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Sodium 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
Calcium (Ca) 8 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 8 in 6f91

Go back to Sodium Binding Sites List in 6f91
Sodium 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 Sodium with other atoms in the Na 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:Na801

b:24.9
occ:1.00
 O A:GLY99 2.2 26.8 1.0
O A:ARG101 2.3 23.4 1.0
O A:PRO96 2.3 27.1 1.0
O A:HOH1208 2.3 29.9 1.0
O A:HOH1185 2.3 24.0 1.0
C A:PRO96 3.2 28.6 1.0
C A:GLY99 3.4 26.4 1.0
C A:ARG101 3.4 23.5 1.0
N A:ARG101 3.8 20.0 1.0
CA A:ASP97 3.8 31.2 1.0
N A:ASP97 3.9 27.3 1.0
C A:TYR100 3.9 21.2 1.0
CA A:ARG101 4.1 22.4 1.0
N A:GLY99 4.2 28.3 1.0
N A:TYR100 4.2 25.5 1.0
CA A:TYR100 4.2 22.7 1.0
C A:ASP97 4.2 30.5 1.0
CA A:PRO96 4.3 25.8 1.0
NZ A:LYS87 4.3 45.2 1.0
O A:TYR100 4.3 21.0 1.0
CB A:PRO96 4.3 25.1 1.0
CA A:GLY99 4.4 27.9 1.0
O A:ASP97 4.4 30.8 1.0
CB A:ARG101 4.5 23.3 1.0
N A:SER102 4.5 23.1 1.0
O A:HOH1029 4.6 42.4 1.0
OH A:TYR123 4.6 23.6 1.0
OD2 A:ASP122 4.6 24.2 1.0
OD1 A:ASP97 4.6 32.8 1.0
CD A:LYS87 4.7 41.1 1.0
CA A:SER102 4.8 22.5 1.0
N A:GLN98 4.9 28.9 1.0

Sodium binding site 2 out of 8 in 6f91

Go back to Sodium Binding Sites List in 6f91
Sodium 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 Sodium with other atoms in the Na 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:Na801

b:21.4
occ:1.00
 O B:ARG101 2.2 18.2 1.0
O B:HOH1173 2.3 27.0 1.0
O B:PRO96 2.3 23.8 1.0
O B:GLY99 2.3 19.4 1.0
O B:HOH1233 2.3 24.4 1.0
C B:PRO96 3.2 31.8 1.0
C B:ARG101 3.3 20.9 1.0
C B:GLY99 3.4 20.9 1.0
N B:ARG101 3.7 19.6 1.0
CA B:ASP97 3.8 28.2 1.0
C B:TYR100 3.9 18.9 1.0
N B:ASP97 3.9 28.8 1.0
CA B:ARG101 4.0 21.0 1.0
N B:TYR100 4.2 19.3 1.0
CA B:TYR100 4.2 18.5 1.0
N B:GLY99 4.2 26.3 1.0
CA B:PRO96 4.2 28.4 1.0
CB B:PRO96 4.2 28.2 1.0
C B:ASP97 4.2 27.0 1.0
O B:HOH1428 4.3 34.6 1.0
O B:TYR100 4.3 20.4 1.0
CA B:GLY99 4.4 22.2 1.0
CB B:ARG101 4.4 21.6 1.0
NZ B:LYS87 4.4 44.3 1.0
N B:SER102 4.4 19.9 1.0
O B:ASP97 4.5 28.1 1.0
OD2 B:ASP122 4.5 25.1 1.0
OD1 B:ASP97 4.6 35.5 1.0
OH B:TYR123 4.7 21.6 1.0
CA B:SER102 4.7 21.7 1.0
CD B:LYS87 4.8 42.1 1.0
N B:GLN98 4.9 25.4 1.0

Sodium binding site 3 out of 8 in 6f91

Go back to Sodium Binding Sites List in 6f91
Sodium 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 Sodium with other atoms in the Na 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:Na801

b:19.1
occ:1.00
 O C:HOH1596 2.2 26.4 1.0
O C:PRO96 2.3 19.7 1.0
O C:ARG101 2.3 17.4 1.0
O C:GLY99 2.3 18.9 1.0
O C:HOH1140 2.3 20.8 1.0
C C:PRO96 3.2 22.8 1.0
C C:ARG101 3.4 18.4 1.0
C C:GLY99 3.4 19.9 1.0
CA C:ASP97 3.8 22.4 1.0
N C:ARG101 3.8 16.6 1.0
N C:ASP97 3.8 21.5 1.0
C C:TYR100 3.9 16.2 1.0
CA C:ARG101 4.1 18.2 1.0
C C:ASP97 4.2 21.5 1.0
N C:GLY99 4.2 20.2 1.0
CA C:PRO96 4.2 21.4 1.0
N C:TYR100 4.2 17.9 1.0
CA C:TYR100 4.3 17.3 1.0
CB C:PRO96 4.3 20.3 1.0
O C:HOH1165 4.3 36.7 1.0
O C:HOH1254 4.3 38.8 1.0
O C:TYR100 4.4 17.6 1.0
CA C:GLY99 4.4 20.1 1.0
O C:ASP97 4.4 24.3 1.0
CB C:ARG101 4.4 16.4 1.0
N C:SER102 4.5 16.9 1.0
OD2 C:ASP122 4.5 22.4 1.0
OD1 C:ASP97 4.6 30.0 1.0
OH C:TYR123 4.7 19.6 1.0
CA C:SER102 4.8 17.9 1.0
N C:GLN98 4.9 21.1 1.0

