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Calcium in PDB 6qgb: Crystal Structure of Ideonella Sakaiensis Mhetase Bound to Benzoic Acid

Enzymatic activity of Crystal Structure of Ideonella Sakaiensis Mhetase Bound to Benzoic Acid

All present enzymatic activity of Crystal Structure of Ideonella Sakaiensis Mhetase Bound to Benzoic Acid:
3.1.1.102;

Protein crystallography data

The structure of Crystal Structure of Ideonella Sakaiensis Mhetase Bound to Benzoic Acid, PDB code: 6qgb 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) 46.09 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 111.141, 184.048, 247.441, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 21.4

Other elements in 6qgb:

The structure of Crystal Structure of Ideonella Sakaiensis Mhetase Bound to Benzoic Acid also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to Benzoic Acid (pdb code 6qgb). 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 Benzoic Acid, PDB code: 6qgb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6qgb

Go back to Calcium Binding Sites List in 6qgb
Calcium binding site 1 out of 6 in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to Benzoic Acid


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 Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:27.4
occ:1.00
 OD1 A:ASP304 2.3 32.5 1.0
O A:ILE313 2.3 30.7 1.0
O A:LEU309 2.4 32.6 1.0
O A:HOH809 2.5 34.8 1.0
O A:ASP304 2.5 32.8 1.0
OD2 A:ASP307 2.5 36.0 1.0
OD1 A:ASP311 2.6 31.2 1.0
OD1 A:ASP307 2.6 31.6 1.0
CG A:ASP307 2.9 31.1 1.0
C A:ASP304 3.4 33.6 1.0
CG A:ASP304 3.5 33.3 1.0
CG A:ASP311 3.5 31.1 1.0
C A:ILE313 3.5 30.3 1.0
C A:LEU309 3.6 33.3 1.0
OD2 A:ASP311 3.9 30.5 1.0
CA A:ASP304 4.0 33.6 1.0
N A:ASP311 4.1 33.1 1.0
N A:ILE313 4.1 30.9 1.0
OD2 A:ASP315 4.2 31.1 1.0
CA A:ILE313 4.3 30.2 1.0
CB A:ASP304 4.3 34.0 1.0
OD2 A:ASP304 4.3 33.7 1.0
CB A:ASP307 4.4 31.0 1.0
CA A:LEU309 4.5 33.2 1.0
N A:ALA305 4.5 34.7 1.0
N A:LEU309 4.5 33.2 1.0
N A:ALA310 4.5 34.2 1.0
N A:VAL314 4.5 30.2 1.0
CA A:ALA310 4.6 34.5 1.0
O A:HOH957 4.6 25.8 1.0
CB A:LEU309 4.6 32.3 1.0
CB A:ILE313 4.6 29.6 1.0
CB A:ASP311 4.7 31.8 1.0
N A:ASP315 4.7 29.6 1.0
CA A:VAL314 4.7 30.4 1.0
C A:ALA310 4.8 33.9 1.0
CA A:ASP311 4.8 32.6 1.0
CA A:ALA305 4.8 35.0 1.0
N A:GLY312 4.8 32.5 1.0

Calcium binding site 2 out of 6 in 6qgb

Go back to Calcium Binding Sites List in 6qgb
Calcium binding site 2 out of 6 in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to Benzoic Acid


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 Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca803

b:28.9
occ:1.00
 O B:LEU309 2.3 33.1 1.0
O B:HOH967 2.4 33.2 1.0
OD1 B:ASP304 2.4 35.7 1.0
OD1 B:ASP311 2.4 34.1 1.0
O B:ILE313 2.4 30.2 1.0
OD1 B:ASP307 2.6 31.9 1.0
OD2 B:ASP307 2.6 30.6 1.0
O B:ASP304 2.7 34.7 1.0
CG B:ASP307 3.0 31.2 1.0
CG B:ASP311 3.4 31.9 1.0
C B:LEU309 3.5 33.9 1.0
C B:ASP304 3.6 32.2 1.0
CG B:ASP304 3.6 33.4 1.0
C B:ILE313 3.6 29.6 1.0
OD2 B:ASP311 3.9 31.9 1.0
N B:ASP311 4.0 33.3 1.0
CA B:ASP304 4.1 31.8 1.0
N B:ILE313 4.2 30.5 1.0
CA B:ILE313 4.4 29.7 1.0
CA B:LEU309 4.4 34.2 1.0
OD2 B:ASP315 4.4 34.1 1.0
N B:LEU309 4.4 34.0 1.0
CB B:ASP304 4.5 32.3 1.0
CB B:LEU309 4.5 33.9 1.0
CB B:ASP307 4.5 31.1 1.0
OD2 B:ASP304 4.5 33.2 1.0
N B:ALA310 4.5 34.6 1.0
O B:HOH955 4.5 26.9 1.0
CA B:ALA310 4.6 34.5 1.0
CB B:ASP311 4.6 32.7 1.0
CB B:ILE313 4.6 29.5 1.0
N B:ALA305 4.7 37.8 1.0
N B:VAL314 4.7 29.0 1.0
CA B:ASP311 4.7 33.1 1.0
C B:ALA310 4.7 34.2 1.0
N B:ASP315 4.7 28.9 1.0
CA B:VAL314 4.8 29.0 1.0
N B:GLY312 4.9 32.2 1.0
CA B:ALA305 5.0 35.0 1.0

