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Zinc in PDB 4dyu: The Crystal Structure of Dna Starvation/Stationary Phase Protection Protein Dps From Yersinia Pestis Kim 10

Protein crystallography data

The structure of The Crystal Structure of Dna Starvation/Stationary Phase Protection Protein Dps From Yersinia Pestis Kim 10, PDB code: 4dyu was solved by K.Tan, M.Gu, K.Kwon, W.F.Anderson, A.Joachimiak, Center For Structuralgenomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.19 / 2.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.414, 105.102, 191.834, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 26.9

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the The Crystal Structure of Dna Starvation/Stationary Phase Protection Protein Dps From Yersinia Pestis Kim 10 (pdb code 4dyu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the The Crystal Structure of Dna Starvation/Stationary Phase Protection Protein Dps From Yersinia Pestis Kim 10, PDB code: 4dyu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 4dyu

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Zinc binding site 1 out of 12 in the The Crystal Structure of Dna Starvation/Stationary Phase Protection Protein Dps From Yersinia Pestis Kim 10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Dna Starvation/Stationary Phase Protection Protein Dps From Yersinia Pestis Kim 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:81.6
occ:1.00
OD2 A:ASP78 2.2 52.9 1.0
OE2 A:GLU82 2.3 44.4 1.0
CE1 C:HIS51 3.0 25.7 1.0
O C:HOH303 3.3 19.7 1.0
CG A:ASP78 3.4 56.1 1.0
CD A:GLU82 3.5 42.5 1.0
ND1 C:HIS51 3.5 26.2 1.0
NE1 C:TRP52 4.0 25.5 1.0
CB A:ASP78 4.0 46.6 1.0
CG A:GLU82 4.1 40.5 1.0
NE2 C:HIS51 4.2 24.3 1.0
CD1 C:TRP52 4.3 27.8 1.0
NZ C:LYS48 4.3 40.8 1.0
OD1 A:ASP78 4.4 61.5 1.0
CE1 C:HIS63 4.5 34.0 1.0
OD1 C:ASP67 4.5 46.9 1.0
NE2 C:HIS63 4.5 31.5 1.0
OE1 A:GLU82 4.6 39.6 1.0
OD2 C:ASP67 4.7 54.9 1.0
CG C:HIS51 4.9 26.9 1.0
CA A:ASP78 4.9 41.0 1.0
O A:ASP78 4.9 28.9 1.0
CG C:ASP67 5.0 48.7 1.0

Zinc binding site 2 out of 12 in 4dyu

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Zinc binding site 2 out of 12 in the The Crystal Structure of Dna Starvation/Stationary Phase Protection Protein Dps From Yersinia Pestis Kim 10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of Dna Starvation/Stationary Phase Protection Protein Dps From Yersinia Pestis Kim 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:81.1
occ:1.00
OE2 B:GLU82 2.2 36.3 1.0
OD1 B:ASP78 2.3 65.1 1.0
NE2 D:HIS51 2.8 32.2 1.0
CG B:ASP78 3.0 60.0 1.0
CE1 D:HIS51 3.3 27.3 1.0
CD B:GLU82 3.4 38.4 1.0
OD2 B:ASP78 3.5 59.5 1.0
OD2 D:ASP67 3.7 47.8 1.0
NZ D:LYS48 3.9 43.5 1.0
CB B:ASP78 4.1 48.5 1.0
CD2 D:HIS51 4.1 34.5 1.0
OE1 B:GLU82 4.2 40.5 1.0
CG B:GLU82 4.3 35.1 1.0
OD1 D:ASP67 4.4 52.5 1.0
CG D:ASP67 4.4 43.0 1.0
O B:HOH308 4.5 53.4 1.0
NE2 D:HIS63 4.5 27.4 1.0
NE1 D:TRP52 4.5 27.4 1.0
ND1 D:HIS51 4.6 29.3 1.0
CE D:LYS48 4.6 38.1 1.0
CE1 D:HIS63 4.7 28.8 1.0
CD1 D:TRP52 4.8 35.4 1.0
O B:ASP78 4.9 35.4 1.0
CA B:ASP78 4.9 35.8 1.0

