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Calcium in PDB 5d0g: Crystal Structure of Triple Mutant (kDa to Egy) of Adenylyl Cyclase MA1120 From Mycobacterium Avium in Complex with Gtp and Calcium Ion

Protein crystallography data

The structure of Crystal Structure of Triple Mutant (kDa to Egy) of Adenylyl Cyclase MA1120 From Mycobacterium Avium in Complex with Gtp and Calcium Ion, PDB code: 5d0g was solved by N.G.Bharambe, K.Suguna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.08 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.070, 55.630, 55.140, 90.00, 108.67, 90.00
R / Rfree (%) 18.9 / 21.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Triple Mutant (kDa to Egy) of Adenylyl Cyclase MA1120 From Mycobacterium Avium in Complex with Gtp and Calcium Ion (pdb code 5d0g). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Triple Mutant (kDa to Egy) of Adenylyl Cyclase MA1120 From Mycobacterium Avium in Complex with Gtp and Calcium Ion, PDB code: 5d0g:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5d0g

Go back to Calcium Binding Sites List in 5d0g
Calcium binding site 1 out of 2 in the Crystal Structure of Triple Mutant (kDa to Egy) of Adenylyl Cyclase MA1120 From Mycobacterium Avium in Complex with Gtp and Calcium 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 Triple Mutant (kDa to Egy) of Adenylyl Cyclase MA1120 From Mycobacterium Avium in Complex with Gtp and Calcium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:15.6
occ:1.00
O A:ILE114 2.2 17.1 1.0
O2A A:GTP301 2.3 21.3 1.0
O1B A:GTP301 2.3 17.7 1.0
OD1 A:ASP113 2.4 19.7 1.0
O1G A:GTP301 2.4 20.2 1.0
OD2 A:ASP157 2.4 18.9 1.0
OD2 A:ASP113 2.4 24.7 1.0
CG A:ASP113 2.7 21.4 1.0
PB A:GTP301 3.4 17.6 1.0
C A:ILE114 3.4 17.7 1.0
CG A:ASP157 3.5 19.5 1.0
PA A:GTP301 3.5 20.9 1.0
PG A:GTP301 3.6 20.2 1.0
HH21 A:ARG195 3.7 37.5 1.0
O3A A:GTP301 3.8 22.4 1.0
H A:SER117 3.8 19.0 1.0
O3B A:GTP301 3.8 19.9 1.0
H A:ILE114 3.9 19.2 1.0
OD1 A:ASP157 3.9 21.9 1.0
HA A:GLU115 4.0 21.6 1.0
N A:ILE114 4.0 16.0 1.0
H A:GLU116 4.1 22.8 1.0
O5' A:GTP301 4.1 23.4 1.0
HB3 A:SER117 4.2 19.2 1.0
CB A:ASP113 4.2 18.6 1.0
HG A:SER117 4.2 19.4 1.0
OG A:SER117 4.2 16.2 1.0
HE A:ARG195 4.3 35.9 1.0
CA A:ILE114 4.3 18.2 1.0
O3G A:GTP301 4.4 22.3 1.0
O A:HOH482 4.4 29.4 1.0
HB A:ILE114 4.4 21.7 1.0
N A:GLU115 4.4 16.9 1.0
C A:ASP113 4.5 14.2 1.0
N A:GLU116 4.5 19.0 1.0
CA A:GLU115 4.6 18.0 1.0
HB2 A:ASP157 4.6 19.9 1.0
NH2 A:ARG195 4.6 31.2 1.0
HB3 A:ASP113 4.6 22.3 1.0
N A:SER117 4.7 15.9 1.0
O A:HOH459 4.7 27.7 1.0
CB A:ASP157 4.7 16.6 1.0
HA A:ASP113 4.7 19.1 1.0
HB2 A:ASP113 4.7 22.3 1.0
CB A:SER117 4.7 16.0 1.0
O2G A:GTP301 4.7 20.0 1.0
CA A:ASP113 4.8 15.9 1.0
O1A A:GTP301 4.8 21.6 1.0
O2B A:GTP301 4.8 16.6 1.0
C A:GLU115 4.8 19.3 1.0
CB A:ILE114 4.9 18.1 1.0
HG22 A:ILE114 4.9 22.2 1.0

