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Zinc in PDB 1yix: Crystal Structure of Ycfh, Tatd Homolog From Escherichia Coli K12, at 1.9 A Resolution

Protein crystallography data

The structure of Crystal Structure of Ycfh, Tatd Homolog From Escherichia Coli K12, at 1.9 A Resolution, PDB code: 1yix was solved by V.N.Malashkevich, D.F.Xiang, F.M.Raushel, S.C.Almo, S.K.Burley, New Yorksgx Research Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.87 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.387, 76.322, 80.738, 90.00, 92.30, 90.00
R / Rfree (%) 19.8 / 25.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ycfh, Tatd Homolog From Escherichia Coli K12, at 1.9 A Resolution (pdb code 1yix). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Ycfh, Tatd Homolog From Escherichia Coli K12, at 1.9 A Resolution, PDB code: 1yix:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1yix

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Zinc binding site 1 out of 4 in the Crystal Structure of Ycfh, Tatd Homolog From Escherichia Coli K12, at 1.9 A Resolution


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 Ycfh, Tatd Homolog From Escherichia Coli K12, at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:21.3
occ:1.00
NE2 A:HIS9 2.1 16.9 1.0
NE2 A:HIS7 2.1 16.1 1.0
OE1 A:GLU94 2.2 16.9 1.0
OD1 A:ASP205 2.4 21.1 1.0
CE1 A:HIS9 3.0 16.6 1.0
CD2 A:HIS7 3.0 13.1 1.0
CD2 A:HIS9 3.1 16.2 1.0
CE1 A:HIS7 3.2 14.6 1.0
CD A:GLU94 3.2 18.8 1.0
CG A:ASP205 3.4 24.2 1.0
ZN A:ZN604 3.4 24.5 1.0
OE2 A:GLU94 3.6 15.2 1.0
CE1 A:HIS155 3.6 15.9 1.0
OD2 A:ASP205 3.6 19.4 1.0
O A:HOH861 3.8 33.8 1.0
NE2 A:HIS155 3.9 19.9 1.0
ND1 A:HIS9 4.1 19.1 1.0
CG A:HIS9 4.2 15.1 1.0
CG A:HIS7 4.2 15.1 1.0
ND1 A:HIS7 4.3 16.8 1.0
ND1 A:HIS155 4.5 11.2 1.0
CG A:GLU94 4.5 19.7 1.0
CG1 A:VAL40 4.6 16.5 1.0
O A:HOH863 4.7 22.4 1.0
CB A:ASP205 4.7 17.0 1.0
CD2 A:HIS155 4.8 19.1 1.0
CB A:VAL40 5.0 17.3 1.0
CA A:ASP205 5.0 17.3 1.0

Zinc binding site 2 out of 4 in 1yix

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Zinc binding site 2 out of 4 in the Crystal Structure of Ycfh, Tatd Homolog From Escherichia Coli K12, at 1.9 A Resolution


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 Ycfh, Tatd Homolog From Escherichia Coli K12, at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn604

b:24.5
occ:1.00
OE2 A:GLU94 2.1 15.2 1.0
NE2 A:HIS155 2.1 19.9 1.0
ND1 A:HIS130 2.3 25.6 1.0
O A:HOH863 2.5 22.4 1.0
CE1 A:HIS155 2.9 15.9 1.0
CD A:GLU94 3.0 18.8 1.0
CG A:HIS130 3.2 23.1 1.0
CD2 A:HIS155 3.2 19.1 1.0
OE1 A:GLU94 3.3 16.9 1.0
CE1 A:HIS130 3.3 25.5 1.0
O A:HOH861 3.4 33.8 1.0
ZN A:ZN601 3.4 21.3 1.0
CB A:HIS130 3.4 20.3 1.0
ND1 A:HIS155 4.1 11.2 1.0
OD2 A:ASP205 4.1 19.4 1.0
CE1 A:HIS67 4.1 17.8 1.0
CG A:HIS155 4.2 16.4 1.0
NE2 A:HIS7 4.3 16.1 1.0
CA A:HIS130 4.3 18.0 1.0
CD2 A:HIS130 4.4 24.1 1.0
CG A:GLU94 4.4 19.7 1.0
NE2 A:HIS130 4.4 25.9 1.0
O A:HOH664 4.6 22.2 1.0
CE1 A:HIS7 4.6 14.6 1.0
OD1 A:ASP205 4.7 21.1 1.0
CG A:ASP205 4.7 24.2 1.0
ND1 A:HIS67 4.8 19.2 1.0
CB A:GLU94 5.0 18.3 1.0
NE2 A:HIS67 5.0 24.5 1.0

Zinc binding site 3 out of 4 in 1yix

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Zinc binding site 3 out of 4 in the Crystal Structure of Ycfh, Tatd Homolog From Escherichia Coli K12, at 1.9 A Resolution


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 Ycfh, Tatd Homolog From Escherichia Coli K12, at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:20.3
occ:1.00
NE2 B:HIS9 2.1 14.9 1.0
NE2 B:HIS7 2.1 19.1 1.0
OE1 B:GLU94 2.2 16.4 1.0
OD1 B:ASP205 2.5 18.3 1.0
CE1 B:HIS7 3.0 17.6 1.0
CE1 B:HIS9 3.0 12.4 1.0
CD B:GLU94 3.1 17.4 1.0
CD2 B:HIS9 3.1 12.4 1.0
CD2 B:HIS7 3.2 15.9 1.0
CG B:ASP205 3.4 23.0 1.0
ZN B:ZN603 3.4 24.3 1.0
OE2 B:GLU94 3.4 15.6 1.0
CE1 B:HIS155 3.5 12.8 1.0
OD2 B:ASP205 3.7 17.5 1.0
NE2 B:HIS155 3.7 15.5 1.0
O B:HOH662 4.0 20.3 1.0
ND1 B:HIS9 4.2 18.0 1.0
ND1 B:HIS7 4.2 16.5 1.0
CG B:HIS9 4.2 16.5 1.0
CG B:HIS7 4.3 14.6 1.0
ND1 B:HIS155 4.4 10.5 1.0
CG B:GLU94 4.5 17.4 1.0
CG1 B:VAL40 4.6 17.6 1.0
O B:HOH636 4.7 15.3 1.0
CB B:ASP205 4.7 17.3 1.0
CD2 B:HIS155 4.8 10.3 1.0
CB B:VAL40 4.9 17.2 1.0
O B:HOH779 4.9 38.4 1.0

Zinc binding site 4 out of 4 in 1yix

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Zinc binding site 4 out of 4 in the Crystal Structure of Ycfh, Tatd Homolog From Escherichia Coli K12, at 1.9 A Resolution


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 Ycfh, Tatd Homolog From Escherichia Coli K12, at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn603

b:24.3
occ:1.00
OE2 B:GLU94 2.0 15.6 1.0
NE2 B:HIS155 2.1 15.5 1.0
ND1 B:HIS130 2.2 16.5 1.0
O B:HOH636 2.4 15.3 1.0
CE1 B:HIS155 2.9 12.8 1.0
CG B:HIS130 3.1 16.3 1.0
CD B:GLU94 3.1 17.4 1.0
CE1 B:HIS130 3.2 20.2 1.0
CD2 B:HIS155 3.2 10.3 1.0
CB B:HIS130 3.3 16.2 1.0
ZN B:ZN602 3.4 20.3 1.0
OE1 B:GLU94 3.4 16.4 1.0
O B:HOH662 3.6 20.3 1.0
NE2 B:HIS67 4.0 18.9 1.0
ND1 B:HIS155 4.1 10.5 1.0
OD2 B:ASP205 4.1 17.5 1.0
CD2 B:HIS130 4.2 16.2 1.0
NE2 B:HIS130 4.2 19.0 1.0
CG B:HIS155 4.3 12.8 1.0
CA B:HIS130 4.3 14.0 1.0
CG B:GLU94 4.4 17.4 1.0
NE2 B:HIS7 4.5 19.1 1.0
CE1 B:HIS7 4.7 17.6 1.0
CD2 B:HIS67 4.7 17.1 1.0
OD1 B:ASP205 4.7 18.3 1.0
O B:HOH619 4.8 19.2 1.0
CG B:ASP205 4.8 23.0 1.0
CE1 B:HIS67 4.9 17.9 1.0
CB B:GLU94 4.9 19.1 1.0

Reference:

V.N.Malashkevich, D.F.Xiang, F.M.Raushel, S.C.Almo. Crystal Structure of Ycfh, Tatd Homolog From Escherichia Coli To Be Published.
Page generated: Wed Dec 16 03:14:29 2020

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