Magnesium in PDB 7yq1: Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Archaeoglobus Fulgidus in Complex with Amp-Pnp and Aps

Enzymatic activity of Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Archaeoglobus Fulgidus in Complex with Amp-Pnp and Aps

All present enzymatic activity of Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Archaeoglobus Fulgidus in Complex with Amp-Pnp and Aps:
2.7.1.25;

Protein crystallography data

The structure of Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Archaeoglobus Fulgidus in Complex with Amp-Pnp and Aps, PDB code: 7yq1 was solved by T.Kawakami, T.Teramoto, Y.Kakuta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.48 / 1.91
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 52.23, 238.24, 132.47, 90, 93.38, 90
R / Rfree (%) 21.4 / 24.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Archaeoglobus Fulgidus in Complex with Amp-Pnp and Aps (pdb code 7yq1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Archaeoglobus Fulgidus in Complex with Amp-Pnp and Aps, PDB code: 7yq1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7yq1

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Magnesium binding site 1 out of 6 in the Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Archaeoglobus Fulgidus in Complex with Amp-Pnp and Aps


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 Adenosine 5'-Phosphosulfate Kinase From Archaeoglobus Fulgidus in Complex with Amp-Pnp and Aps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:13.0
occ:1.00
 O1G A:ANP302 2.0 18.2 1.0
O2B A:ANP302 2.0 13.2 1.0
O A:HOH440 2.1 16.1 1.0
O A:HOH448 2.1 13.3 1.0
OG1 A:THR16 2.1 14.4 1.0
O A:HOH435 2.2 11.5 1.0
PG A:ANP302 3.2 15.0 1.0
CB A:THR16 3.2 11.6 1.0
PB A:ANP302 3.2 11.5 1.0
N3B A:ANP302 3.5 13.0 1.0
OD1 A:ASP37 3.8 13.2 1.0
N A:THR16 4.0 11.4 1.0
O3G A:ANP302 4.0 17.3 1.0
NZ A:LYS117 4.1 23.3 1.0
O A:HOH465 4.1 15.0 1.0
O2A A:ANP302 4.1 15.8 1.0
CA A:THR16 4.2 11.6 1.0
CG2 A:THR16 4.2 11.7 1.0
O A:HOH568 4.3 31.0 1.0
O1B A:ANP302 4.3 15.2 1.0
O2G A:ANP302 4.3 20.7 1.0
O A:HOH529 4.3 29.5 1.0
OD2 A:ASP37 4.3 14.2 1.0
O3A A:ANP302 4.3 17.6 1.0
CG A:ASP37 4.5 12.9 1.0
PA A:ANP302 4.6 12.2 1.0
O1A A:ANP302 4.7 13.8 1.0
OG A:SER80 4.7 13.2 0.3
CE A:LYS15 4.7 11.0 1.0
NZ A:LYS15 4.8 11.8 1.0
O3' A:ADX301 4.9 24.9 1.0
CB A:LYS15 5.0 11.2 1.0

Magnesium binding site 2 out of 6 in 7yq1

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Magnesium binding site 2 out of 6 in the Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Archaeoglobus Fulgidus in Complex with Amp-Pnp and Aps


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 Adenosine 5'-Phosphosulfate Kinase From Archaeoglobus Fulgidus in Complex with Amp-Pnp and Aps within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:11.5
occ:1.00
 O3G B:ANP302 2.0 16.9 1.0
OG1 B:THR16 2.1 11.4 1.0
O B:HOH487 2.1 14.5 1.0
O B:HOH488 2.1 17.2 1.0
O2B B:ANP302 2.1 11.6 1.0
O B:HOH484 2.3 11.4 1.0
PG B:ANP302 3.2 17.2 1.0
CB B:THR16 3.2 11.5 1.0
PB B:ANP302 3.3 14.1 1.0
N3B B:ANP302 3.5 12.1 1.0
OD1 B:ASP37 3.8 11.3 1.0
N B:THR16 3.9 11.3 1.0
O1G B:ANP302 4.0 14.8 1.0
O B:HOH463 4.1 20.9 1.0
CA B:THR16 4.2 12.1 1.0
O1A B:ANP302 4.2 15.7 1.0
CG2 B:THR16 4.3 12.9 1.0
O1B B:ANP302 4.3 12.7 1.0
O2G B:ANP302 4.3 19.5 1.0
NZ B:LYS117 4.3 29.1 1.0
O B:HOH492 4.4 33.1 1.0
O3A B:ANP302 4.4 14.8 1.0
OD2 B:ASP37 4.4 15.5 1.0
CG B:ASP37 4.6 14.2 1.0
OG B:SER80 4.6 11.2 0.3
O B:HOH557 4.7 31.9 1.0
PA B:ANP302 4.7 13.6 1.0
O2A B:ANP302 4.7 15.3 1.0
CE B:LYS15 4.8 11.1 1.0
NZ B:LYS15 4.8 10.9 1.0
O3' B:ADX301 4.9 25.0 1.0

