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Calcium in PDB 6f91: Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron

Protein crystallography data

The structure of Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron, PDB code: 6f91 was solved by A.J.Thompson, R.J.Spears, Y.Zhu, M.D.L.Suits, 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) 48.08 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 111.919, 184.542, 183.661, 90.00, 90.80, 90.00
R / Rfree (%) 16 / 18.5

Other elements in 6f91:

The structure of Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms
Sodium (Na) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron (pdb code 6f91). 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 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron, PDB code: 6f91:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6f91

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Calcium binding site 1 out of 8 in the Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron


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 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca802

b:38.1
occ:0.60
 O A:HOH1046 2.3 44.2 1.0
O A:GLY589 2.3 34.7 1.0
OD2 A:ASP633 2.3 35.4 1.0
O A:HOH1410 2.3 36.8 1.0
O A:HOH1191 2.3 38.0 1.0
OE1 A:GLU591 2.4 29.4 1.0
CD A:GLU591 3.3 29.0 1.0
CG A:ASP633 3.3 36.8 1.0
C A:GLY589 3.5 35.2 1.0
OE2 A:GLU591 3.5 32.5 1.0
OD1 A:ASP633 3.6 42.2 1.0
O A:HOH927 3.7 32.5 1.0
CA A:GLY589 4.2 34.3 1.0
O A:HOH1255 4.3 32.6 1.0
O A:ASN631 4.3 21.4 1.0
N A:GLU591 4.5 30.2 1.0
N A:ASN590 4.5 34.2 1.0
OD1 A:ASP344 4.6 28.4 1.0
CG A:GLU591 4.7 27.9 1.0
CA A:ASN590 4.7 35.7 1.0
CB A:ASP633 4.7 28.8 1.0
SD A:MET637 4.8 31.7 1.0
O A:HOH1040 4.8 48.5 1.0
OE1 A:GLU531 4.9 53.0 0.5

Calcium binding site 2 out of 8 in 6f91

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Calcium binding site 2 out of 8 in the Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron


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 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca802

b:31.9
occ:0.60
 O B:GLY589 2.3 27.6 1.0
OD2 B:ASP633 2.3 30.4 1.0
OE1 B:GLU591 2.3 27.6 1.0
O B:HOH1396 2.3 31.4 1.0
O B:HOH1032 2.3 35.9 1.0
O B:HOH1271 2.4 30.3 1.0
CD B:GLU591 3.2 25.2 1.0
CG B:ASP633 3.3 32.7 1.0
C B:GLY589 3.5 26.3 1.0
OE2 B:GLU591 3.5 25.2 1.0
OD1 B:ASP633 3.6 39.5 1.0
O B:HOH969 3.9 22.4 1.0
O B:HOH1312 4.2 27.8 1.0
CA B:GLY589 4.2 26.9 1.0
O B:HOH1592 4.3 46.4 1.0
O B:ASN631 4.3 21.2 1.0
N B:GLU591 4.4 22.7 1.0
N B:ASN590 4.5 24.5 1.0
OD1 B:ASP344 4.6 28.2 1.0
CG B:GLU591 4.7 22.5 1.0
CA B:ASN590 4.7 27.8 1.0
CB B:ASP633 4.7 27.8 1.0
SD B:MET637 4.8 25.3 1.0
O B:HOH1098 5.0 42.6 1.0

Calcium binding site 3 out of 8 in 6f91

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Calcium binding site 3 out of 8 in the Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron


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 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca802

b:27.4
occ:0.60
 O C:GLY589 2.3 21.5 1.0
O C:HOH1263 2.3 34.5 1.0
O C:HOH1497 2.3 24.7 1.0
OD2 C:ASP633 2.4 27.9 1.0
O C:HOH1315 2.4 24.3 1.0
OE1 C:GLU591 2.4 23.5 1.0
CD C:GLU591 3.3 22.8 1.0
CG C:ASP633 3.4 27.8 1.0
C C:GLY589 3.5 20.0 1.0
OE2 C:GLU591 3.6 21.8 1.0
OD1 C:ASP633 3.6 32.6 1.0
O C:HOH988 3.9 28.2 1.0
CA C:GLY589 4.2 19.4 1.0
O C:ASN631 4.3 18.2 1.0
O C:HOH1350 4.3 25.1 1.0
O C:HOH1008 4.4 62.4 1.0
O C:HOH907 4.4 47.8 1.0
N C:GLU591 4.5 17.2 1.0
N C:ASN590 4.5 19.8 1.0
OD1 C:ASP344 4.6 21.8 1.0
SD C:MET637 4.7 21.5 1.0
CA C:ASN590 4.8 21.6 0.5
CA C:ASN590 4.8 18.3 0.5
CG C:GLU591 4.8 21.3 1.0
CB C:ASP633 4.8 22.2 1.0
OE1 C:GLU531 4.9 45.5 1.0

