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Magnesium in PDB 6ki8: Pyrophosphatase Mutant K149R From Acinetobacter Baumannii

Enzymatic activity of Pyrophosphatase Mutant K149R From Acinetobacter Baumannii

All present enzymatic activity of Pyrophosphatase Mutant K149R From Acinetobacter Baumannii:
3.6.1.1;

Protein crystallography data

The structure of Pyrophosphatase Mutant K149R From Acinetobacter Baumannii, PDB code: 6ki8 was solved by J.Su, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 1.79
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 116.755, 116.755, 109.704, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 18.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pyrophosphatase Mutant K149R From Acinetobacter Baumannii (pdb code 6ki8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Pyrophosphatase Mutant K149R From Acinetobacter Baumannii, PDB code: 6ki8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 6ki8

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Magnesium binding site 1 out of 9 in the Pyrophosphatase Mutant K149R From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyrophosphatase Mutant K149R From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:21.9
occ:1.00
 OD2 A:ASP97 2.4 23.8 1.0
O A:HOH335 2.4 20.8 1.0
O3 A:DPO201 2.4 19.0 1.0
OD2 A:ASP102 2.4 26.1 1.0
O5 A:DPO201 2.5 20.3 1.0
O A:HOH387 2.8 31.5 1.0
CG A:ASP102 3.3 29.8 1.0
P1 A:DPO201 3.4 20.7 1.0
O A:HOH315 3.4 31.5 1.0
CG A:ASP97 3.4 24.1 1.0
P2 A:DPO201 3.6 18.4 1.0
O1 A:DPO201 3.6 22.9 1.0
NZ A:LYS142 3.6 19.9 1.0
O A:HOH313 3.7 21.1 1.0
O4 A:DPO201 3.9 20.3 1.0
OH A:TYR141 3.9 18.7 1.0
NZ A:LYS104 3.9 23.0 1.0
OD1 A:ASP102 4.0 31.1 1.0
O7 A:DPO201 4.1 20.2 1.0
CB A:ASP97 4.1 22.3 1.0
CB A:ASP102 4.2 24.3 1.0
OD1 A:ASP97 4.2 22.2 1.0
CE A:LYS104 4.4 21.4 1.0
O A:HOH324 4.4 39.1 1.0
O A:HOH346 4.5 20.6 1.0
O A:HOH326 4.6 34.2 1.0
CE A:LYS142 4.7 20.7 1.0
O2 A:DPO201 4.7 21.8 1.0
O6 A:DPO201 4.9 18.6 1.0

Magnesium binding site 2 out of 9 in 6ki8

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Magnesium binding site 2 out of 9 in the Pyrophosphatase Mutant K149R From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pyrophosphatase Mutant K149R From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:45.5
occ:1.00
 O A:HOH352 2.6 50.6 1.0
OD2 A:ASP70 2.8 29.0 1.0
O1 A:DPO201 2.9 22.9 1.0
OD1 A:ASP70 2.9 29.2 1.0
CG A:ASP70 3.2 29.1 1.0
O A:HOH332 3.2 40.2 1.0
O A:HOH345 3.5 41.3 1.0
O2 A:DPO201 3.6 21.8 1.0
MG A:MG204 3.7 41.6 1.0
O A:HOH446 3.7 36.0 1.0
P1 A:DPO201 3.8 20.7 1.0
OH A:TYR55 3.8 25.7 1.0
O A:HOH364 3.8 33.2 1.0
O A:HOH387 4.0 31.5 1.0
O A:HOH430 4.0 41.6 1.0
NZ A:LYS104 4.4 23.0 1.0
O3 A:DPO201 4.4 19.0 1.0
O A:HOH303 4.6 24.9 1.0
CB A:ASP70 4.7 21.6 1.0
O A:HOH329 4.7 26.5 1.0
O A:HOH324 4.8 39.1 1.0
OD1 A:ASP102 4.8 31.1 1.0
CB A:ASP67 5.0 35.8 1.0