Magnesium binding site 3 out of 6 in 7yq1

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Magnesium binding site 3 out of 6 in the Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Archaeoglobus Fulgidus in Complex with Amp-Pnp and Aps


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 Adenosine 5'-Phosphosulfate Kinase From Archaeoglobus Fulgidus in Complex with Amp-Pnp and Aps within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:18.6
occ:1.00
 O C:HOH444 2.0 23.7 1.0
O2B C:ANP302 2.1 18.3 1.0
O C:HOH420 2.1 23.0 1.0
O2G C:ANP302 2.1 23.6 1.0
O C:HOH429 2.2 17.6 1.0
OG1 C:THR16 2.2 17.1 1.0
PG C:ANP302 3.3 23.5 1.0
CB C:THR16 3.3 20.1 1.0
PB C:ANP302 3.3 20.2 1.0
N3B C:ANP302 3.6 19.5 1.0
OD1 C:ASP37 3.7 20.6 1.0
O1G C:ANP302 3.9 20.9 1.0
NZ C:LYS117 3.9 28.2 1.0
N C:THR16 4.0 22.3 1.0
O2A C:ANP302 4.1 16.8 1.0
O C:HOH428 4.1 23.0 1.0
CA C:THR16 4.2 19.0 1.0
O1B C:ANP302 4.3 18.3 1.0
OD2 C:ASP37 4.3 19.6 1.0
CG2 C:THR16 4.3 19.5 1.0
O C:HOH539 4.4 31.6 1.0
O3A C:ANP302 4.4 25.3 1.0
CG C:ASP37 4.4 22.3 1.0
O3G C:ANP302 4.5 24.5 1.0
OG C:SER80 4.6 18.5 0.3
PA C:ANP302 4.6 18.5 1.0
O1A C:ANP302 4.6 19.9 1.0
O C:HOH497 4.7 33.6 1.0
CE C:LYS15 4.7 16.1 1.0
NZ C:LYS15 4.9 18.6 1.0
O3' C:ADX301 4.9 26.6 1.0
CB C:LYS15 4.9 21.1 1.0

Magnesium binding site 4 out of 6 in 7yq1

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Magnesium binding site 4 out of 6 in the Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Archaeoglobus Fulgidus in Complex with Amp-Pnp and Aps


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 Adenosine 5'-Phosphosulfate Kinase From Archaeoglobus Fulgidus in Complex with Amp-Pnp and Aps within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg303