Calcium binding site 4 out of 8 in 6f91

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Calcium binding site 4 out of 8 in the Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron


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 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca802

b:30.9
occ:0.60
 O D:GLY589 2.3 26.5 1.0
O D:HOH1066 2.3 39.8 1.0
O D:HOH1500 2.3 30.9 1.0
OD2 D:ASP633 2.3 27.9 1.0
O D:HOH1205 2.4 26.0 1.0
OE1 D:GLU591 2.4 24.8 1.0
CD D:GLU591 3.3 25.0 1.0
CG D:ASP633 3.3 26.6 1.0
C D:GLY589 3.4 25.2 1.0
OE2 D:GLU591 3.5 25.3 1.0
OD1 D:ASP633 3.6 36.6 1.0
O D:HOH1017 3.9 26.6 1.0
CA D:GLY589 4.1 21.7 1.0
O D:ASN631 4.3 20.6 1.0
O D:HOH1303 4.3 26.9 1.0
N D:ASN590 4.5 23.1 1.0
N D:GLU591 4.5 22.0 1.0
OD1 D:ASP344 4.6 22.0 1.0
CA D:ASN590 4.7 24.4 1.0
SD D:MET637 4.7 24.0 1.0
CB D:ASP633 4.7 22.8 1.0
CG D:GLU591 4.7 22.2 1.0

Calcium binding site 5 out of 8 in 6f91

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Calcium binding site 5 out of 8 in the Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron


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 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca802

b:29.1
occ:0.60
 O E:HOH1392 2.3 36.0 1.0
O E:GLY589 2.3 25.4 1.0
O E:HOH1534 2.3 27.3 1.0
OD2 E:ASP633 2.3 24.5 1.0
O E:HOH1285 2.4 24.5 1.0
OE1 E:GLU591 2.4 26.6 1.0
CD E:GLU591 3.3 24.4 1.0
CG E:ASP633 3.3 22.8 1.0
C E:GLY589 3.5 26.0 1.0
OE2 E:GLU591 3.5 23.9 1.0
OD1 E:ASP633 3.6 28.2 1.0
O E:HOH994 3.8 25.3 1.0
CA E:GLY589 4.2 23.1 1.0
O E:HOH1249 4.3 31.0 1.0
O E:ASN631 4.3 20.3 1.0
O E:HOH904 4.4 42.6 1.0
N E:GLU591 4.5 22.9 1.0
N E:ASN590 4.5 24.6 1.0
OD1 E:ASP344 4.6 20.8 1.0
CG E:GLU591 4.7 21.9 1.0
CA E:ASN590 4.7 24.0 0.5
CA E:ASN590 4.7 24.4 0.5
CB E:ASP633 4.8 20.2 1.0
SD E:MET637 4.8 23.4 1.0
O E:HOH902 4.9 36.4 1.0

Calcium binding site 6 out of 8 in 6f91

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Calcium binding site 6 out of 8 in the Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron


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 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca802

b:42.8
occ:0.60
 O F:HOH1252 2.3 44.4 1.0
OD2 F:ASP633 2.3 42.0 1.0
O F:HOH1318 2.3 43.7 1.0
O F:HOH1157 2.3 45.0 1.0
O F:GLY589 2.3 47.0 1.0
OE1 F:GLU591 2.4 37.1 1.0
CD F:GLU591 3.3 33.7 1.0
CG F:ASP633 3.3 40.5 1.0
C F:GLY589 3.5 42.2 1.0
OE2 F:GLU591 3.5 34.0 1.0
O F:HOH969 3.5 38.2 1.0
OD1 F:ASP633 3.5 51.9 1.0
O F:HOH1180 4.2 50.0 1.0
CA F:GLY589 4.3 38.7 1.0
O F:ASN631 4.3 31.8 1.0
O F:HOH920 4.5 51.6 1.0
N F:GLU591 4.5 33.7 1.0
N F:ASN590 4.5 38.6 1.0
OD1 F:ASP344 4.5 31.3 1.0
CB F:ASP633 4.7 39.1 1.0
CG F:GLU591 4.7 35.7 1.0
CA F:ASN590 4.7 42.7 1.0
SD F:MET637 4.8 42.3 1.0

