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Sodium in PDB 1hhy: Deglucobalhimycin in Complex with D-Ala-D-Ala

Protein crystallography data

The structure of Deglucobalhimycin in Complex with D-Ala-D-Ala, PDB code: 1hhy was solved by C.Lehmann, G.Bunkoczi, G.M.Sheldrick, L.Vertesy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.06 / 0.89
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 48.444, 48.444, 43.086, 90.00, 90.00, 120.00
R / Rfree (%) 12.1 / 13.9

Other elements in 1hhy:

The structure of Deglucobalhimycin in Complex with D-Ala-D-Ala also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Deglucobalhimycin in Complex with D-Ala-D-Ala (pdb code 1hhy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Deglucobalhimycin in Complex with D-Ala-D-Ala, PDB code: 1hhy:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1hhy

Go back to Sodium Binding Sites List in 1hhy
Sodium binding site 1 out of 2 in the Deglucobalhimycin in Complex with D-Ala-D-Ala


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Deglucobalhimycin in Complex with D-Ala-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1001

b:6.5
occ:1.00
N A:MLU1 3.1 7.2 0.6
O A:HOH2002 3.2 13.8 0.4
O A:HOH2023 3.2 15.9 1.0
CN A:MLU1 3.6 8.8 0.6
CA A:MLU1 3.7 6.9 0.6
CB A:MLU1 4.1 8.1 0.6
OXT A:DAL12 4.5 10.6 1.0
N A:MLU1 4.8 14.3 0.4
CA A:MLU1 4.8 11.3 0.4
CA A:DAL12 4.9 10.6 1.0
CG A:MLU1 5.0 8.7 0.6

Sodium binding site 2 out of 2 in 1hhy

Go back to Sodium Binding Sites List in 1hhy
Sodium binding site 2 out of 2 in the Deglucobalhimycin in Complex with D-Ala-D-Ala


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Deglucobalhimycin in Complex with D-Ala-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1002

b:7.7
occ:0.33
O2 B:PGO1001 2.4 11.7 1.0
O1 B:PGO1001 2.5 7.0 1.0
C1 B:PGO1001 3.2 7.6 1.0
C2 B:PGO1001 3.3 7.1 1.0
O4 B:GHP4 3.7 6.5 1.0
O4 A:GHP4 4.5 9.4 1.0
O B:HOH2030 4.6 32.7 1.0
C3 B:PGO1001 4.6 8.4 1.0
C4 B:GHP4 4.9 5.7 1.0

Reference:

C.Lehmann, G.Bunkoczi, L.Vertesy, G.M.Sheldrick. Structures of Glycopeptide Antibiotics with Peptides That Model Bacterial Cell-Wall Precursors J.Mol.Biol. V. 318 723 2002.
ISSN: ISSN 0022-2836
PubMed: 12054818
DOI: 10.1016/S0022-2836(02)00146-8
Page generated: Tue Dec 15 05:25:21 2020

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