Zinc binding site 3 out of 12 in 4dyu

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Zinc binding site 3 out of 12 in the The Crystal Structure of Dna Starvation/Stationary Phase Protection Protein Dps From Yersinia Pestis Kim 10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of Dna Starvation/Stationary Phase Protection Protein Dps From Yersinia Pestis Kim 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:73.4
occ:1.00
OE2 C:GLU82 2.5 50.1 1.0
OD2 C:ASP78 2.5 55.9 1.0
NE2 A:HIS51 2.6 29.8 1.0
OD1 C:ASP78 2.8 55.5 1.0
CG C:ASP78 3.0 51.6 1.0
CE1 A:HIS51 3.1 21.4 1.0
CD C:GLU82 3.3 51.1 1.0
OD2 A:ASP67 3.5 38.4 1.0
OE1 C:GLU82 3.8 46.8 1.0
CD2 A:HIS51 3.8 33.3 1.0
NE2 A:HIS63 3.8 44.8 1.0
NZ A:LYS48 3.9 33.2 1.0
CE1 A:HIS63 3.9 44.9 1.0
CG A:ASP67 4.3 36.9 1.0
ND1 A:HIS51 4.3 26.3 1.0
OD1 A:ASP67 4.3 47.0 1.0
CG C:GLU82 4.4 47.5 1.0
CB C:ASP78 4.4 42.0 1.0
NE1 A:TRP52 4.6 32.5 1.0
CD1 A:TRP52 4.6 35.4 1.0
CG A:HIS51 4.7 29.9 1.0
CD2 A:HIS63 4.9 40.3 1.0
CE A:LYS48 5.0 38.3 1.0

Zinc binding site 4 out of 12 in 4dyu

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Zinc binding site 4 out of 12 in the The Crystal Structure of Dna Starvation/Stationary Phase Protection Protein Dps From Yersinia Pestis Kim 10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of Dna Starvation/Stationary Phase Protection Protein Dps From Yersinia Pestis Kim 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:68.7
occ:1.00
OE2 D:GLU82 2.2 33.6 1.0
OD2 D:ASP78 2.3 48.7 1.0
NE2 B:HIS51 2.5 22.6 1.0
CG D:ASP78 3.1 43.9 1.0
O D:HOH301 3.3 31.2 1.0
OD1 D:ASP78 3.3 51.0 1.0
CD2 B:HIS51 3.3 22.1 1.0
CD D:GLU82 3.4 37.9 1.0
CE1 B:HIS51 3.5 26.7 1.0
OD2 B:ASP67 3.9 56.9 1.0
NE2 B:HIS63 4.1 42.3 1.0
NZ B:LYS48 4.1 42.3 1.0
OE1 D:GLU82 4.1 38.1 1.0
CG D:GLU82 4.3 33.3 1.0
NE1 B:TRP52 4.4 27.4 1.0
OD1 B:ASP67 4.4 54.5 1.0
CB D:ASP78 4.5 30.3 1.0
CG B:HIS51 4.5 25.9 1.0
CD1 B:TRP52 4.5 24.9 1.0
CG B:ASP67 4.6 49.4 1.0
ND1 B:HIS51 4.6 29.6 1.0
CE1 B:HIS63 4.6 41.0 1.0
CD2 B:HIS63 5.0 40.6 1.0
O D:ASP78 5.0 27.4 1.0

Zinc binding site 5 out of 12 in 4dyu

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Zinc binding site 5 out of 12 in the The Crystal Structure of Dna Starvation/Stationary Phase Protection Protein Dps From Yersinia Pestis Kim 10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Crystal Structure of Dna Starvation/Stationary Phase Protection Protein Dps From Yersinia Pestis Kim 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn201

b:73.7
occ:1.00
CE1 G:HIS51 2.3 17.4 1.0
OD1 E:ASP78 2.5 55.6 1.0
OE2 E:GLU82 2.5 35.5 1.0
OD2 E:ASP78 2.6 62.3 1.0
CG E:ASP78 2.9 52.7 1.0
ND1 G:HIS51 3.3 16.2 1.0
NE2 G:HIS51 3.3 21.9 1.0
CD E:GLU82 3.4 32.0 1.0
OD2 G:ASP67 3.6 40.1 1.0
OE1 E:GLU82 4.1 30.4 1.0
NZ G:LYS48 4.1 38.1 1.0
CG E:GLU82 4.1 21.1 1.0
NE2 G:HIS63 4.2 22.8 1.0
NE1 G:TRP52 4.3 39.8 1.0
OD1 G:ASP67 4.3 49.9 1.0
CE1 G:HIS63 4.3 31.9 1.0
CG G:ASP67 4.4 42.4 1.0
CB E:ASP78 4.4 35.8 1.0
CD2 G:HIS51 4.5 25.8 1.0
CG G:HIS51 4.5 21.8 1.0
CD1 G:TRP52 4.5 40.1 1.0
CE G:LYS48 4.6 33.3 1.0
O E:ASP78 4.9 20.5 1.0