Calcium binding site 7 out of 8 in 6f91

Go back to Calcium Binding Sites List in 6f91
Calcium binding site 7 out of 8 in the Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron


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 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca802

b:38.8
occ:0.60
 O G:HOH1375 2.3 43.9 0.5
O G:HOH1375 2.3 43.8 0.5
O G:HOH1283 2.3 38.7 1.0
O G:HOH1594 2.3 41.3 1.0
O G:HOH1220 2.4 24.4 0.5
OD2 G:ASP633 2.4 35.7 1.0
OE1 G:GLU591 2.4 27.7 1.0
O G:GLY589 2.4 35.8 1.0
CD G:GLU591 3.3 28.6 1.0
CG G:ASP633 3.4 29.6 1.0
OD1 G:ASP633 3.6 49.0 1.0
C G:GLY589 3.6 28.8 1.0
OE2 G:GLU591 3.6 25.4 1.0
O G:HOH1336 4.1 30.6 1.0
O G:ASN631 4.4 21.3 1.0
O G:HOH1220 4.4 17.0 0.5
CA G:GLY589 4.4 27.6 1.0
N G:GLU591 4.4 28.4 1.0
OD1 G:ASP344 4.5 26.0 1.0
N G:ASN590 4.6 35.5 1.0
CA G:ASN590 4.7 39.0 1.0
CG G:GLU591 4.7 25.1 1.0
CB G:ASP633 4.8 28.2 1.0
O G:HOH914 4.9 42.1 1.0
O G:HOH1186 4.9 41.5 1.0
N G:ASN631 5.0 24.8 1.0

Calcium binding site 8 out of 8 in 6f91

Go back to Calcium Binding Sites List in 6f91
Calcium binding site 8 out of 8 in the Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron


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 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca802

b:39.6
occ:0.60
 O H:HOH3312 2.3 45.9 0.5
O H:HOH3312 2.3 45.9 0.5
O H:HOH3693 2.3 39.3 1.0
OE1 H:GLU591 2.3 27.6 1.0
O H:HOH3482 2.3 42.0 1.0
O H:HOH3122 2.4 26.8 0.5
OD2 H:ASP633 2.4 40.8 1.0
O H:GLY589 2.4 37.6 1.0
CD H:GLU591 3.3 25.8 1.0
CG H:ASP633 3.4 33.7 1.0
C H:GLY589 3.6 29.2 1.0
OD1 H:ASP633 3.6 47.2 1.0
OE2 H:GLU591 3.6 27.9 1.0
O H:HOH3447 4.0 35.3 1.0
N H:GLU591 4.4 27.8 1.0
CA H:GLY589 4.4 30.6 1.0
O H:ASN631 4.5 23.1 1.0
OD1 H:ASP344 4.5 25.6 1.0
O H:HOH3122 4.5 20.8 0.5
N H:ASN590 4.5 36.2 1.0
CE H:MET637 4.7 30.1 0.5
CA H:ASN590 4.7 35.6 0.5
CA H:ASN590 4.7 36.5 0.5
CG H:GLU591 4.7 22.8 1.0
CB H:ASP633 4.8 30.4 1.0
O H:HOH3136 4.9 40.9 1.0
O H:HOH3309 4.9 49.1 1.0
C H:ASN590 5.0 32.8 1.0

Reference:

A.J.Thompson, R.J.Spears, Y.Zhu, M.D.L.Suits, S.J.Williams, H.J.Gilbert, G.J.Davies. Bacteroides Thetaiotaomicron Generates Diverse Alpha-Mannosidase Activities Through Subtle Evolution of A Distal Substrate-Binding Motif. Acta Crystallogr D Struct V. 74 394 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 29717710
DOI: 10.1107/S2059798318002942
Page generated: Tue Jul 16 07:41:14 2024

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