Atomistry » Nickel » PDB 7fbw-7odg » 7lnp
Atomistry »
  Nickel »
    PDB 7fbw-7odg »
      7lnp »

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

Go back to Nickel Binding Sites List in 7lnp
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: Thu Oct 10 09:16:03 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy