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Zinc in PDB 6qg9: Crystal Structure of Ideonella Sakaiensis Mhetase

Enzymatic activity of Crystal Structure of Ideonella Sakaiensis Mhetase

All present enzymatic activity of Crystal Structure of Ideonella Sakaiensis Mhetase:
3.1.1.102;

Protein crystallography data

The structure of Crystal Structure of Ideonella Sakaiensis Mhetase, PDB code: 6qg9 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) 40.00 / 2.05
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 111.286, 137.949, 137.051, 83.01, 66.88, 68.45
R / Rfree (%) 21 / 26.2

Other elements in 6qg9:

The structure of Crystal Structure of Ideonella Sakaiensis Mhetase also contains other interesting chemical elements:

Calcium (Ca) 10 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Ideonella Sakaiensis Mhetase (pdb code 6qg9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 11 binding sites of Zinc where determined in the Crystal Structure of Ideonella Sakaiensis Mhetase, PDB code: 6qg9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in 6qg9

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Zinc binding site 1 out of 11 in the Crystal Structure of Ideonella Sakaiensis Mhetase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Ideonella Sakaiensis Mhetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:57.4
occ:1.00
 OE2 A:GLU93 2.3 34.6 1.0
O A:HOH1139 2.8 35.4 1.0
OE1 A:GLU93 2.8 31.2 1.0
CD A:GLU93 2.9 31.3 1.0
O A:HOH1125 3.2 33.9 1.0
O A:HOH900 3.2 40.0 1.0
O A:HOH813 3.7 25.9 1.0
NH2 A:ARG76 3.9 34.7 1.0
NH2 A:ARG116 3.9 23.0 1.0
NE A:ARG114 4.1 35.4 1.0
CG A:GLU93 4.4 26.6 1.0
NH1 A:ARG116 4.6 27.0 1.0
NE A:ARG76 4.6 34.8 1.0
CZ A:ARG114 4.6 36.5 1.0
CZ A:ARG76 4.6 35.8 1.0
NH2 A:ARG114 4.7 34.0 1.0
CZ A:ARG116 4.7 26.0 1.0
CD A:ARG114 4.7 30.4 1.0

Zinc binding site 2 out of 11 in 6qg9

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Zinc binding site 2 out of 11 in the Crystal Structure of Ideonella Sakaiensis Mhetase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Ideonella Sakaiensis Mhetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:71.4
occ:1.00
 OD2 A:ASP347 2.2 42.9 1.0
O F:HOH999 2.6 34.4 1.0
CG A:ASP347 2.9 43.0 1.0
OD1 A:ASP347 2.9 44.7 1.0
NZ F:LYS256 3.8 20.6 1.0
O F:HOH900 4.1 52.7 1.0
CB A:ASP347 4.3 40.8 1.0
CZ2 F:TRP453 4.8 31.5 1.0
CE F:LYS256 4.9 20.1 1.0

Zinc binding site 3 out of 11 in 6qg9

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Zinc binding site 3 out of 11 in the Crystal Structure of Ideonella Sakaiensis Mhetase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Ideonella Sakaiensis Mhetase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:63.2
occ:1.00
 OE1 B:GLU93 2.4 30.4 1.0
OE2 B:GLU93 2.5 35.4 1.0
O B:HOH1199 2.6 39.7 1.0
CD B:GLU93 2.8 30.4 1.0
O B:HOH1118 2.9 43.1 1.0
O B:HOH1161 3.1 49.4 1.0
NH2 B:ARG116 3.7 35.2 1.0
O B:HOH867 4.0 29.9 1.0
CG B:GLU93 4.2 31.8 1.0
NE B:ARG114 4.2 33.8 1.0
NH2 B:ARG76 4.2 36.4 1.0
O B:HOH1263 4.3 57.3 1.0
CZ B:ARG116 4.6 34.5 1.0
NH1 B:ARG116 4.7 31.1 1.0
CZ B:ARG114 4.8 33.1 1.0
CD B:ARG114 4.8 31.7 1.0
NH2 B:ARG114 4.8 33.4 1.0
CZ B:ARG76 4.8 38.2 1.0
NE B:ARG76 4.9 39.2 1.0

Zinc binding site 4 out of 11 in 6qg9

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Zinc binding site 4 out of 11 in the Crystal Structure of Ideonella Sakaiensis Mhetase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Ideonella Sakaiensis Mhetase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn702

b:68.1
occ:1.00
 OE2 C:GLU93 2.5 35.1 1.0
O C:HOH1132 2.6 37.9 1.0
OE1 C:GLU93 2.7 31.8 1.0
CD C:GLU93 3.0 32.1 1.0
O C:HOH1156 3.1 42.0 1.0
O C:HOH1136 3.3 37.4 1.0
O C:HOH884 3.5 38.9 1.0
NH2 C:ARG76 4.0 34.6 1.0
NH2 C:ARG116 4.1 29.0 1.0
NE C:ARG114 4.2 32.2 1.0
NE C:ARG76 4.5 31.6 1.0
CG C:GLU93 4.5 28.9 1.0
NH2 C:ARG114 4.5 29.8 1.0
CZ C:ARG76 4.6 33.2 1.0
NH1 C:ARG116 4.7 24.7 1.0
CZ C:ARG114 4.7 30.6 1.0
CZ C:ARG116 4.9 27.2 1.0

Zinc binding site 5 out of 11 in 6qg9

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Zinc binding site 5 out of 11 in the Crystal Structure of Ideonella Sakaiensis Mhetase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Ideonella Sakaiensis Mhetase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn703

b:68.4
occ:1.00
 OE2 D:GLU93 2.5 44.0 1.0
O D:HOH1127 2.7 31.2 1.0
OE1 D:GLU93 2.9 37.5 1.0
CD D:GLU93 3.0 39.4 1.0
O D:HOH1100 3.2 47.9 1.0
O D:HOH1125 3.3 37.6 1.0
O D:HOH953 3.6 30.3 1.0
NH2 D:ARG76 3.6 33.5 1.0
NH2 D:ARG116 3.9 30.6 1.0
NE D:ARG114 4.1 25.8 1.0
CZ D:ARG76 4.4 34.7 1.0
CG D:GLU93 4.5 32.6 1.0
NH1 D:ARG116 4.5 24.9 1.0
NE D:ARG76 4.5 32.0 1.0
CZ D:ARG114 4.6 29.2 1.0
CZ D:ARG116 4.6 30.8 1.0
NH2 D:ARG114 4.6 32.4 1.0
CD D:ARG114 4.7 26.8 1.0

Zinc binding site 6 out of 11 in 6qg9

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Zinc binding site 6 out of 11 in the Crystal Structure of Ideonella Sakaiensis Mhetase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Ideonella Sakaiensis Mhetase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn702

b:62.8
occ:1.00
 OD1 E:ASP175 2.3 58.0 1.0
OD2 E:ASP175 2.8 61.4 1.0
CG E:ASP175 2.9 57.6 1.0
CG E:PRO174 4.3 47.8 1.0
CB E:ASP175 4.4 53.1 1.0
N E:ASP175 4.9 45.7 1.0
CB E:PRO174 4.9 46.4 1.0

Zinc binding site 7 out of 11 in 6qg9

Go back to Zinc Binding Sites List in 6qg9
Zinc binding site 7 out of 11 in the Crystal Structure of Ideonella Sakaiensis Mhetase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Ideonella Sakaiensis Mhetase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn703

b:67.2
occ:1.00
 OE2 E:GLU93 2.0 35.8 1.0
CD E:GLU93 2.7 32.6 1.0
OE1 E:GLU93 2.8 31.6 1.0
NH2 E:ARG116 3.6 27.7 1.0
O E:HOH901 3.6 32.3 1.0
NE E:ARG114 4.0 30.8 1.0
NH2 E:ARG76 4.1 27.0 1.0
CG E:GLU93 4.2 28.6 1.0
CZ E:ARG116 4.4 30.1 1.0
NH1 E:ARG116 4.4 32.8 1.0
NH2 E:ARG114 4.4 31.3 1.0
CZ E:ARG114 4.5 31.9 1.0
NE E:ARG76 4.5 31.1 1.0
CZ E:ARG76 4.7 31.3 1.0
CD E:ARG114 4.7 29.1 1.0

