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Magnesium in PDB 5c5v: Recombinant Inorganic Pyrophosphatase From T Brucei Brucei

Protein crystallography data

The structure of Recombinant Inorganic Pyrophosphatase From T Brucei Brucei, PDB code: 5c5v was solved by A.Jamwal, M.Yogavel, A.Sharma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.83 / 2.35
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 104.210, 104.210, 215.513, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 23.8

Other elements in 5c5v:

The structure of Recombinant Inorganic Pyrophosphatase From T Brucei Brucei also contains other interesting chemical elements:

Bromine (Br) 1 atom
Chlorine (Cl) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Recombinant Inorganic Pyrophosphatase From T Brucei Brucei (pdb code 5c5v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Recombinant Inorganic Pyrophosphatase From T Brucei Brucei, PDB code: 5c5v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5c5v

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Magnesium binding site 1 out of 8 in the Recombinant Inorganic Pyrophosphatase From T Brucei Brucei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Recombinant Inorganic Pyrophosphatase From T Brucei Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:55.6
occ:1.00
 OD2 A:ASP328 2.0 55.6 1.0
O A:HOH637 2.1 55.4 1.0
O2 A:2PN501 2.1 54.3 1.0
O A:HOH631 2.2 54.2 1.0
OD2 A:ASP323 2.3 58.2 1.0
O5 A:2PN501 2.3 52.9 1.0
CG A:ASP328 3.1 55.3 1.0
P1 A:2PN501 3.3 55.2 1.0
CG A:ASP323 3.3 58.2 1.0
O A:HOH662 3.4 55.0 0.4
P2 A:2PN501 3.4 54.1 0.8
N1 A:2PN501 3.4 54.4 1.0
MG A:MG503 3.5 54.2 1.0
OD1 A:ASP328 3.7 55.3 1.0
CB A:ASP323 3.8 56.9 1.0
OD1 A:ASP291 3.9 55.0 1.0
OH A:TYR368 4.0 55.9 1.0
NZ A:LYS330 4.0 54.3 1.0
HN1 A:2PN501 4.0 63.6 1.0
NZ A:LYS369 4.1 58.4 1.0
O3 A:2PN501 4.2 55.5 1.0
O4 A:2PN501 4.2 55.2 1.0
O A:HOH636 4.3 57.4 1.0
CB A:ASP328 4.3 54.5 1.0
O1 A:2PN501 4.4 56.5 1.0
OD1 A:ASP323 4.4 58.9 1.0
OD2 A:ASP296 4.5 53.0 1.0
CE A:MET321 4.6 57.7 1.0
O6 A:2PN501 4.6 53.3 1.0
O A:HOH612 4.6 52.8 1.0
O A:HOH662 4.7 55.9 0.6
CG A:ASP291 4.9 55.2 1.0
CE A:LYS369 4.9 58.6 1.0
CE A:LYS330 4.9 54.0 1.0

Magnesium binding site 2 out of 8 in 5c5v

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Magnesium binding site 2 out of 8 in the Recombinant Inorganic Pyrophosphatase From T Brucei Brucei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Recombinant Inorganic Pyrophosphatase From T Brucei Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:54.2
occ:1.00
 O A:HOH612 1.9 52.8 1.0
OD2 A:ASP296 2.0 53.0 1.0
OD1 A:ASP328 2.0 55.3 1.0
O5 A:2PN501 2.1 52.9 1.0
O A:HOH632 2.2 53.5 1.0
OD1 A:ASP291 2.2 55.0 1.0
CG A:ASP328 2.9 55.3 1.0
CG A:ASP296 3.0 52.8 1.0
OD2 A:ASP328 3.1 55.6 1.0
CG A:ASP291 3.1 55.2 1.0
P2 A:2PN501 3.2 54.1 0.8
MG A:MG505 3.3 54.3 1.0
OD1 A:ASP296 3.4 53.2 1.0
O6 A:2PN501 3.5 53.3 1.0
OD2 A:ASP291 3.5 54.9 1.0
MG A:MG502 3.5 55.6 1.0
O A:HOH631 3.7 54.2 1.0
O4 A:2PN501 3.8 55.2 1.0
NZ A:LYS330 4.0 54.3 1.0
O A:HOH605 4.2 52.4 1.0
O A:HOH662 4.3 55.0 0.4
CB A:ASP328 4.3 54.5 1.0
CB A:ASP296 4.3 51.6 1.0
CB A:ASP291 4.4 55.1 1.0
CB A:ASP293 4.4 54.8 1.0
O A:HOH637 4.4 55.4 1.0
O A:HOH622 4.5 50.5 1.0
N1 A:2PN501 4.6 54.4 1.0
OH A:TYR270 4.6 52.9 1.0
O A:PRO294 4.7 51.1 1.0
CA A:ASP328 4.7 54.0 1.0
OD2 A:ASP293 4.8 56.4 1.0
O2 A:2PN501 4.9 54.3 1.0
O A:HOH647 5.0 52.8 1.0

