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Zinc in PDB 5uyw: Yfea Ancillary Sites That Co-Load with Site 2

Protein crystallography data

The structure of Yfea Ancillary Sites That Co-Load with Site 2, PDB code: 5uyw was solved by C.D.Radka, L.J.Delucas, S.G.Aller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.14 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.277, 66.358, 67.086, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 22.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Yfea Ancillary Sites That Co-Load with Site 2 (pdb code 5uyw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Yfea Ancillary Sites That Co-Load with Site 2, PDB code: 5uyw:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5uyw

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Zinc binding site 1 out of 6 in the Yfea Ancillary Sites That Co-Load with Site 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Yfea Ancillary Sites That Co-Load with Site 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:27.2
occ:1.00
OD2 A:ASP282 2.1 21.6 1.0
NE2 A:HIS76 2.1 19.6 1.0
NE2 A:HIS141 2.1 20.4 1.0
OE1 A:GLU207 2.2 17.1 1.0
OE2 A:GLU207 2.6 17.9 1.0
CD A:GLU207 2.7 18.7 1.0
OD1 A:ASP282 2.7 21.1 1.0
CG A:ASP282 2.7 22.3 1.0
CE1 A:HIS76 3.0 17.0 1.0
CE1 A:HIS141 3.1 18.6 1.0
CD2 A:HIS76 3.1 18.3 1.0
CD2 A:HIS141 3.1 16.9 1.0
ND2 A:ASN228 3.9 23.3 1.0
ND1 A:HIS76 4.1 18.8 1.0
ND1 A:HIS141 4.2 18.0 1.0
CG A:GLU207 4.2 25.1 1.0
CB A:ASP282 4.2 19.9 1.0
O A:HOH552 4.2 31.4 1.0
CG A:HIS76 4.2 20.8 1.0
CG A:HIS141 4.3 17.6 1.0
CB A:ALA209 4.3 16.8 1.0
CG A:ASN228 4.3 24.3 1.0
O A:HOH532 4.4 22.1 1.0
OD1 A:ASN228 4.7 25.2 1.0
CB A:ASN228 4.9 22.2 1.0
CD1 A:LEU101 5.0 16.6 1.0

Zinc binding site 2 out of 6 in 5uyw

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Zinc binding site 2 out of 6 in the Yfea Ancillary Sites That Co-Load with Site 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Yfea Ancillary Sites That Co-Load with Site 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:47.0
occ:1.00
NE2 A:HIS163 2.0 28.4 1.0
O A:HOH648 2.2 23.1 1.0
O A:HOH659 2.7 41.3 1.0
O A:HOH676 2.7 50.3 1.0
CE1 A:HIS163 2.8 27.5 1.0
CD2 A:HIS163 3.1 29.1 1.0
ND1 A:HIS163 4.0 30.0 1.0
CG A:HIS163 4.1 31.3 1.0
CG A:GLU162 4.3 41.9 1.0
CB A:PRO116 4.6 23.3 1.0
O A:HOH667 4.8 34.8 1.0
CB A:GLU162 4.8 36.5 1.0

Zinc binding site 3 out of 6 in 5uyw

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Zinc binding site 3 out of 6 in the Yfea Ancillary Sites That Co-Load with Site 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Yfea Ancillary Sites That Co-Load with Site 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:0.2
occ:1.00
NE2 A:HIS167 2.3 51.5 1.0
CE1 A:HIS167 3.2 52.2 1.0
CD2 A:HIS167 3.3 48.7 1.0
ND1 A:HIS167 4.3 48.3 1.0
CG A:HIS167 4.4 46.1 1.0
CG2 A:THR38 4.7 77.5 1.0

Zinc binding site 4 out of 6 in 5uyw

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Zinc binding site 4 out of 6 in the Yfea Ancillary Sites That Co-Load with Site 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Yfea Ancillary Sites That Co-Load with Site 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:0.4
occ:1.00
O A:HOH631 1.9 39.3 1.0
OE1 A:GLU131 2.6 61.6 1.0
NE2 A:GLN237 2.6 61.8 1.0
OE2 A:GLU131 2.7 57.9 1.0
CD A:GLU131 3.0 58.2 1.0
O A:HOH640 3.1 51.0 1.0
CD A:GLN237 3.6 67.4 1.0
CD2 A:HIS240 3.8 76.2 1.0
OE1 A:GLN237 3.8 73.2 1.0
NE2 A:HIS240 4.1 77.6 1.0
CG A:GLU131 4.5 46.2 1.0
O A:TYR223 4.6 33.4 1.0
CE1 A:TYR223 4.6 39.0 1.0
CD1 A:ILE244 4.9 68.4 1.0
CZ A:TYR223 4.9 39.7 1.0
CG A:GLN237 5.0 56.3 1.0
CG A:HIS240 5.0 76.4 1.0

Zinc binding site 5 out of 6 in 5uyw

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Zinc binding site 5 out of 6 in the Yfea Ancillary Sites That Co-Load with Site 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Yfea Ancillary Sites That Co-Load with Site 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:0.1
occ:1.00
OE1 A:GLU169 2.9 67.2 1.0
CD A:GLU169 4.1 67.9 1.0
OE2 A:GLU169 4.5 69.5 1.0
NH1 A:ARG173 4.7 53.6 1.0

Zinc binding site 6 out of 6 in 5uyw

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Zinc binding site 6 out of 6 in the Yfea Ancillary Sites That Co-Load with Site 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Yfea Ancillary Sites That Co-Load with Site 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:92.9
occ:1.00
CE1 A:HIS167 3.0 52.2 1.0
OD1 A:ASP164 3.1 44.5 1.0
ND1 A:HIS167 3.2 48.3 1.0
OD2 A:ASP164 3.5 36.2 1.0
CG A:ASP164 3.7 39.7 1.0
CB A:PHE42 4.1 32.0 1.0
NE2 A:HIS167 4.3 51.5 1.0
N A:PHE42 4.4 34.5 1.0
O A:HOH531 4.5 42.5 1.0
CG A:HIS167 4.5 46.1 1.0
O A:VAL62 4.8 43.8 1.0
CA A:PHE42 4.8 34.6 1.0
CG A:PHE42 5.0 29.4 1.0

Reference:

C.D.Radka, L.J.Delucas, L.S.Wilson, M.B.Lawrenz, R.D.Perry, S.G.Aller. Crystal Structure of Yersinia Pestis Virulence Factor Yfea Reveals Two Polyspecific Metal-Binding Sites. Acta Crystallogr D Struct V. 73 557 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 28695856
DOI: 10.1107/S2059798317006349
Page generated: Wed Dec 16 11:07:32 2020

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