Magnesium binding site 3 out of 9 in 6ki8

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Magnesium binding site 3 out of 9 in the Pyrophosphatase Mutant K149R From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pyrophosphatase Mutant K149R From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:41.6
occ:1.00
 O A:HOH446 2.3 36.0 1.0
O2 A:DPO201 2.9 21.8 1.0
OE1 A:GLU20 3.2 24.7 1.0
O A:HOH364 3.3 33.2 1.0
O A:HOH329 3.4 26.5 1.0
NZ A:LYS29 3.4 23.9 1.0
O A:HOH358 3.5 36.9 1.0
O A:HOH344 3.5 23.2 1.0
MG A:MG203 3.7 45.5 1.0
CG A:GLU31 3.8 24.7 1.0
CD A:GLU31 3.9 31.2 1.0
OE1 A:GLU31 3.9 28.8 1.0
OH A:TYR55 3.9 25.7 1.0
CD A:GLU20 4.0 22.7 1.0
OE2 A:GLU20 4.0 21.8 1.0
P1 A:DPO201 4.1 20.7 1.0
O A:HOH352 4.1 50.6 1.0
O1 A:DPO201 4.1 22.9 1.0
CE2 A:TYR55 4.2 20.9 1.0
O A:HOH332 4.2 40.2 1.0
CZ A:TYR55 4.5 24.7 1.0
OE2 A:GLU31 4.5 30.6 1.0
O4 A:DPO201 4.6 20.3 1.0
OD1 A:ASP70 4.6 29.2 1.0
CB A:GLU31 4.7 23.6 1.0
CE A:LYS29 4.9 21.0 1.0

Magnesium binding site 4 out of 9 in 6ki8

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Magnesium binding site 4 out of 9 in the Pyrophosphatase Mutant K149R From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pyrophosphatase Mutant K149R From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:22.9
occ:1.00
 OD2 B:ASP97 2.3 24.9 1.0
O3 B:DPO201 2.3 21.2 1.0
O B:HOH343 2.4 22.5 1.0
O7 B:DPO201 2.4 22.3 1.0
OD2 B:ASP102 2.4 26.4 1.0
O B:HOH372 2.6 30.9 1.0
P1 B:DPO201 3.3 22.1 1.0
CG B:ASP97 3.4 28.3 1.0
CG B:ASP102 3.4 29.4 1.0
P2 B:DPO201 3.5 20.9 1.0
O1 B:DPO201 3.5 24.9 1.0
NZ B:LYS142 3.6 20.3 1.0
O B:HOH316 3.8 25.1 1.0
O4 B:DPO201 3.8 20.4 1.0
NZ B:LYS104 3.9 22.9 1.0
OH B:TYR141 3.9 17.5 1.0
CB B:ASP97 4.0 22.6 1.0
O6 B:DPO201 4.0 20.2 1.0
OD1 B:ASP102 4.0 28.5 1.0
OD1 B:ASP97 4.2 25.2 1.0
O B:HOH402 4.3 33.3 1.0
CB B:ASP102 4.3 24.1 1.0
CE B:LYS104 4.4 20.8 1.0
CE B:LYS142 4.6 20.4 1.0
O B:HOH323 4.6 35.0 1.0
O B:HOH307 4.7 39.9 1.0
O2 B:DPO201 4.7 23.5 1.0
O B:HOH352 4.7 20.0 1.0
O5 B:DPO201 4.8 20.7 1.0
O B:HOH374 4.9 39.6 1.0

Magnesium binding site 5 out of 9 in 6ki8

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Magnesium binding site 5 out of 9 in the Pyrophosphatase Mutant K149R From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Pyrophosphatase Mutant K149R From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:43.3
occ:1.00
 O B:HOH310 2.1 37.8 1.0
OD2 B:ASP70 2.5 27.9 1.0
O1 B:DPO201 2.6 24.9 1.0
OD2 B:ASP65 2.9 47.0 1.0
O B:HOH302 3.0 45.2 1.0
O B:HOH319 3.0 40.5 1.0
O B:HOH307 3.1 39.9 1.0
OD1 B:ASP70 3.3 28.4 1.0
CG B:ASP70 3.3 28.2 1.0
O B:HOH372 3.3 30.9 1.0
MG B:MG204 3.6 44.0 1.0
P1 B:DPO201 3.6 22.1 1.0
O2 B:DPO201 3.8 23.5 1.0
O B:HOH453 3.8 44.3 1.0
CG B:ASP65 4.1 49.1 1.0
O B:HOH305 4.1 27.4 1.0
O B:HOH393 4.1 32.1 1.0
OD1 B:ASP102 4.1 28.5 1.0
O3 B:DPO201 4.1 21.2 1.0
NZ B:LYS104 4.1 22.9 1.0
OH B:TYR55 4.2 21.7 1.0
OD1 B:ASP65 4.5 47.7 1.0
O B:HOH428 4.6 36.0 1.0
O B:HOH400 4.6 31.8 1.0
CB B:ASP70 4.7 25.1 1.0
O B:HOH402 4.8 33.3 1.0
CG B:ASP102 4.9 29.4 1.0

