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Calcium in PDB 2wzs: Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Mannoimidazole

Protein crystallography data

The structure of Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Mannoimidazole, PDB code: 2wzs was solved by Y.Zhu, M.D.L.Suits, A.Thompson, S.Chavan, Z.Dinev, C.Dumon, N.Smith, K.W.Moremen, Y.Xiang, A.Siriwardena, S.J.Williams, H.J.Gilbert, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 218.22 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 109.190, 152.390, 221.450, 90.00, 94.21, 90.00
R / Rfree (%) 20.038 / 24.227

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Mannoimidazole (pdb code 2wzs). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Mannoimidazole, PDB code: 2wzs:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 2wzs

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Calcium binding site 1 out of 8 in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Mannoimidazole


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Mannoimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca800

b:20.3
occ:1.00
 OD2 A:ASP644 2.3 20.4 1.0
O A:HOH2283 2.4 10.8 1.0
O3 A:MVL801 2.5 13.0 1.0
O2 A:MVL801 2.5 16.4 1.0
OD1 A:ASN601 2.5 19.4 1.0
OE1 A:GLN602 2.5 18.0 1.0
O A:HOH2271 2.6 13.2 1.0
O A:HOH2306 2.7 19.4 1.0
CG A:ASP644 3.3 20.4 1.0
CD A:GLN602 3.5 19.7 1.0
C2 A:MVL801 3.5 15.5 1.0
C3 A:MVL801 3.6 14.8 1.0
OD1 A:ASP644 3.7 20.6 1.0
NE2 A:GLN602 3.7 20.9 1.0
CG A:ASN601 3.8 19.7 1.0
CB A:ASP642 4.0 17.8 1.0
OD2 A:ASP348 4.2 19.1 1.0
C1 A:MVL801 4.3 15.3 1.0
O A:HOH2274 4.4 10.0 1.0
CB A:ASP644 4.5 19.3 1.0
C4 A:MVL801 4.6 15.0 1.0
CA A:ASN601 4.6 19.6 1.0
N1 A:MVL801 4.6 16.9 1.0
ND2 A:ASN601 4.6 17.6 1.0
O A:GLY600 4.6 19.7 1.0
O A:ASP642 4.7 17.5 1.0
OD2 A:ASP642 4.7 20.0 1.0
OE2 A:GLU533 4.7 22.4 1.0
CZ3 A:TRP347 4.7 19.0 1.0
CB A:ASN601 4.7 19.3 1.0
N A:GLN602 4.7 19.6 1.0
CG A:ASP642 4.8 17.6 1.0
CG A:GLN602 4.9 19.6 1.0
CA A:ASP642 5.0 17.5 1.0

Calcium binding site 2 out of 8 in 2wzs

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Calcium binding site 2 out of 8 in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Mannoimidazole


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Mannoimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca800

b:17.1
occ:1.00
 OD1 B:ASN601 2.3 15.7 1.0
OD2 B:ASP644 2.3 19.4 1.0
O2 B:MVL801 2.4 10.9 1.0
O B:HOH2233 2.4 6.3 1.0
O3 B:MVL801 2.5 14.2 1.0
O B:HOH2265 2.6 4.0 1.0
O B:HOH2241 2.6 6.0 1.0
OE1 B:GLN602 2.6 17.6 1.0
CG B:ASP644 3.4 19.6 1.0
C2 B:MVL801 3.4 13.9 1.0
C3 B:MVL801 3.5 14.2 1.0
CG B:ASN601 3.5 18.2 1.0
CD B:GLN602 3.6 19.0 1.0
OD1 B:ASP644 3.8 19.3 1.0
NE2 B:GLN602 3.9 19.7 1.0
C1 B:MVL801 4.1 14.8 1.0
OD2 B:ASP348 4.3 17.3 1.0
CB B:ASP642 4.3 16.6 1.0
O B:HOH2237 4.3 6.7 1.0
ND2 B:ASN601 4.4 17.1 1.0
OE2 B:GLU533 4.4 21.6 1.0
C4 B:MVL801 4.5 14.2 1.0
N1 B:MVL801 4.5 15.8 1.0
CA B:ASN601 4.5 18.6 1.0
CB B:ASN601 4.6 18.3 1.0
CZ3 B:TRP347 4.6 18.5 1.0
CB B:ASP644 4.6 18.1 1.0
O B:GLY600 4.7 18.6 1.0
OE2 B:GLU585 4.7 19.3 1.0
N B:GLN602 4.7 18.3 1.0
OD2 B:ASP642 4.8 17.6 1.0
O B:ASP642 4.9 15.7 1.0
CG B:GLN602 5.0 18.8 1.0
CG B:ASP642 5.0 17.5 1.0

Calcium binding site 3 out of 8 in 2wzs

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Calcium binding site 3 out of 8 in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Mannoimidazole


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Mannoimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca800

b:22.1
occ:1.00
 O2 C:MVL801 2.3 19.3 1.0
O C:HOH2278 2.4 16.2 1.0
OD1 C:ASN601 2.4 18.6 1.0
O C:HOH2279 2.4 11.5 1.0
O3 C:MVL801 2.5 17.6 1.0
OD2 C:ASP644 2.5 18.7 1.0
O C:HOH2210 2.5 7.5 1.0
OE1 C:GLN602 2.6 17.1 1.0
C2 C:MVL801 3.3 19.6 1.0
C3 C:MVL801 3.4 18.8 1.0
CG C:ASP644 3.4 19.6 1.0
CD C:GLN602 3.6 18.8 1.0
CG C:ASN601 3.6 19.6 1.0
OD1 C:ASP644 3.9 19.2 1.0
NE2 C:GLN602 3.9 19.1 1.0
CB C:ASP642 4.1 18.0 1.0
C1 C:MVL801 4.1 20.5 1.0
OD2 C:ASP348 4.2 17.8 1.0
OE2 C:GLU533 4.5 23.0 1.0
C4 C:MVL801 4.5 19.0 1.0
ND2 C:ASN601 4.5 18.1 1.0
N1 C:MVL801 4.5 20.6 1.0
O C:HOH2207 4.5 12.8 1.0
CA C:ASN601 4.6 19.1 1.0
CZ3 C:TRP347 4.6 19.2 1.0
CB C:ASN601 4.6 19.1 1.0
CB C:ASP644 4.7 18.5 1.0
OD2 C:ASP642 4.7 20.4 1.0
O C:GLY600 4.7 19.7 1.0
N C:GLN602 4.8 18.9 1.0
OE2 C:GLU585 4.8 21.0 1.0
CG C:ASP642 4.9 18.6 1.0
O C:ASP642 4.9 17.0 1.0
CG C:GLN602 4.9 19.3 1.0

Calcium binding site 4 out of 8 in 2wzs

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Calcium binding site 4 out of 8 in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Mannoimidazole


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Mannoimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca800

b:17.5
occ:1.00
 O2 D:MVL801 2.4 21.0 1.0
OD2 D:ASP644 2.4 19.1 1.0
OD1 D:ASN601 2.5 16.4 1.0
O3 D:MVL801 2.5 14.3 1.0
O D:HOH2261 2.5 4.6 1.0
OE1 D:GLN602 2.5 17.6 1.0
O D:HOH2259 2.6 4.8 1.0
O D:HOH2236 2.6 8.8 1.0
CG D:ASP644 3.4 19.1 1.0
C2 D:MVL801 3.4 18.1 1.0
CD D:GLN602 3.5 18.2 1.0
C3 D:MVL801 3.5 17.2 1.0
CG D:ASN601 3.7 18.4 1.0
NE2 D:GLN602 3.8 17.7 1.0
OD1 D:ASP644 3.8 18.4 1.0
C1 D:MVL801 4.1 17.5 1.0
CB D:ASP642 4.1 16.7 1.0
OD2 D:ASP348 4.2 17.5 1.0
O D:HOH2238 4.4 8.3 1.0
N1 D:MVL801 4.5 18.8 1.0
C4 D:MVL801 4.5 17.2 1.0
OE2 D:GLU533 4.5 22.2 1.0
ND2 D:ASN601 4.5 16.6 1.0
CA D:ASN601 4.5 18.6 1.0
O D:GLY600 4.6 19.2 1.0
CZ3 D:TRP347 4.6 19.6 1.0
CB D:ASP644 4.7 18.0 1.0
OE2 D:GLU585 4.7 20.8 1.0
CB D:ASN601 4.7 18.5 1.0
N D:GLN602 4.7 18.4 1.0
OD2 D:ASP642 4.8 19.0 1.0
O D:ASP642 4.8 16.0 1.0
CG D:GLN602 4.9 18.4 1.0
CG D:ASP642 5.0 17.2 1.0