Magnesium binding site 3 out of 8 in 5c5v

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Magnesium binding site 3 out of 8 in the Recombinant Inorganic Pyrophosphatase From T Brucei Brucei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Recombinant Inorganic Pyrophosphatase From T Brucei Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:56.1
occ:1.00
 O A:HOH670 2.0 56.1 1.0
O A:HOH662 2.1 55.9 0.6
O1 A:2PN501 2.1 56.5 1.0
OE2 A:GLU239 2.2 54.2 1.0
O A:HOH652 2.2 56.8 1.0
O4 A:2PN501 2.3 55.2 1.0
O A:HOH662 2.5 55.0 0.4
CD A:GLU239 3.2 54.7 1.0
P1 A:2PN501 3.3 55.2 1.0
P2 A:2PN501 3.5 54.1 0.8
N1 A:2PN501 3.6 54.4 1.0
OE1 A:GLU239 3.7 55.5 1.0
NZ A:LYS237 3.9 51.2 1.0
O2 A:2PN501 3.9 54.3 1.0
NH1 A:ARG259 4.0 53.5 1.0
OD2 A:ASP293 4.1 56.4 1.0
OD2 A:ASP252 4.1 56.1 1.0
O A:HOH644 4.2 57.8 1.0
O A:HOH647 4.2 52.8 1.0
HN1 A:2PN501 4.3 63.6 1.0
O5 A:2PN501 4.4 52.9 1.0
CG A:GLU239 4.5 54.2 1.0
O6 A:2PN501 4.5 53.3 1.0
O3 A:2PN501 4.6 55.5 1.0
CE A:LYS237 4.6 51.7 1.0
O A:HOH612 4.8 52.8 1.0
CG A:ASP252 4.9 57.0 1.0
O A:HOH631 4.9 54.2 1.0

Magnesium binding site 4 out of 8 in 5c5v

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Magnesium binding site 4 out of 8 in the Recombinant Inorganic Pyrophosphatase From T Brucei Brucei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Recombinant Inorganic Pyrophosphatase From T Brucei Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:54.3
occ:1.00
 O6 A:2PN501 1.9 53.3 1.0
OD1 A:ASP296 2.0 53.2 1.0
O A:HOH612 2.1 52.8 1.0
O A:HOH603 2.1 51.2 1.0
O A:HOH647 2.3 52.8 1.0
O A:HOH622 2.3 50.5 1.0
P2 A:2PN501 2.8 54.1 0.8
CG A:ASP296 2.9 52.8 1.0
O4 A:2PN501 3.0 55.2 1.0
OD2 A:ASP296 3.1 53.0 1.0
MG A:MG503 3.3 54.2 1.0
O5 A:2PN501 3.3 52.9 1.0
OH A:TYR270 3.8 52.9 1.0
O A:HOH632 3.9 53.5 1.0
O A:PRO294 4.2 51.1 1.0
CB A:ASP293 4.3 54.8 1.0
CB A:ASP296 4.3 51.6 1.0
O A:HOH613 4.3 51.5 1.0
N1 A:2PN501 4.3 54.4 1.0
OD2 A:ASP293 4.3 56.4 1.0
CG A:ASP293 4.4 56.0 1.0
HN1 A:2PN501 4.5 63.6 1.0
NZ A:LYS237 4.5 51.2 1.0
OE1 A:GLU229 4.6 51.9 1.0
CZ A:TYR270 4.7 52.3 1.0
CE2 A:TYR270 4.7 53.1 1.0
OD1 A:ASP291 4.7 55.0 1.0
O A:HOH630 4.8 53.3 1.0
CA A:ASP296 4.8 51.2 1.0
O A:HOH609 5.0 51.5 1.0
O A:GLY271 5.0 50.9 1.0

