Sodium in PDB 8rzk: The Michaelis Complex of ZGGH129 D486N From Zobellia Galactanivorans with Neo-B/K-Oligo-Carrageenan Tetrasaccharide (Beta-Kappa Neo-Oligo- Carrageenan DP4).

Protein crystallography data

The structure of The Michaelis Complex of ZGGH129 D486N From Zobellia Galactanivorans with Neo-B/K-Oligo-Carrageenan Tetrasaccharide (Beta-Kappa Neo-Oligo- Carrageenan DP4)., PDB code: 8rzk was solved by T.Roret, M.Czjzek, E.Ficko-Blean, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.82 / 2.29
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.734, 105.943, 213.664, 90, 111.23, 90
R / Rfree (%) 16.9 / 20.2

Other elements in 8rzk:

The structure of The Michaelis Complex of ZGGH129 D486N From Zobellia Galactanivorans with Neo-B/K-Oligo-Carrageenan Tetrasaccharide (Beta-Kappa Neo-Oligo- Carrageenan DP4). also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Michaelis Complex of ZGGH129 D486N From Zobellia Galactanivorans with Neo-B/K-Oligo-Carrageenan Tetrasaccharide (Beta-Kappa Neo-Oligo- Carrageenan DP4). (pdb code 8rzk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the The Michaelis Complex of ZGGH129 D486N From Zobellia Galactanivorans with Neo-B/K-Oligo-Carrageenan Tetrasaccharide (Beta-Kappa Neo-Oligo- Carrageenan DP4)., PDB code: 8rzk:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 8rzk

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Sodium binding site 1 out of 4 in the The Michaelis Complex of ZGGH129 D486N From Zobellia Galactanivorans with Neo-B/K-Oligo-Carrageenan Tetrasaccharide (Beta-Kappa Neo-Oligo- Carrageenan DP4).


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Michaelis Complex of ZGGH129 D486N From Zobellia Galactanivorans with Neo-B/K-Oligo-Carrageenan Tetrasaccharide (Beta-Kappa Neo-Oligo- Carrageenan DP4). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na703

b:80.9
occ:1.00
 O A:LEU512 2.5 45.5 1.0
OD2 A:ASP528 2.9 46.6 1.0
OD1 A:ASN514 3.0 52.4 1.0
O A:HOH902 3.6 45.5 1.0
C A:LEU512 3.7 44.9 1.0
OD1 A:ASP508 3.8 62.4 1.0
CG A:ASP528 3.8 42.9 1.0
CG A:ASN514 3.8 49.2 1.0
NH1 A:ARG326 3.9 59.8 1.0
OD1 A:ASP528 4.0 46.0 1.0
N A:ASN514 4.1 42.9 1.0
O A:HOH897 4.3 51.0 1.0
N A:LEU512 4.3 48.5 1.0
CA A:VAL513 4.4 42.0 1.0
N A:VAL513 4.5 42.5 1.0
ND2 A:ASN514 4.5 50.6 1.0
C A:ASN511 4.6 47.5 1.0
OD1 A:ASN511 4.7 50.0 1.0
CA A:LEU512 4.7 44.8 1.0
CB A:ASN514 4.7 43.1 1.0
CA A:ASN511 4.7 47.5 1.0
C A:VAL513 4.7 44.7 1.0
ND2 A:ASN327 4.8 48.7 1.0
O A:TYR526 4.8 44.9 1.0
CG A:ASP508 4.9 59.1 1.0
CZ A:ARG326 4.9 60.5 1.0
CA A:ASN514 5.0 44.3 1.0

Sodium binding site 2 out of 4 in 8rzk

Go back to Sodium Binding Sites List in 8rzk
Sodium binding site 2 out of 4 in the The Michaelis Complex of ZGGH129 D486N From Zobellia Galactanivorans with Neo-B/K-Oligo-Carrageenan Tetrasaccharide (Beta-Kappa Neo-Oligo- Carrageenan DP4).


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Michaelis Complex of ZGGH129 D486N From Zobellia Galactanivorans with Neo-B/K-Oligo-Carrageenan Tetrasaccharide (Beta-Kappa Neo-Oligo- Carrageenan DP4). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na703

b:78.6
occ:1.00
 OD2 B:ASP528 2.5 46.5 1.0
OD1 B:ASN514 2.5 55.0 1.0
O B:HOH904 2.5 54.0 1.0
O B:LEU512 3.1 48.5 1.0
CG B:ASP528 3.1 43.3 1.0
O B:HOH1016 3.1 51.5 1.0
OD1 B:ASP528 3.2 45.2 1.0
CG B:ASN514 3.6 52.9 1.0
O B:HOH882 3.8 49.5 1.0
N B:ASN514 4.0 45.3 1.0
OD1 B:ASP508 4.2 63.9 1.0
C B:LEU512 4.2 47.9 1.0
O B:HOH953 4.3 56.9 1.0
ND2 B:ASN514 4.3 55.1 1.0
N B:ASP528 4.3 41.3 1.0
CB B:ASP528 4.4 39.1 1.0
O B:TYR526 4.4 43.1 1.0
C B:PHE527 4.5 42.7 1.0
NH1 B:ARG326 4.6 59.0 1.0
CA B:VAL513 4.6 43.7 1.0
CB B:ASN514 4.6 46.5 1.0
CA B:PHE527 4.7 38.1 1.0
C B:VAL513 4.8 47.4 1.0
CA B:ASN514 4.8 51.0 1.0
O B:ASN514 4.8 46.6 1.0
CA B:ASP528 4.9 37.8 1.0
N B:VAL513 4.9 43.6 1.0
C B:TYR526 4.9 42.1 1.0

