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Sodium in PDB 5kd8: BT_4244 Metallopeptidase in Complex with Tn Antigen.

Protein crystallography data

The structure of BT_4244 Metallopeptidase in Complex with Tn Antigen., PDB code: 5kd8 was solved by I.Noach, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.72 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.450, 88.230, 98.650, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 24.2

Other elements in 5kd8:

The structure of BT_4244 Metallopeptidase in Complex with Tn Antigen. also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the BT_4244 Metallopeptidase in Complex with Tn Antigen. (pdb code 5kd8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the BT_4244 Metallopeptidase in Complex with Tn Antigen., PDB code: 5kd8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5kd8

Go back to Sodium Binding Sites List in 5kd8
Sodium binding site 1 out of 2 in the BT_4244 Metallopeptidase in Complex with Tn Antigen.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of BT_4244 Metallopeptidase in Complex with Tn Antigen. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:48.6
occ:1.00
OD1 A:ASP451 2.1 53.1 1.0
O A:HOH1124 2.2 46.0 1.0
O A:HOH1144 2.4 45.7 1.0
CG A:ASP451 2.9 54.7 1.0
OD2 A:ASP451 3.0 63.2 1.0
NE A:ARG476 3.9 50.8 1.0
CB A:LYS453 4.1 83.6 1.0
N A:LYS453 4.3 65.5 1.0
CD A:LYS453 4.4 0.2 1.0
O A:GLY477 4.4 46.8 1.0
CG A:ARG476 4.4 46.5 1.0
CB A:ASP451 4.4 49.1 1.0
CD A:ARG476 4.4 48.8 1.0
NZ A:LYS453 4.5 0.6 1.0
CZ A:ARG476 4.6 53.7 1.0
CG A:LYS453 4.7 94.3 1.0
NH2 A:ARG476 4.7 61.7 1.0
O A:ARG476 4.8 46.7 1.0
CA A:LYS453 4.8 74.1 1.0
N A:LEU452 4.9 54.4 1.0
CE A:LYS453 4.9 0.5 1.0
O A:HOH1068 5.0 50.4 1.0

Sodium binding site 2 out of 2 in 5kd8

Go back to Sodium Binding Sites List in 5kd8
Sodium binding site 2 out of 2 in the BT_4244 Metallopeptidase in Complex with Tn Antigen.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of BT_4244 Metallopeptidase in Complex with Tn Antigen. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:45.7
occ:1.00
O A:HOH1071 2.0 57.0 1.0
OE1 A:GLU454 2.2 82.8 1.0
OE1 A:GLU327 2.2 73.0 1.0
CD A:GLU327 2.8 80.2 1.0
OE2 A:GLU327 2.8 89.1 1.0
CD A:GLU454 2.8 71.2 1.0
OE2 A:GLU454 3.2 70.4 1.0
CG A:GLU454 3.9 69.8 1.0
NE2 A:HIS455 4.1 59.9 1.0
CG A:GLU327 4.2 71.8 1.0
CD2 A:HIS455 4.5 64.2 1.0
O A:GLU327 4.6 51.0 1.0
NH2 A:ARG331 4.7 47.2 1.0
NH1 A:ARG331 4.8 46.4 1.0
CB A:GLU454 4.8 66.5 1.0
CB A:GLU327 4.9 67.7 1.0
CA A:GLU327 5.0 62.4 1.0

Reference:

I.Noach, E.Ficko-Blean, B.Pluvinage, C.Stuart, M.L.Jenkins, D.Brochu, N.Buenbrazo, W.Wakarchuk, J.E.Burke, M.Gilbert, A.B.Boraston. Recognition of Protein-Linked Glycans As A Determinant of Peptidase Activity. Proc. Natl. Acad. Sci. V. 114 E679 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28096352
DOI: 10.1073/PNAS.1615141114
Page generated: Tue Dec 15 11:10:09 2020

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