Calcium binding site 3 out of 6 in 6qgb

Go back to Calcium Binding Sites List in 6qgb
Calcium binding site 3 out of 6 in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to Benzoic Acid


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 Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca702

b:33.7
occ:1.00
 O C:HOH887 2.4 31.5 1.0
O C:LEU309 2.4 40.4 1.0
OD1 C:ASP304 2.4 35.8 1.0
O C:ASP304 2.4 36.0 1.0
O C:ILE313 2.4 33.7 1.0
OD1 C:ASP307 2.5 43.1 1.0
OD2 C:ASP307 2.5 40.0 1.0
OD1 C:ASP311 2.5 37.0 1.0
CG C:ASP307 2.8 36.1 1.0
C C:ASP304 3.4 36.5 1.0
C C:LEU309 3.6 37.7 1.0
CG C:ASP311 3.6 36.8 1.0
CG C:ASP304 3.6 36.2 1.0
C C:ILE313 3.6 33.1 1.0
CA C:ASP304 4.0 36.0 1.0
OD2 C:ASP311 4.1 37.2 1.0
N C:ASP311 4.2 36.9 1.0
O C:HOH815 4.3 31.4 1.0
CB C:ASP307 4.3 34.9 1.0
N C:ILE313 4.3 33.9 1.0
OD2 C:ASP315 4.3 35.1 1.0
CB C:ASP304 4.4 36.5 1.0
N C:ALA305 4.4 37.4 1.0
CA C:ILE313 4.4 33.0 1.0
CA C:LEU309 4.5 37.9 1.0
OD2 C:ASP304 4.5 36.6 1.0
N C:ALA310 4.5 38.4 1.0
CA C:ALA310 4.5 38.3 1.0
N C:LEU309 4.5 38.0 1.0
N C:ASP315 4.6 33.3 1.0
N C:VAL314 4.6 32.6 1.0
CB C:LEU309 4.7 37.3 1.0
CA C:ALA305 4.7 38.0 1.0
CB C:ILE313 4.7 32.6 1.0
CA C:VAL314 4.7 32.7 1.0
C C:ALA310 4.8 37.8 1.0
CB C:ASP311 4.8 35.9 1.0
CA C:ASP311 4.9 36.4 1.0
N C:ASP307 5.0 36.1 1.0

Calcium binding site 4 out of 6 in 6qgb

Go back to Calcium Binding Sites List in 6qgb
Calcium binding site 4 out of 6 in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to Benzoic Acid


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 Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca702

b:29.1
occ:1.00
 O D:LEU309 2.3 28.1 1.0
O D:ILE313 2.4 27.2 1.0
OD1 D:ASP304 2.4 28.4 1.0
O D:HOH923 2.4 27.9 1.0
OD2 D:ASP307 2.6 28.7 1.0
O D:ASP304 2.6 28.2 1.0
OD1 D:ASP307 2.6 28.6 1.0
OD1 D:ASP311 2.8 32.4 1.0
CG D:ASP307 3.0 28.0 1.0
C D:LEU309 3.5 28.3 1.0
C D:ASP304 3.5 28.6 1.0
C D:ILE313 3.6 27.1 1.0
CG D:ASP304 3.6 28.7 1.0
CG D:ASP311 3.7 27.6 1.0
CA D:ASP304 4.0 28.6 1.0
OD2 D:ASP311 4.1 27.1 1.0
N D:ASP311 4.1 28.5 1.0
N D:ILE313 4.2 27.6 1.0
CA D:ILE313 4.3 27.1 1.0
CA D:LEU309 4.4 28.2 1.0
CB D:ASP304 4.4 29.0 1.0
N D:ALA310 4.4 28.8 1.0
CB D:ASP307 4.5 27.1 1.0
N D:LEU309 4.5 28.2 1.0
CB D:LEU309 4.5 27.8 1.0
OD2 D:ASP304 4.5 29.0 1.0
CA D:ALA310 4.5 29.1 1.0
N D:VAL314 4.6 32.0 1.0
OD2 D:ASP315 4.6 26.1 1.0
O D:HOH900 4.6 23.8 1.0
N D:ASP315 4.6 26.4 1.0
N D:ALA305 4.6 29.1 1.0
CB D:ILE313 4.7 26.8 1.0
CA D:VAL314 4.7 27.0 1.0
CB D:ASP311 4.8 27.9 1.0
C D:ALA310 4.8 28.9 1.0
CA D:ASP311 4.9 28.4 1.0
CA D:ALA305 5.0 29.1 1.0
N D:GLY312 5.0 28.5 1.0

