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Manganese in PDB 3tr4: Structure of An Inorganic Pyrophosphatase (Ppa) From Coxiella Burnetii

Enzymatic activity of Structure of An Inorganic Pyrophosphatase (Ppa) From Coxiella Burnetii

All present enzymatic activity of Structure of An Inorganic Pyrophosphatase (Ppa) From Coxiella Burnetii:
3.6.1.1;

Protein crystallography data

The structure of Structure of An Inorganic Pyrophosphatase (Ppa) From Coxiella Burnetii, PDB code: 3tr4 was solved by J.Cheung, M.C.Franklin, M.Rudolph, M.Cassidy, E.Gary, F.Burshteyn, J.Love, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.46 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.910, 108.654, 74.664, 90.00, 104.44, 90.00
R / Rfree (%) 18.1 / 22.6

Other elements in 3tr4:

The structure of Structure of An Inorganic Pyrophosphatase (Ppa) From Coxiella Burnetii also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of An Inorganic Pyrophosphatase (Ppa) From Coxiella Burnetii (pdb code 3tr4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Structure of An Inorganic Pyrophosphatase (Ppa) From Coxiella Burnetii, PDB code: 3tr4:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 3tr4

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Manganese binding site 1 out of 6 in the Structure of An Inorganic Pyrophosphatase (Ppa) From Coxiella Burnetii


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of An Inorganic Pyrophosphatase (Ppa) From Coxiella Burnetii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn176

b:56.7
occ:0.76
 OD2 A:ASP69 2.4 49.1 1.0
O A:HOH214 2.6 42.9 1.0
OD2 A:ASP64 2.7 57.8 1.0
OD2 A:ASP101 2.8 66.3 1.0
OD1 A:ASP101 2.8 60.0 1.0
CG A:ASP69 3.1 37.4 1.0
OD1 A:ASP69 3.1 34.0 1.0
CG A:ASP101 3.1 62.8 1.0
CG A:ASP64 3.7 56.5 1.0
OD1 A:ASP64 4.1 48.5 1.0
O A:HOH216 4.2 27.7 0.9
OH A:TYR54 4.4 57.1 1.0
O A:HOH213 4.5 32.6 1.0
CB A:ASP66 4.5 40.7 1.0
CB A:ASP69 4.5 31.7 1.0
CB A:ASP101 4.6 61.4 1.0
NZ A:LYS103 4.7 44.1 1.0
O A:PRO67 4.7 31.2 1.0
CB A:ASP64 4.8 53.6 1.0
OD2 A:ASP66 4.9 58.4 1.0

Manganese binding site 2 out of 6 in 3tr4

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Manganese binding site 2 out of 6 in the Structure of An Inorganic Pyrophosphatase (Ppa) From Coxiella Burnetii


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of An Inorganic Pyrophosphatase (Ppa) From Coxiella Burnetii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn176

b:55.4
occ:0.93
 O B:HOH226 2.0 45.1 1.0
OD2 B:ASP69 2.4 35.4 1.0
O B:HOH353 2.5 37.2 0.9
OD1 B:ASP101 2.5 41.5 1.0
OD1 B:ASP69 3.0 41.7 1.0
OD1 B:ASP64 3.0 53.4 1.0
CG B:ASP69 3.0 36.5 1.0
CG B:ASP101 3.4 45.6 1.0
OD2 B:ASP101 3.5 49.2 1.0
CG B:ASP64 4.0 58.6 1.0
OH B:TYR54 4.1 58.8 1.0
O B:HOH199 4.2 36.5 1.0
O B:HOH200 4.3 32.9 1.0
OD2 B:ASP64 4.4 59.5 1.0
CB B:ASP69 4.5 30.4 1.0
NZ B:LYS103 4.6 36.8 1.0
OD2 B:ASP66 4.6 69.7 1.0
O B:HOH233 4.6 50.4 1.0
CB B:ASP66 4.7 55.8 1.0
CB B:ASP101 4.8 39.9 1.0
O B:PRO67 4.8 31.5 1.0

Manganese binding site 3 out of 6 in 3tr4

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Manganese binding site 3 out of 6 in the Structure of An Inorganic Pyrophosphatase (Ppa) From Coxiella Burnetii


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of An Inorganic Pyrophosphatase (Ppa) From Coxiella Burnetii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn176

b:69.5
occ:0.75
 OD2 C:ASP69 2.5 47.4 1.0
OD2 C:ASP64 2.9 94.4 1.0
OD1 C:ASP101 2.9 59.8 1.0
OD2 C:ASP101 3.1 61.3 1.0
CG C:ASP69 3.2 42.7 1.0
OD1 C:ASP69 3.3 42.6 1.0
CG C:ASP101 3.3 60.8 1.0
CG C:ASP64 3.4 94.1 1.0
OD1 C:ASP64 3.4 96.3 1.0
OD2 C:ASP66 4.3 71.8 1.0
O C:HOH195 4.3 35.4 0.8
CB C:ASP66 4.4 69.8 1.0
O C:HOH193 4.5 35.4 0.8
O C:HOH323 4.6 54.2 1.0
CB C:ASP69 4.6 36.4 1.0
CB C:ASP64 4.6 91.2 1.0
OH C:TYR54 4.7 61.5 1.0
O C:PRO67 4.7 35.9 1.0
CB C:ASP101 4.8 58.3 1.0
CG C:ASP66 4.9 72.1 1.0

