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Magnesium in PDB 7epq: Crystal Structure of Exopolyphosphatase (Ppx) From Porphyromonas Gingivalis in Complex with Sulfate and Magnesium Ions

Protein crystallography data

The structure of Crystal Structure of Exopolyphosphatase (Ppx) From Porphyromonas Gingivalis in Complex with Sulfate and Magnesium Ions, PDB code: 7epq was solved by A.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.40 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.43, 86.61, 122.92, 90, 90, 90
R / Rfree (%) 18 / 24

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Exopolyphosphatase (Ppx) From Porphyromonas Gingivalis in Complex with Sulfate and Magnesium Ions (pdb code 7epq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of Exopolyphosphatase (Ppx) From Porphyromonas Gingivalis in Complex with Sulfate and Magnesium Ions, PDB code: 7epq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 7epq

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Magnesium binding site 1 out of 7 in the Crystal Structure of Exopolyphosphatase (Ppx) From Porphyromonas Gingivalis in Complex with Sulfate and Magnesium Ions


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 Exopolyphosphatase (Ppx) From Porphyromonas Gingivalis in Complex with Sulfate and Magnesium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:31.3
occ:1.00
 O3 A:SO4401 2.0 29.4 1.0
O A:HOH652 2.0 32.7 1.0
O A:HOH519 2.1 26.9 1.0
O A:HOH513 2.1 30.5 1.0
O A:HOH522 2.1 27.3 1.0
O A:HOH554 2.2 28.2 1.0
S A:SO4401 3.3 33.1 1.0
O4 A:SO4401 3.5 29.6 1.0
O A:HOH660 3.8 45.7 1.0
MG A:MG407 3.9 41.2 1.0
O A:HOH518 4.0 31.6 1.0
OG1 A:THR86 4.1 30.2 1.0
OE2 A:GLU118 4.1 32.3 1.0
OD1 A:ASP10 4.1 29.5 1.0
O2 A:SO4401 4.1 26.4 1.0
OD2 A:ASP10 4.1 33.9 1.0
O A:HOH574 4.2 34.1 1.0
O1 A:SO4401 4.2 32.7 1.0
O A:HOH607 4.3 26.6 1.0
CA A:GLY12 4.5 23.1 1.0
CG A:ASP10 4.6 30.9 1.0
OD2 A:ASP141 4.7 45.4 1.0
CA A:GLY143 4.8 28.0 1.0
CD1 A:LEU285 4.8 30.8 1.0
CG2 A:THR86 4.9 25.8 1.0
CB A:THR86 4.9 30.7 1.0
O A:HOH502 4.9 39.2 1.0
O A:HOH600 5.0 33.6 1.0

Magnesium binding site 2 out of 7 in 7epq

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Magnesium binding site 2 out of 7 in the Crystal Structure of Exopolyphosphatase (Ppx) From Porphyromonas Gingivalis in Complex with Sulfate and Magnesium Ions


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 Exopolyphosphatase (Ppx) From Porphyromonas Gingivalis in Complex with Sulfate and Magnesium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:35.7
occ:1.00
 O A:HOH565 2.0 36.9 1.0
OD1 A:ASP292 2.0 33.2 1.0
O A:HOH599 2.0 39.6 1.0
O A:HOH572 2.1 36.5 1.0
O A:HOH527 2.1 32.4 1.0
O A:HOH545 2.2 30.7 1.0
CG A:ASP292 2.9 33.3 1.0
OD2 A:ASP292 3.1 32.9 1.0
O A:GLY288 4.2 31.8 1.0
O A:VAL122 4.2 35.7 1.0
CB A:ASP292 4.2 34.5 1.0
O A:ARG120 4.3 31.3 1.0
OE1 A:GLU291 4.3 41.4 1.0
OD2 A:ASP124 4.4 43.3 1.0
O A:HOH556 4.5 43.1 1.0
CA A:ASP292 4.6 36.4 1.0
N A:ASP292 4.6 33.1 1.0
CD1 A:LEU121 4.9 31.7 1.0
O A:HOH621 4.9 37.9 1.0

Magnesium binding site 3 out of 7 in 7epq

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Magnesium binding site 3 out of 7 in the Crystal Structure of Exopolyphosphatase (Ppx) From Porphyromonas Gingivalis in Complex with Sulfate and Magnesium Ions


