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Calcium in PDB 6qga: Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta

Enzymatic activity of Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta

All present enzymatic activity of Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta:
3.1.1.102;

Protein crystallography data

The structure of Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta, PDB code: 6qga was solved by G.J.Palm, L.Reisky, D.Boettcher, H.Mueller, E.A.P.Michels, C.Walczak, L.Berndt, M.S.Weiss, U.T.Bornscheuer, G.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.11 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 112.153, 183.646, 246.752, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 19.8

Other elements in 6qga:

The structure of Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta (pdb code 6qga). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta, PDB code: 6qga:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6qga

Go back to Calcium Binding Sites List in 6qga
Calcium binding site 1 out of 6 in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta


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 Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca706

b:25.8
occ:1.00
 OD1 A:ASP304 2.3 32.1 1.0
O A:ILE313 2.4 29.9 1.0
O A:LEU309 2.4 32.2 1.0
OD1 A:ASP311 2.6 30.6 1.0
OD2 A:ASP307 2.6 29.9 1.0
O A:HOH822 2.6 25.8 1.0
O A:ASP304 2.6 32.2 1.0
OD1 A:ASP307 2.7 30.9 1.0
CG A:ASP307 3.0 30.3 1.0
C A:ASP304 3.4 33.1 1.0
CG A:ASP304 3.5 33.0 1.0
CG A:ASP311 3.5 30.4 1.0
C A:ILE313 3.6 29.4 1.0
C A:LEU309 3.6 32.9 1.0
OD2 A:ASP311 3.9 29.7 1.0
CA A:ASP304 3.9 33.1 1.0
N A:ASP311 4.0 32.6 1.0
N A:ILE313 4.2 30.2 1.0
CB A:ASP304 4.3 33.6 1.0
OD2 A:ASP315 4.4 36.4 1.0
CA A:ILE313 4.4 29.3 1.0
OD2 A:ASP304 4.4 33.4 1.0
N A:ALA305 4.5 34.2 1.0
CA A:LEU309 4.5 32.8 1.0
CB A:ASP307 4.5 30.1 1.0
N A:ALA310 4.5 33.8 1.0
O A:HOH936 4.5 24.8 1.0
N A:LEU309 4.5 32.7 1.0
N A:VAL314 4.6 29.2 1.0
CA A:ALA310 4.6 34.1 1.0
N A:ASP315 4.7 28.4 1.0
CB A:LEU309 4.7 31.8 1.0
CB A:ASP311 4.7 31.1 1.0
CA A:VAL314 4.7 29.4 1.0
CB A:ILE313 4.7 28.5 1.0
C A:ALA310 4.8 33.5 1.0
CA A:ALA305 4.8 34.4 1.0
CA A:ASP311 4.8 32.0 1.0
N A:GLY312 4.9 32.0 1.0
O A:HOH1055 4.9 25.8 1.0

Calcium binding site 2 out of 6 in 6qga

Go back to Calcium Binding Sites List in 6qga
Calcium binding site 2 out of 6 in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta


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 Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca706

b:23.9
occ:1.00
 O B:LEU309 2.3 28.8 1.0
O B:ILE313 2.4 25.9 1.0
OD1 B:ASP304 2.5 27.9 1.0
O B:ASP304 2.5 27.6 1.0
OD1 B:ASP311 2.5 27.4 1.0
O B:HOH870 2.6 25.6 1.0
OD1 B:ASP307 2.6 27.5 1.0
OD2 B:ASP307 2.7 26.1 1.0
CG B:ASP307 3.0 26.7 1.0
C B:ASP304 3.5 28.0 1.0
CG B:ASP311 3.5 27.7 1.0
C B:LEU309 3.5 29.6 1.0
C B:ILE313 3.6 25.4 1.0
CG B:ASP304 3.7 28.3 1.0
OD2 B:ASP311 4.0 28.5 1.0
N B:ASP311 4.0 29.3 1.0
CA B:ASP304 4.1 27.6 1.0
N B:ILE313 4.2 26.4 1.0
CA B:LEU309 4.4 29.8 1.0
CA B:ILE313 4.4 25.5 1.0
N B:ALA310 4.4 30.4 1.0
CB B:ASP304 4.5 28.3 1.0
N B:LEU309 4.5 29.6 1.0
N B:ALA305 4.5 28.8 1.0
CB B:LEU309 4.5 29.3 1.0
O B:HOH865 4.5 20.6 1.0
CA B:ALA310 4.5 30.4 1.0
CB B:ASP307 4.5 26.5 1.0
OD2 B:ASP304 4.6 28.8 1.0
CB B:ASP311 4.6 28.6 1.0
N B:VAL314 4.6 24.8 1.0
OD2 B:ASP315 4.7 33.9 1.0
CB B:ILE313 4.7 25.3 1.0
C B:ALA310 4.7 30.2 1.0
N B:ASP315 4.7 24.4 1.0
CA B:ALA305 4.7 29.4 1.0
CA B:ASP311 4.8 29.1 1.0
CA B:VAL314 4.8 24.7 1.0
N B:GLY312 5.0 28.2 1.0