Zinc binding site 6 out of 12 in 4dyu

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Zinc binding site 6 out of 12 in the The Crystal Structure of Dna Starvation/Stationary Phase Protection Protein Dps From Yersinia Pestis Kim 10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Crystal Structure of Dna Starvation/Stationary Phase Protection Protein Dps From Yersinia Pestis Kim 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn202

b:72.2
occ:1.00
OE2 G:GLU82 2.4 61.9 1.0
NE2 E:HIS51 2.6 44.3 1.0
O E:HOH311 2.6 22.1 1.0
O G:HOH312 2.7 28.1 1.0
OD2 G:ASP78 2.8 56.4 1.0
CD2 E:HIS51 3.4 37.8 1.0
CD G:GLU82 3.5 55.0 1.0
CE1 E:HIS51 3.6 43.9 1.0
OD2 E:ASP67 3.9 54.9 1.0
NE2 E:HIS63 3.9 21.0 1.0
CG G:ASP78 3.9 46.5 1.0
NZ E:LYS48 4.0 35.1 1.0
OE1 G:GLU82 4.4 51.9 1.0
CG G:GLU82 4.4 42.6 1.0
CB G:ASP78 4.4 33.6 1.0
CE1 E:HIS63 4.4 18.9 1.0
CG E:HIS51 4.6 39.5 1.0
ND1 E:HIS51 4.7 41.7 1.0
CG E:ASP67 4.7 48.7 1.0
OD1 E:ASP67 4.8 50.6 1.0
NE1 E:TRP52 4.9 26.3 1.0
CD1 E:TRP52 4.9 26.7 1.0
OD1 G:ASP78 4.9 47.5 1.0
CD2 E:HIS63 4.9 26.5 1.0

Zinc binding site 7 out of 12 in 4dyu

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Zinc binding site 7 out of 12 in the The Crystal Structure of Dna Starvation/Stationary Phase Protection Protein Dps From Yersinia Pestis Kim 10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Crystal Structure of Dna Starvation/Stationary Phase Protection Protein Dps From Yersinia Pestis Kim 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn201

b:71.6
occ:1.00
OE2 F:GLU82 2.3 65.3 1.0
NE2 H:HIS51 2.6 27.5 1.0
OD1 F:ASP78 2.7 47.5 1.0
OD2 F:ASP78 2.7 42.9 1.0
CG F:ASP78 3.1 44.2 1.0
CD F:GLU82 3.3 64.0 1.0
CE1 H:HIS51 3.3 20.2 1.0
CG F:GLU82 3.6 61.2 1.0
CD2 H:HIS51 3.7 31.5 1.0
NE2 H:HIS63 3.9 31.5 1.0
CE1 H:HIS63 4.0 35.5 1.0
OD2 H:ASP67 4.1 36.0 1.0
NZ H:LYS48 4.3 24.8 1.0
CD1 H:TRP52 4.4 34.9 1.0
OE1 F:GLU82 4.4 61.2 1.0
NE1 H:TRP52 4.4 36.1 1.0
ND1 H:HIS51 4.5 30.7 1.0
CB F:ASP78 4.6 36.7 1.0
CG H:HIS51 4.8 32.5 1.0
OD1 H:ASP67 4.8 46.8 1.0
CG H:ASP67 4.8 41.8 1.0
O F:ASP78 4.9 27.5 1.0

Zinc binding site 8 out of 12 in 4dyu

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Zinc binding site 8 out of 12 in the The Crystal Structure of Dna Starvation/Stationary Phase Protection Protein Dps From Yersinia Pestis Kim 10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Crystal Structure of Dna Starvation/Stationary Phase Protection Protein Dps From Yersinia Pestis Kim 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn201

