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Sodium in PDB 3mvk: The Crystal Structure of Fucu From Bifidobacterium Longum to 1.65A

Protein crystallography data

The structure of The Crystal Structure of Fucu From Bifidobacterium Longum to 1.65A, PDB code: 3mvk was solved by A.J.Stein, X.Xu, H.Cui, A.Savchenko, A.Joachimiak, Midwest Center Forstructural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.72 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 66.047, 83.859, 144.813, 90.00, 95.11, 90.00
R / Rfree (%) 18.2 / 20.5

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Sodium atom in the The Crystal Structure of Fucu From Bifidobacterium Longum to 1.65A (pdb code 3mvk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 15 binding sites of Sodium where determined in the The Crystal Structure of Fucu From Bifidobacterium Longum to 1.65A, PDB code: 3mvk:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 15 in 3mvk

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Sodium binding site 1 out of 15 in the The Crystal Structure of Fucu From Bifidobacterium Longum to 1.65A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of Fucu From Bifidobacterium Longum to 1.65A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na149

b:23.4
occ:1.00
O A:HOH1295 2.3 42.5 1.0
OG1 A:THR67 2.9 21.5 1.0
N A:VAL143 3.1 23.9 1.0
N A:THR67 3.2 20.3 1.0
CA A:GLY142 3.6 19.1 1.0
OD1 A:ASP66 3.7 19.7 1.0
CB A:THR67 3.8 22.4 1.0
CD2 A:TYR68 3.8 24.9 1.0
CG2 A:THR67 3.8 22.9 1.0
C A:GLY142 3.9 22.0 1.0
CB A:VAL143 3.9 26.3 1.0
CE2 A:TYR68 4.0 28.4 1.0
CA A:THR67 4.0 21.9 1.0
CA A:ASP66 4.1 17.8 1.0
CG2 A:VAL143 4.1 26.0 1.0
CA A:VAL143 4.1 26.0 1.0
C A:ASP66 4.1 19.3 1.0
O A:HOH1064 4.2 39.3 1.0
O A:LEU65 4.2 18.3 1.0
O A:VAL143 4.5 27.7 1.0
N A:TYR68 4.6 22.4 1.0
CE1 A:HIS22 4.7 17.5 1.0
CG A:ASP66 4.7 17.6 1.0
C A:THR67 4.7 22.8 1.0
C A:VAL143 4.8 27.3 1.0
N A:GLY142 4.9 16.6 1.0
C A:LEU65 4.9 17.7 1.0
N A:ASP66 5.0 17.3 1.0

Sodium binding site 2 out of 15 in 3mvk

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Sodium binding site 2 out of 15 in the The Crystal Structure of Fucu From Bifidobacterium Longum to 1.65A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of Fucu From Bifidobacterium Longum to 1.65A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na150

b:27.2
occ:1.00
O A:HOH735 2.5 30.8 1.0
OD1 A:ASP30 2.7 16.2 1.0
C1 A:GOL152 2.7 31.1 1.0
O1 A:GOL152 2.8 27.3 1.0
OD1 A:ASN136 3.0 18.8 1.0
OD2 A:ASP30 3.3 15.6 1.0
CG A:ASP30 3.4 15.9 1.0
N A:PHE33 3.5 14.5 1.0
CA A:PHE33 3.5 13.7 1.0
ND2 A:ASN136 3.6 11.4 1.0
CB A:PHE33 3.6 13.1 1.0
O2 A:GOL152 3.7 34.7 1.0
CG A:ASN136 3.7 15.8 1.0
C2 A:GOL152 3.7 33.2 1.0
CD1 A:PHE33 3.7 12.6 1.0
C A:ASN32 3.8 15.3 1.0
O3 A:GOL152 4.1 39.9 1.0
O A:ASN32 4.1 15.1 1.0
CB A:ASN32 4.1 16.8 1.0
CG A:PHE33 4.2 13.0 1.0
C3 A:GOL152 4.4 35.1 1.0
CA A:ASN32 4.4 15.5 1.0
CE A:MSE76 4.6 15.4 1.0
SE A:MSE76 4.7 25.1 1.0
N A:ASN32 4.8 15.0 1.0
CB A:ASP30 4.8 14.5 1.0
CE1 A:PHE33 4.9 12.0 1.0
OH A:TYR116 4.9 21.5 1.0
C A:PHE33 5.0 13.5 1.0
CD A:PRO34 5.0 14.5 1.0

Sodium binding site 3 out of 15 in 3mvk

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Sodium binding site 3 out of 15 in the The Crystal Structure of Fucu From Bifidobacterium Longum to 1.65A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of Fucu From Bifidobacterium Longum to 1.65A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na149

b:22.3
occ:1.00
OG1 B:THR67 2.9 21.3 1.0
N B:THR67 3.1 17.9 1.0
N B:VAL143 3.2 22.1 1.0
CA B:GLY142 3.6 18.6 1.0
CG2 B:VAL143 3.6 26.6 1.0
CB B:THR67 3.7 19.9 1.0
OD1 B:ASP66 3.8 16.1 1.0
CD1 B:TYR68 3.8 23.7 1.0
CG2 B:THR67 3.8 20.9 1.0
C B:GLY142 3.9 20.2 1.0
CE1 B:TYR68 3.9 25.7 1.0
CA B:THR67 3.9 19.6 1.0
CA B:ASP66 4.0 16.5 1.0
C B:ASP66 4.0 16.8 1.0
O B:LEU65 4.1 17.2 1.0
CG1 B:VAL143 4.2 25.1 1.0
CB B:VAL143 4.2 24.5 1.0
CA B:VAL143 4.2 24.2 1.0
O B:HOH782 4.3 30.1 1.0
N B:TYR68 4.5 19.1 1.0
O B:VAL143 4.5 25.8 1.0
CE1 B:HIS22 4.6 16.4 1.0
C B:THR67 4.6 19.4 1.0
CG B:ASP66 4.8 16.4 1.0
C B:LEU65 4.9 17.1 1.0
N B:ASP66 4.9 16.1 1.0
C B:VAL143 4.9 25.5 1.0
N B:GLY142 4.9 15.6 1.0

Sodium binding site 4 out of 15 in 3mvk

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Sodium binding site 4 out of 15 in the The Crystal Structure of Fucu From Bifidobacterium Longum to 1.65A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Crystal Structure of Fucu From Bifidobacterium Longum to 1.65A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na150

b:27.0
occ:1.00
O B:HOH1296 2.4 29.0 1.0
O1 B:GOL152 2.6 34.4 1.0
OD1 B:ASP30 2.7 15.5 1.0
ND2 B:ASN136 3.0 16.3 1.0
C1 B:GOL152 3.0 39.2 1.0
OD2 B:ASP30 3.3 16.2 1.0
CG B:ASP30 3.4 15.3 1.0
CA B:PHE33 3.5 13.1 1.0
N B:PHE33 3.5 14.3 1.0
OD1 B:ASN136 3.6 13.5 1.0
CB B:PHE33 3.6 13.5 1.0
CG B:ASN136 3.7 15.7 1.0
O2 B:GOL152 3.7 39.9 1.0
C B:ASN32 3.8 15.1 1.0
CD1 B:PHE33 3.8 14.0 1.0
C2 B:GOL152 3.9 39.3 1.0
O3 B:GOL152 4.0 41.7 1.0
CB B:ASN32 4.1 16.9 1.0
O B:ASN32 4.1 15.7 1.0
CG B:PHE33 4.2 12.8 1.0
CA B:ASN32 4.4 15.8 1.0
C3 B:GOL152 4.6 40.7 1.0
SE B:MSE76 4.6 24.9 1.0
CE B:MSE76 4.7 14.8 1.0
N B:ASN32 4.8 15.8 1.0
CB B:ASP30 4.8 14.7 1.0
C B:PHE33 5.0 13.3 1.0
CE1 B:PHE33 5.0 14.2 1.0
OH B:TYR116 5.0 18.9 1.0

