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Nickel 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:

Zinc (Zn) 1 atom
Sodium (Na) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total 2 binding sites of Nickel where determined in the BT_4244 Metallopeptidase in Complex with Tn Antigen., PDB code: 5kd8:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 5kd8

Go back to Nickel Binding Sites List in 5kd8
Nickel 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 Nickel with other atoms in the Ni 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:Ni903

b:60.5
occ:1.00
O A:HOH1139 2.0 29.0 1.0
NE2 A:HIS438 2.3 71.6 1.0
O A:HOH1142 2.4 35.1 1.0
O A:HOH1146 2.5 47.4 1.0
O A:HOH1003 2.7 50.2 1.0
CE1 A:HIS438 3.1 73.7 1.0
CD2 A:HIS438 3.5 72.5 1.0
CD1 A:ILE330 3.8 73.4 1.0
NZ A:LYS326 3.8 91.0 1.0
ND1 A:HIS438 4.3 74.6 1.0
CA A:PRO440 4.3 78.7 1.0
CG1 A:ILE330 4.4 66.0 1.0
N A:LEU441 4.5 71.5 1.0
CG A:HIS438 4.5 69.4 1.0
CB A:PRO440 4.6 77.5 1.0
CE A:LYS326 4.9 90.5 1.0
C A:PRO440 5.0 76.1 1.0
CG A:LEU441 5.0 77.4 1.0

Nickel binding site 2 out of 2 in 5kd8

Go back to Nickel Binding Sites List in 5kd8
Nickel 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 Nickel with other atoms in the Ni 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:Ni904

b:54.8
occ:1.00
O A:HOH1037 1.7 37.4 1.0
O A:HOH1008 1.9 42.6 1.0
OE2 A:GLU708 2.0 43.4 1.0
O A:HOH1004 2.2 50.5 1.0
OE1 A:GLU714 2.2 54.4 1.0
O A:HOH1083 2.3 46.5 1.0
CD A:GLU708 2.9 43.9 1.0
OE1 A:GLU708 3.2 48.1 1.0
CD A:GLU714 3.3 61.2 1.0
OE2 A:GLU714 3.6 66.1 1.0
O A:PHE713 3.9 53.4 1.0
O A:HOH1075 3.9 40.2 1.0
NH2 A:ARG622 4.0 47.5 1.0
CG A:GLU708 4.3 40.7 1.0
CG A:GLU714 4.6 60.0 1.0
O A:HOH1094 4.7 55.3 1.0
C A:PHE713 4.7 48.0 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: Wed Dec 16 01:41:24 2020

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