Calcium binding site 5 out of 6 in 6qgb

Go back to Calcium Binding Sites List in 6qgb
Calcium binding site 5 out of 6 in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to Benzoic Acid


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 Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca702

b:23.1
occ:1.00
 O E:ILE313 2.3 28.9 1.0
OD1 E:ASP311 2.3 29.9 1.0
O E:HOH837 2.4 34.9 1.0
O E:LEU309 2.4 31.1 1.0
OD1 E:ASP304 2.4 35.4 1.0
O E:ASP304 2.5 30.3 1.0
OD1 E:ASP307 2.6 30.2 1.0
OD2 E:ASP307 2.6 31.4 1.0
CG E:ASP307 2.9 29.6 1.0
CG E:ASP311 3.4 30.1 1.0
C E:ASP304 3.5 30.6 1.0
C E:ILE313 3.5 28.4 1.0
C E:LEU309 3.7 31.7 1.0
CG E:ASP304 3.7 31.7 1.0
OD2 E:ASP311 3.9 29.8 1.0
N E:ASP311 4.0 31.2 1.0
CA E:ASP304 4.0 30.3 1.0
N E:ILE313 4.2 29.0 1.0
OD2 E:ASP315 4.2 28.3 1.0
CA E:ILE313 4.4 28.4 1.0
CB E:ASP307 4.4 29.6 1.0
CB E:ASP304 4.5 30.7 1.0
CA E:LEU309 4.5 31.9 1.0
N E:VAL314 4.5 28.0 1.0
N E:ALA305 4.6 31.3 1.0
OD2 E:ASP304 4.6 30.9 1.0
CB E:LEU309 4.6 31.5 1.0
CB E:ASP311 4.6 30.7 1.0
N E:LEU309 4.6 31.8 1.0
N E:ALA310 4.6 32.3 1.0
N E:ASP315 4.6 27.9 1.0
O E:HOH934 4.6 19.0 1.0
CA E:ALA310 4.6 32.2 1.0
CB E:ILE313 4.7 28.2 1.0
CA E:VAL314 4.7 28.0 1.0
CA E:ASP311 4.8 31.0 1.0
C E:ALA310 4.8 31.9 1.0
CA E:ALA305 4.8 31.7 1.0
N E:GLY312 4.9 30.3 1.0

Calcium binding site 6 out of 6 in 6qgb

Go back to Calcium Binding Sites List in 6qgb
Calcium binding site 6 out of 6 in the Crystal Structure of Ideonella Sakaiensis Mhetase Bound to Benzoic Acid


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 Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca702

b:25.4
occ:1.00
 O F:LEU309 2.3 27.8 1.0
OD1 F:ASP304 2.4 34.4 1.0
OD1 F:ASP311 2.4 27.5 1.0
O F:ILE313 2.4 26.5 1.0
O F:HOH814 2.5 30.6 1.0
OD2 F:ASP307 2.5 32.9 1.0
OD1 F:ASP307 2.6 27.6 1.0
O F:ASP304 2.6 32.4 1.0
CG F:ASP307 2.9 26.5 1.0
CG F:ASP311 3.4 28.1 1.0
C F:ASP304 3.5 27.5 1.0
C F:LEU309 3.5 28.3 1.0
CG F:ASP304 3.6 29.3 1.0
C F:ILE313 3.6 26.4 1.0
OD2 F:ASP311 3.8 30.5 1.0
N F:ASP311 4.0 28.8 1.0
CA F:ASP304 4.1 27.5 1.0
OD2 F:ASP315 4.2 27.5 1.0
N F:ILE313 4.2 27.2 1.0
CA F:ILE313 4.4 26.6 1.0
CB F:ASP307 4.4 26.3 1.0
CA F:LEU309 4.4 28.3 1.0
CB F:ASP304 4.4 28.7 1.0
N F:ALA310 4.5 28.9 1.0
N F:LEU309 4.5 28.0 1.0
OD2 F:ASP304 4.5 28.4 1.0
CA F:ALA310 4.5 29.0 1.0
N F:ALA305 4.5 28.0 1.0
CB F:LEU309 4.6 28.1 1.0
CB F:ASP311 4.6 28.4 1.0
O F:HOH940 4.6 22.8 1.0
CB F:ILE313 4.6 26.6 1.0
N F:VAL314 4.6 26.1 1.0
N F:ASP315 4.7 25.6 1.0
C F:ALA310 4.7 31.2 1.0
CA F:ASP311 4.7 28.7 1.0
CA F:ALA305 4.8 28.1 1.0
CA F:VAL314 4.8 26.2 1.0
N F:GLY312 4.9 28.4 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: Tue Jul 16 13:50:48 2024

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