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Zinc in PDB 1xvx: Crystal Structure of Iron-Loaded Yersinia Enterocolitica Yfua

Protein crystallography data

The structure of Crystal Structure of Iron-Loaded Yersinia Enterocolitica Yfua, PDB code: 1xvx was solved by S.R.Shouldice, D.E.Mcree, D.R.Dougan, L.W.Tari, A.B.Schryvers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.86 / 1.53
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 108.392, 46.951, 62.454, 90.00, 103.51, 90.00
R / Rfree (%) 16.1 / 19.3

Other elements in 1xvx:

The structure of Crystal Structure of Iron-Loaded Yersinia Enterocolitica Yfua also contains other interesting chemical elements:

Iron (Fe) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Iron-Loaded Yersinia Enterocolitica Yfua (pdb code 1xvx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Iron-Loaded Yersinia Enterocolitica Yfua, PDB code: 1xvx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 1xvx

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Zinc binding site 1 out of 5 in the Crystal Structure of Iron-Loaded Yersinia Enterocolitica Yfua


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Iron-Loaded Yersinia Enterocolitica Yfua within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn314

b:24.0
occ:1.00
OE2 A:GLU42 2.0 16.1 1.0
CD A:GLU42 2.7 15.4 1.0
OE1 A:GLU42 2.7 18.7 1.0
O A:HOH546 2.9 34.4 1.0
CG A:GLU42 4.1 14.5 1.0
N A:GLY39 4.2 15.8 1.0
CA A:GLY38 4.3 16.3 1.0
O A:HOH777 4.4 39.5 1.0
O A:HOH505 4.7 20.9 1.0
C A:GLY38 4.7 15.9 1.0

Zinc binding site 2 out of 5 in 1xvx

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Zinc binding site 2 out of 5 in the Crystal Structure of Iron-Loaded Yersinia Enterocolitica Yfua


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Iron-Loaded Yersinia Enterocolitica Yfua within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn315

b:15.1
occ:1.00
O A:HOH615 2.1 9.4 1.0
O A:HOH616 2.1 9.7 1.0
O A:HOH614 2.1 10.7 1.0
OD2 A:ASP191 2.2 12.6 1.0
OD1 A:ASP191 2.3 12.0 1.0
O3 A:CO3319 2.3 10.1 1.0
CG A:ASP191 2.6 12.4 1.0
C A:CO3319 3.3 14.9 1.0
O2 A:CO3319 3.5 14.5 1.0
CB A:ASP191 4.1 12.6 1.0
O A:HOH659 4.1 36.0 1.0
NE A:ARG135 4.1 10.7 1.0
O A:HOH431 4.1 8.1 1.0
O A:LYS114 4.2 13.5 1.0
O1 A:CO3319 4.3 16.0 1.0
NZ A:LYS114 4.5 23.3 1.0
CG A:ARG135 4.7 11.4 1.0
CE A:LYS114 4.7 23.3 1.0
NH2 A:ARG135 4.7 13.5 1.0
CD A:ARG135 4.8 10.5 1.0
CZ A:ARG135 4.9 12.5 1.0
CA A:ASP191 4.9 12.1 1.0

Zinc binding site 3 out of 5 in 1xvx

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Zinc binding site 3 out of 5 in the Crystal Structure of Iron-Loaded Yersinia Enterocolitica Yfua


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Iron-Loaded Yersinia Enterocolitica Yfua within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn316

b:26.5
occ:1.00
ND1 A:HIS217 2.1 18.5 1.0
OE2 A:GLU117 2.3 23.3 1.0
OE1 A:GLU117 2.4 25.5 1.0
O A:HOH484 2.5 14.2 1.0
CD A:GLU117 2.7 22.9 1.0
O A:HOH597 2.9 18.8 1.0
CE1 A:HIS217 3.0 19.3 1.0
CG A:HIS217 3.2 15.8 1.0
CB A:HIS217 3.7 13.6 1.0
CA A:HIS217 3.8 12.9 1.0
NE2 A:HIS217 4.1 18.9 1.0
CG A:GLU117 4.2 19.4 1.0
CD2 A:HIS217 4.3 17.7 1.0
N A:TYR218 4.4 12.2 1.0
CD1 A:LEU120 4.4 16.2 1.0
C A:HIS217 4.6 12.6 1.0
O A:LEU216 4.6 13.4 1.0
O A:HOH756 4.8 32.6 1.0
O A:TYR218 4.9 12.7 1.0
N A:HIS217 4.9 12.2 1.0

Zinc binding site 4 out of 5 in 1xvx

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Zinc binding site 4 out of 5 in the Crystal Structure of Iron-Loaded Yersinia Enterocolitica Yfua


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Iron-Loaded Yersinia Enterocolitica Yfua within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn317

b:13.2
occ:1.00
OD2 A:ASP4 2.0 14.3 1.0
OE1 A:GLU244 2.0 12.7 1.0
ND1 A:HIS241 2.0 11.0 1.0
CG A:ASP4 2.8 14.5 1.0
CD A:GLU244 2.8 12.0 1.0
OE2 A:GLU244 2.9 14.4 1.0
OD1 A:ASP4 2.9 14.7 1.0
CE1 A:HIS241 3.0 12.4 1.0
CG A:HIS241 3.1 11.9 1.0
CB A:HIS241 3.4 12.2 1.0
CA A:HIS241 4.0 11.9 1.0
NE2 A:HIS241 4.1 13.1 1.0
CD2 A:HIS241 4.2 13.4 1.0
CB A:ASP4 4.2 15.8 1.0
CG A:GLU244 4.2 10.7 1.0
O A:HOH365 4.4 18.6 1.0
O A:HOH506 4.5 18.7 1.0
O A:GLY6 4.7 13.3 1.0
CB A:GLU244 4.7 11.8 1.0
O A:LYS240 4.8 11.6 1.0
O A:HOH470 4.8 10.9 1.0
N A:GLY6 4.9 14.2 1.0

Zinc binding site 5 out of 5 in 1xvx

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Zinc binding site 5 out of 5 in the Crystal Structure of Iron-Loaded Yersinia Enterocolitica Yfua


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Iron-Loaded Yersinia Enterocolitica Yfua within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn318

b:23.9
occ:1.00
ND1 A:HIS221 2.1 14.6 1.0
O A:HOH487 2.2 12.6 0.5
O A:HOH728 2.2 23.4 1.0
CE1 A:HIS221 3.0 15.5 1.0
CG A:HIS221 3.2 13.6 1.0
CB A:HIS221 3.5 12.7 1.0
O A:HOH322 3.9 6.8 0.5
NE2 A:HIS221 4.2 14.8 1.0
CA A:HIS221 4.3 12.4 1.0
CD2 A:HIS221 4.3 14.6 1.0
O A:HOH323 4.3 33.4 1.0
O A:HOH603 4.6 17.7 1.0
O A:HIS221 4.6 12.1 1.0
O A:HOH632 4.9 10.0 0.5
C A:HIS221 5.0 12.0 1.0

Reference:

S.R.Shouldice, D.E.Mcree, D.R.Dougan, L.W.Tari, A.B.Schryvers. Novel Anion-Independent Iron Coordination By Members of A Third Class of Bacterial Periplasmic Ferric Ion-Binding Proteins J.Biol.Chem. V. 280 5820 2005.
ISSN: ISSN 0021-9258
PubMed: 15576371
DOI: 10.1074/JBC.M411238200
Page generated: Wed Dec 16 03:13:18 2020

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