Magnesium binding site 6 out of 9 in 6ki8

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Magnesium binding site 6 out of 9 in the Pyrophosphatase Mutant K149R From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Pyrophosphatase Mutant K149R From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:44.0
occ:1.00
 O B:HOH435 2.2 38.6 1.0
O B:HOH310 2.6 37.8 1.0
O2 B:DPO201 2.7 23.5 1.0
O B:HOH453 2.8 44.3 1.0
O B:HOH313 3.1 25.1 1.0
O B:HOH393 3.2 32.1 1.0
O B:HOH428 3.4 36.0 1.0
OD1 B:ASP70 3.5 28.4 1.0
OH B:TYR55 3.6 21.7 1.0
MG B:MG203 3.6 43.3 1.0
O1 B:DPO201 3.6 24.9 1.0
P1 B:DPO201 3.7 22.1 1.0
NZ B:LYS29 3.9 21.5 1.0
OE1 B:GLU20 3.9 25.2 1.0
O B:HOH341 4.2 22.4 1.0
CE2 B:TYR55 4.2 19.6 1.0
CG B:ASP70 4.3 28.2 1.0
CZ B:TYR55 4.3 23.3 1.0
OE1 B:GLU31 4.5 27.9 1.0
OD2 B:ASP70 4.5 27.9 1.0
O4 B:DPO201 4.5 20.4 1.0
O B:HOH302 4.6 45.2 1.0
CD B:GLU31 4.7 31.5 1.0
CD B:GLU20 4.8 21.7 1.0
OE2 B:GLU20 4.8 23.0 1.0
O B:HOH371 4.9 40.2 1.0
O3 B:DPO201 4.9 21.2 1.0
CG B:GLU31 4.9 26.3 1.0
O B:HOH319 5.0 40.5 1.0

Magnesium binding site 7 out of 9 in 6ki8

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Magnesium binding site 7 out of 9 in the Pyrophosphatase Mutant K149R From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Pyrophosphatase Mutant K149R From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:22.6
occ:1.00
 OD2 C:ASP102 2.4 24.6 1.0
OD2 C:ASP97 2.4 22.1 1.0
O3 C:DPO201 2.4 19.5 1.0
O C:HOH386 2.4 30.2 1.0
O5 C:DPO201 2.4 18.8 1.0
O C:HOH354 2.5 20.6 1.0
CG C:ASP102 3.3 27.8 1.0
CG C:ASP97 3.4 24.5 1.0
P1 C:DPO201 3.4 19.8 1.0
NZ C:LYS142 3.5 18.6 1.0
P2 C:DPO201 3.6 18.4 1.0
O1 C:DPO201 3.6 22.8 1.0
OD1 C:ASP102 3.8 27.5 1.0
O4 C:DPO201 3.9 19.5 1.0
NZ C:LYS104 3.9 21.6 1.0
O C:HOH340 3.9 21.9 1.0
OH C:TYR141 3.9 16.5 1.0
CB C:ASP97 4.0 21.4 1.0
O C:HOH385 4.0 34.2 1.0
O7 C:DPO201 4.0 19.6 1.0
OD1 C:ASP97 4.2 24.0 1.0
CB C:ASP102 4.3 20.9 1.0
CE C:LYS104 4.5 20.0 1.0
O C:HOH317 4.5 36.8 1.0
CE C:LYS142 4.6 20.1 1.0
O C:HOH304 4.6 39.5 1.0
O C:HOH368 4.7 34.3 1.0
O2 C:DPO201 4.8 20.9 1.0
O C:HOH362 4.8 20.9 1.0
O6 C:DPO201 4.8 19.5 1.0