Sodium binding site 5 out of 15 in 3mvk

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Sodium binding site 5 out of 15 in the The Crystal Structure of Fucu From Bifidobacterium Longum to 1.65A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Crystal Structure of Fucu From Bifidobacterium Longum to 1.65A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na149

b:24.1
occ:1.00
O C:HOH1013 2.8 33.0 1.0
OG1 C:THR67 2.8 21.9 1.0
N C:VAL143 3.1 21.8 1.0
N C:THR67 3.1 19.6 1.0
CA C:GLY142 3.6 19.5 1.0
CB C:THR67 3.7 20.6 1.0
OD1 C:ASP66 3.7 18.8 1.0
CD2 C:TYR68 3.8 18.9 1.0
CB C:VAL143 3.8 23.3 1.0
CG2 C:THR67 3.8 22.2 1.0
C C:GLY142 3.9 21.1 1.0
CA C:THR67 3.9 20.5 1.0
CE2 C:TYR68 3.9 21.8 1.0
CG2 C:VAL143 4.0 24.1 1.0
CA C:VAL143 4.0 23.6 1.0
C C:ASP66 4.1 19.5 1.0
CA C:ASP66 4.1 19.0 1.0
O C:LEU65 4.2 19.6 1.0
CE2 C:PHE145 4.3 34.9 1.0
O C:VAL143 4.4 24.5 1.0
CZ C:PHE145 4.5 35.3 1.0
N C:TYR68 4.5 19.5 1.0
NE2 C:HIS22 4.6 17.3 1.0
C C:THR67 4.6 20.7 1.0
C C:VAL143 4.7 24.8 1.0
CG C:ASP66 4.7 18.9 1.0
N C:GLY142 4.9 17.2 1.0
C C:LEU65 4.9 20.1 1.0
N C:ASP66 5.0 18.6 1.0

Sodium binding site 6 out of 15 in 3mvk

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Sodium binding site 6 out of 15 in the The Crystal Structure of Fucu From Bifidobacterium Longum to 1.65A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Crystal Structure of Fucu From Bifidobacterium Longum to 1.65A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na149

b:20.9
occ:1.00
O D:HOH1027 2.8 38.6 1.0
OG1 D:THR67 2.8 23.2 1.0
N D:THR67 3.1 19.6 1.0
N D:VAL143 3.1 20.6 1.0
CA D:GLY142 3.6 17.9 1.0
CB D:THR67 3.7 21.3 1.0
OD1 D:ASP66 3.7 17.8 1.0
CG2 D:THR67 3.8 22.3 1.0
CD1 D:TYR68 3.9 19.3 1.0
C D:GLY142 3.9 19.3 1.0
CA D:THR67 3.9 20.7 1.0
CB D:VAL143 3.9 22.6 1.0
C D:ASP66 4.0 19.0 1.0
CA D:ASP66 4.0 17.8 1.0
CE1 D:TYR68 4.0 22.0 1.0
CA D:VAL143 4.0 22.8 1.0
CE2 D:PHE145 4.2 37.3 1.0
O D:LEU65 4.2 18.7 1.0
CZ D:PHE145 4.3 37.8 1.0
CG2 D:VAL143 4.3 23.6 1.0
O D:VAL143 4.4 24.3 1.0
N D:TYR68 4.5 18.8 1.0
C D:THR67 4.6 20.0 1.0
NE2 D:HIS22 4.6 15.4 1.0
O D:HOH437 4.6 30.9 1.0
CG D:ASP66 4.7 18.1 1.0
C D:VAL143 4.7 23.9 1.0
N D:GLY142 4.9 16.6 1.0
N D:ASP66 4.9 17.5 1.0
C D:LEU65 4.9 18.1 1.0
CB D:ASP66 5.0 17.8 1.0