b:81.9
occ:1.00
OD2 H:ASP78 2.3 47.9 1.0
OE2 H:GLU82 2.4 36.9 1.0
NE2 F:HIS51 2.6 44.1 1.0
OD1 H:ASP78 2.8 54.4 1.0
CG H:ASP78 2.9 44.6 1.0
CD2 F:HIS51 3.1 41.2 1.0
CD H:GLU82 3.2 43.3 1.0
O H:HOH311 3.3 19.2 1.0
NZ F:LYS48 3.4 34.4 1.0
OE1 H:GLU82 3.7 39.7 1.0
OD2 F:ASP67 3.8 41.4 1.0
CE1 F:HIS51 3.8 42.7 1.0
O H:HOH312 3.9 25.3 1.0
OD1 F:ASP67 4.2 47.0 1.0
NE2 F:HIS63 4.2 38.2 1.0
CG H:GLU82 4.3 14.1 1.0
NE1 F:TRP52 4.3 41.5 1.0
CG F:HIS51 4.4 45.6 1.0
CG F:ASP67 4.4 42.3 1.0
CB H:ASP78 4.4 27.2 1.0
O H:HOH313 4.5 26.8 1.0
CE1 F:HIS63 4.5 38.4 1.0
CD1 F:TRP52 4.6 42.9 1.0
ND1 F:HIS51 4.7 44.0 1.0
CE F:LYS48 4.8 34.1 1.0

Zinc binding site 9 out of 12 in 4dyu

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Zinc binding site 9 out of 12 in the The Crystal Structure of Dna Starvation/Stationary Phase Protection Protein Dps From Yersinia Pestis Kim 10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The Crystal Structure of Dna Starvation/Stationary Phase Protection Protein Dps From Yersinia Pestis Kim 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:82.8
occ:1.00
OD1 I:ASP78 2.3 67.0 1.0
NE2 K:HIS51 2.4 31.7 1.0
OE2 I:GLU82 2.7 39.6 1.0
CD2 K:HIS51 3.2 30.9 1.0
CD I:GLU82 3.3 34.2 1.0
CG I:ASP78 3.3 61.4 1.0
CE1 K:HIS51 3.5 24.9 1.0
CG I:GLU82 3.8 27.8 1.0
CB I:ASP78 3.8 48.6 1.0
NE1 K:TRP52 3.9 24.4 1.0
OD2 K:ASP67 3.9 49.1 1.0
OE1 I:GLU82 4.0 37.4 1.0
CD1 K:TRP52 4.1 28.3 1.0
OD2 I:ASP78 4.3 62.8 1.0
CE K:LYS48 4.4 16.3 1.0
CG K:HIS51 4.4 31.6 1.0
NE2 K:HIS63 4.4 30.9 1.0
NZ K:LYS48 4.5 15.4 1.0
CE1 K:HIS63 4.5 27.3 1.0
ND1 K:HIS51 4.5 23.2 1.0
OD1 K:ASP67 4.6 46.0 1.0
O I:ASP78 4.7 35.5 1.0
CG K:ASP67 4.7 43.7 1.0
CA I:ASP78 4.7 37.0 1.0
C I:ASP78 5.0 35.0 1.0

Zinc binding site 10 out of 12 in 4dyu

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Zinc binding site 10 out of 12 in the The Crystal Structure of Dna Starvation/Stationary Phase Protection Protein Dps From Yersinia Pestis Kim 10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of The Crystal Structure of Dna Starvation/Stationary Phase Protection Protein Dps From Yersinia Pestis Kim 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn201

b:98.5
occ:1.00
OE2 J:GLU82 2.1 32.6 1.0
OD2 J:ASP78 2.6 64.5 1.0
OD1 J:ASP78 2.6 73.7 1.0
NE2 L:HIS51 2.7 42.0 1.0
CG J:ASP78 3.0 63.8 1.0
CD J:GLU82 3.2 37.8 1.0
OD2 L:ASP67 3.4 47.4 1.0
O C:HOH313 3.4 22.5 1.0
CD2 L:HIS51 3.6 37.4 1.0
CE1 L:HIS51 3.6 41.9 1.0
OE1 J:GLU82 3.7 42.6 1.0
NZ L:LYS48 3.9 30.3 1.0
CG L:ASP67 4.3 44.6 1.0
CG J:GLU82 4.4 32.6 1.0
CE1 L:HIS63 4.4 29.4 1.0
OD1 L:ASP67 4.4 42.3 1.0
CB J:ASP78 4.5 48.5 1.0
NE2 L:HIS63 4.7 30.4 1.0
ND1 L:HIS51 4.7 41.3 1.0
CG L:HIS51 4.7 37.2 1.0
NE1 L:TRP52 4.9 44.8 1.0
CD1 L:TRP52 5.0 44.5 1.0

Reference:

K.Tan, M.Gu, K.Kwon, W.F.Anderson, A.Joachimiak. The Crystal Structure of Dna Starvation/Stationary Phase Protection Protein Dps From Yersinia Pestis Kim 10 To Be Published.
Page generated: Wed Dec 16 05:15:19 2020

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