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Sodium in PDB 7lnp: Structure of the Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside

Protein crystallography data

The structure of Structure of the Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside, PDB code: 7lnp was solved by A.B.Boraston, C.S.Robb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.57 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.325, 106.637, 155.896, 90, 114.97, 90
R / Rfree (%) 23 / 28.4

Other elements in 7lnp:

The structure of Structure of the Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Nickel (Ni) 9 atoms
Calcium (Ca) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside (pdb code 7lnp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Structure of the Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside, PDB code: 7lnp:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 7lnp

Go back to Sodium Binding Sites List in 7lnp
Sodium binding site 1 out of 10 in the Structure of the Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside


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 Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:26.4
occ:1.00
 OG A:SER451 4.0 16.0 1.0
CB A:SER451 4.4 14.8 1.0
CG1 A:VAL489 4.8 13.3 1.0

Sodium binding site 2 out of 10 in 7lnp

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Sodium binding site 2 out of 10 in the Structure of the Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside


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 Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na606

b:24.2
occ:1.00
 O A:LEU182 3.0 16.9 1.0
CA A:LYS178 3.9 21.4 1.0
N A:PHE184 3.9 14.4 1.0
N A:LYS178 4.0 19.1 1.0
CG2 A:THR177 4.0 11.8 1.0
CB A:PHE184 4.0 13.2 1.0
CB A:LYS178 4.2 19.7 1.0
C A:LEU182 4.2 16.9 1.0
C A:THR177 4.2 18.2 1.0
CA A:ARG183 4.3 15.1 1.0
O A:THR177 4.4 17.0 1.0
O A:HOH852 4.4 19.1 1.0
C A:ARG183 4.4 15.4 1.0
CB A:THR177 4.5 16.9 1.0
O A:HOH724 4.6 18.1 1.0
OE2 A:GLU259 4.6 26.7 1.0
CA A:PHE184 4.6 13.4 1.0
CG A:LYS178 4.7 21.9 1.0
N A:ARG183 4.7 12.7 1.0
O A:LYS174 4.7 18.5 1.0

Sodium binding site 3 out of 10 in 7lnp

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Sodium binding site 3 out of 10 in the Structure of the Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside


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 Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na607

b:23.1
occ:1.00
 N A:HIS220 4.1 23.5 1.0
CD1 A:TYR234 4.2 25.1 1.0
CD2 A:HIS220 4.3 36.6 1.0
CB A:LEU219 4.3 24.5 1.0
CD2 A:LEU219 4.5 19.7 1.0
CB A:HIS220 4.5 29.0 1.0
CG A:HIS220 4.8 36.3 1.0
CA A:LEU219 4.8 24.4 1.0
CB A:TYR234 4.8 29.0 1.0
CG A:LEU219 4.9 23.9 1.0
CG A:TYR234 4.9 27.7 1.0
CE1 A:TYR234 4.9 33.7 1.0
CA A:HIS220 4.9 25.5 1.0

Sodium binding site 4 out of 10 in 7lnp

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Sodium binding site 4 out of 10 in the Structure of the Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside


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 Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na606

b:22.6
occ:1.00
 O C:HOH868 2.7 29.5 1.0
OD1 C:ASP111 3.0 14.2 1.0
OD2 C:ASP111 3.6 22.3 1.0
O C:LYS106 3.6 32.2 1.0
CG C:ASP111 3.7 18.8 1.0
CE C:LYS110 3.9 17.8 1.0
NZ C:LYS110 3.9 24.7 1.0
C C:LYS106 4.7 26.1 1.0
O C:HOH832 5.0 13.4 1.0

Sodium binding site 5 out of 10 in 7lnp

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Sodium binding site 5 out of 10 in the Structure of the Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside


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 Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na607

b:15.9
occ:1.00
 O C:HOH836 2.5 10.0 1.0
O C:HOH805 3.0 9.7 1.0
O C:HOH706 3.2 14.3 1.0
N C:VAL294 3.5 11.6 1.0
CA C:GLU293 3.7 12.4 1.0
CE1 C:TYR52 3.8 11.8 1.0
CG2 C:VAL294 3.9 11.6 1.0
CB C:ALA287 4.1 12.5 1.0
CD1 C:TYR52 4.1 13.2 1.0
C C:GLU293 4.1 11.2 1.0
CB C:GLU293 4.2 11.7 1.0
O C:LYS292 4.2 16.8 1.0
CG C:GLU293 4.2 10.1 1.0
CD1 C:TYR284 4.5 12.5 1.0
O C:VAL294 4.5 11.4 1.0
CA C:VAL294 4.6 12.5 1.0
CB C:VAL294 4.8 12.8 1.0
N C:GLU293 4.8 13.3 1.0
O C:TYR284 4.9 13.8 1.0
CG C:TYR284 4.9 14.0 1.0
C C:VAL294 4.9 11.9 1.0
C C:LYS292 4.9 13.6 1.0
CA C:TYR284 5.0 16.7 1.0
CZ C:TYR52 5.0 13.2 1.0
CB C:TYR284 5.0 14.5 1.0