Zinc binding site 8 out of 11 in 6qg9

Go back to Zinc Binding Sites List in 6qg9
Zinc binding site 8 out of 11 in the Crystal Structure of Ideonella Sakaiensis Mhetase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Ideonella Sakaiensis Mhetase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn703

b:69.6
occ:1.00
 OE2 F:GLU93 2.3 34.9 1.0
OE1 F:GLU93 2.7 35.9 1.0
CD F:GLU93 2.9 35.7 1.0
O F:HOH1079 3.4 35.8 1.0
O F:HOH1173 3.4 37.0 1.0
O F:HOH1106 3.7 34.5 1.0
NH2 F:ARG76 3.9 33.8 1.0
NH2 F:ARG116 4.1 28.0 1.0
NE F:ARG114 4.1 33.0 1.0
CG F:GLU93 4.4 34.9 1.0
CZ F:ARG76 4.7 33.9 1.0
NE F:ARG76 4.7 31.7 1.0
NH2 F:ARG114 4.7 30.6 1.0
CZ F:ARG114 4.7 29.7 1.0
CD F:ARG114 4.7 30.4 1.0
NH1 F:ARG116 4.9 27.0 1.0
CZ F:ARG116 4.9 28.7 1.0

Zinc binding site 9 out of 11 in 6qg9

Go back to Zinc Binding Sites List in 6qg9
Zinc binding site 9 out of 11 in the Crystal Structure of Ideonella Sakaiensis Mhetase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Ideonella Sakaiensis Mhetase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn702

b:90.3
occ:1.00
 OE2 G:GLU93 2.5 44.6 1.0
OE1 G:GLU93 2.5 44.4 1.0
CD G:GLU93 2.8 44.7 1.0
O G:HOH1027 3.0 37.3 1.0
O G:HOH878 3.7 48.8 1.0
NH2 G:ARG116 3.7 35.6 1.0
NH2 G:ARG76 3.9 47.3 1.0
NE G:ARG114 4.3 42.9 1.0
CG G:GLU93 4.4 43.4 1.0
NE G:ARG76 4.4 47.9 1.0
CZ G:ARG116 4.5 36.3 1.0
CZ G:ARG76 4.6 48.7 1.0
NH1 G:ARG116 4.6 42.4 1.0
CZ G:ARG114 4.7 41.3 1.0
CD G:ARG114 4.8 42.4 1.0
NH2 G:ARG114 4.8 40.7 1.0

Zinc binding site 10 out of 11 in 6qg9

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Zinc binding site 10 out of 11 in the Crystal Structure of Ideonella Sakaiensis Mhetase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Ideonella Sakaiensis Mhetase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn702

b:76.0
occ:1.00
 OE1 H:GLU93 2.5 46.2 1.0
OE2 H:GLU93 2.9 48.7 1.0
CD H:GLU93 3.0 45.7 1.0
O H:HOH1027 3.1 41.8 1.0
O H:HOH844 3.6 29.3 1.0
NH2 H:ARG76 3.8 47.0 1.0
NH2 H:ARG116 4.0 32.1 1.0
NE H:ARG114 4.3 38.5 1.0
CG H:GLU93 4.5 44.6 1.0
CZ H:ARG76 4.5 48.7 1.0
NH2 H:ARG114 4.6 31.9 1.0
NE H:ARG76 4.7 47.6 1.0
CZ H:ARG114 4.7 35.0 1.0
CZ H:ARG116 4.9 34.0 1.0
NH1 H:ARG116 4.9 35.1 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 Oct 29 05:39:08 2024

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