Sodium binding site 7 out of 15 in 3mvk

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Sodium binding site 7 out of 15 in the The Crystal Structure of Fucu From Bifidobacterium Longum to 1.65A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Crystal Structure of Fucu From Bifidobacterium Longum to 1.65A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na149

b:24.1
occ:1.00
O E:HOH538 2.7 37.6 1.0
OG1 E:THR67 2.7 22.2 1.0
N E:VAL143 3.1 21.9 1.0
N E:THR67 3.2 20.6 1.0
CA E:GLY142 3.6 18.5 1.0
CB E:THR67 3.7 21.2 1.0
OD1 E:ASP66 3.7 19.1 1.0
CD2 E:TYR68 3.8 20.9 1.0
CG2 E:THR67 3.8 22.4 1.0
CB E:VAL143 3.8 24.0 1.0
C E:GLY142 3.9 20.6 1.0
CE2 E:TYR68 3.9 21.8 1.0
CA E:THR67 4.0 21.5 1.0
CA E:VAL143 4.1 24.0 1.0
CE2 E:PHE145 4.1 39.5 1.0
CZ E:PHE145 4.1 40.1 1.0
CA E:ASP66 4.1 19.5 1.0
C E:ASP66 4.1 19.9 1.0
CG2 E:VAL143 4.1 23.9 1.0
O E:LEU65 4.2 20.7 1.0
O E:VAL143 4.4 25.4 1.0
O E:HOH551 4.4 35.3 1.0
N E:TYR68 4.5 21.0 1.0
C E:THR67 4.7 21.6 1.0
C E:VAL143 4.7 26.0 1.0
NE2 E:HIS22 4.7 17.3 1.0
CG E:ASP66 4.8 19.3 1.0
N E:GLY142 4.9 17.4 1.0
C E:LEU65 5.0 19.8 1.0

Sodium binding site 8 out of 15 in 3mvk

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Sodium binding site 8 out of 15 in the The Crystal Structure of Fucu From Bifidobacterium Longum to 1.65A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of The Crystal Structure of Fucu From Bifidobacterium Longum to 1.65A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na150

b:27.1
occ:1.00
O E:HOH937 2.6 35.5 1.0
C1 E:GOL153 2.6 36.0 1.0
OD1 E:ASP30 2.7 15.5 1.0
O1 E:GOL153 2.8 34.2 1.0
ND2 E:ASN136 3.0 17.9 1.0
OD2 E:ASP30 3.3 16.3 1.0
CG E:ASP30 3.4 16.6 1.0
CA E:PHE33 3.4 13.8 1.0
N E:PHE33 3.5 14.0 1.0
OD1 E:ASN136 3.6 16.7 1.0
CB E:PHE33 3.6 14.2 1.0
O2 E:GOL153 3.7 39.9 1.0
C2 E:GOL153 3.7 37.1 1.0
CG E:ASN136 3.7 16.4 1.0
CD1 E:PHE33 3.7 13.3 1.0
C E:ASN32 3.7 14.7 1.0
O E:ASN32 4.1 15.6 1.0
CB E:ASN32 4.1 16.3 1.0
O3 E:GOL153 4.1 35.8 1.0
CG E:PHE33 4.2 14.6 1.0
CA E:ASN32 4.4 15.2 1.0
C3 E:GOL153 4.5 37.7 1.0
CE E:MSE76 4.7 19.7 1.0
N E:ASN32 4.8 15.2 1.0
SE E:MSE76 4.8 24.9 1.0
CB E:ASP30 4.8 14.1 1.0
C E:PHE33 4.9 13.5 1.0
CE1 E:PHE33 4.9 13.7 1.0
CD E:PRO34 5.0 14.6 1.0