Calcium binding site 2 out of 2 in 5d0g

Go back to Calcium Binding Sites List in 5d0g
Calcium binding site 2 out of 2 in the Crystal Structure of Triple Mutant (kDa to Egy) of Adenylyl Cyclase MA1120 From Mycobacterium Avium in Complex with Gtp and Calcium 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 Triple Mutant (kDa to Egy) of Adenylyl Cyclase MA1120 From Mycobacterium Avium in Complex with Gtp and Calcium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:16.9
occ:1.00
O1A B:GTP301 2.3 18.5 1.0
O B:ILE114 2.3 19.5 1.0
O1B B:GTP301 2.3 18.9 1.0
O2G B:GTP301 2.4 23.3 1.0
OD2 B:ASP157 2.4 20.5 1.0
OD1 B:ASP113 2.4 24.9 1.0
OD2 B:ASP113 2.5 24.8 1.0
CG B:ASP113 2.8 22.9 1.0
PB B:GTP301 3.4 19.1 1.0
PA B:GTP301 3.5 22.6 1.0
CG B:ASP157 3.5 20.9 1.0
C B:ILE114 3.5 17.8 1.0
HH12 B:ARG195 3.5 37.5 1.0
PG B:GTP301 3.6 22.9 1.0
O3A B:GTP301 3.7 22.3 1.0
H B:SER117 3.8 24.2 1.0
HH11 B:ARG195 3.8 37.5 1.0
O3B B:GTP301 3.9 21.8 1.0
OD1 B:ASP157 3.9 20.8 1.0
H B:ILE114 4.0 19.4 1.0
NH1 B:ARG195 4.0 31.2 1.0
N B:ILE114 4.1 16.2 1.0
H B:GLU116 4.1 25.4 1.0
O5' B:GTP301 4.1 27.8 1.0
HA B:GLU115 4.1 25.8 1.0
HB3 B:SER117 4.1 21.9 1.0
HG B:SER117 4.2 22.0 1.0
CB B:ASP113 4.3 17.2 1.0
OG B:SER117 4.3 18.3 1.0
O1G B:GTP301 4.3 24.0 1.0
CA B:ILE114 4.3 16.0 1.0
HB B:ILE114 4.4 21.8 1.0
O B:HOH494 4.4 33.7 1.0
N B:GLU115 4.4 17.8 1.0
N B:GLU116 4.5 21.1 1.0
C B:ASP113 4.5 16.8 1.0
O B:HOH425 4.5 34.3 1.0
CA B:GLU115 4.6 21.5 1.0
HB2 B:ASP157 4.6 23.8 1.0
N B:SER117 4.6 20.1 1.0
O3G B:GTP301 4.6 24.2 1.0
HB3 B:ASP113 4.7 20.7 1.0
O2B B:GTP301 4.7 22.4 1.0
CB B:SER117 4.7 18.2 1.0
O2A B:GTP301 4.7 25.8 1.0
CB B:ASP157 4.7 19.9 1.0
HA B:ASP113 4.7 19.3 1.0
C B:GLU115 4.8 21.9 1.0
HB2 B:ASP113 4.8 20.7 1.0
CA B:ASP113 4.8 16.1 1.0
CB B:ILE114 4.9 18.1 1.0
HG22 B:ILE114 5.0 22.6 1.0

Reference:

N.G.Bharambe, D.V.Barathy, W.Syed, S.S.Visweswariah, M.Cola Sigmaf O, S.Misquith, K.Suguna. Substrate Specificity Determinants of Class III Nucleotidyl Cyclases Febs J. V. 283 3723 2016.
ISSN: ISSN 1742-464X
PubMed: 27542992
DOI: 10.1111/FEBS.13837
Page generated: Sun Jul 14 17:40:55 2024

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