Sodium binding site 6 out of 10 in 7lnp

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Sodium binding site 6 out of 10 in the Structure of the Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside


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 Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na605

b:24.4
occ:1.00
 O D:HOH851 2.6 27.4 1.0
CB D:LYS482 3.9 25.7 1.0
C D:TYR481 4.1 27.4 1.0
N D:LYS482 4.2 27.9 1.0
CA D:TYR481 4.3 25.5 1.0
N D:TYR481 4.4 29.5 1.0
C D:ASP480 4.5 29.6 1.0
O D:ASP480 4.5 31.7 1.0
O D:TYR481 4.5 31.4 1.0
O D:VAL489 4.6 27.1 1.0
CB D:ASP480 4.6 33.1 1.0
CA D:LYS482 4.7 27.3 1.0
CG1 D:VAL489 4.8 21.9 1.0

Sodium binding site 7 out of 10 in 7lnp

Go back to Sodium Binding Sites List in 7lnp
Sodium binding site 7 out of 10 in the Structure of the Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside


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 Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na606

b:25.2
occ:1.00
 O D:HOH725 2.4 30.7 1.0
O D:HOH767 3.4 28.8 1.0
O D:HOH763 3.8 20.7 1.0
CD1 D:TYR234 3.9 36.6 1.0
ND1 D:HIS220 4.3 42.0 1.0
CE1 D:TYR234 4.5 37.6 1.0
CD2 D:LEU219 4.6 15.4 1.0
N D:HIS220 4.7 21.7 1.0
CB D:LEU219 4.7 19.8 1.0
CG D:TYR234 4.9 35.5 1.0
CB D:TYR234 5.0 30.2 1.0
CB D:HIS220 5.0 31.2 1.0

Sodium binding site 8 out of 10 in 7lnp

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Sodium binding site 8 out of 10 in the Structure of the Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside


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 Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na605

b:16.5
occ:1.00
 O E:HOH823 2.5 13.4 1.0
OD1 E:ASN438 3.0 19.7 1.0
O E:HOH728 3.1 18.0 1.0
N E:SER562 3.5 15.6 1.0
C E:LYS561 3.6 18.2 1.0
O E:ASN533 3.9 18.5 1.0
O E:SER562 3.9 14.5 1.0
CA E:SER562 3.9 15.2 1.0
O E:HOH790 3.9 15.3 1.0
C E:SER562 3.9 17.2 1.0
CA E:LYS561 4.1 17.8 1.0
ND1 E:HIS534 4.1 17.1 1.0
CG E:ASN438 4.1 18.2 1.0
O E:LYS561 4.1 17.4 1.0
CA E:ASN438 4.1 14.2 1.0
CE1 E:HIS534 4.2 16.6 1.0
C E:ASN533 4.5 18.5 1.0
CB E:ASN438 4.6 12.1 1.0
CG E:HIS534 4.6 18.7 1.0
N E:GLU563 4.7 16.6 1.0
CA E:HIS534 4.7 19.0 1.0
NE2 E:HIS534 4.7 14.0 1.0
OG1 E:THR435 4.8 16.5 1.0
N E:ASN438 4.8 12.6 1.0
N E:HIS534 4.8 18.4 1.0
CB E:LYS561 4.8 12.7 1.0
N E:ASN533 4.9 14.8 1.0
CB E:ALA532 4.9 11.7 1.0
CD2 E:HIS534 4.9 17.1 1.0

Sodium binding site 9 out of 10 in 7lnp

Go back to Sodium Binding Sites List in 7lnp
Sodium binding site 9 out of 10 in the Structure of the Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Structure of the Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na606

b:21.4
occ:1.00
 O E:HOH860 2.7 28.0 1.0
OE1 E:GLN257 5.0 22.0 1.0

Sodium binding site 10 out of 10 in 7lnp

Go back to Sodium Binding Sites List in 7lnp
Sodium binding site 10 out of 10 in the Structure of the Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Structure of the Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na607

b:20.4
occ:1.00
 NZ E:LYS505 4.4 18.2 1.0

Reference:

C.S.Robb, J.K.Hobbs, B.Pluvinage, G.Reintjes, L.Klassen, S.Monteith, G.Giljan, C.Amundsen, C.Vickers, A.G.Hettle, R.Hills, X.Xing, T.Montina, W.F.Zandberg, D.W.Abbott, A.B.Boraston. Metabolism of A Hybrid Algal Galactan By Members of the Human Gut Microbiome. Nat.Chem.Biol. V. 18 501 2022.
ISSN: ESSN 1552-4469
PubMed: 35289327
DOI: 10.1038/S41589-022-00983-Y
Page generated: Tue Oct 8 17:39:17 2024

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