Sodium binding site 3 out of 4 in 8rzk

Go back to Sodium Binding Sites List in 8rzk
Sodium binding site 3 out of 4 in the The Michaelis Complex of ZGGH129 D486N From Zobellia Galactanivorans with Neo-B/K-Oligo-Carrageenan Tetrasaccharide (Beta-Kappa Neo-Oligo- Carrageenan DP4).


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Michaelis Complex of ZGGH129 D486N From Zobellia Galactanivorans with Neo-B/K-Oligo-Carrageenan Tetrasaccharide (Beta-Kappa Neo-Oligo- Carrageenan DP4). within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na702

b:79.1
occ:1.00
 O C:LEU512 2.4 48.4 1.0
OD1 C:ASN514 2.6 53.7 1.0
OD2 C:ASP528 2.8 49.6 1.0
CG C:ASP528 3.5 46.2 1.0
OD1 C:ASP528 3.6 50.9 1.0
NH2 C:ARG326 3.6 67.7 1.0
CG C:ASN514 3.6 49.8 1.0
C C:LEU512 3.6 47.8 1.0
N C:ASN514 3.9 50.8 1.0
O C:HOH847 4.0 54.3 1.0
OD1 C:ASP508 4.2 64.6 1.0
O C:HOH890 4.2 56.1 1.0
CA C:VAL513 4.4 48.2 1.0
N C:LEU512 4.4 56.5 1.0
N C:VAL513 4.4 46.1 1.0
ND2 C:ASN514 4.4 49.3 1.0
CB C:ASN514 4.5 47.2 1.0
C C:VAL513 4.6 50.8 1.0
CA C:LEU512 4.7 51.7 1.0
OD1 C:ASN511 4.7 60.3 1.0
CZ C:ARG326 4.7 66.2 1.0
CA C:ASN514 4.8 47.8 1.0
CB C:ASP528 4.8 39.8 1.0
N C:ASP528 4.9 41.0 1.0
C C:ASN511 4.9 54.2 1.0
O C:TYR526 5.0 48.9 1.0
ND2 C:ASN327 5.0 49.6 1.0

Sodium binding site 4 out of 4 in 8rzk

Go back to Sodium Binding Sites List in 8rzk
Sodium binding site 4 out of 4 in the The Michaelis Complex of ZGGH129 D486N From Zobellia Galactanivorans with Neo-B/K-Oligo-Carrageenan Tetrasaccharide (Beta-Kappa Neo-Oligo- Carrageenan DP4).


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Michaelis Complex of ZGGH129 D486N From Zobellia Galactanivorans with Neo-B/K-Oligo-Carrageenan Tetrasaccharide (Beta-Kappa Neo-Oligo- Carrageenan DP4). within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na702

b:68.6
occ:1.00
 O D:LEU512 2.4 51.5 1.0
O D:HOH989 2.4 60.4 1.0
OD2 D:ASP528 2.8 45.9 1.0
ND2 D:ASN514 2.8 55.9 1.0
OD1 D:ASN514 3.1 55.1 1.0
CG D:ASN514 3.2 52.4 1.0
C D:LEU512 3.6 48.9 1.0
CG D:ASP528 3.6 43.3 1.0
OD1 D:ASP508 3.7 64.5 1.0
OD1 D:ASP528 3.8 41.9 1.0
N D:ASN514 3.9 44.5 1.0
O D:HOH802 3.9 45.6 1.0
NH1 D:ARG326 4.2 53.8 1.0
N D:LEU512 4.2 48.6 1.0
CA D:VAL513 4.4 44.6 1.0
CB D:ASN514 4.4 43.0 1.0
N D:VAL513 4.4 46.2 1.0
ND2 D:ASN327 4.5 49.1 1.0
CA D:LEU512 4.6 46.3 1.0
C D:VAL513 4.6 44.9 1.0
C D:ASN511 4.7 49.4 1.0
CA D:ASN514 4.7 46.0 1.0
OD1 D:ASN511 4.8 56.2 1.0
O D:TYR526 4.8 43.1 1.0
CA D:ASN511 4.9 52.6 1.0
CB D:ASP528 4.9 41.6 1.0
CG D:ASP508 5.0 60.8 1.0
N D:ASP528 5.0 41.0 1.0

Reference:

M.D.Wallace, I.Cuxart, T.Roret, L.Guee, A.W.Debowski, M.Czjzek, C.Rovira, K.A.Stubbs, E.Ficko-Blean. Constrained Catalytic Itinerary of A Retaining 3,6-Anhydro-D-Galactosidase, A Key Enzyme in Red Algal Cell Wall Degradation. Angew.Chem.Int.Ed.Engl. 11171 2024.
ISSN: ESSN 1521-3773
PubMed: 39022920
DOI: 10.1002/ANIE.202411171
Page generated: Wed Oct 9 13:24:50 2024

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