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Magnesium in PDB 4h54: Crystal Structure of the Diguanylate Cyclase Dgcz

Enzymatic activity of Crystal Structure of the Diguanylate Cyclase Dgcz

All present enzymatic activity of Crystal Structure of the Diguanylate Cyclase Dgcz:
2.7.7.65;

Protein crystallography data

The structure of Crystal Structure of the Diguanylate Cyclase Dgcz, PDB code: 4h54 was solved by F.Zaehringer, T.Schirmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.20 / 3.90
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 102.593, 102.593, 129.156, 90.00, 90.00, 120.00
R / Rfree (%) 24.2 / 24.1

Other elements in 4h54:

The structure of Crystal Structure of the Diguanylate Cyclase Dgcz also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Diguanylate Cyclase Dgcz (pdb code 4h54). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Diguanylate Cyclase Dgcz, PDB code: 4h54:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4h54

Go back to Magnesium Binding Sites List in 4h54
Magnesium binding site 1 out of 2 in the Crystal Structure of the Diguanylate Cyclase Dgcz


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 the Diguanylate Cyclase Dgcz within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:19.9
occ:1.00
OD2 A:ASP165 1.7 19.4 0.5
O3G A:GAV402 1.9 23.8 1.0
O A:ILE166 2.0 16.1 1.0
OE2 A:GLU208 2.4 19.2 1.0
OE1 A:GLU208 2.5 16.2 1.0
O2B A:GAV402 2.6 18.8 1.0
CD A:GLU208 2.8 17.0 1.0
PG A:GAV402 2.8 31.6 1.0
CG A:ASP165 2.9 19.2 0.5
O3B A:GAV402 3.0 27.0 1.0
PB A:GAV402 3.2 22.2 1.0
C A:ILE166 3.2 15.0 1.0
NZ A:LYS277 3.3 24.9 1.0
O3A A:GAV402 3.5 22.1 1.0
O2G A:GAV402 3.5 45.6 1.0
OD1 A:ASP165 3.6 19.8 0.5
C A:ASP165 3.8 15.3 1.0
N A:ILE166 3.9 13.6 1.0
CE A:LYS277 3.9 28.3 1.0
O A:ASP165 3.9 16.8 1.0
CB A:ASP165 4.0 18.7 0.5
N A:ASP167 4.1 15.9 1.0
O1G A:GAV402 4.1 42.8 1.0
CA A:ILE166 4.1 13.2 1.0
CA A:ASP167 4.1 18.1 1.0
CG A:GLU208 4.2 16.0 1.0
N A:ARG168 4.4 19.3 1.0
CA A:ASP165 4.5 15.8 0.5
O1B A:GAV402 4.6 25.0 1.0
C A:ASP167 4.6 17.3 1.0
PA A:GAV402 4.8 26.4 1.0
CB A:ILE166 4.8 11.8 1.0
OD1 A:ASP167 4.9 22.5 1.0
CD A:LYS277 4.9 44.0 1.0
NH1 A:ARG281 4.9 45.6 1.0

Magnesium binding site 2 out of 2 in 4h54

Go back to Magnesium Binding Sites List in 4h54
Magnesium binding site 2 out of 2 in the Crystal Structure of the Diguanylate Cyclase Dgcz


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 the Diguanylate Cyclase Dgcz within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:39.8
occ:1.00
O3G B:GAV402 1.7 51.5 1.0
O B:ILE166 1.7 38.7 1.0
O2B B:GAV402 2.1 50.5 1.0
OD2 B:ASP165 2.2 31.4 0.5
OE1 B:GLU208 2.6 35.8 1.0
PG B:GAV402 2.7 58.6 1.0
O3B B:GAV402 2.7 53.8 1.0
PB B:GAV402 2.9 54.3 1.0
OE2 B:GLU208 2.9 33.9 1.0
C B:ILE166 2.9 39.1 1.0
CD B:GLU208 3.1 33.0 1.0
NZ B:LYS277 3.4 41.6 1.0
CG B:ASP165 3.4 27.0 0.5
O3A B:GAV402 3.6 47.5 1.0
CA B:ASP167 3.6 67.5 1.0
O2G B:GAV402 3.7 57.1 1.0
N B:ASP167 3.7 49.8 1.0
O1G B:GAV402 3.7 74.9 1.0
N B:ARG168 3.8 83.0 1.0
N B:ILE166 3.9 28.6 1.0
CA B:ILE166 4.0 34.2 1.0
O B:ASP165 4.0 30.0 1.0
C B:ASP165 4.0 27.0 1.0
C B:ASP167 4.1 78.0 1.0
OD1 B:ASP165 4.1 26.0 0.5
CE B:LYS277 4.1 35.5 1.0
O1B B:GAV402 4.2 69.6 1.0
CB B:ASP165 4.5 23.6 0.5
CG B:GLU208 4.5 28.6 1.0
N B:PHE169 4.6 68.5 1.0
NH1 B:ARG281 4.6 89.8 1.0
CB B:ILE166 4.7 35.4 1.0
OD1 B:ASP167 4.7 67.1 1.0
CA B:ARG168 4.8 94.9 1.0
CA B:ASP165 4.8 22.2 0.5
PA B:GAV402 4.9 53.4 1.0
CB B:ASP167 5.0 84.0 1.0

Reference:

F.Zahringer, E.Lacanna, U.Jenal, T.Schirmer, A.Boehm. Structure and Signaling Mechanism of A Zinc-Sensory Diguanylate Cyclase. Structure V. 21 1149 2013.
ISSN: ISSN 0969-2126
PubMed: 23769666
DOI: 10.1016/J.STR.2013.04.026
Page generated: Mon Dec 14 17:12:03 2020

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