Magnesium in PDB 6h9v: Crystal Structure of Deaminated P Domain From Norovirus Strain Saga Gii-4 in Complex with Fuc

Protein crystallography data

The structure of Crystal Structure of Deaminated P Domain From Norovirus Strain Saga Gii-4 in Complex with Fuc, PDB code: 6h9v was solved by P.H.O.Meyer, B.S.Blaum, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.58 / 1.52
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.290, 83.950, 65.130, 90.00, 95.78, 90.00
R / Rfree (%) 14.7 / 18.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Deaminated P Domain From Norovirus Strain Saga Gii-4 in Complex with Fuc (pdb code 6h9v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Deaminated P Domain From Norovirus Strain Saga Gii-4 in Complex with Fuc, PDB code: 6h9v:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6h9v

Go back to Magnesium Binding Sites List in 6h9v
Magnesium binding site 1 out of 2 in the Crystal Structure of Deaminated P Domain From Norovirus Strain Saga Gii-4 in Complex with Fuc


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Deaminated P Domain From Norovirus Strain Saga Gii-4 in Complex with Fuc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:32.1
occ:1.00
H A:GLU488 2.2 23.6 1.0
HG2 A:GLU488 2.8 29.8 1.0
O A:ALA528 2.8 25.6 1.0
HA A:PHE487 2.8 23.8 1.0
HB2 A:PHE487 2.8 27.3 1.0
HB1 A:ALA528 3.0 37.1 1.0
N A:GLU488 3.0 19.7 1.0
HB3 A:MET530 3.0 44.6 1.0
O A:HOH892 3.1 38.1 1.0
CA A:PHE487 3.4 19.9 1.0
O A:PRO529 3.4 34.3 1.0
CB A:PHE487 3.5 22.8 1.0
O A:HOH832 3.6 18.3 1.0
C A:ALA528 3.6 27.7 1.0
CG A:GLU488 3.6 24.8 1.0
C A:PHE487 3.7 20.7 1.0
HG3 A:GLU488 3.8 29.8 1.0
CB A:ALA528 3.8 30.9 1.0
O A:GLU488 3.8 21.6 1.0
HB3 A:PHE487 3.8 27.3 1.0
C A:PRO529 3.9 29.7 1.0
CB A:MET530 3.9 37.2 1.0
HB2 A:ALA528 4.0 37.1 1.0
HA A:MET530 4.0 40.6 1.0
CA A:GLU488 4.1 18.6 1.0
N A:MET530 4.2 30.5 1.0
CA A:ALA528 4.2 26.7 1.0
CA A:MET530 4.3 33.9 1.0
CB A:GLU488 4.3 25.9 1.0
C A:GLU488 4.4 19.9 1.0
H A:ALA528 4.4 31.3 1.0
HB2 A:MET530 4.5 44.6 1.0
HG2 A:MET530 4.5 45.4 1.0
N A:PRO529 4.5 27.1 1.0
HD1 A:PHE487 4.5 25.9 1.0
HB3 A:GLU488 4.6 31.1 1.0
HB3 A:ALA528 4.6 37.1 1.0
N A:ALA528 4.6 26.1 1.0
H A:MET530 4.6 36.6 1.0
CD A:GLU488 4.7 30.2 1.0
CA A:PRO529 4.7 29.5 1.0
N A:PHE487 4.7 20.7 1.0
HB3 A:LEU527 4.8 27.4 1.0
CG A:PHE487 4.8 20.0 1.0
CG A:MET530 4.8 37.8 1.0
O A:LEU486 4.9 27.4 1.0
HA A:GLU488 4.9 22.3 1.0
O A:PHE487 4.9 20.6 1.0

Magnesium binding site 2 out of 2 in 6h9v

Go back to Magnesium Binding Sites List in 6h9v
Magnesium binding site 2 out of 2 in the Crystal Structure of Deaminated P Domain From Norovirus Strain Saga Gii-4 in Complex with Fuc


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Deaminated P Domain From Norovirus Strain Saga Gii-4 in Complex with Fuc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:32.5
occ:1.00
H B:GLU488 2.3 22.2 1.0
O B:ALA528 2.7 25.9 1.0
HG2 B:GLU488 2.7 23.6 1.0
HA B:PHE487 2.8 23.1 1.0
HA B:MET530 2.9 38.1 0.6
O B:HOH790 2.9 33.0 1.0
HB3 B:ALA528 3.0 36.7 1.0
HB2 B:PHE487 3.0 22.6 1.0
N B:GLU488 3.1 18.5 1.0
O B:HOH984 3.2 38.5 1.0
O B:PRO529 3.3 32.8 1.0
HA B:MET530 3.4 43.2 0.4
CA B:PHE487 3.4 19.2 1.0
C B:ALA528 3.6 24.9 1.0
CG B:GLU488 3.6 19.7 1.0
CB B:PHE487 3.6 18.9 1.0
O B:HOH837 3.7 21.2 1.0
CA B:MET530 3.7 31.8 0.6
C B:PRO529 3.7 35.8 1.0
HG3 B:GLU488 3.7 23.6 1.0
C B:PHE487 3.7 19.6 1.0
CB B:ALA528 3.8 30.6 1.0
O B:GLU488 3.9 19.2 1.0
N B:MET530 3.9 31.8 0.6
HB1 B:ALA528 3.9 36.7 1.0
N B:MET530 4.0 32.0 0.4
HB3 B:PHE487 4.0 22.6 1.0
CA B:MET530 4.1 36.0 0.4
CA B:GLU488 4.1 21.0 1.0
CA B:ALA528 4.2 30.7 1.0
C B:MET530 4.3 35.4 0.6
CB B:GLU488 4.4 21.4 1.0
OXT B:MET530 4.4 39.8 0.6
HB2 B:MET530 4.4 40.5 0.4
N B:PRO529 4.4 25.6 1.0
H B:ALA528 4.4 28.6 1.0
C B:GLU488 4.5 19.7 1.0
H B:MET530 4.5 38.5 0.4
H B:MET530 4.6 38.2 0.6
HB2 B:ALA528 4.6 36.7 1.0
N B:ALA528 4.6 23.9 1.0
HB3 B:GLU488 4.6 25.7 1.0
CA B:PRO529 4.6 25.9 1.0
CD B:GLU488 4.7 37.5 1.0
HD1 B:PHE487 4.7 25.6 1.0
HB3 B:LEU527 4.7 27.8 1.0
N B:PHE487 4.8 19.8 1.0
CB B:MET530 4.8 33.8 0.4
O B:LEU486 4.8 22.8 1.0
CB B:MET530 4.8 33.4 0.6
HB2 B:MET530 4.9 40.1 0.6
HG3 B:MET530 4.9 42.9 0.4
HG3 B:MET530 4.9 41.8 0.6
CG B:PHE487 4.9 19.7 1.0
O B:PHE487 4.9 19.3 1.0
HA B:GLU488 4.9 25.1 1.0
OE2 B:GLU488 5.0 30.8 1.0
HA B:PRO529 5.0 31.1 1.0

Reference:

A.Mallagaray, R.Creutznacher, J.Dulfer, P.H.O.Mayer, L.L.Grimm, J.M.Orduna, E.Trabjerg, T.Stehle, K.D.Rand, B.S.Blaum, C.Uetrecht, T.Peters. A Post-Translational Modification of Human Norovirus Capsid Protein Attenuates Glycan Binding. Nat Commun V. 10 1320 2019.
ISSN: ESSN 2041-1723
PubMed: 30899001
DOI: 10.1038/S41467-019-09251-5
Page generated: Mon Dec 14 22:48:42 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy