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Calcium 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:

Magnesium (Mg) 3 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 3 in 4wp9

Go back to Calcium Binding Sites List in 4wp9
Calcium 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 Calcium with other atoms in the Ca 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:Ca304

b:16.9
occ:1.00
 O2B A:ZDA303 2.2 18.0 1.0
OD1 A:ASP61 2.3 20.1 1.0
O2A A:ZDA303 2.3 17.1 1.0
OD2 A:ASP105 2.3 20.5 1.0
O A:ILE62 2.3 15.9 1.0
O3G A:ZDA303 2.3 20.5 1.0
OD2 A:ASP61 2.8 21.5 1.0
CG A:ASP61 2.8 18.7 1.0
PB A:ZDA303 3.3 16.9 1.0
CG A:ASP105 3.3 17.0 1.0
PA A:ZDA303 3.4 19.4 1.0
C A:ILE62 3.5 14.1 1.0
MG A:MG302 3.5 27.1 1.0
PG A:ZDA303 3.5 21.6 1.0
O3A A:ZDA303 3.7 20.4 1.0
O3B A:ZDA303 3.7 16.0 1.0
H A:SER65 3.7 20.2 1.0
OD1 A:ASP105 3.8 19.8 1.0
HG A:SER65 3.9 19.0 1.0
H A:ILE62 3.9 19.4 1.0
OG A:SER65 4.0 15.8 1.0
N A:ILE62 4.0 16.2 1.0
O A:HOH416 4.1 30.1 1.0
HA A:GLU63 4.1 22.5 1.0
HB3 A:SER65 4.2 19.2 1.0
H A:GLU64 4.2 22.3 1.0
HH11 A:ARG143 4.2 34.1 1.0
HB A:ILE62 4.3 18.7 1.0
CA A:ILE62 4.3 15.4 1.0
CB A:ASP61 4.3 16.9 1.0
O A:HOH448 4.4 27.7 1.0
O2G A:ZDA303 4.4 24.9 1.0
C A:ASP61 4.4 15.5 1.0
O3' A:ZDA303 4.5 24.4 1.0
N A:GLU63 4.5 15.9 1.0
HB2 A:ASP105 4.5 22.0 1.0
N A:GLU64 4.6 18.6 1.0
CB A:ASP105 4.6 18.3 1.0
HH12 A:ARG143 4.6 34.1 1.0
N A:SER65 4.6 16.9 1.0
CB A:SER65 4.6 16.0 1.0
O1A A:ZDA303 4.6 23.6 1.0
O1G A:ZDA303 4.6 23.1 1.0
CA A:GLU63 4.6 18.8 1.0
H12 A:ZDA303 4.6 26.9 1.0
HA A:ASP61 4.7 18.6 1.0
HB2 A:ASP61 4.7 20.3 1.0
O1B A:ZDA303 4.7 20.0 1.0
NH1 A:ARG143 4.7 28.4 1.0
CA A:ASP61 4.8 15.5 1.0
CB A:ILE62 4.8 15.6 1.0
HB3 A:ASP61 4.8 20.3 1.0
C A:GLU63 4.8 18.6 1.0
HG22 A:ILE62 4.9 18.8 1.0
C3' A:ZDA303 5.0 22.4 1.0
HB3 A:ASP105 5.0 22.0 1.0

Calcium binding site 2 out of 3 in 4wp9

Go back to Calcium Binding Sites List in 4wp9
Calcium 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 Calcium with other atoms in the Ca 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:Ca305

b:25.4
occ:1.00
 HE21 A:GLN172 2.0 71.5 1.0
HE A:ARG168 2.1 43.3 1.0
HE22 A:GLN172 2.2 71.5 1.0
NE2 A:GLN172 2.3 59.6 1.0
NH2 A:ARG168 2.5 46.5 1.0
HA A:LEU204 2.8 25.3 1.0
NE A:ARG168 2.8 36.1 1.0
CZ A:ARG168 3.1 44.2 1.0
HB3 A:ARG168 3.1 23.5 1.0
N A:LYS205 3.2 22.5 1.0
HH22 A:ARG168 3.2 55.8 1.0
HD23 A:LEU204 3.5 26.2 1.0
HB2 A:LYS205 3.5 28.2 1.0
CD A:GLN172 3.6 41.3 1.0
HD22 A:LEU204 3.6 26.2 1.0
CA A:LEU204 3.7 21.1 1.0
HB3 A:LEU204 3.9 23.8 1.0
O A:HOH406 3.9 32.0 1.0
HB3 A:LYS205 3.9 28.2 1.0
HG2 A:GLN172 3.9 30.2 1.0
C A:LEU204 3.9 23.7 1.0
CD2 A:LEU204 4.0 21.8 1.0
CB A:ARG168 4.0 19.6 1.0
CB A:LYS205 4.0 23.5 1.0
CD A:ARG168 4.1 29.6 1.0
O A:GLU203 4.1 26.2 1.0
HG3 A:ARG168 4.2 27.3 1.0
CA A:LYS205 4.2 23.8 1.0
CB A:LEU204 4.2 19.8 1.0
HB3 A:ALA171 4.3 22.4 1.0
O A:ARG168 4.3 16.5 1.0
CG A:ARG168 4.3 22.7 1.0
CG A:GLN172 4.3 25.1 1.0
HA A:ARG168 4.3 20.5 1.0
NH1 A:ARG168 4.4 45.7 1.0
OE1 A:GLN172 4.4 34.3 1.0
HD3 A:ARG168 4.6 35.5 1.0
CA A:ARG168 4.6 17.1 1.0
HD2 A:ARG168 4.7 35.5 1.0
HB2 A:ARG168 4.7 23.5 1.0
HG3 A:GLN172 4.7 30.2 1.0
HA A:LYS205 4.8 28.5 1.0
HD21 A:LEU204 4.8 26.2 1.0
N A:LEU204 4.8 19.9 1.0
CG A:LEU204 4.8 22.2 1.0
C A:ARG168 4.8 15.1 1.0
HH12 A:ARG168 4.8 54.9 1.0
C A:GLU203 4.9 23.5 1.0
HH11 A:ARG168 4.9 54.9 1.0

Calcium binding site 3 out of 3 in 4wp9

Go back to Calcium Binding Sites List in 4wp9
Calcium 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 Calcium with other atoms in the Ca 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:Ca303

b:15.6
occ:1.00
 OD1 B:ASP61 2.2 16.1 1.0
O B:ILE62 2.3 17.5 1.0
O3G B:ZDA301 2.3 15.7 1.0
O1B B:ZDA301 2.3 16.7 1.0
OD2 B:ASP105 2.3 19.1 1.0
O1A B:ZDA301 2.4 18.0 1.0
CG B:ASP61 3.4 17.6 1.0
PB B:ZDA301 3.4 15.5 1.0
CG B:ASP105 3.4 19.3 1.0
C B:ILE62 3.4 16.0 1.0
PG B:ZDA301 3.5 16.4 1.0
PA B:ZDA301 3.5 18.1 1.0
O3B B:ZDA301 3.7 13.6 1.0
O3A B:ZDA301 3.8 16.4 1.0
HH22 B:ARG143 3.8 25.9 1.0
H B:SER65 3.8 20.3 1.0
OD1 B:ASP105 3.8 20.0 1.0
H12 B:ZDA301 3.8 23.8 1.0
H B:ILE62 3.9 16.8 1.0
HE21 B:GLN103 3.9 26.8 1.0
N B:ILE62 3.9 14.0 1.0
HE22 B:GLN103 3.9 26.8 1.0
OD2 B:ASP61 3.9 23.0 1.0
HG B:SER65 4.0 22.9 1.0
MG B:MG302 4.0 28.7 1.0
HB3 B:SER65 4.1 24.2 1.0
OG B:SER65 4.1 19.1 1.0
NH1 B:ARG143 4.2 22.5 1.0
CA B:ILE62 4.2 16.1 1.0
H B:GLU64 4.2 20.1 1.0
HB B:ILE62 4.2 20.6 1.0
NE2 B:GLN103 4.3 22.4 1.0
O1G B:ZDA301 4.3 18.6 1.0
HA B:GLU63 4.3 21.0 1.0
C B:ASP61 4.3 15.3 1.0
NH2 B:ARG143 4.4 21.6 1.0
N B:GLU63 4.5 16.3 1.0
CB B:ASP61 4.5 15.0 1.0
HA B:ASP61 4.5 17.3 1.0
N B:GLU64 4.6 16.7 1.0
HB2 B:ASP105 4.6 23.1 1.0
CB B:SER65 4.6 20.2 1.0
HB3 B:ASP61 4.6 18.0 1.0
O2G B:ZDA301 4.6 18.3 1.0
N B:SER65 4.6 16.9 1.0
O3' B:ZDA301 4.7 20.4 1.0
CB B:ASP105 4.7 19.3 1.0
CZ B:ARG143 4.7 20.3 1.0
C3' B:ZDA301 4.7 19.8 1.0
HH11 B:ARG143 4.7 27.0 1.0
O2A B:ZDA301 4.7 17.4 1.0
CA B:ASP61 4.7 14.4 1.0
CA B:GLU63 4.7 17.5 1.0
CB B:ILE62 4.7 17.1 1.0
HG22 B:ILE62 4.8 22.0 1.0
O2B B:ZDA301 4.8 16.9 1.0
C B:GLU63 4.8 17.9 1.0
O B:ASP61 4.9 16.8 1.0
HH21 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: Sun Jul 14 14:20:26 2024

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