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Zinc in PDB 3s6l: Crystal Structure of A Yada-Like Head Domain of the Trimeric Autotransporter Adhesin Boaa From Burkholderia Pseudomallei Solved By Iodide Ion Sad Phasing

Protein crystallography data

The structure of Crystal Structure of A Yada-Like Head Domain of the Trimeric Autotransporter Adhesin Boaa From Burkholderia Pseudomallei Solved By Iodide Ion Sad Phasing, PDB code: 3s6l was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.30
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 144.000, 144.000, 144.000, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 20.7

Other elements in 3s6l:

The structure of Crystal Structure of A Yada-Like Head Domain of the Trimeric Autotransporter Adhesin Boaa From Burkholderia Pseudomallei Solved By Iodide Ion Sad Phasing also contains other interesting chemical elements:

Iodine (I) 53 atoms
Chlorine (Cl) 25 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of A Yada-Like Head Domain of the Trimeric Autotransporter Adhesin Boaa From Burkholderia Pseudomallei Solved By Iodide Ion Sad Phasing (pdb code 3s6l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 17 binding sites of Zinc where determined in the Crystal Structure of A Yada-Like Head Domain of the Trimeric Autotransporter Adhesin Boaa From Burkholderia Pseudomallei Solved By Iodide Ion Sad Phasing, PDB code: 3s6l:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 17 in 3s6l

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Zinc binding site 1 out of 17 in the Crystal Structure of A Yada-Like Head Domain of the Trimeric Autotransporter Adhesin Boaa From Burkholderia Pseudomallei Solved By Iodide Ion Sad Phasing


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 A Yada-Like Head Domain of the Trimeric Autotransporter Adhesin Boaa From Burkholderia Pseudomallei Solved By Iodide Ion Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn185

b:37.2
occ:1.00
NE2 A:HIS59 2.1 28.6 1.0
OD2 A:ASP45 2.3 31.2 1.0
O A:HOH223 2.3 21.3 1.0
O A:HOH224 2.4 15.6 1.0
O A:HOH225 2.7 29.3 1.0
CD2 A:HIS59 3.1 25.6 1.0
CE1 A:HIS59 3.1 28.9 1.0
CG A:ASP45 3.3 27.0 1.0
O A:HOH227 4.0 28.4 1.0
O B:HOH237 4.1 15.6 1.0
OD1 A:ASP45 4.1 29.7 1.0
CB A:ASP45 4.2 23.6 1.0
ND1 A:HIS59 4.2 27.2 1.0
CG A:HIS59 4.2 24.6 1.0
OG1 A:THR44 4.8 31.9 1.0
O A:HOH267 4.9 27.2 1.0

Zinc binding site 2 out of 17 in 3s6l

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Zinc binding site 2 out of 17 in the Crystal Structure of A Yada-Like Head Domain of the Trimeric Autotransporter Adhesin Boaa From Burkholderia Pseudomallei Solved By Iodide Ion Sad Phasing


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 A Yada-Like Head Domain of the Trimeric Autotransporter Adhesin Boaa From Burkholderia Pseudomallei Solved By Iodide Ion Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn186

b:46.8
occ:1.00
NE2 A:HIS108 2.1 27.7 1.0
OE1 A:GLN93 2.1 24.6 1.0
CE1 A:HIS108 2.9 26.3 1.0
I E:IOD176 2.9 47.0 0.5
CD A:GLN93 3.0 22.6 1.0
CD2 A:HIS108 3.2 22.6 1.0
NE2 A:GLN93 3.3 18.3 1.0
NH1 E:ARG136 3.9 45.0 1.0
ND1 A:HIS108 4.1 24.5 1.0
CZ E:ARG136 4.1 46.5 1.0
CG A:HIS108 4.3 22.3 1.0
NH2 E:ARG136 4.3 47.1 1.0
CG A:GLN93 4.4 18.7 1.0
NE E:ARG136 4.6 41.7 1.0
CA C:GLY73 4.9 22.5 1.0
CB A:GLN93 4.9 18.0 1.0
O C:HOH203 4.9 13.4 1.0

Zinc binding site 3 out of 17 in 3s6l

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Zinc binding site 3 out of 17 in the Crystal Structure of A Yada-Like Head Domain of the Trimeric Autotransporter Adhesin Boaa From Burkholderia Pseudomallei Solved By Iodide Ion Sad Phasing