Magnesium binding site 8 out of 9 in 6ki8

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Magnesium binding site 8 out of 9 in the Pyrophosphatase Mutant K149R From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Pyrophosphatase Mutant K149R From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg203

b:36.5
occ:1.00
 O C:HOH308 2.3 22.5 1.0
OD2 C:ASP70 2.5 27.1 1.0
OD2 C:ASP65 2.6 32.0 1.0
O1 C:DPO201 2.7 22.8 1.0
O C:HOH323 3.0 30.0 1.0
O C:HOH304 3.2 39.5 1.0
OD1 C:ASP70 3.2 24.7 1.0
CG C:ASP70 3.2 24.8 1.0
O C:HOH386 3.4 30.2 1.0
MG C:MG204 3.6 34.3 1.0
CG C:ASP65 3.8 38.3 1.0
P1 C:DPO201 3.8 19.8 1.0
O C:HOH363 3.8 32.0 1.0
O C:HOH337 3.9 27.4 1.0
O C:HOH339 3.9 43.2 1.0
OD1 C:ASP102 4.0 27.5 1.0
O2 C:DPO201 4.0 20.9 1.0
O C:HOH384 4.1 27.2 1.0
O C:HOH408 4.2 26.5 1.0
O3 C:DPO201 4.2 19.5 1.0
OD1 C:ASP65 4.2 31.3 1.0
NZ C:LYS104 4.3 21.6 1.0
OH C:TYR55 4.5 20.4 1.0
O C:HOH372 4.7 25.5 1.0
O C:HOH385 4.7 34.2 1.0
CB C:ASP70 4.7 18.4 1.0
CG C:ASP102 4.9 27.8 1.0

Magnesium binding site 9 out of 9 in 6ki8

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Magnesium binding site 9 out of 9 in the Pyrophosphatase Mutant K149R From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Pyrophosphatase Mutant K149R From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg204

b:34.3
occ:1.00
 O C:HOH308 2.5 22.5 1.0
O C:HOH411 2.6 31.8 1.0
O2 C:DPO201 2.7 20.9 1.0
O C:HOH322 2.9 23.4 1.0
O C:HOH363 3.2 32.0 1.0
O C:HOH384 3.3 27.2 1.0
OD1 C:ASP70 3.3 24.7 1.0
O C:HOH372 3.5 25.5 1.0
O1 C:DPO201 3.5 22.8 1.0
OH C:TYR55 3.6 20.4 1.0
MG C:MG203 3.6 36.5 1.0
P1 C:DPO201 3.7 19.8 1.0
NZ C:LYS29 3.9 20.9 1.0
O C:HOH477 4.0 35.2 1.0
CG C:ASP70 4.0 24.8 1.0
OE1 C:GLU20 4.1 22.6 1.0
CE2 C:TYR55 4.2 19.8 1.0
O C:HOH360 4.2 20.8 1.0
OD2 C:ASP70 4.2 27.1 1.0
CZ C:TYR55 4.3 22.0 1.0
OE1 C:GLU31 4.4 27.4 1.0
O4 C:DPO201 4.6 19.5 1.0
O C:HOH494 4.7 37.7 1.0
CD C:GLU31 4.8 29.3 1.0
O3 C:DPO201 4.8 19.5 1.0
OE2 C:GLU20 4.9 21.1 1.0
CD C:GLU20 5.0 22.1 1.0
O C:HOH307 5.0 40.6 1.0

Reference:

Y.Si, X.Wang, G.Yang, T.Yang, Y.Li, G.J.Ayala, X.Li, H.Wang, J.Su. Crystal Structures of Pyrophosphatase From Acinetobacter Baumannii: Snapshots of Pyrophosphate Binding and Identification of A Phosphorylated Enzyme Intermediate. Int J Mol Sci V. 20 2019.
ISSN: ESSN 1422-0067
PubMed: 31500178
DOI: 10.3390/IJMS20184394
Page generated: Wed Aug 13 10:31:42 2025

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