Magnesium binding site 5 out of 8 in 5c5v

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Magnesium binding site 5 out of 8 in the Recombinant Inorganic Pyrophosphatase From T Brucei Brucei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Recombinant Inorganic Pyrophosphatase From T Brucei Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:60.0
occ:1.00
 O B:HOH643 1.9 59.5 1.0
OD2 B:ASP296 2.1 59.2 1.0
O3 B:2PN501 2.1 59.4 1.0
OD1 B:ASP328 2.2 60.9 1.0
O B:HOH622 2.2 59.0 1.0
OD2 B:ASP291 2.3 61.4 1.0
CG B:ASP296 3.0 58.4 1.0
CG B:ASP328 3.1 61.4 1.0
P1 B:2PN501 3.1 60.3 1.0
MG B:MG503 3.2 59.0 1.0
OD2 B:ASP328 3.3 62.0 1.0
CG B:ASP291 3.3 61.3 1.0
O1 B:2PN501 3.3 58.1 1.0
OD1 B:ASP296 3.4 58.9 1.0
O B:HOH646 3.6 62.0 1.0
O2 B:2PN501 3.7 61.9 1.0
MG B:MG505 3.7 61.9 1.0
OD1 B:ASP291 3.7 60.5 1.0
O B:HOH629 3.8 60.8 0.4
NZ B:LYS330 4.0 60.4 1.0
O B:HOH608 4.2 57.2 1.0
CB B:ASP293 4.3 60.7 1.0
CB B:ASP296 4.4 56.7 1.0
OD2 B:ASP293 4.4 63.2 1.0
O B:HOH613 4.4 57.1 1.0
CB B:ASP328 4.5 60.8 1.0
N1 B:2PN501 4.5 60.7 1.0
OH B:TYR270 4.5 58.3 1.0
CB B:ASP291 4.6 62.1 1.0
O B:PRO294 4.6 56.5 1.0
O B:HOH621 4.7 59.5 1.0
O B:HOH668 4.8 58.5 1.0
CG B:ASP293 4.8 62.6 1.0
CA B:ASP328 4.9 59.5 1.0
O5 B:2PN501 5.0 62.3 1.0
O B:HOH629 5.0 61.6 0.6

Magnesium binding site 6 out of 8 in 5c5v

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Magnesium binding site 6 out of 8 in the Recombinant Inorganic Pyrophosphatase From T Brucei Brucei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Recombinant Inorganic Pyrophosphatase From T Brucei Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:59.0
occ:1.00
 O B:HOH643 1.9 59.5 1.0
OD1 B:ASP296 2.0 58.9 1.0
O1 B:2PN501 2.0 58.1 1.0
O B:HOH668 2.2 58.5 1.0
O B:HOH613 2.2 57.1 1.0
O B:HOH605 2.3 54.6 1.0
CG B:ASP296 3.0 58.4 1.0
P1 B:2PN501 3.1 60.3 1.0
MG B:MG502 3.2 60.0 1.0
OD2 B:ASP296 3.3 59.2 1.0
O2 B:2PN501 3.3 61.9 1.0
O3 B:2PN501 3.7 59.4 1.0
OH B:TYR270 4.0 58.3 1.0
O B:HOH622 4.0 59.0 1.0
O B:PRO294 4.0 56.5 1.0
CB B:ASP293 4.2 60.7 1.0
OD2 B:ASP293 4.3 63.2 1.0
CB B:ASP296 4.4 56.7 1.0
CG B:ASP293 4.4 62.6 1.0
OE1 B:GLU229 4.5 57.4 1.0
N1 B:2PN501 4.5 60.7 1.0
O B:HOH654 4.5 60.0 1.0
NZ B:LYS237 4.5 59.6 1.0
HN1 B:2PN501 4.7 65.2 1.0
CE2 B:TYR270 4.7 57.6 1.0
CZ B:TYR270 4.7 57.3 1.0
OD2 B:ASP291 4.8 61.4 1.0
CA B:ASP296 4.9 55.8 1.0
O B:HOH620 4.9 57.4 1.0
O B:HOH629 4.9 60.8 0.4