Calcium binding site 5 out of 8 in 2wzs

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Calcium binding site 5 out of 8 in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Mannoimidazole


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Mannoimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca800

b:18.9
occ:1.00
 OD2 E:ASP644 2.3 21.5 1.0
O2 E:MVL801 2.3 14.5 1.0
O E:HOH2239 2.4 11.4 1.0
O E:HOH2215 2.4 25.3 1.0
OE1 E:GLN602 2.5 19.5 1.0
OD1 E:ASN601 2.6 19.4 1.0
O3 E:MVL801 2.6 13.2 1.0
O E:HOH2238 2.6 10.2 1.0
CG E:ASP644 3.3 20.9 1.0
C2 E:MVL801 3.4 14.7 1.0
C3 E:MVL801 3.6 14.8 1.0
CD E:GLN602 3.6 19.5 1.0
OD1 E:ASP644 3.7 20.6 1.0
CG E:ASN601 3.8 20.3 1.0
NE2 E:GLN602 4.0 19.9 1.0
CB E:ASP642 4.1 17.8 1.0
C1 E:MVL801 4.2 16.0 1.0
OD2 E:ASP348 4.2 18.2 1.0
O E:HOH2222 4.4 13.2 1.0
OE2 E:GLU533 4.5 23.9 1.0
N1 E:MVL801 4.5 18.2 1.0
C4 E:MVL801 4.5 15.3 1.0
CA E:ASN601 4.5 20.2 1.0
CZ3 E:TRP347 4.6 20.3 1.0
CB E:ASP644 4.6 19.5 1.0
OD2 E:ASP642 4.6 21.6 1.0
ND2 E:ASN601 4.7 17.4 1.0
O E:GLY600 4.7 19.3 1.0
CB E:ASN601 4.7 19.9 1.0
N E:GLN602 4.7 20.2 1.0
CG E:ASP642 4.8 19.0 1.0
OE2 E:GLU585 4.9 23.1 1.0
O E:ASP642 4.9 18.1 1.0
CG E:GLN602 4.9 19.6 1.0

Calcium binding site 6 out of 8 in 2wzs

Go back to Calcium Binding Sites List in 2wzs
Calcium binding site 6 out of 8 in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Mannoimidazole


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Mannoimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca800

b:23.5
occ:1.00
 OD2 F:ASP644 2.3 21.4 1.0
O2 F:MVL801 2.4 24.8 1.0
O3 F:MVL801 2.5 23.5 1.0
O F:HOH2173 2.5 21.6 1.0
OD1 F:ASN601 2.5 20.1 1.0
OE1 F:GLN602 2.6 19.4 1.0
O F:HOH2172 2.6 12.6 1.0
CG F:ASP644 3.3 21.1 1.0
C2 F:MVL801 3.4 26.2 1.0
C3 F:MVL801 3.5 25.3 1.0
CD F:GLN602 3.5 20.7 1.0
OD1 F:ASP644 3.7 22.0 1.0
CG F:ASN601 3.7 20.5 1.0
NE2 F:GLN602 3.9 22.1 1.0
CB F:ASP642 4.1 18.5 1.0
C1 F:MVL801 4.1 28.1 1.0
OD2 F:ASP348 4.4 21.3 1.0
N1 F:MVL801 4.5 29.0 1.0
C4 F:MVL801 4.5 25.1 1.0
ND2 F:ASN601 4.5 20.7 1.0
CA F:ASN601 4.6 20.7 1.0
OE2 F:GLU533 4.6 23.8 1.0
CB F:ASP644 4.6 20.3 1.0
OD2 F:ASP642 4.6 20.3 1.0
O F:GLY600 4.6 21.1 1.0
O F:HOH2153 4.6 24.6 1.0
CZ3 F:TRP347 4.7 21.4 1.0
CB F:ASN601 4.7 20.4 1.0
OE2 F:GLU585 4.8 23.3 1.0
N F:GLN602 4.8 21.0 1.0
CG F:ASP642 4.8 19.1 1.0
O F:ASP642 4.9 19.1 1.0
CG F:GLN602 4.9 20.6 1.0

Calcium binding site 7 out of 8 in 2wzs

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Calcium binding site 7 out of 8 in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Mannoimidazole


