 in the Crystal Structure of Adenylyl Cyclase MA1120 From Mycobacterium Avium Bound to 2'5'-Dd-3'-Atp, Calcium and Magnesium Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Adenylyl Cyclase MA1120 From Mycobacterium Avium Bound to 2'5'-Dd-3'-Atp, Calcium and Magnesium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:42.3
occ:1.00
 O A:HOH433 1.9 30.8 1.0
O A:PHE207 1.9 25.0 1.0
O A:LEU204 2.0 23.9 1.0
H A:PHE207 2.4 25.8 1.0
O A:HOH405 2.7 36.9 1.0
O A:HOH475 2.9 21.1 1.0
C A:PHE207 3.0 23.6 1.0
N A:PHE207 3.0 21.5 1.0
C A:LEU204 3.1 23.7 1.0
H A:LEU204 3.1 23.8 1.0
HB2 A:PHE207 3.3 25.7 1.0
H A:GLY206 3.4 25.7 1.0
CA A:PHE207 3.4 20.6 1.0
N A:LEU204 3.5 19.9 1.0
HB3 A:GLU203 3.5 28.8 1.0
N A:GLY206 3.7 21.4 1.0
HA A:LYS205 3.8 28.5 1.0
CB A:PHE207 3.9 21.4 1.0
CA A:LEU204 3.9 21.1 1.0
N A:LYS205 4.0 22.5 1.0
C A:LYS205 4.1 22.2 1.0
C A:GLY206 4.1 22.3 1.0
N A:SER208 4.1 25.4 1.0
CA A:LYS205 4.1 23.8 1.0
HA A:SER208 4.2 32.4 1.0
HB2 A:LEU204 4.2 23.8 1.0
HA A:PHE207 4.3 24.7 1.0
C A:GLU203 4.3 23.5 1.0
HB3 A:PHE207 4.4 25.7 1.0
CB A:GLU203 4.4 24.0 1.0
CA A:GLY206 4.5 22.6 1.0
O A:HOH441 4.5 35.8 1.0
CA A:SER208 4.6 27.0 1.0
HA A:LEU204 4.6 25.3 1.0
HD2 A:PHE207 4.6 23.6 1.0
CB A:LEU204 4.7 19.8 1.0
HA A:GLU203 4.7 29.0 1.0
CA A:GLU203 4.8 24.1 1.0
HB2 A:GLU203 4.8 28.8 1.0
O A:GLY209 4.8 25.9 1.0
OE2 A:GLU203 4.9 33.9 1.0
O A:LYS205 4.9 22.7 1.0
H A:SER208 4.9 30.4 1.0
C A:SER208 4.9 25.4 1.0
HA2 A:GLY206 4.9 27.1 1.0

