Magnesium in PDB 5yol: Crystal Structure of Octameric Form of Nucleoside Diphosphate Kinase From Acinetobacter Baumannii at 2.2 A Resolution

Enzymatic activity of Crystal Structure of Octameric Form of Nucleoside Diphosphate Kinase From Acinetobacter Baumannii at 2.2 A Resolution

All present enzymatic activity of Crystal Structure of Octameric Form of Nucleoside Diphosphate Kinase From Acinetobacter Baumannii at 2.2 A Resolution:
2.7.4.6;

Protein crystallography data

The structure of Crystal Structure of Octameric Form of Nucleoside Diphosphate Kinase From Acinetobacter Baumannii at 2.2 A Resolution, PDB code: 5yol was solved by P.K.Singh, J.Sikarwar, P.Kaur, S.Sharma, T.P.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.32 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.100, 69.930, 71.700, 80.51, 69.94, 89.76
R / Rfree (%) 21.3 / 25.8

Magnesium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Octameric Form of Nucleoside Diphosphate Kinase From Acinetobacter Baumannii at 2.2 A Resolution (pdb code 5yol). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Crystal Structure of Octameric Form of Nucleoside Diphosphate Kinase From Acinetobacter Baumannii at 2.2 A Resolution, PDB code: 5yol:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 5yol

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Magnesium binding site 1 out of 12 in the Crystal Structure of Octameric Form of Nucleoside Diphosphate Kinase From Acinetobacter Baumannii at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Octameric Form of Nucleoside Diphosphate Kinase From Acinetobacter Baumannii at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:28.4
occ:1.00
 O A:HOH316 2.2 47.6 1.0
ND2 A:ASN136 2.3 29.8 1.0
O A:ASN136 2.3 31.6 1.0
O A:HOH320 2.3 35.4 1.0
OD1 G:ASP46 2.4 44.4 1.0
O A:HOH375 3.0 57.1 1.0
CG A:ASN136 3.4 30.1 1.0
C A:ASN136 3.4 30.5 1.0
CG G:ASP46 3.5 40.5 1.0
CA A:ASN136 3.8 29.6 1.0
CB A:ASN136 4.2 29.5 1.0
OD1 A:ASN136 4.2 31.7 1.0
O G:HOH308 4.3 41.6 1.0
OD2 G:ASP46 4.4 42.4 1.0
CB G:ASP46 4.4 35.6 1.0
CA G:ASP46 4.4 33.5 1.0
N A:GLU137 4.6 33.3 1.0
OH G:TYR131 4.8 23.4 1.0
N G:ASP46 4.8 30.7 1.0
O A:ILE138 4.8 35.2 1.0
O D:HOH353 5.0 38.6 1.0

Magnesium binding site 2 out of 12 in 5yol

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Magnesium binding site 2 out of 12 in the Crystal Structure of Octameric Form of Nucleoside Diphosphate Kinase From Acinetobacter Baumannii at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Octameric Form of Nucleoside Diphosphate Kinase From Acinetobacter Baumannii at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:62.1
occ:1.00
 O A:HOH303 2.2 38.6 1.0
OD2 A:ASP120 2.4 42.6 1.0
O A:HOH365 2.5 55.1 1.0
CG A:ASP120 3.2 39.4 1.0
OD1 A:ASP120 3.4 43.8 1.0
CB A:ASP120 4.5 35.4 1.0
OE2 A:GLU53 4.5 62.7 1.0

Magnesium binding site 3 out of 12 in 5yol

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Magnesium binding site 3 out of 12 in the Crystal Structure of Octameric Form of Nucleoside Diphosphate Kinase From Acinetobacter Baumannii at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Octameric Form of Nucleoside Diphosphate Kinase From Acinetobacter Baumannii at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:27.1
occ:1.00
 O F:HOH313 2.0 48.8 1.0
O B:HOH331 2.3 38.3 1.0
OD1 F:ASP46 2.3 44.7 1.0
OD1 B:ASN136 2.4 47.7 1.0
O B:ASN136 2.4 42.2 1.0
CG B:ASN136 3.4 40.8 1.0
C B:ASN136 3.4 39.1 1.0
CG F:ASP46 3.5 37.6 1.0
CA B:ASN136 3.9 37.1 1.0
CB B:ASN136 4.2 37.0 1.0
ND2 B:ASN136 4.2 40.6 1.0
OD2 F:ASP46 4.3 35.3 1.0
CA F:ASP46 4.3 33.7 1.0
CB F:ASP46 4.3 35.6 1.0
N B:GLU137 4.6 38.8 1.0
O B:HOH348 4.6 40.0 1.0
N F:ASP46 4.7 31.7 1.0
OH F:TYR131 4.7 35.9 1.0
O B:ILE138 4.9 33.0 1.0
O F:HOH319 5.0 47.3 1.0