Sodium binding site 4 out of 8 in 6f91

Go back to Sodium Binding Sites List in 6f91
Sodium 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 Sodium with other atoms in the Na 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:Na801

b:24.7
occ:1.00
 O D:PRO96 2.2 26.6 1.0
O D:GLY99 2.2 25.3 1.0
O D:ARG101 2.2 23.8 1.0
O D:HOH1566 2.3 29.1 1.0
O D:HOH1282 2.3 28.9 1.0
C D:PRO96 3.2 32.2 1.0
C D:GLY99 3.4 26.5 1.0
C D:ARG101 3.4 24.4 1.0
N D:ARG101 3.7 22.7 1.0
CA D:ASP97 3.8 33.2 1.0
N D:ASP97 3.9 32.5 1.0
C D:TYR100 3.9 19.7 1.0
CA D:ARG101 4.0 22.6 1.0
N D:TYR100 4.2 21.3 1.0
CA D:TYR100 4.2 21.3 1.0
N D:GLY99 4.2 30.3 1.0
C D:ASP97 4.2 29.5 1.0
CA D:PRO96 4.2 30.7 1.0
CB D:PRO96 4.3 31.7 1.0
O D:TYR100 4.3 22.2 1.0
CA D:GLY99 4.3 24.7 1.0
O D:ASP97 4.4 32.6 1.0
CB D:ARG101 4.4 21.0 1.0
O D:HOH1136 4.4 41.0 1.0
O D:HOH1152 4.4 44.5 1.0
N D:SER102 4.5 25.1 1.0
OH D:TYR123 4.6 23.0 1.0
OD2 D:ASP122 4.6 29.2 1.0
OD1 D:ASP97 4.6 38.5 1.0
CA D:SER102 4.8 25.2 1.0
N D:GLN98 4.9 29.0 1.0

Sodium binding site 5 out of 8 in 6f91

Go back to Sodium Binding Sites List in 6f91
Sodium 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 Sodium with other atoms in the Na 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:Na801

b:24.2
occ:1.00
 O E:PRO96 2.2 27.4 1.0
O E:ARG101 2.3 20.0 1.0
O E:GLY99 2.3 24.1 1.0
O E:HOH1193 2.3 23.5 1.0
O E:HOH1391 2.3 28.1 1.0
C E:PRO96 3.2 26.6 1.0
C E:ARG101 3.4 21.3 1.0
C E:GLY99 3.4 23.1 1.0
N E:ARG101 3.8 20.0 1.0
CA E:ASP97 3.8 27.8 1.0
N E:ASP97 3.8 27.4 1.0
C E:TYR100 3.9 19.1 1.0
CA E:ARG101 4.0 19.4 1.0
N E:GLY99 4.2 24.9 1.0
C E:ASP97 4.2 24.4 1.0
CA E:PRO96 4.2 27.2 1.0
N E:TYR100 4.2 20.6 1.0
CA E:TYR100 4.2 19.3 1.0
CB E:PRO96 4.3 27.4 1.0
O E:TYR100 4.3 18.9 1.0
CA E:GLY99 4.4 23.4 1.0
O E:HOH1336 4.4 37.2 1.0
O E:ASP97 4.4 27.2 1.0
CB E:ARG101 4.4 19.4 1.0
N E:SER102 4.5 21.3 1.0
NZ E:LYS87 4.5 28.6 0.5
OD2 E:ASP122 4.6 27.3 1.0
OD1 E:ASP97 4.6 29.9 1.0
OH E:TYR123 4.6 24.1 1.0
CA E:SER102 4.8 23.8 1.0
CD E:LYS87 4.8 30.8 0.5
N E:GLN98 4.9 26.7 1.0