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Mannoimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca800

b:28.1
occ:1.00
 OD2 G:ASP644 2.3 24.4 1.0
O G:HOH2074 2.4 20.1 1.0
O2 G:MVL801 2.5 29.6 1.0
O3 G:MVL801 2.5 27.9 1.0
OE1 G:GLN602 2.5 22.9 1.0
OD1 G:ASN601 2.6 21.2 1.0
O G:HOH2072 2.7 22.6 1.0
CG G:ASP644 3.4 22.8 1.0
C2 G:MVL801 3.5 30.6 1.0
CD G:GLN602 3.5 22.0 1.0
C3 G:MVL801 3.5 29.9 1.0
NE2 G:GLN602 3.7 23.5 1.0
CG G:ASN601 3.8 21.8 1.0
OD1 G:ASP644 3.8 23.7 1.0
CB G:ASP642 4.1 19.6 1.0
C1 G:MVL801 4.2 31.8 1.0
OE2 G:GLU533 4.4 25.1 1.0
OD2 G:ASP348 4.4 21.8 1.0
OD2 G:ASP642 4.4 21.1 1.0
O G:GLY600 4.5 21.9 1.0
N1 G:MVL801 4.5 32.8 1.0
CA G:ASN601 4.5 21.2 1.0
C4 G:MVL801 4.6 30.8 1.0
CZ3 G:TRP347 4.6 21.0 1.0
O G:HOH2060 4.7 23.2 1.0
ND2 G:ASN601 4.7 21.2 1.0
CB G:ASP644 4.7 21.4 1.0
CG G:ASP642 4.7 20.1 1.0
CB G:ASN601 4.7 21.3 1.0
N G:GLN602 4.8 21.3 1.0
CG G:GLN602 4.9 21.6 1.0
O G:ASP642 5.0 20.2 1.0
OE2 G:GLU585 5.0 24.2 1.0

Calcium binding site 8 out of 8 in 2wzs

Go back to Calcium Binding Sites List in 2wzs
Calcium binding site 8 out of 8 in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Mannoimidazole


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Mannoimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca800

b:33.2
occ:1.00
 O2 H:MVL801 2.2 33.3 1.0
O H:HOH2057 2.3 31.8 1.0
O H:HOH2070 2.3 27.1 1.0
OD2 H:ASP644 2.4 22.6 1.0
OE1 H:GLN602 2.5 23.6 1.0
O3 H:MVL801 2.5 36.3 1.0
OD1 H:ASN601 2.6 22.2 1.0
C2 H:MVL801 3.3 34.1 1.0
C3 H:MVL801 3.5 34.4 1.0
CD H:GLN602 3.5 22.6 1.0
CG H:ASP644 3.5 22.0 1.0
NE2 H:GLN602 3.8 23.4 1.0
CG H:ASN601 3.8 22.1 1.0
OD1 H:ASP644 3.9 22.5 1.0
C1 H:MVL801 4.0 34.8 1.0
O H:HOH2058 4.3 21.3 1.0
OD2 H:ASP348 4.3 21.9 1.0
CB H:ASP642 4.3 20.6 1.0
N1 H:MVL801 4.5 34.5 1.0
OE2 H:GLU533 4.5 26.0 1.0
C4 H:MVL801 4.5 34.5 1.0
CA H:ASN601 4.5 21.9 1.0
O H:GLY600 4.5 22.1 1.0
CZ3 H:TRP347 4.6 20.7 1.0
ND2 H:ASN601 4.7 21.6 1.0
N H:GLN602 4.7 21.8 1.0
CB H:ASP644 4.7 21.5 1.0
OD2 H:ASP642 4.7 23.5 1.0
CB H:ASN601 4.7 22.1 1.0
OE2 H:GLU585 4.8 24.1 1.0
CG H:GLN602 4.9 21.6 1.0
CG H:ASP642 5.0 21.4 1.0

Reference:

Y.Zhu, M.D.L.Suits, A.Thompson, S.Chavan, Z.Dinev, C.Dumon, N.Smith, K.W.Moremen, Y.Xiang, A.Siriwardena, S.J.Williams, H.J.Gilbert, G.J.Davies. Mechanistic Insights Into A CA2+-Dependent Family of A-Mannosidases in A Human Gut Symbiont. Nat.Chem.Biol. V. 6 125 2010.
ISSN: ISSN 1552-4450
PubMed: 20081828
DOI: 10.1038/NCHEMBIO.278
Page generated: Fri Jul 12 18:58:57 2024

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