Sodium binding site 9 out of 15 in 3mvk

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Sodium binding site 9 out of 15 in the The Crystal Structure of Fucu From Bifidobacterium Longum to 1.65A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of The Crystal Structure of Fucu From Bifidobacterium Longum to 1.65A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na149

b:27.7
occ:1.00
O F:HOH1294 2.5 38.7 1.0
OG1 F:THR67 2.8 25.7 1.0
N F:THR67 3.1 22.1 1.0
N F:VAL143 3.2 24.0 1.0
CA F:GLY142 3.6 20.8 1.0
CB F:THR67 3.7 23.8 1.0
CB F:VAL143 3.9 26.6 1.0
CG2 F:THR67 3.9 24.4 1.0
OD1 F:ASP66 3.9 23.2 1.0
CD1 F:TYR68 3.9 26.9 1.0
C F:GLY142 3.9 22.9 1.0
CA F:THR67 3.9 23.3 1.0
CE1 F:TYR68 4.0 29.6 1.0
CA F:ASP66 4.1 20.3 1.0
C F:ASP66 4.1 21.3 1.0
CA F:VAL143 4.1 26.9 1.0
O F:HOH470 4.2 29.5 1.0
O F:LEU65 4.2 22.1 1.0
O F:VAL143 4.5 29.1 1.0
CG2 F:VAL143 4.5 27.7 1.0
N F:TYR68 4.6 23.5 1.0
C F:THR67 4.7 23.6 1.0
CE1 F:HIS22 4.8 17.5 1.0
C F:VAL143 4.8 28.1 1.0
CG F:ASP66 4.9 21.7 1.0
C F:LEU65 4.9 21.5 1.0
CG1 F:VAL143 4.9 28.5 1.0
N F:GLY142 4.9 19.4 1.0
N F:ASP66 4.9 20.4 1.0

Sodium binding site 10 out of 15 in 3mvk

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Sodium binding site 10 out of 15 in the The Crystal Structure of Fucu From Bifidobacterium Longum to 1.65A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of The Crystal Structure of Fucu From Bifidobacterium Longum to 1.65A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na150

b:28.9
occ:1.00
O1 F:GOL152 2.8 29.3 1.0
OD1 F:ASP30 2.8 17.8 1.0
C1 F:GOL152 2.9 35.7 1.0
ND2 F:ASN136 3.0 16.8 1.0
OD2 F:ASP30 3.4 18.3 1.0
CG F:ASP30 3.5 16.2 1.0
N F:PHE33 3.5 15.2 1.0
CA F:PHE33 3.5 14.1 1.0
O3 F:GOL152 3.6 42.8 1.0
OD1 F:ASN136 3.7 15.1 1.0
CD1 F:PHE33 3.7 13.7 1.0
C F:ASN32 3.7 16.0 1.0
CB F:PHE33 3.8 14.4 1.0
CG F:ASN136 3.8 15.9 1.0
C3 F:GOL152 3.9 36.7 1.0
C2 F:GOL152 4.0 36.6 1.0
O F:ASN32 4.0 17.6 1.0
CB F:ASN32 4.1 17.3 1.0
CG F:PHE33 4.2 15.0 1.0
CA F:ASN32 4.4 16.7 1.0
O2 F:GOL152 4.5 39.5 1.0
CE F:MSE76 4.8 19.5 1.0
SE F:MSE76 4.8 26.8 1.0
N F:ASN32 4.8 15.8 1.0
CE1 F:PHE33 4.9 12.5 1.0
OH F:TYR116 4.9 21.1 1.0
CD F:PRO34 4.9 13.9 1.0
C F:PHE33 4.9 13.6 1.0
CB F:ASP30 4.9 15.3 1.0

Reference:

A.J.Stein, X.Xu, H.Cui, A.Savchenko, A.Joachimiak. The Crystal Structure of Fucu From Bifidobacterium Longum to 1.65A To Be Published.
Page generated: Tue Dec 15 06:18:26 2020

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