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Nickel 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
Sodium (Na) 10 atoms
Calcium (Ca) 4 atoms

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total 9 binding sites of Nickel 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 Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Nickel binding site 1 out of 9 in 7lnp

Go back to Nickel Binding Sites List in 7lnp
Nickel binding site 1 out of 9 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 Nickel with other atoms in the Ni 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:Ni603

b:27.0
occ:1.00
 O A:HOH853 2.3 13.2 1.0
O A:HOH790 2.9 15.2 1.0
NE2 A:HIS502 3.4 13.3 1.0
N A:TYR500 3.6 11.8 1.0
CE1 A:HIS502 3.6 15.2 1.0
NZ A:LYS496 3.7 17.1 1.0
O A:HOH811 3.8 14.4 1.0
CB A:TRP447 3.9 14.7 1.0
CA A:GLU499 4.0 18.2 1.0
C A:GLU499 4.0 14.4 1.0
N A:TRP447 4.2 15.8 1.0
CB A:GLU499 4.4 18.1 1.0
CE A:LYS496 4.4 18.6 1.0
CA A:TYR500 4.4 14.4 1.0
O A:TYR500 4.6 14.8 1.0
CD A:LYS496 4.6 17.1 1.0
C A:TYR500 4.7 14.4 1.0
CA A:TRP447 4.7 15.0 1.0
CD2 A:HIS502 4.7 13.8 1.0
ND1 A:HIS502 4.9 15.0 1.0
C A:ALA446 4.9 16.4 1.0
O A:GLU499 5.0 15.9 1.0
CA A:ALA446 5.0 18.0 1.0
CG A:TRP447 5.0 16.9 1.0

Nickel binding site 2 out of 9 in 7lnp

Go back to Nickel Binding Sites List in 7lnp
Nickel binding site 2 out of 9 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 Nickel with other atoms in the Ni 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:Ni604

b:35.7
occ:1.00
 NZ A:LYS332 3.5 29.8 1.0
OG A:SER345 3.6 18.4 1.0
CD2 A:HIS348 3.6 20.5 1.0
CE A:LYS332 3.8 30.7 1.0
N A:SER345 3.9 16.8 1.0
CB A:HIS348 3.9 17.7 1.0
CD A:LYS423 4.0 24.6 1.0
CG A:HIS348 4.0 20.5 1.0
CB A:SER345 4.2 18.8 1.0
CA A:LYS344 4.4 16.1 1.0
CB A:LYS423 4.5 19.0 1.0
C A:LYS344 4.7 17.2 1.0
CA A:SER345 4.7 16.5 1.0
NE2 A:HIS348 4.8 21.1 1.0
CG A:LYS423 4.8 19.2 1.0
CB A:LYS344 4.8 18.5 1.0

Nickel binding site 3 out of 9 in 7lnp

Go back to Nickel Binding Sites List in 7lnp
Nickel binding site 3 out of 9 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 Nickel with other atoms in the Ni 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
C:Ni603

b:39.2
occ:1.00
 NE2 C:HIS502 3.5 16.5 1.0
N C:TYR500 3.6 13.8 1.0
NZ C:LYS496 3.7 22.0 1.0
CE1 C:HIS502 3.8 17.2 1.0
CB C:TRP447 4.0 16.4 1.0
CA C:GLU499 4.0 17.5 1.0
C C:GLU499 4.1 15.3 1.0
N C:TRP447 4.3 18.5 1.0
CB C:GLU499 4.4 15.9 1.0
CE C:LYS496 4.4 21.9 1.0
CA C:TYR500 4.5 15.7 1.0
CD C:LYS496 4.6 16.6 1.0
O C:TYR500 4.7 15.4 1.0
C C:TYR500 4.7 15.4 1.0
CA C:TRP447 4.8 14.9 1.0
CG C:GLU499 4.8 17.3 1.0
CD2 C:HIS502 4.8 17.0 1.0
C C:ALA446 4.9 20.8 1.0
O C:GLU499 5.0 18.2 1.0
CA C:ALA446 5.0 19.8 1.0

Nickel binding site 4 out of 9 in 7lnp

Go back to Nickel Binding Sites List in 7lnp
Nickel binding site 4 out of 9 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 Nickel with other atoms in the Ni 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:Ni604

b:38.4
occ:1.00
 O C:HOH716 2.0 20.5 1.0
NZ C:LYS332 3.4 28.1 1.0
CD2 C:HIS348 3.4 20.6 1.0
OG C:SER345 3.6 15.4 1.0
CE C:LYS332 3.8 31.1 1.0
N C:SER345 3.8 15.1 1.0
CB C:HIS348 3.9 17.1 1.0
CD C:LYS423 3.9 19.6 1.0
CG C:HIS348 4.0 22.6 1.0
CB C:SER345 4.2 18.2 1.0
CA C:LYS344 4.4 19.4 1.0
CB C:LYS423 4.5 21.9 1.0
NE2 C:HIS348 4.6 22.2 1.0
C C:LYS344 4.6 16.6 1.0
CA C:SER345 4.7 16.9 1.0
CG C:LYS423 4.7 17.6 1.0
CE C:LYS423 4.7 15.6 1.0
CB C:LYS344 4.8 24.2 1.0

