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Sodium in PDB 6fhn: Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase (Pt Derivative)

Protein crystallography data

The structure of Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase (Pt Derivative), PDB code: 6fhn was solved by O.V.Moroz, P.F.Jensen, S.P.Mcdonald, N.Mcgregor, E.Blagova, G.Comamala, D.R.Segura, L.Anderson, S.M.Vasu, V.P.Rao, L.Giger, R.N.Monrad, A.Svendsen, J.E.Nielsen, B.Henrissat, G.J.Davies, H.Brumer, K.Rand, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.29 / 2.00
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 103.270, 103.270, 210.350, 90.00, 90.00, 120.00
R / Rfree (%) 17.3 / 21

Other elements in 6fhn:

The structure of Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase (Pt Derivative) also contains other interesting chemical elements:

Platinum (Pt) 2 atoms
Calcium (Ca) 5 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase (Pt Derivative) (pdb code 6fhn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase (Pt Derivative), PDB code: 6fhn:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6fhn

Go back to Sodium Binding Sites List in 6fhn
Sodium binding site 1 out of 3 in the Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase (Pt Derivative)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase (Pt Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3011

b:38.1
occ:1.00
O A:HOH3533 2.3 40.0 1.0
O A:HOH3527 2.3 35.2 1.0
O A:PHE474 2.4 31.9 1.0
O A:HOH3671 2.4 44.2 1.0
OD1 A:ASN473 2.4 42.2 1.0
OD2 A:ASP476 2.4 37.9 1.0
CG A:ASP476 3.2 36.7 1.0
C A:PHE474 3.5 31.9 1.0
N A:PHE474 3.5 34.5 1.0
OD1 A:ASP476 3.6 36.8 1.0
CG A:ASN473 3.6 40.9 1.0
CA A:PHE474 4.1 33.3 1.0
C A:ASN473 4.1 35.9 1.0
O A:HOH3420 4.1 42.0 1.0
OD2 A:ASP521 4.2 32.6 1.0
CA A:ASN473 4.2 38.1 1.0
CB A:ASP476 4.4 35.2 1.0
CB A:ASN473 4.5 39.9 1.0
O A:HOH3766 4.5 49.0 1.0
N A:ASP476 4.5 31.6 1.0
N A:THR475 4.5 30.4 1.0
ND2 A:ASN473 4.6 40.8 1.0
CD1 A:ILE464 4.8 31.6 1.0
CA A:THR475 4.9 29.8 1.0
C A:THR475 4.9 30.2 1.0
O A:HOH3737 4.9 46.4 1.0
CD1 A:PHE474 5.0 35.6 1.0

Sodium binding site 2 out of 3 in 6fhn

Go back to Sodium Binding Sites List in 6fhn
Sodium binding site 2 out of 3 in the Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase (Pt Derivative)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase (Pt Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3012

b:47.1
occ:1.00
O A:HOH3418 2.2 48.5 1.0
OD2 A:ASP901 2.2 39.0 1.0
OD2 A:ASP846 2.2 46.9 1.0
O A:THR818 2.3 44.5 0.3
O A:THR818 2.4 46.2 0.7
O A:HOH3345 2.5 38.6 1.0
CG A:ASP846 3.3 47.2 1.0
CG A:ASP901 3.4 37.5 1.0
C A:THR818 3.6 44.3 0.3
C A:THR818 3.6 45.0 0.7
OD1 A:ASP846 3.6 48.0 1.0
CB A:GLN850 3.9 49.2 1.0
N A:THR818 4.1 46.3 0.3
N A:THR818 4.1 46.8 0.7
CD A:PRO820 4.2 38.6 1.0
CB A:ASP901 4.2 36.2 1.0
OD1 A:ASP901 4.3 36.7 1.0
CG A:GLN850 4.3 49.7 1.0
N A:PRO820 4.3 39.8 1.0
C A:ALA819 4.5 40.8 1.0
CA A:THR818 4.5 46.0 0.3
N A:ALA819 4.5 43.5 1.0
CA A:ALA819 4.5 42.0 1.0
CA A:THR818 4.5 47.0 0.7
CB A:ASP846 4.5 46.4 1.0
OG1 A:THR904 4.6 34.1 1.0
CG2 A:THR904 4.8 36.8 1.0
C A:GLY817 4.8 46.8 1.0
OG1 A:THR818 5.0 49.4 0.7

Sodium binding site 3 out of 3 in 6fhn

Go back to Sodium Binding Sites List in 6fhn
Sodium binding site 3 out of 3 in the Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase (Pt Derivative)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase (Pt Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3013

b:46.4
occ:1.00
O A:HOH3672 2.2 40.1 1.0
O A:ASP807 2.4 42.8 1.0
O A:THR699 2.4 50.1 1.0
OD1 A:ASP807 2.5 46.5 1.0
O A:ASP663 2.5 45.2 1.0
O A:HOH3491 2.7 59.5 1.0
C A:ASP807 3.3 43.0 1.0
C A:ASP663 3.5 43.5 1.0
CG2 A:THR699 3.6 52.8 1.0
CG A:ASP807 3.6 46.4 1.0
C A:THR699 3.6 50.5 1.0
O A:HOH3447 3.8 46.9 1.0
CA A:ASP807 3.8 43.6 1.0
CA A:ASP663 4.1 42.2 1.0
CG A:GLU808 4.1 45.6 1.0
CB A:ASP807 4.3 44.8 1.0
CB A:ASP663 4.3 42.5 1.0
N A:THR699 4.3 52.9 1.0
CA A:THR699 4.3 53.2 1.0
N A:GLU808 4.5 41.7 1.0
CB A:THR699 4.5 54.6 1.0
OD2 A:ASP807 4.5 47.7 1.0
N A:PHE664 4.6 43.3 1.0
N A:VAL700 4.6 49.8 1.0
CB A:PHE664 4.6 44.9 1.0
CA A:VAL700 4.8 47.3 1.0
OE2 A:GLU808 4.9 49.4 1.0
CA A:GLU808 5.0 41.9 1.0
CA A:PHE664 5.0 45.0 1.0
CD1 A:PHE664 5.0 42.2 1.0

Reference:

O.V.Moroz, P.F.Jensen, S.P.Mcdonald, N.Mcgregor, E.Blagova, G.Comamala, D.R.Segura, L.Anderson, S.M.Vasu, V.P.Rao, L.Giger, R.N.Monrad, A.Svendsen, J.E.Nielsen, B.Henrissat, G.J.Davies, H.Brumer, K.Rand, K.S.Wilson. Structural Dynamics and Catalytic Properties of A Multimodular Xanthanase Acs Catalysis 2018.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.8B00666
Page generated: Tue Dec 15 12:15:13 2020

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