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 A Yada-Like Head Domain of the Trimeric Autotransporter Adhesin Boaa From Burkholderia Pseudomallei Solved By Iodide Ion Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn187

b:63.6
occ:1.00
NE2 A:HIS138 2.1 36.7 1.0
NE2 E:HIS138 2.2 38.4 1.0
O E:HOH284 2.5 32.8 1.0
CE1 A:HIS138 2.8 36.3 1.0
O A:HOH238 2.9 19.8 1.0
CE1 E:HIS138 3.0 36.5 1.0
O E:HOH228 3.0 2.0 1.0
CD2 E:HIS138 3.1 32.1 1.0
CD2 A:HIS138 3.3 32.7 1.0
O E:HOH229 3.4 26.7 1.0
ND1 A:HIS138 4.0 34.0 1.0
ND1 E:HIS138 4.0 33.4 1.0
CG E:HIS138 4.1 31.1 1.0
CG A:HIS138 4.3 31.3 1.0

Zinc binding site 4 out of 17 in 3s6l

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Zinc binding site 4 out of 17 in the Crystal Structure of A Yada-Like Head Domain of the Trimeric Autotransporter Adhesin Boaa From Burkholderia Pseudomallei Solved By Iodide Ion Sad Phasing


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 A Yada-Like Head Domain of the Trimeric Autotransporter Adhesin Boaa From Burkholderia Pseudomallei Solved By Iodide Ion Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn188

b:62.0
occ:0.56
O A:HOH194 2.1 14.2 1.0
OD1 A:ASP101 2.4 27.3 1.0
O A:HOH232 3.1 33.3 1.0
CG A:ASP101 3.1 26.2 1.0
I D:IOD182 3.1 50.5 0.3
OD2 A:ASP101 3.1 34.1 1.0
O B:HOH242 3.6 38.8 1.0
O A:ASP86 3.9 22.3 1.0
CG2 A:THR100 4.2 24.5 1.0
C A:ASP86 4.2 21.6 1.0
CA A:GLY87 4.2 20.2 1.0
I A:IOD174 4.3 38.8 0.5
N A:GLY87 4.4 21.0 1.0
CB A:ASP101 4.4 23.3 1.0
N A:ASP101 4.7 22.6 1.0
CB A:ASP86 4.7 23.0 1.0
CA A:ASP101 4.8 22.0 1.0

Zinc binding site 5 out of 17 in 3s6l

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Zinc binding site 5 out of 17 in the Crystal Structure of A Yada-Like Head Domain of the Trimeric Autotransporter Adhesin Boaa From Burkholderia Pseudomallei Solved By Iodide Ion Sad Phasing


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 A Yada-Like Head Domain of the Trimeric Autotransporter Adhesin Boaa From Burkholderia Pseudomallei Solved By Iodide Ion Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn184

b:29.1
occ:1.00
OE1 B:GLN93 2.0 24.0 1.0
NE2 B:HIS108 2.1 26.5 1.0
I A:IOD174 2.5 38.8 0.5
CL B:CL189 2.5 51.7 1.0
CE1 B:HIS108 2.6 26.0 1.0
O B:HOH273 2.7 27.0 1.0
CD B:GLN93 3.0 21.8 1.0
NE2 B:GLN93 3.3 22.8 1.0
CD2 B:HIS108 3.4 23.8 1.0
O B:HOH241 3.8 35.4 1.0
ND1 B:HIS108 3.8 25.4 1.0
CG B:HIS108 4.2 22.8 1.0
CG B:GLN93 4.4 19.3 1.0
O B:HOH242 4.6 38.8 1.0
CA A:GLY73 4.7 20.2 1.0
CB B:GLN93 4.8 15.8 1.0
O B:GLN93 4.9 16.9 1.0
CG D:ARG136 5.0 32.4 1.0

Zinc binding site 6 out of 17 in 3s6l

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Zinc binding site 6 out of 17 in the Crystal Structure of A Yada-Like Head Domain of the Trimeric Autotransporter Adhesin Boaa From Burkholderia Pseudomallei Solved By Iodide Ion Sad Phasing


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of A Yada-Like Head Domain of the Trimeric Autotransporter Adhesin Boaa From Burkholderia Pseudomallei Solved By Iodide Ion Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn185

b:57.6
occ:1.00
NE2 B:HIS138 2.0 36.6 1.0
NE2 D:HIS138 2.0 35.6 1.0
O B:HOH226 2.3 25.1 1.0
O B:HOH234 2.4 19.4 1.0
CL D:CL192 2.6 42.8 1.0
CE1 D:HIS138 2.8 33.1 1.0
CE1 B:HIS138 2.9 33.7 1.0
CD2 B:HIS138 3.1 32.7 1.0
CD2 D:HIS138 3.2 30.2 1.0
ND1 D:HIS138 4.0 31.2 1.0
ND1 B:HIS138 4.0 32.8 1.0
CG B:HIS138 4.2 30.6 1.0
CG D:HIS138 4.2 30.0 1.0
O B:HOH233 5.0 24.8 1.0