Nickel binding site 5 out of 9 in 7lnp

Go back to Nickel Binding Sites List in 7lnp
Nickel binding site 5 out of 9 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 Nickel with other atoms in the Ni 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:Ni605

b:51.6
occ:1.00
 O C:HOH866 2.7 29.6 1.0
NZ C:LYS59 3.4 29.7 1.0
NE C:ARG401 3.8 14.4 1.0
CD C:ARG401 4.2 10.5 1.0
CE C:LYS59 4.3 25.0 1.0
CD C:LYS59 4.4 16.7 1.0
O C:HOH820 4.7 21.3 1.0
CG C:ARG401 4.8 10.7 1.0
CZ C:ARG401 4.9 14.8 1.0

Nickel binding site 6 out of 9 in 7lnp

Go back to Nickel Binding Sites List in 7lnp
Nickel binding site 6 out of 9 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 Nickel with other atoms in the Ni 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:Ni603

b:36.0
occ:1.00
 OG D:SER345 3.5 22.3 1.0
N D:SER345 3.6 22.7 1.0
CB D:HIS348 3.9 21.3 1.0
CB D:SER345 4.0 24.5 1.0
CE D:LYS332 4.1 27.3 1.0
CG D:HIS348 4.1 28.0 1.0
NZ D:LYS332 4.1 23.9 1.0
CA D:LYS344 4.2 23.8 1.0
ND1 D:HIS348 4.3 30.4 1.0
C D:LYS344 4.4 21.6 1.0
CA D:SER345 4.4 22.6 1.0
CB D:LYS344 4.6 20.7 1.0
CD2 D:HIS348 4.8 35.3 1.0
CG D:LYS344 4.9 27.1 1.0

Nickel binding site 7 out of 9 in 7lnp

Go back to Nickel Binding Sites List in 7lnp
Nickel binding site 7 out of 9 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 Nickel with other atoms in the Ni 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:Ni604

b:42.3
occ:1.00
 NE2 D:HIS502 3.5 18.6 1.0
N D:TYR500 3.7 18.1 1.0
NZ D:LYS496 3.7 20.7 1.0
CE1 D:HIS502 3.8 18.7 1.0
CB D:TRP447 4.0 18.6 1.0
C D:GLU499 4.3 20.1 1.0
CA D:GLU499 4.3 22.5 1.0
CE D:LYS496 4.4 21.9 1.0
CA D:TYR500 4.4 19.2 1.0
N D:TRP447 4.4 23.0 1.0
O D:TYR500 4.4 21.6 1.0
C D:TYR500 4.6 20.8 1.0
CB D:GLU499 4.7 18.8 1.0
CD D:LYS496 4.7 14.1 1.0
CD2 D:HIS502 4.8 18.1 1.0
CA D:TRP447 4.8 18.4 1.0

Nickel binding site 8 out of 9 in 7lnp

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Nickel binding site 8 out of 9 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 Nickel with other atoms in the Ni 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:Ni603

b:38.7
occ:1.00
 O E:HOH832 2.2 12.9 1.0
NE2 E:HIS502 3.4 16.7 1.0
N E:TYR500 3.5 18.1 1.0
NZ E:LYS496 3.6 16.4 1.0
CE1 E:HIS502 3.7 18.4 1.0
CB E:TRP447 4.0 17.8 1.0
C E:GLU499 4.1 19.8 1.0
CA E:GLU499 4.1 21.3 1.0
CE E:LYS496 4.2 18.1 1.0
CA E:TYR500 4.3 17.0 1.0
N E:TRP447 4.4 21.5 1.0
O E:TYR500 4.4 20.2 1.0
O E:HOH859 4.4 22.8 1.0
CB E:GLU499 4.5 19.4 1.0
C E:TYR500 4.5 17.2 1.0
O E:HOH841 4.5 11.9 1.0
CD E:LYS496 4.7 12.6 1.0
CD2 E:HIS502 4.8 16.4 1.0
CA E:TRP447 4.8 17.0 1.0
O E:HOH826 4.8 23.5 1.0
O E:GLU499 4.9 18.6 1.0
ND1 E:HIS502 5.0 19.2 1.0
C E:ALA446 5.0 19.4 1.0

Nickel binding site 9 out of 9 in 7lnp

Go back to Nickel Binding Sites List in 7lnp
Nickel binding site 9 out of 9 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 Nickel with other atoms in the Ni 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:Ni604

b:28.9
occ:1.00
 OG E:SER345 3.5 20.1 1.0
N E:SER345 3.5 19.6 1.0
NZ E:LYS332 3.9 36.9 1.0
CB E:SER345 3.9 16.6 1.0
CE E:LYS332 3.9 31.3 1.0
ND1 E:HIS348 4.0 25.3 1.0
CB E:HIS348 4.0 19.8 1.0
CA E:LYS344 4.2 23.7 1.0
CG E:HIS348 4.3 23.6 1.0
CA E:SER345 4.4 19.1 1.0
C E:LYS344 4.4 21.9 1.0
CB E:LYS344 4.5 21.4 1.0
CG E:LYS344 4.9 24.6 1.0
CE1 E:HIS348 4.9 24.2 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: Fri Apr 7 19:10:35 2023

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