Magnesium binding site 2 out of 3 in 4wp9

Go back to Magnesium Binding Sites List in 4wp9
Magnesium binding site 2 out of 3 in the Crystal Structure of Adenylyl Cyclase MA1120 From Mycobacterium Avium Bound to 2'5'-Dd-3'-Atp, Calcium and Magnesium Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Adenylyl Cyclase MA1120 From Mycobacterium Avium Bound to 2'5'-Dd-3'-Atp, Calcium and Magnesium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:27.1
occ:1.00
 OD1 A:ASP61 2.3 20.1 1.0
O A:HOH503 2.3 25.4 1.0
OD1 A:ASP105 2.4 19.8 1.0
O A:HOH476 2.4 27.2 1.0
O A:HOH448 2.4 27.7 1.0
O2A A:ZDA303 2.6 17.1 1.0
CG A:ASP105 3.3 17.0 1.0
CG A:ASP61 3.4 18.7 1.0
H2 A:ZDA303 3.4 23.7 1.0
OD2 A:ASP105 3.5 20.5 1.0
CA A:CA304 3.5 16.9 1.0
HB2 A:ASP61 3.8 20.3 1.0
O3' A:ZDA303 3.8 24.4 1.0
PA A:ZDA303 3.9 19.4 1.0
CB A:ASP61 4.1 16.9 1.0
H A:ASP105 4.2 20.6 1.0
HA A:ASP61 4.2 18.6 1.0
O A:GLN103 4.3 19.0 1.0
OD2 A:ASP61 4.3 21.5 1.0
C2' A:ZDA303 4.3 19.8 1.0
O A:HOH490 4.3 26.3 1.0
HB2 A:GLN103 4.5 27.2 1.0
C3' A:ZDA303 4.5 22.4 1.0
H1 A:ZDA303 4.6 23.7 1.0
O1A A:ZDA303 4.6 23.6 1.0
HA3 A:GLY106 4.7 17.6 1.0
CB A:ASP105 4.7 18.3 1.0
CA A:ASP61 4.7 15.5 1.0
C A:ASP105 4.7 16.1 1.0
HB3 A:GLN103 4.8 27.2 1.0
H A:ILE62 4.8 19.4 1.0
O A:HOH416 4.9 30.1 1.0
N A:GLY106 4.9 14.8 1.0
N A:ASP105 4.9 17.1 1.0
O A:ASP105 4.9 18.3 1.0
HB3 A:ASP61 4.9 20.3 1.0
H12 A:ZDA303 4.9 26.9 1.0

Magnesium binding site 3 out of 3 in 4wp9

Go back to Magnesium Binding Sites List in 4wp9
Magnesium binding site 3 out of 3 in the Crystal Structure of Adenylyl Cyclase MA1120 From Mycobacterium Avium Bound to 2'5'-Dd-3'-Atp, Calcium and Magnesium Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Adenylyl Cyclase MA1120 From Mycobacterium Avium Bound to 2'5'-Dd-3'-Atp, Calcium and Magnesium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:28.7
occ:1.00
 OD2 B:ASP61 2.6 23.0 1.0
O B:HOH410 2.8 24.1 1.0
O1A B:ZDA301 2.8 18.0 1.0
HH11 B:ARG143 2.9 27.0 1.0
HE22 B:GLN103 2.9 26.8 1.0
NH1 B:ARG143 3.2 22.5 1.0
O2A B:ZDA301 3.4 17.4 1.0
CG B:ASP61 3.5 17.6 1.0
PA B:ZDA301 3.6 18.1 1.0
OD1 B:ASP61 3.7 16.1 1.0
O3G B:ZDA301 3.7 15.7 1.0
NE2 B:GLN103 3.7 22.4 1.0
O B:HOH526 4.0 26.0 1.0
CA B:CA303 4.0 15.6 1.0
O B:HOH557 4.2 28.3 1.0
HE21 B:GLN103 4.2 26.8 1.0
HZ3 A:LYS205 4.3 30.0 1.0
O B:HOH461 4.3 29.8 1.0
O2G B:ZDA301 4.3 18.3 1.0
CZ B:ARG143 4.4 20.3 1.0
OE1 B:GLN103 4.5 26.8 1.0
PG B:ZDA301 4.5 16.4 1.0
CD B:GLN103 4.6 24.8 1.0
O3' B:ZDA301 4.6 20.4 1.0
HZ1 A:LYS205 4.6 30.0 1.0
NZ A:LYS205 4.8 25.0 1.0
CB B:ASP61 4.9 15.0 1.0
O3B B:ZDA301 4.9 13.6 1.0
O3A B:ZDA301 4.9 16.4 1.0
HH22 B:ARG143 5.0 25.9 1.0

Reference:

D.V.Barathy, N.G.Bharambe, W.Syed, A.Zaveri, S.S.Visweswariah, M.Cola Sigmaf O, S.Misquith, K.Suguna. Autoinhibitory Mechanism and Activity-Related Structural Changes in A Mycobacterial Adenylyl Cyclase J.Struct.Biol. V. 190 304 2015.
ISSN: ESSN 1095-8657
PubMed: 25916753
DOI: 10.1016/J.JSB.2015.04.013
Page generated: Tue Aug 20 13:54:00 2024

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