Manganese binding site 4 out of 6 in 3tr4

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Manganese binding site 4 out of 6 in the Structure of An Inorganic Pyrophosphatase (Ppa) From Coxiella Burnetii


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of An Inorganic Pyrophosphatase (Ppa) From Coxiella Burnetii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn176

b:70.9
occ:0.75
 OD2 D:ASP69 2.4 45.7 1.0
O D:HOH307 2.5 42.3 1.0
OD2 D:ASP64 2.5 97.8 1.0
OD1 D:ASP101 2.7 49.9 1.0
OD2 D:ASP101 2.8 50.2 1.0
CG D:ASP101 3.0 48.9 1.0
CG D:ASP69 3.3 42.2 1.0
CG D:ASP64 3.4 98.6 1.0
OD1 D:ASP69 3.5 44.8 1.0
CB D:ASP64 3.8 90.8 1.0
OD2 D:ASP66 4.1 81.0 1.0
O D:HOH191 4.3 29.4 0.9
OD1 D:ASP64 4.4 0.0 1.0
CB D:ASP66 4.4 68.3 1.0
CB D:ASP101 4.5 44.1 1.0
O D:HOH190 4.6 50.0 1.0
CB D:ASP69 4.7 34.4 1.0
CG D:ASP66 4.7 79.7 1.0
OH D:TYR54 4.8 59.0 1.0
O D:PRO67 4.8 31.7 1.0

Manganese binding site 5 out of 6 in 3tr4

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Manganese binding site 5 out of 6 in the Structure of An Inorganic Pyrophosphatase (Ppa) From Coxiella Burnetii


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of An Inorganic Pyrophosphatase (Ppa) From Coxiella Burnetii within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn176

b:63.2
occ:0.60
 O E:HOH192 2.4 46.7 1.0
OD2 E:ASP69 2.4 51.2 1.0
O E:HOH203 2.5 51.7 1.0
OD2 E:ASP101 2.8 70.0 1.0
OD1 E:ASP64 3.0 86.9 1.0
OD1 E:ASP101 3.2 65.6 1.0
CG E:ASP101 3.3 64.8 1.0
CG E:ASP69 3.4 44.9 1.0
CG E:ASP64 3.8 82.8 1.0
OD1 E:ASP69 3.9 46.4 1.0
O E:HOH191 4.0 34.8 1.0
CB E:ASP64 4.2 72.6 1.0
NZ E:LYS103 4.3 56.5 1.0
CB E:ASP101 4.6 55.9 1.0
CB E:ASP69 4.7 35.0 1.0
OD2 E:ASP64 4.7 84.0 1.0
OH E:TYR54 5.0 62.3 1.0

Manganese binding site 6 out of 6 in 3tr4

Go back to Manganese Binding Sites List in 3tr4
Manganese binding site 6 out of 6 in the Structure of An Inorganic Pyrophosphatase (Ppa) From Coxiella Burnetii


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structure of An Inorganic Pyrophosphatase (Ppa) From Coxiella Burnetii within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn176

b:39.0
occ:0.53
 O F:HOH264 2.3 43.1 1.0
O F:HOH317 2.4 45.1 1.0
OD2 F:ASP69 2.4 48.8 1.0
OD2 F:ASP64 2.6 60.6 1.0
OD1 F:ASP101 2.6 57.0 1.0
OD2 F:ASP101 2.8 51.5 1.0
OD1 F:ASP69 2.9 43.0 1.0
CG F:ASP69 3.0 42.6 1.0
CG F:ASP101 3.1 53.2 1.0
CG F:ASP64 3.6 63.6 1.0
OD1 F:ASP64 4.0 63.7 1.0
O F:HOH237 4.2 41.6 1.0
OH F:TYR54 4.3 53.6 1.0
O F:HOH181 4.3 41.8 1.0
O F:HOH364 4.4 59.2 1.0
CB F:ASP69 4.4 38.8 1.0
CB F:ASP66 4.5 61.5 1.0
NZ F:LYS103 4.5 42.7 1.0
CB F:ASP101 4.6 50.5 1.0
O F:PRO67 4.7 38.7 1.0
CB F:ASP64 4.8 65.4 1.0
OD2 F:ASP66 4.9 73.5 1.0

Reference:

M.C.Franklin, J.Cheung, M.J.Rudolph, F.Burshteyn, M.Cassidy, E.Gary, B.Hillerich, Z.K.Yao, P.R.Carlier, M.Totrov, J.D.Love. Structural Genomics For Drug Design Against the Pathogen Coxiella Burnetii. Proteins V. 83 2124 2015.
ISSN: ISSN 0887-3585
PubMed: 26033498
DOI: 10.1002/PROT.24841
Page generated: Sat Oct 5 18:01:55 2024

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