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 Exopolyphosphatase (Ppx) From Porphyromonas Gingivalis in Complex with Sulfate and Magnesium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg407

b:41.2
occ:1.00
 O A:HOH518 2.1 31.6 1.0
O A:HOH502 2.1 39.2 1.0
OE2 A:GLU118 2.2 32.3 1.0
O1 A:SO4401 2.4 32.7 1.0
OG A:SER146 2.4 29.8 1.0
O3 A:SO4401 2.5 29.4 1.0
S A:SO4401 2.9 33.1 1.0
CD A:GLU118 3.3 31.0 1.0
OE1 A:GLU148 3.4 38.1 1.0
O A:HOH513 3.4 30.5 1.0
O A:SER146 3.6 31.6 1.0
OE1 A:GLU118 3.6 30.2 1.0
OE2 A:GLU148 3.7 33.2 1.0
CB A:SER146 3.7 29.7 1.0
O2 A:SO4401 3.7 26.4 1.0
OG A:SER87 3.9 43.2 1.0
N A:SER146 3.9 24.5 1.0
C A:SER146 3.9 29.5 1.0
CD A:GLU148 3.9 36.2 1.0
MG A:MG405 3.9 31.3 1.0
CA A:SER146 4.0 30.4 1.0
O4 A:SO4401 4.2 29.6 1.0
O A:HOH652 4.2 32.7 1.0
OG1 A:THR86 4.4 30.2 1.0
CB A:THR86 4.5 30.7 1.0
CA A:GLY143 4.5 28.0 1.0
CG A:GLU118 4.6 32.3 1.0
N A:THR147 4.8 32.6 1.0
N A:GLY143 4.8 26.0 1.0
CB A:SER87 4.8 33.9 1.0
N A:SER87 4.9 29.8 1.0
NH2 A:ARG90 4.9 35.3 1.0
CG2 A:THR86 5.0 25.8 1.0
O A:HOH519 5.0 26.9 1.0
C A:GLY145 5.0 31.3 1.0

Magnesium binding site 4 out of 7 in 7epq

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Magnesium binding site 4 out of 7 in the Crystal Structure of Exopolyphosphatase (Ppx) From Porphyromonas Gingivalis in Complex with Sulfate and Magnesium Ions


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 Exopolyphosphatase (Ppx) From Porphyromonas Gingivalis in Complex with Sulfate and Magnesium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg405

b:28.6
occ:1.00
 O1 B:SO4402 2.0 25.4 1.0
O B:HOH623 2.0 28.2 1.0
O B:HOH517 2.1 23.4 1.0
O B:HOH570 2.1 20.1 1.0
O B:HOH585 2.1 20.7 1.0
O B:HOH510 2.1 28.3 1.0
S B:SO4402 3.2 26.4 1.0
O2 B:SO4402 3.4 24.9 1.0
O B:HOH531 3.9 24.5 1.0
MG B:MG407 3.9 33.3 1.0
OE2 B:GLU118 3.9 28.7 1.0
O3 B:SO4402 3.9 25.0 1.0
OG1 B:THR86 4.1 23.9 1.0
OD1 B:ASP10 4.2 25.1 1.0
O B:HOH648 4.2 25.0 1.0
O4 B:SO4402 4.3 25.0 1.0
OD2 B:ASP10 4.3 29.3 1.0
O B:HOH646 4.3 31.1 1.0
OD1 B:ASP141 4.4 44.8 1.0
CA B:GLY12 4.6 21.4 1.0
CA B:GLY143 4.6 27.2 1.0
CG B:ASP10 4.7 27.3 1.0
O B:HOH610 4.8 21.5 1.0
CD1 B:LEU285 4.9 32.1 1.0

Magnesium binding site 5 out of 7 in 7epq

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Magnesium binding site 5 out of 7 in the Crystal Structure of Exopolyphosphatase (Ppx) From Porphyromonas Gingivalis in Complex with Sulfate and Magnesium Ions


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 Exopolyphosphatase (Ppx) From Porphyromonas Gingivalis in Complex with Sulfate and Magnesium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg406

b:32.2
occ:1.00
 OD1 B:ASP292 2.0 29.1 1.0
O B:HOH507 2.1 27.2 1.0
O B:HOH560 2.1 28.2 1.0
O B:HOH542 2.1 24.1 1.0
O B:HOH556 2.1 27.4 1.0
O B:HOH650 2.1 30.5 1.0
CG B:ASP292 3.0 28.3 1.0
OD2 B:ASP292 3.3 25.5 1.0
O B:VAL122 4.1 29.9 1.0
OD2 B:ASP124 4.1 33.6 1.0
O B:HOH680 4.1 47.5 1.0
O B:HOH508 4.2 38.9 1.0
O B:GLY288 4.2 20.8 1.0
O B:ARG120 4.2 28.9 1.0
O B:HOH699 4.2 40.6 1.0
OE1 B:GLU291 4.3 29.8 1.0
CB B:ASP292 4.4 26.4 1.0
CA B:ASP292 4.7 28.7 1.0
N B:ASP292 4.7 25.7 1.0
CD1 B:LEU121 4.8 25.4 1.0
N B:VAL122 4.9 22.9 1.0
O B:HOH657 4.9 40.4 1.0

