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Zinc in PDB 5kds: Zmpb Metallopeptidase in Complex with An O-Glycopeptide (A2,6- Sialylated Core-3 Pentapeptide).

Protein crystallography data

The structure of Zmpb Metallopeptidase in Complex with An O-Glycopeptide (A2,6- Sialylated Core-3 Pentapeptide)., PDB code: 5kds was solved by I.Noach, E.Ficko-Blean, C.Stuart, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.180, 68.950, 171.570, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 18.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Zmpb Metallopeptidase in Complex with An O-Glycopeptide (A2,6- Sialylated Core-3 Pentapeptide). (pdb code 5kds). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Zmpb Metallopeptidase in Complex with An O-Glycopeptide (A2,6- Sialylated Core-3 Pentapeptide)., PDB code: 5kds:

Zinc binding site 1 out of 1 in 5kds

Go back to Zinc Binding Sites List in 5kds
Zinc binding site 1 out of 1 in the Zmpb Metallopeptidase in Complex with An O-Glycopeptide (A2,6- Sialylated Core-3 Pentapeptide).


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zmpb Metallopeptidase in Complex with An O-Glycopeptide (A2,6- Sialylated Core-3 Pentapeptide). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1101

b:25.4
occ:1.00
O11 A:TLA1102 2.0 26.6 1.0
OE1 A:GLU771 2.1 24.9 1.0
NE2 A:HIS760 2.1 22.1 1.0
NE2 A:HIS756 2.2 18.6 1.0
O2 A:TLA1102 2.2 28.6 1.0
O A:HOH1222 2.2 23.3 1.0
C1 A:TLA1102 2.8 32.1 1.0
C2 A:TLA1102 3.0 31.5 1.0
CD A:GLU771 3.0 27.1 1.0
CD2 A:HIS760 3.1 21.4 1.0
CD2 A:HIS756 3.1 16.9 1.0
CE1 A:HIS756 3.2 17.5 1.0
CE1 A:HIS760 3.2 20.9 1.0
OE2 A:GLU771 3.3 28.7 1.0
N G:THR4 3.8 22.2 1.0
O1 A:TLA1102 4.0 30.7 1.0
O3 A:TLA1102 4.1 34.7 1.0
C3 A:TLA1102 4.1 32.2 1.0
CA G:THR4 4.2 22.2 1.0
CG A:HIS760 4.2 21.1 1.0
OE1 A:GLU757 4.2 17.9 1.0
ND1 A:HIS760 4.2 22.2 1.0
ND1 A:HIS756 4.3 17.9 1.0
CG A:HIS756 4.3 16.1 1.0
CG A:GLU771 4.4 23.2 1.0
O A:HOH1400 4.4 25.7 1.0
ND2 A:ASN774 4.5 18.4 1.0
OE2 A:GLU757 4.7 20.3 1.0
CB G:THR4 4.8 21.2 1.0
C4 A:TLA1102 4.8 37.0 1.0
CB A:GLU771 4.9 20.1 1.0
CD A:GLU757 4.9 17.4 1.0
CA A:GLU771 4.9 19.4 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: Wed Dec 16 06:27:04 2020

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