Magnesium binding site 7 out of 8 in 5c5v

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Magnesium binding site 7 out of 8 in the Recombinant Inorganic Pyrophosphatase From T Brucei Brucei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Recombinant Inorganic Pyrophosphatase From T Brucei Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg504

b:62.8
occ:1.00
 O B:HOH609 2.0 62.6 1.0
O2 B:2PN501 2.0 61.9 1.0
O B:HOH656 2.1 64.0 1.0
O B:HOH638 2.1 63.5 1.0
OE2 B:GLU239 2.1 63.0 1.0
O6 B:2PN501 2.3 63.9 1.0
CD B:GLU239 3.1 63.4 1.0
P1 B:2PN501 3.2 60.3 1.0
P2 B:2PN501 3.3 62.4 1.0
N1 B:2PN501 3.3 60.7 1.0
O B:HOH629 3.5 60.8 0.4
OE1 B:GLU239 3.7 63.9 1.0
NZ B:LYS237 3.8 59.6 1.0
O5 B:2PN501 3.9 62.3 1.0
OD2 B:ASP293 4.0 63.2 1.0
HN1 B:2PN501 4.0 65.2 1.0
O B:HOH668 4.0 58.5 1.0
NH1 B:ARG259 4.0 64.1 1.0
OD2 B:ASP252 4.2 65.3 1.0
O3 B:2PN501 4.2 59.4 1.0
O1 B:2PN501 4.2 58.1 1.0
O B:HOH629 4.3 61.6 0.6
CG B:GLU239 4.4 62.2 1.0
CE B:LYS237 4.5 60.7 1.0
O4 B:2PN501 4.6 62.6 1.0
O B:HOH643 4.7 59.5 1.0
O B:HOH646 4.9 62.0 1.0
CG B:ASP252 4.9 65.2 1.0

Magnesium binding site 8 out of 8 in 5c5v

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Magnesium binding site 8 out of 8 in the Recombinant Inorganic Pyrophosphatase From T Brucei Brucei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Recombinant Inorganic Pyrophosphatase From T Brucei Brucei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg505

b:61.9
occ:1.00
 O B:HOH646 2.0 62.0 1.0
O5 B:2PN501 2.0 62.3 1.0
OD2 B:ASP328 2.1 62.0 1.0
O3 B:2PN501 2.2 59.4 1.0
OD2 B:ASP323 2.2 65.7 1.0
O B:HOH621 2.4 59.5 1.0
CG B:ASP328 3.2 61.4 1.0
CG B:ASP323 3.2 65.7 1.0
P2 B:2PN501 3.3 62.4 1.0
P1 B:2PN501 3.4 60.3 1.0
N1 B:2PN501 3.4 60.7 1.0
CB B:ASP323 3.7 64.2 1.0
MG B:MG502 3.7 60.0 1.0
OD1 B:ASP328 3.8 60.9 1.0
OD2 B:ASP291 4.0 61.4 1.0
O B:HOH609 4.0 62.6 1.0
HN1 B:2PN501 4.1 65.2 1.0
OH B:TYR368 4.1 60.2 1.0
O2 B:2PN501 4.1 61.9 1.0
NZ B:LYS369 4.1 64.5 1.0
O4 B:2PN501 4.2 62.6 1.0
O6 B:2PN501 4.2 63.9 1.0
O B:HOH633 4.2 65.9 1.0
NZ B:LYS330 4.3 60.4 1.0
O B:HOH629 4.3 60.8 0.4
OD1 B:ASP323 4.3 66.7 1.0
CB B:ASP328 4.4 60.8 1.0
O1 B:2PN501 4.7 58.1 1.0
OD2 B:ASP296 4.7 59.2 1.0
CE B:MET321 4.7 64.6 1.0
O B:HOH643 4.8 59.5 1.0
CE B:LYS369 4.9 64.2 1.0

Reference:

A.Jamwal, A.R.Round, L.Bannwarth, C.Venien-Bryan, H.Belrhali, M.Yogavel, A.Sharma. Structural and Functional Highlights of Vacuolar Soluble Protein 1 From Pathogen Trypanosoma Brucei Brucei J.Biol.Chem. V. 290 30498 2015.
ISSN: ESSN 1083-351X
PubMed: 26494625
DOI: 10.1074/JBC.M115.674176
Page generated: Sun Sep 29 01:58:53 2024

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