Magnesium binding site 6 out of 7 in 7epq

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Magnesium binding site 6 out of 7 in the Crystal Structure of Exopolyphosphatase (Ppx) From Porphyromonas Gingivalis in Complex with Sulfate and Magnesium Ions


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 Exopolyphosphatase (Ppx) From Porphyromonas Gingivalis in Complex with Sulfate and Magnesium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg407

b:33.3
occ:1.00
 O B:HOH531 2.0 24.5 1.0
O B:HOH516 2.2 35.6 1.0
OG B:SER146 2.2 25.1 1.0
O1 B:SO4402 2.2 25.4 1.0
O4 B:SO4402 2.3 25.0 1.0
OE2 B:GLU118 2.3 28.7 1.0
S B:SO4402 2.7 26.4 1.0
CD B:GLU118 3.2 26.3 1.0
O3 B:SO4402 3.3 25.0 1.0
O B:SER146 3.4 27.1 1.0
OE1 B:GLU118 3.5 25.8 1.0
CB B:SER146 3.5 24.9 1.0
O B:HOH510 3.6 28.3 1.0
N B:SER146 3.7 24.6 1.0
OE1 B:GLU148 3.7 28.5 1.0
C B:SER146 3.8 23.0 1.0
OE2 B:GLU148 3.8 30.3 1.0
CA B:SER146 3.9 26.2 1.0
MG B:MG405 3.9 28.6 1.0
O2 B:SO4402 4.0 24.9 1.0
O B:HOH623 4.1 28.2 1.0
CD B:GLU148 4.2 29.4 1.0
OG1 B:THR86 4.3 23.9 1.0
CB B:SER87 4.4 26.3 1.0
CB B:THR86 4.4 23.8 1.0
CA B:GLY143 4.4 27.2 1.0
CG B:GLU118 4.5 20.7 1.0
N B:SER87 4.7 25.9 1.0
C B:GLY145 4.8 24.4 1.0
N B:THR147 4.8 23.8 1.0
N B:GLY143 4.8 23.9 1.0
O B:HOH517 4.9 23.4 1.0
NH2 B:ARG90 4.9 30.0 1.0
N B:GLY145 4.9 22.3 1.0

Magnesium binding site 7 out of 7 in 7epq

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Magnesium binding site 7 out of 7 in the Crystal Structure of Exopolyphosphatase (Ppx) From Porphyromonas Gingivalis in Complex with Sulfate and Magnesium Ions


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 Exopolyphosphatase (Ppx) From Porphyromonas Gingivalis in Complex with Sulfate and Magnesium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg408

b:40.7
occ:1.00
 CA B:GLY203 2.7 36.5 1.0
O B:HOH535 2.7 42.4 1.0
O B:THR202 2.7 30.5 1.0
C B:GLY203 3.1 42.9 1.0
N B:ILE206 3.2 33.4 1.0
C B:THR202 3.3 31.9 1.0
N B:GLY203 3.3 35.6 1.0
O B:GLY203 3.5 38.5 1.0
N B:ASN205 3.5 34.6 1.0
O B:VAL142 3.6 26.3 1.0
CB B:ILE206 3.7 36.8 1.0
CB B:ASN205 3.8 32.7 1.0
N B:GLY204 3.9 39.9 1.0
CG2 B:ILE206 3.9 30.8 1.0
CE2 B:PHE266 4.0 33.4 1.0
CA B:ASN205 4.0 34.1 1.0
C B:ASN205 4.1 34.5 1.0
CA B:ILE206 4.1 34.1 1.0
CB B:VAL142 4.1 31.1 1.0
CZ B:PHE266 4.4 26.3 1.0
C B:GLY204 4.4 43.1 1.0
N B:VAL142 4.5 28.8 1.0
C B:VAL142 4.5 30.1 1.0
CA B:VAL142 4.6 29.2 1.0
CA B:THR202 4.6 28.5 1.0
CG1 B:VAL142 4.7 27.7 1.0
CA B:GLY204 4.8 46.0 1.0
ND2 B:ASN205 4.8 30.7 1.0
CG B:ASN205 4.9 36.4 1.0
N B:THR202 5.0 26.2 1.0

Reference:

A.Zhang, Z.Lu, Y.Xu, T.Qi, W.Li, L.Zhang, Z.Cui. The Structure of Exopolyphosphatase (Ppx) From Porphyromonas Gingivalis in Complex with Substrate Analogs and Magnesium Ions Reveals the Basis For Polyphosphate Processivity. J.Struct.Biol. V. 213 07767 2021.
ISSN: ESSN 1095-8657
PubMed: 34214602
DOI: 10.1016/J.JSB.2021.107767
Page generated: Wed Oct 2 20:54:56 2024

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