Magnesium binding site 4 out of 12 in 5yol

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Magnesium binding site 4 out of 12 in the Crystal Structure of Octameric Form of Nucleoside Diphosphate Kinase From Acinetobacter Baumannii at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Octameric Form of Nucleoside Diphosphate Kinase From Acinetobacter Baumannii at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:45.6
occ:1.00
 O E:HOH337 1.9 32.5 1.0
O C:HOH303 2.8 27.7 1.0
O C:HOH345 2.9 44.1 1.0
OD1 C:ASN136 3.7 43.2 1.0
O C:ASN136 4.2 38.0 1.0
OH E:TYR131 4.3 31.4 1.0
OD1 E:ASP46 4.4 43.5 1.0
O C:ILE138 4.5 40.4 1.0
CA C:ASN136 4.7 34.8 1.0
C C:ASN136 4.8 37.0 1.0
O E:ALA45 4.9 29.8 1.0
CG C:ASN136 4.9 42.5 1.0

Magnesium binding site 5 out of 12 in 5yol

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Magnesium binding site 5 out of 12 in the Crystal Structure of Octameric Form of Nucleoside Diphosphate Kinase From Acinetobacter Baumannii at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Octameric Form of Nucleoside Diphosphate Kinase From Acinetobacter Baumannii at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg201

b:50.1
occ:1.00
 O D:HOH343 2.3 46.7 1.0
OD1 D:ASN136 2.3 49.1 1.0
O H:HOH302 2.5 37.7 1.0
O D:ASN136 2.5 33.5 1.0
OD1 H:ASP46 2.7 42.3 1.0
O D:HOH370 2.9 35.1 1.0
CG D:ASN136 3.3 45.9 1.0
C D:ASN136 3.6 32.7 1.0
CG H:ASP46 3.8 41.9 1.0
CA D:ASN136 4.0 39.1 1.0
ND2 D:ASN136 4.1 47.4 1.0
CB D:ASN136 4.2 46.1 1.0
O H:HOH310 4.4 35.8 1.0
O A:HOH353 4.5 38.4 1.0
OD2 H:ASP46 4.6 39.3 1.0
N D:GLU137 4.8 34.1 1.0
CB H:ASP46 4.8 43.5 1.0
CA H:ASP46 4.8 37.4 1.0
O D:ILE138 5.0 36.4 1.0

Magnesium binding site 6 out of 12 in 5yol

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Magnesium binding site 6 out of 12 in the Crystal Structure of Octameric Form of Nucleoside Diphosphate Kinase From Acinetobacter Baumannii at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Octameric Form of Nucleoside Diphosphate Kinase From Acinetobacter Baumannii at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg201

b:30.4
occ:1.00
 O E:HOH307 1.9 39.0 1.0
OD2 A:ASP112 2.0 51.8 1.0
O E:HOH301 2.4 31.2 1.0
OD1 E:ASP120 2.4 55.2 1.0
O E:HOH314 2.4 36.5 1.0
OD2 E:ASP120 2.6 54.0 1.0
OG E:SER124 2.7 63.2 1.0
CG A:ASP112 2.9 49.6 1.0
CG E:ASP120 2.9 48.4 1.0
OD1 A:ASP112 3.0 56.9 1.0
OE2 E:GLU53 3.5 61.7 1.0
CB E:SER124 3.8 42.6 1.0
OE1 E:GLU53 4.0 61.9 1.0
CD E:GLU53 4.2 60.0 1.0
O A:HOH356 4.2 41.7 1.0
CB A:ASP112 4.3 46.7 1.0
O E:HOH311 4.3 24.0 1.0
OD2 A:ASP62 4.3 49.0 1.0
CB E:ASP120 4.4 45.4 1.0
OG E:SER121 4.5 43.5 1.0
O A:HOH348 4.5 41.1 1.0
CA E:SER124 4.9 40.1 1.0
O A:HOH366 4.9 42.6 1.0

Magnesium binding site 7 out of 12 in 5yol

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Magnesium binding site 7 out of 12 in the Crystal Structure of Octameric Form of Nucleoside Diphosphate Kinase From Acinetobacter Baumannii at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Octameric Form of Nucleoside Diphosphate Kinase From Acinetobacter Baumannii at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg202