Zinc binding site 7 out of 17 in 3s6l

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Zinc binding site 7 out of 17 in the Crystal Structure of A Yada-Like Head Domain of the Trimeric Autotransporter Adhesin Boaa From Burkholderia Pseudomallei Solved By Iodide Ion Sad Phasing


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of A Yada-Like Head Domain of the Trimeric Autotransporter Adhesin Boaa From Burkholderia Pseudomallei Solved By Iodide Ion Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn186

b:80.8
occ:1.00
O B:HOH230 1.9 7.0 1.0
OD2 B:ASP45 2.2 34.6 1.0
O B:HOH302 2.4 34.5 1.0
O C:HOH301 2.7 17.7 1.0
NE2 B:HIS59 2.9 35.1 1.0
CG B:ASP45 3.5 26.5 1.0
CD2 B:HIS59 3.6 27.8 1.0
CE1 B:HIS59 4.1 34.9 1.0
OD1 B:ASP45 4.2 26.2 1.0
CB B:ASP45 4.5 25.1 1.0
NE2 C:GLN79 4.6 23.4 1.0
CG B:HIS59 4.9 27.5 1.0
OE1 C:GLN65 4.9 21.1 1.0

Zinc binding site 8 out of 17 in 3s6l

Go back to Zinc Binding Sites List in 3s6l
Zinc binding site 8 out of 17 in the Crystal Structure of A Yada-Like Head Domain of the Trimeric Autotransporter Adhesin Boaa From Burkholderia Pseudomallei Solved By Iodide Ion Sad Phasing


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of A Yada-Like Head Domain of the Trimeric Autotransporter Adhesin Boaa From Burkholderia Pseudomallei Solved By Iodide Ion Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn184

b:74.1
occ:1.00
OE1 C:GLN93 2.1 27.8 1.0
NE2 C:HIS108 2.2 30.3 1.0
O C:HOH213 2.9 12.2 1.0
CL C:CL188 3.0 44.9 1.0
CD C:GLN93 3.1 23.5 1.0
CD2 C:HIS108 3.1 25.7 1.0
CE1 C:HIS108 3.2 29.1 1.0
NE2 C:GLN93 3.5 24.4 1.0
ND1 C:HIS108 4.3 28.2 1.0
CG C:HIS108 4.3 24.8 1.0
CG C:GLN93 4.4 19.6 1.0
O C:GLN93 4.8 19.4 1.0
CB C:GLN93 4.9 18.5 1.0

Zinc binding site 9 out of 17 in 3s6l

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Zinc binding site 9 out of 17 in the Crystal Structure of A Yada-Like Head Domain of the Trimeric Autotransporter Adhesin Boaa From Burkholderia Pseudomallei Solved By Iodide Ion Sad Phasing


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of A Yada-Like Head Domain of the Trimeric Autotransporter Adhesin Boaa From Burkholderia Pseudomallei Solved By Iodide Ion Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn185

b:70.9
occ:1.00
OD2 C:ASP45 1.9 35.7 1.0
CG C:ASP45 3.0 27.5 1.0
OD1 C:ASP45 3.5 29.2 1.0
NE2 C:HIS59 3.6 33.3 1.0
CD2 C:HIS59 4.1 27.1 1.0
CB C:ASP45 4.3 25.2 1.0
OE1 A:GLN65 4.6 21.9 1.0
CE1 C:HIS59 4.9 34.4 1.0
NE2 A:GLN79 4.9 21.6 1.0

Zinc binding site 10 out of 17 in 3s6l

Go back to Zinc Binding Sites List in 3s6l
Zinc binding site 10 out of 17 in the Crystal Structure of A Yada-Like Head Domain of the Trimeric Autotransporter Adhesin Boaa From Burkholderia Pseudomallei Solved By Iodide Ion Sad Phasing


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of A Yada-Like Head Domain of the Trimeric Autotransporter Adhesin Boaa From Burkholderia Pseudomallei Solved By Iodide Ion Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn186

b:78.3
occ:1.00
NE2 C:HIS138 2.4 38.4 1.0
CD2 C:HIS138 3.2 34.2 1.0
CE1 C:HIS138 3.5 37.4 1.0
CG C:HIS138 4.4 32.8 1.0
ND1 C:HIS138 4.5 35.6 1.0
O C:HOH309 4.8 21.4 1.0
O C:ARG136 5.0 32.2 1.0

Reference:

T.E.Edwards, A.S.Gardberg, E.R.Lafontaine, Seattle Structural Genomics Center For Infectious Disease(Ssgcid). Crystal Structure of A Yada-Like Head Domain of the Trimeric Autotransporter Adhesin Boaa From Burkholderia Pseudomallei To Be Published.
Page generated: Wed Dec 16 04:49:25 2020

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