Calcium binding site 3 out of 6 in 6qga

Go back to Calcium Binding Sites List in 6qga
Calcium binding site 3 out of 6 in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta


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 Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca703

b:30.9
occ:1.00
 O C:ASP304 2.4 34.6 1.0
OD1 C:ASP304 2.4 35.5 1.0
O C:ILE313 2.4 32.2 1.0
O C:LEU309 2.4 36.2 1.0
OD1 C:ASP311 2.4 34.1 1.0
OD1 C:ASP307 2.5 34.2 1.0
O C:HOH826 2.5 27.2 1.0
OD2 C:ASP307 2.6 32.5 1.0
CG C:ASP307 2.9 33.2 1.0
C C:ASP304 3.4 35.3 1.0
CG C:ASP311 3.5 34.3 1.0
C C:ILE313 3.6 31.5 1.0
CG C:ASP304 3.6 35.5 1.0
C C:LEU309 3.6 37.3 1.0
N C:ASP311 4.0 36.6 1.0
CA C:ASP304 4.0 34.8 1.0
OD2 C:ASP311 4.0 34.8 1.0
N C:ILE313 4.2 32.7 1.0
OD2 C:ASP315 4.3 35.8 1.0
N C:ALA305 4.4 36.5 1.0
CA C:ILE313 4.4 31.5 1.0
CB C:ASP307 4.4 33.0 1.0
CB C:ASP304 4.4 35.6 1.0
O C:HOH824 4.4 26.5 1.0
CA C:LEU309 4.5 37.5 1.0
OD2 C:ASP304 4.5 36.0 1.0
N C:LEU309 4.5 37.3 1.0
N C:ALA310 4.6 38.4 1.0
CB C:LEU309 4.6 36.7 1.0
CA C:ALA310 4.6 38.3 1.0
CB C:ASP311 4.6 35.6 1.0
N C:VAL314 4.6 30.7 1.0
N C:ASP315 4.6 30.2 1.0
CA C:ALA305 4.7 37.3 1.0
CB C:ILE313 4.7 31.0 1.0
C C:ALA310 4.7 37.9 1.0
CA C:VAL314 4.8 30.7 1.0
CA C:ASP311 4.8 36.2 1.0
N C:GLY312 5.0 35.2 1.0
N C:ASP307 5.0 34.5 1.0

Calcium binding site 4 out of 6 in 6qga

Go back to Calcium Binding Sites List in 6qga
Calcium binding site 4 out of 6 in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca702

b:21.9
occ:1.00
 O D:LEU309 2.3 25.0 1.0
O D:ILE313 2.4 23.8 1.0
OD1 D:ASP304 2.4 25.9 1.0
O D:HOH824 2.5 24.4 1.0
OD2 D:ASP307 2.6 26.4 1.0
O D:ASP304 2.6 24.8 1.0
OD1 D:ASP311 2.7 24.5 1.0
OD1 D:ASP307 2.7 24.9 1.0
CG D:ASP307 3.0 25.9 1.0
C D:ASP304 3.5 25.3 1.0
C D:LEU309 3.5 25.5 1.0
C D:ILE313 3.6 23.7 1.0
CG D:ASP304 3.6 25.7 1.0
CG D:ASP311 3.6 26.2 1.0
OD2 D:ASP311 4.0 27.3 1.0
CA D:ASP304 4.0 25.4 1.0
N D:ASP311 4.0 25.8 1.0
N D:ILE313 4.2 24.5 1.0
CA D:ILE313 4.3 23.8 1.0
CB D:ASP304 4.4 25.9 1.0
OD2 D:ASP315 4.4 29.4 1.0
CA D:LEU309 4.4 25.3 1.0
N D:ALA310 4.4 26.1 1.0
N D:LEU309 4.5 25.1 1.0
OD2 D:ASP304 4.5 26.2 1.0
CA D:ALA310 4.5 26.4 1.0
CB D:ASP307 4.5 23.4 1.0
N D:VAL314 4.6 23.4 1.0
N D:ALA305 4.6 28.9 1.0
CB D:LEU309 4.6 24.9 1.0
O D:HOH963 4.6 21.4 1.0
N D:ASP315 4.7 22.6 1.0
CB D:ILE313 4.7 23.4 1.0
CB D:ASP311 4.7 25.5 1.0
C D:ALA310 4.8 26.4 1.0
CA D:VAL314 4.8 23.4 1.0
CA D:ASP311 4.8 25.8 1.0
CA D:ALA305 4.9 26.2 1.0
N D:GLY312 5.0 25.8 1.0