b:30.3
occ:1.00
 O E:HOH335 2.0 46.0 1.0
OD1 E:ASN136 2.4 48.1 1.0
OD1 C:ASP46 2.5 39.3 1.0
O E:ASN136 2.5 32.1 1.0
O C:HOH338 2.6 36.4 1.0
O E:HOH326 2.6 46.9 1.0
O C:HOH346 2.6 45.7 1.0
O E:HOH338 2.8 53.7 1.0
CG E:ASN136 3.4 38.3 1.0
C E:ASN136 3.6 31.7 1.0
CG C:ASP46 3.6 34.7 1.0
CA E:ASN136 4.0 34.2 1.0
ND2 E:ASN136 4.2 37.5 1.0
CB E:ASN136 4.3 36.8 1.0
OD2 C:ASP46 4.4 31.2 1.0
CA C:ASP46 4.5 35.5 1.0
CB C:ASP46 4.5 34.2 1.0
O C:HOH337 4.7 45.3 1.0
N E:GLU137 4.8 33.7 1.0
O F:HOH335 4.8 37.8 1.0
N C:ASP46 4.9 36.5 1.0
OH C:TYR131 4.9 33.7 1.0
O E:ILE138 4.9 34.0 1.0

Magnesium binding site 8 out of 12 in 5yol

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Magnesium binding site 8 out of 12 in the Crystal Structure of Octameric Form of Nucleoside Diphosphate Kinase From Acinetobacter Baumannii at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Octameric Form of Nucleoside Diphosphate Kinase From Acinetobacter Baumannii at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg201

b:31.0
occ:1.00
 O F:HOH320 2.0 43.5 1.0
O F:HOH306 2.3 31.0 1.0
OD1 B:ASP46 2.4 41.1 1.0
O F:ASN136 2.4 37.1 1.0
ND2 F:ASN136 2.5 43.5 1.0
O F:HOH337 3.0 40.8 1.0
CG F:ASN136 3.3 45.8 1.0
C F:ASN136 3.5 35.1 1.0
CG B:ASP46 3.6 38.5 1.0
CA F:ASN136 3.9 41.3 1.0
OD1 F:ASN136 3.9 49.0 1.0
CB F:ASN136 4.2 41.1 1.0
O B:HOH333 4.2 33.6 1.0
OD2 B:ASP46 4.4 42.6 1.0
CA B:ASP46 4.5 32.5 1.0
CB B:ASP46 4.5 35.7 1.0
N F:GLU137 4.7 30.2 1.0
N B:ASP46 4.8 32.3 1.0
OH B:TYR131 4.9 26.4 1.0

Magnesium binding site 9 out of 12 in 5yol

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Magnesium binding site 9 out of 12 in the Crystal Structure of Octameric Form of Nucleoside Diphosphate Kinase From Acinetobacter Baumannii at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Octameric Form of Nucleoside Diphosphate Kinase From Acinetobacter Baumannii at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg201

b:31.1
occ:1.00
 O A:HOH329 2.1 46.6 1.0
OD1 G:ASN136 2.3 41.0 1.0
OD1 A:ASP46 2.4 44.5 1.0
O G:HOH333 2.4 36.7 1.0
O G:ASN136 2.4 40.3 1.0
O A:HOH343 2.5 46.7 1.0
O A:HOH372 2.8 52.1 1.0
CG G:ASN136 3.3 35.4 1.0
C G:ASN136 3.5 35.5 1.0
CG A:ASP46 3.6 44.6 1.0
CA G:ASN136 3.8 34.4 1.0
CB G:ASN136 4.1 33.1 1.0
ND2 G:ASN136 4.2 31.8 1.0
CA A:ASP46 4.4 33.8 1.0
CB A:ASP46 4.4 38.6 1.0
OD2 A:ASP46 4.4 46.9 1.0
O H:HOH361 4.4 45.5 1.0
O A:HOH334 4.6 46.9 1.0
N G:GLU137 4.7 36.8 1.0
O G:HOH354 4.7 43.2 1.0
OH A:TYR131 4.7 26.1 1.0
N A:ASP46 4.8 30.2 1.0
O G:ILE138 4.9 43.3 1.0

Magnesium binding site 10 out of 12 in 5yol

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Magnesium binding site 10 out of 12 in the Crystal Structure of Octameric Form of Nucleoside Diphosphate Kinase From Acinetobacter Baumannii at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Octameric Form of Nucleoside Diphosphate Kinase From Acinetobacter Baumannii at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg202

b:59.6
occ:1.00
 O G:HOH355 2.0 53.7 1.0
O G:HOH302 2.7 44.4 1.0
OD2 G:ASP112 3.3 63.1 1.0
OD1 G:ASP112 3.6 68.2 1.0
CG G:ASP112 3.9 61.4 1.0
OD2 G:ASP62 4.5 56.4 1.0

Reference:

P.K.Singh, J.Sikarwar, P.Kaur, S.Sharma, T.P.Singh. Crystal Structure of Octameric Form of Nucleoside Diphosphate Kinase From Acinetobacter Baumannii at 2.2 A Resolution To Be Published.
Page generated: Mon Dec 14 22:14:05 2020

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