Sodium binding site 6 out of 8 in 6f91

Go back to Sodium Binding Sites List in 6f91
Sodium 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 Sodium with other atoms in the Na 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:Na801

b:34.4
occ:1.00
 O F:ARG101 2.2 34.7 1.0
O F:PRO96 2.3 35.3 1.0
O F:HOH1102 2.3 33.9 1.0
O F:HOH997 2.3 34.7 1.0
O F:GLY99 2.3 30.7 1.0
C F:PRO96 3.2 41.5 1.0
C F:ARG101 3.4 31.1 1.0
C F:GLY99 3.4 32.1 1.0
N F:ARG101 3.8 26.7 1.0
CA F:ASP97 3.8 41.4 1.0
N F:ASP97 3.9 40.3 1.0
C F:TYR100 3.9 26.7 1.0
CA F:ARG101 4.0 30.7 1.0
CA F:TYR100 4.2 26.8 1.0
N F:TYR100 4.2 27.0 1.0
N F:GLY99 4.2 34.7 1.0
C F:ASP97 4.2 37.8 1.0
CA F:PRO96 4.3 38.6 1.0
CB F:PRO96 4.3 39.4 1.0
O F:TYR100 4.3 26.0 1.0
NZ F:LYS87 4.4 63.1 1.0
CA F:GLY99 4.4 30.4 1.0
O F:HOH1139 4.4 41.0 1.0
O F:ASP97 4.4 41.1 1.0
CB F:ARG101 4.5 30.6 1.0
N F:SER102 4.5 32.5 1.0
OH F:TYR123 4.6 31.8 1.0
OD2 F:ASP122 4.6 40.0 1.0
OD1 F:ASP97 4.6 43.2 1.0
CA F:SER102 4.8 32.1 1.0
CD F:LYS87 4.8 59.7 1.0
N F:GLN98 4.9 35.7 1.0

Sodium binding site 7 out of 8 in 6f91

Go back to Sodium Binding Sites List in 6f91
Sodium 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 Sodium with other atoms in the Na 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:Na801

b:24.3
occ:1.00
 O G:PRO96 2.2 24.2 1.0
O G:GLY99 2.3 24.0 1.0
O G:HOH1099 2.3 33.8 1.0
O G:ARG101 2.3 24.9 1.0
O G:HOH1227 2.3 24.9 1.0
C G:PRO96 3.2 30.4 1.0
C G:GLY99 3.4 27.2 1.0
C G:ARG101 3.4 23.4 1.0
CA G:ASP97 3.7 31.9 1.0
N G:ASP97 3.8 28.8 1.0
N G:ARG101 3.8 22.6 1.0
C G:TYR100 3.9 21.8 1.0
CA G:ARG101 4.1 22.4 1.0
C G:ASP97 4.2 29.2 1.0
N G:GLY99 4.2 30.5 1.0
CA G:PRO96 4.2 28.9 1.0
N G:TYR100 4.2 23.9 1.0
CB G:PRO96 4.3 28.3 1.0
CA G:TYR100 4.3 22.7 1.0
O G:ASP97 4.4 32.9 1.0
CA G:GLY99 4.4 28.5 1.0
NZ G:LYS87 4.4 38.8 0.5
O G:TYR100 4.4 24.2 1.0
CB G:ARG101 4.5 23.8 1.0
O G:HOH1143 4.5 46.5 1.0
N G:SER102 4.5 22.6 1.0
OD2 G:ASP122 4.6 30.6 1.0
OD1 G:ASP97 4.6 31.8 1.0
OH G:TYR123 4.7 25.4 1.0
CD G:LYS87 4.8 38.6 0.5
CA G:SER102 4.8 20.9 1.0
N G:GLN98 4.8 31.0 1.0

Sodium binding site 8 out of 8 in 6f91

Go back to Sodium Binding Sites List in 6f91
Sodium 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 Sodium with other atoms in the Na 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:Na801

b:27.3
occ:1.00
 O H:PRO96 2.2 30.4 1.0
O H:GLY99 2.2 27.8 1.0
O H:ARG101 2.3 25.6 1.0
O H:HOH3407 2.3 31.9 1.0
O H:HOH3420 2.3 28.6 1.0
C H:PRO96 3.2 36.0 1.0
C H:GLY99 3.4 28.8 1.0
C H:ARG101 3.4 25.4 1.0
N H:ARG101 3.7 23.2 1.0
CA H:ASP97 3.8 37.9 1.0
N H:ASP97 3.8 37.1 1.0
C H:TYR100 3.9 22.8 1.0
CA H:ARG101 4.0 23.9 1.0
N H:GLY99 4.2 31.4 1.0
N H:TYR100 4.2 23.4 1.0
CA H:PRO96 4.2 34.4 1.0
C H:ASP97 4.2 33.8 1.0
CA H:TYR100 4.2 25.9 1.0
CB H:PRO96 4.3 32.7 1.0
O H:HOH3195 4.3 46.0 1.0
CA H:GLY99 4.3 29.1 1.0
O H:TYR100 4.3 22.9 1.0
CB H:ARG101 4.4 26.3 1.0
NZ H:LYS87 4.4 54.6 1.0
O H:ASP97 4.4 37.5 1.0
N H:SER102 4.5 26.1 1.0
OD2 H:ASP122 4.6 35.6 1.0
OD1 H:ASP97 4.6 42.5 1.0
OH H:TYR123 4.7 26.3 1.0
CD H:LYS87 4.8 52.9 1.0
CA H:SER102 4.8 27.4 1.0
N H:GLN98 4.9 35.5 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 Oct 8 08:42:31 2024

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