Calcium binding site 5 out of 6 in 6qga

Go back to Calcium Binding Sites List in 6qga
Calcium binding site 5 out of 6 in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca705

b:26.2
occ:1.00
 OD1 E:ASP304 2.3 30.2 1.0
O E:ILE313 2.3 24.3 1.0
OD1 E:ASP311 2.4 25.2 1.0
O E:LEU309 2.4 26.4 1.0
OD2 E:ASP307 2.5 27.6 1.0
O E:HOH812 2.6 26.1 1.0
OD1 E:ASP307 2.6 27.8 1.0
O E:ASP304 2.7 25.8 1.0
CG E:ASP307 2.9 26.1 1.0
CG E:ASP311 3.4 25.4 1.0
C E:ILE313 3.5 23.9 1.0
C E:ASP304 3.5 29.9 1.0
CG E:ASP304 3.6 28.9 1.0
C E:LEU309 3.6 27.0 1.0
OD2 E:ASP311 3.8 25.4 1.0
N E:ASP311 4.0 26.4 1.0
CA E:ASP304 4.0 25.7 1.0
N E:ILE313 4.1 24.4 1.0
CA E:ILE313 4.3 23.9 1.0
OD2 E:ASP315 4.3 30.9 1.0
CB E:ASP304 4.4 26.0 1.0
OD2 E:ASP304 4.4 26.2 1.0
CB E:ASP307 4.5 25.2 1.0
CA E:LEU309 4.5 27.2 1.0
O E:HOH940 4.5 19.6 1.0
N E:ALA310 4.5 27.5 1.0
N E:VAL314 4.6 23.6 1.0
CA E:ALA310 4.6 27.3 1.0
CB E:ASP311 4.6 26.0 1.0
N E:ALA305 4.6 26.7 1.0
CB E:ILE313 4.6 23.7 1.0
N E:LEU309 4.6 27.1 1.0
CB E:LEU309 4.6 26.9 1.0
N E:ASP315 4.7 24.0 1.0
CA E:ASP311 4.7 26.2 1.0
CA E:VAL314 4.7 23.6 1.0
C E:ALA310 4.8 27.1 1.0
N E:GLY312 4.9 25.6 1.0
CA E:ALA305 4.9 27.1 1.0

Calcium binding site 6 out of 6 in 6qga

Go back to Calcium Binding Sites List in 6qga
Calcium binding site 6 out of 6 in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Ideonella Sakaiensis Mhetase Bound to the Non- Hydrolyzable Ligand Mheta within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca706

b:24.8
occ:1.00
 O F:ILE313 2.3 25.3 1.0
O F:LEU309 2.4 27.5 1.0
OD1 F:ASP311 2.4 26.6 1.0
OD1 F:ASP304 2.4 26.9 1.0
O F:HOH860 2.5 26.8 1.0
OD2 F:ASP307 2.5 25.4 1.0
O F:ASP304 2.6 26.6 1.0
OD1 F:ASP307 2.7 27.7 1.0
CG F:ASP307 3.0 25.8 1.0
CG F:ASP311 3.5 26.9 1.0
C F:ASP304 3.5 26.9 1.0
C F:ILE313 3.5 24.9 1.0
C F:LEU309 3.6 28.2 1.0
CG F:ASP304 3.6 27.2 1.0
OD2 F:ASP311 4.0 26.6 1.0
N F:ASP311 4.0 28.0 1.0
CA F:ASP304 4.0 26.7 1.0
N F:ILE313 4.1 25.8 1.0
CA F:ILE313 4.3 25.1 1.0
CB F:ASP304 4.4 27.2 1.0
O F:HOH947 4.4 19.1 1.0
CA F:LEU309 4.5 28.4 1.0
CB F:ASP307 4.5 25.7 1.0
N F:ALA310 4.5 28.9 1.0
OD2 F:ASP315 4.5 31.9 1.0
CA F:ALA310 4.5 28.8 1.0
N F:ALA305 4.5 27.6 1.0
OD2 F:ASP304 4.5 27.6 1.0
N F:LEU309 4.5 28.1 1.0
N F:VAL314 4.6 24.4 1.0
CB F:LEU309 4.6 28.1 1.0
CB F:ILE313 4.6 24.9 1.0
CB F:ASP311 4.6 27.7 1.0
N F:ASP315 4.7 24.1 1.0
C F:ALA310 4.7 28.7 1.0
CA F:ASP311 4.7 28.0 1.0
CA F:VAL314 4.8 24.3 1.0
CA F:ALA305 4.8 28.0 1.0
N F:GLY312 4.9 27.3 1.0

Reference:

G.J.Palm, L.Reisky, D.Bottcher, H.Muller, E.A.P.Michels, M.C.Walczak, L.Berndt, M.S.Weiss, U.T.Bornscheuer, G.Weber. Structure of the Plastic-Degrading Ideonella Sakaiensis Mhetase Bound to A Substrate. Nat Commun V. 10 1717 2019.
ISSN: ESSN 2041-1723
PubMed: 30979881
DOI: 10.1038/S41467-019-09326-3
Page generated: Wed Jul 9 17:11:41 2025

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