Zinc in PDB 6y4e: X-Ray Structure of the Zn-Dependent Receptor-Binding Domain of Proteus Mirabilis Mr/P Fimbrial Adhesin Mrph

Protein crystallography data

The structure of X-Ray Structure of the Zn-Dependent Receptor-Binding Domain of Proteus Mirabilis Mr/P Fimbrial Adhesin Mrph, PDB code: 6y4e was solved by S.D.Knight, W.Ubhayasekera, W.Jiang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.15 / 1.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 25.561, 53.139, 40.158, 90.00, 102.84, 90.00
R / Rfree (%) 10.7 / 12.8

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Structure of the Zn-Dependent Receptor-Binding Domain of Proteus Mirabilis Mr/P Fimbrial Adhesin Mrph (pdb code 6y4e). 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 X-Ray Structure of the Zn-Dependent Receptor-Binding Domain of Proteus Mirabilis Mr/P Fimbrial Adhesin Mrph, PDB code: 6y4e:

Zinc binding site 1 out of 1 in 6y4e

Go back to Zinc Binding Sites List in 6y4e
Zinc binding site 1 out of 1 in the X-Ray Structure of the Zn-Dependent Receptor-Binding Domain of Proteus Mirabilis Mr/P Fimbrial Adhesin Mrph


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of the Zn-Dependent Receptor-Binding Domain of Proteus Mirabilis Mr/P Fimbrial Adhesin Mrph within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:8.3
occ:1.00
O1 A:TLA202 2.0 9.9 1.0
ND1 A:HIS74 2.0 8.1 1.0
NE2 A:HIS72 2.0 7.9 1.0
ND1 A:HIS117 2.0 8.5 1.0
C1 A:TLA202 2.8 9.5 1.0
HA A:HIS117 2.9 11.6 1.0
CE1 A:HIS74 2.9 8.8 1.0
O11 A:TLA202 2.9 9.1 1.0
CE1 A:HIS117 3.0 8.6 1.0
CE1 A:HIS72 3.0 8.2 1.0
HE1 A:HIS74 3.0 10.5 1.0
CD2 A:HIS72 3.0 7.8 1.0
HE1 A:HIS117 3.1 10.4 1.0
CG A:HIS117 3.1 9.1 1.0
CG A:HIS74 3.1 8.2 1.0
HA A:HIS74 3.1 8.9 1.0
HE1 A:HIS72 3.2 9.9 1.0
HD2 A:HIS72 3.2 9.3 1.0
HB2 A:HIS74 3.3 9.8 1.0
HB2 A:HIS117 3.4 11.1 1.0
H A:ARG118 3.4 12.8 1.0
HA3 A:GLY81 3.5 9.7 1.0
CB A:HIS117 3.5 9.3 1.0
CA A:HIS117 3.6 9.7 1.0
CB A:HIS74 3.6 8.2 1.0
CA A:HIS74 3.8 7.4 1.0
N A:ARG118 4.0 10.7 1.0
NE2 A:HIS74 4.1 9.0 1.0
NE2 A:HIS117 4.1 9.6 1.0
ND1 A:HIS72 4.1 7.6 1.0
CG A:HIS72 4.2 7.7 1.0
CD2 A:HIS74 4.2 8.9 1.0
CD2 A:HIS117 4.2 9.6 1.0
C2 A:TLA202 4.2 14.6 1.0
C A:HIS117 4.2 10.4 1.0
HA2 A:GLY81 4.2 9.7 1.0
CA A:GLY81 4.3 8.1 1.0
O A:ARG118 4.4 11.7 1.0
O A:THR116 4.4 9.5 0.4
HB3 A:HIS117 4.5 11.1 1.0
H A:ASN82 4.5 9.5 1.0
HB3 A:HIS74 4.5 9.8 1.0
O3 A:TLA202 4.6 17.5 1.0
O2 A:TLA202 4.6 18.3 1.0
O A:HIS74 4.6 9.2 1.0
HA3 A:GLY119 4.6 14.6 1.0
C A:ARG118 4.7 11.3 1.0
HA A:TLA202 4.7 21.9 1.0
C A:HIS74 4.7 7.5 1.0
H2 A:TLA202 4.7 17.5 1.0
N A:HIS117 4.8 9.7 1.0
HD12 A:ILE140 4.8 12.3 1.0
O A:THR116 4.8 14.1 0.6
HE2 A:HIS74 4.8 10.8 1.0
N A:HIS74 4.8 7.4 1.0
HE2 A:HIS117 4.9 11.5 1.0
O A:LYS73 4.9 8.8 1.0
HD1 A:HIS72 4.9 9.1 1.0

Reference:

W.Jiang, W.Ubhayasekera, M.C.Breed, A.N.Norsworthy, N.Serr, H.L.T.Mobley, M.M.Pearson, S.D.Knight. Mrph, A New Class of Metal-Binding Adhesin, Requires Zinc to Mediate Biofilm Formation. Plos Pathog. V. 16 08707 2020.
ISSN: ESSN 1553-7374
PubMed: 32780778
DOI: 10.1371/JOURNAL.PPAT.1008707
Page generated: Wed Dec 16 13:14:17 2020

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