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Zinc in PDB 3men: Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak

Protein crystallography data

The structure of Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak, PDB code: 3men 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 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.700, 162.120, 173.070, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 23.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak (pdb code 3men). 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 Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak, PDB code: 3men:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3men

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Zinc binding site 1 out of 4 in the Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak


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 Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:36.0
occ:1.00
OD2 A:ASP192 2.1 16.7 1.0
O4 A:SO4401 2.2 31.2 1.0
OD2 A:ASP281 2.2 19.7 1.0
ND1 A:HIS194 2.2 14.6 1.0
O2 A:SO4401 2.7 28.9 1.0
S A:SO4401 2.9 23.7 1.0
CG A:ASP192 2.9 12.3 1.0
OD1 A:ASP192 3.0 11.2 1.0
CE1 A:HIS194 3.1 10.4 1.0
CG A:ASP281 3.2 15.6 1.0
CG A:HIS194 3.2 13.2 1.0
OD1 A:ASP281 3.4 12.6 1.0
CB A:HIS194 3.6 10.7 1.0
O1 A:SO4401 3.6 30.5 1.0
N A:HIS194 3.8 10.0 1.0
O3 A:SO4401 4.1 33.4 1.0
N A:MET193 4.1 10.4 1.0
NE2 A:HIS156 4.3 10.5 1.0
NE2 A:HIS194 4.3 12.2 1.0
CB A:ASP192 4.3 11.1 1.0
CA A:HIS194 4.3 10.5 1.0
CD2 A:HIS194 4.4 14.7 1.0
CB A:MET193 4.4 10.9 1.0
CA A:GLY318 4.4 16.9 1.0
CB A:ASP281 4.5 15.0 1.0
CE1 A:HIS156 4.5 11.0 1.0
CA A:MET193 4.6 10.8 1.0
C A:MET193 4.6 11.0 1.0
CE2 A:TYR320 4.6 23.6 1.0
OH A:TYR320 4.7 22.9 1.0
C A:ASP192 4.7 10.2 1.0
NE2 A:HIS157 4.7 13.6 1.0
N A:GLY318 4.8 15.5 1.0
CA A:ASP192 5.0 10.5 1.0

Zinc binding site 2 out of 4 in 3men

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Zinc binding site 2 out of 4 in the Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak


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 Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn400

b:43.4
occ:1.00
OD2 B:ASP281 2.1 21.9 1.0
OD2 B:ASP192 2.1 23.2 1.0
ND1 B:HIS194 2.2 19.0 1.0
O4 B:SO4401 2.3 37.4 1.0
O2 B:SO4401 2.7 35.3 1.0
CG B:ASP192 2.9 17.9 1.0
OD1 B:ASP192 3.0 19.9 1.0
CG B:ASP281 3.0 18.1 1.0
S B:SO4401 3.0 29.6 1.0
CE1 B:HIS194 3.1 19.5 1.0
CG B:HIS194 3.3 18.9 1.0
OD1 B:ASP281 3.3 15.4 1.0
CB B:HIS194 3.7 17.6 1.0
N B:HIS194 3.7 16.8 1.0
O1 B:SO4401 3.8 40.0 1.0
N B:MET193 4.0 15.6 1.0
O3 B:SO4401 4.2 38.5 1.0
NE2 B:HIS194 4.2 22.8 1.0
CB B:MET193 4.2 16.5 1.0
CB B:ASP192 4.3 17.3 1.0
CA B:HIS194 4.3 17.2 1.0
CD2 B:HIS194 4.4 21.9 1.0
CB B:ASP281 4.4 18.4 1.0
NE2 B:HIS156 4.5 17.1 1.0
CA B:MET193 4.5 16.2 1.0
C B:MET193 4.5 15.5 1.0
CE2 B:TYR320 4.6 24.6 1.0
CA B:GLY318 4.6 18.9 1.0
C B:ASP192 4.7 15.9 1.0
OH B:TYR320 4.8 27.6 1.0
CE1 B:HIS156 4.8 15.3 1.0
NE2 B:HIS157 4.9 13.5 1.0
CA B:ASP192 4.9 16.9 1.0
N B:GLY318 4.9 18.6 1.0

Zinc binding site 3 out of 4 in 3men

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Zinc binding site 3 out of 4 in the Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak


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 Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn400

b:55.3
occ:1.00
OD2 C:ASP281 2.0 38.0 1.0
OD2 C:ASP192 2.1 33.0 1.0
ND1 C:HIS194 2.2 26.8 1.0
O4 C:SO4401 2.4 55.1 1.0
O2 C:SO4401 2.7 50.4 1.0
CG C:ASP192 2.8 30.5 1.0
OD1 C:ASP192 2.8 32.1 1.0
S C:SO4401 3.0 47.9 1.0
CG C:ASP281 3.0 35.7 1.0
CE1 C:HIS194 3.0 25.0 1.0
CG C:HIS194 3.3 28.2 1.0
OD1 C:ASP281 3.3 36.2 1.0
O1 C:SO4401 3.5 49.9 1.0
N C:HIS194 3.7 27.7 1.0
CB C:HIS194 3.7 26.4 1.0
N C:MET193 4.0 29.5 1.0
NE2 C:HIS194 4.2 29.6 1.0
CB C:ASP192 4.3 29.8 1.0
CB C:MET193 4.3 31.1 1.0
O3 C:SO4401 4.3 52.9 1.0
CA C:HIS194 4.3 27.2 1.0
CD2 C:HIS194 4.3 28.9 1.0
NE2 C:HIS156 4.3 25.4 1.0
CA C:GLY318 4.3 35.5 1.0
CB C:ASP281 4.4 36.1 1.0
CA C:MET193 4.4 29.8 1.0
C C:MET193 4.4 28.7 1.0
CE2 C:TYR320 4.5 41.8 1.0
CE1 C:HIS156 4.6 26.4 1.0
C C:ASP192 4.6 29.6 1.0
N C:GLY318 4.7 34.5 1.0
OH C:TYR320 4.8 43.3 1.0
CA C:ASP192 4.9 30.5 1.0
NE2 C:HIS157 4.9 27.9 1.0
OE1 C:GLN288 5.0 54.2 1.0

Zinc binding site 4 out of 4 in 3men

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Zinc binding site 4 out of 4 in the Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak


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 Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn400

b:50.8
occ:1.00
OD2 D:ASP192 2.0 21.6 1.0
O4 D:SO4401 2.1 40.9 1.0
OD2 D:ASP281 2.2 34.2 1.0
ND1 D:HIS194 2.3 21.0 1.0
CG D:ASP192 2.8 20.3 1.0
O2 D:SO4401 2.8 33.8 1.0
OD1 D:ASP192 2.9 18.4 1.0
S D:SO4401 3.0 35.1 1.0
CE1 D:HIS194 3.1 23.9 1.0
CG D:ASP281 3.2 30.1 1.0
CG D:HIS194 3.4 20.4 1.0
OD1 D:ASP281 3.4 32.6 1.0
N D:HIS194 3.6 19.8 1.0
CB D:HIS194 3.8 19.4 1.0
O1 D:SO4401 3.9 38.9 1.0
N D:MET193 4.0 22.1 1.0
O3 D:SO4401 4.1 39.6 1.0
CB D:ASP192 4.2 20.4 1.0
CB D:MET193 4.2 24.0 1.0
NE2 D:HIS156 4.3 19.2 1.0
NE2 D:HIS194 4.3 23.6 1.0
CA D:HIS194 4.3 19.1 1.0
CA D:MET193 4.4 22.4 1.0
CD2 D:HIS194 4.5 24.9 1.0
C D:MET193 4.5 21.6 1.0
CA D:GLY318 4.5 25.6 1.0
CB D:ASP281 4.5 28.9 1.0
OH D:TYR320 4.6 36.6 1.0
CE1 D:HIS156 4.6 17.5 1.0
CE2 D:TYR320 4.6 35.8 1.0
C D:ASP192 4.6 20.9 1.0
CA D:ASP192 4.8 20.7 1.0
N D:GLY318 4.8 24.2 1.0
NE2 D:HIS157 4.9 15.7 1.0

Reference:

J.Abendroth, A.S.Gardberg, J.I.Robinson, J.S.Christensen, B.L.Staker, P.J.Myler, L.J.Stewart, T.E.Edwards. Sad Phasing Using Iodide Ions in A High-Throughput Structural Genomics Environment. J Struct Funct Genomics V. 12 83 2011.
PubMed: 21359836
DOI: 10.1007/S10969-011-9101-7
Page generated: Sat Sep 26 11:43:24 2020
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