b:18.2
occ:1.00
 O3G D:ANP302 2.0 23.1 1.0
OG1 D:THR16 2.1 19.6 1.0
O D:HOH420 2.1 15.3 1.0
O2B D:ANP302 2.1 15.6 1.0
O D:HOH421 2.2 20.5 1.0
O D:HOH448 2.3 22.8 1.0
CB D:THR16 3.2 19.0 1.0
PG D:ANP302 3.3 23.6 1.0
PB D:ANP302 3.4 20.1 1.0
N3B D:ANP302 3.6 21.0 1.0
OD1 D:ASP37 3.8 18.9 1.0
O1G D:ANP302 4.0 19.2 1.0
N D:THR16 4.0 18.1 1.0
O D:HOH458 4.0 27.4 1.0
O1A D:ANP302 4.1 18.5 1.0
NZ D:LYS117 4.1 25.1 1.0
CA D:THR16 4.2 23.1 1.0
CG2 D:THR16 4.2 21.9 1.0
OG D:SER80 4.2 19.1 0.3
OD2 D:ASP37 4.3 20.3 1.0
O D:HOH445 4.3 30.8 1.0
O D:HOH529 4.3 30.8 1.0
O1B D:ANP302 4.4 17.2 1.0
O2G D:ANP302 4.4 24.4 1.0
CG D:ASP37 4.4 20.0 1.0
O3A D:ANP302 4.5 24.6 1.0
O2A D:ANP302 4.5 19.4 1.0
PA D:ANP302 4.6 19.3 1.0
O3' D:ADX301 4.8 26.7 1.0
CE D:LYS15 4.9 21.5 1.0
CE D:LYS117 4.9 30.0 1.0
CB D:LYS15 5.0 23.1 1.0

Magnesium binding site 5 out of 6 in 7yq1

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Magnesium binding site 5 out of 6 in the Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Archaeoglobus Fulgidus in Complex with Amp-Pnp and Aps


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 Adenosine 5'-Phosphosulfate Kinase From Archaeoglobus Fulgidus in Complex with Amp-Pnp and Aps within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg303

b:22.8
occ:1.00
 O E:HOH434 2.0 22.7 1.0
OG1 E:THR16 2.1 23.9 1.0
O2B E:ANP302 2.1 20.9 1.0
O E:HOH440 2.2 20.4 1.0
O E:HOH416 2.2 20.8 1.0
O2G E:ANP302 2.2 30.3 1.0
CB E:THR16 3.1 24.3 1.0
PG E:ANP302 3.3 24.7 1.0
PB E:ANP302 3.4 23.0 1.0
OD1 E:ASP37 3.6 24.3 1.0
N3B E:ANP302 3.6 28.2 1.0
O1G E:ANP302 3.9 25.7 1.0
N E:THR16 4.0 23.1 1.0
O E:HOH471 4.0 27.6 1.0
NZ E:LYS117 4.1 34.4 1.0
CA E:THR16 4.1 24.7 1.0
CG2 E:THR16 4.1 24.5 1.0
O2A E:ANP302 4.2 23.0 1.0
OD2 E:ASP37 4.2 24.5 1.0
CG E:ASP37 4.3 25.4 1.0
O1B E:ANP302 4.3 27.5 1.0
O3A E:ANP302 4.5 31.2 1.0
O1A E:ANP302 4.6 21.0 1.0
O3G E:ANP302 4.6 26.8 1.0
PA E:ANP302 4.6 24.8 1.0
OG E:SER80 4.7 36.0 1.0
O3' E:ADX301 4.9 32.4 1.0
CB E:LYS15 5.0 23.0 1.0

Magnesium binding site 6 out of 6 in 7yq1

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Magnesium binding site 6 out of 6 in the Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Archaeoglobus Fulgidus in Complex with Amp-Pnp and Aps


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 Adenosine 5'-Phosphosulfate Kinase From Archaeoglobus Fulgidus in Complex with Amp-Pnp and Aps within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg303

b:22.0
occ:1.00
 O F:HOH411 2.0 21.8 1.0
O F:HOH446 2.0 20.7 1.0
O2B F:ANP302 2.0 20.5 1.0
OG1 F:THR16 2.1 25.2 1.0
O2G F:ANP302 2.1 27.0 1.0
O F:HOH408 2.2 21.9 1.0
CB F:THR16 3.1 22.9 1.0
PG F:ANP302 3.3 25.7 1.0
PB F:ANP302 3.3 26.1 1.0
N3B F:ANP302 3.6 30.5 1.0
OD1 F:ASP37 3.6 27.1 1.0
O F:HOH474 3.8 31.8 1.0
O F:HOH426 4.0 32.1 1.0
O1G F:ANP302 4.0 27.7 1.0
N F:THR16 4.0 25.9 1.0
CA F:THR16 4.1 24.8 1.0
CG2 F:THR16 4.1 29.2 1.0
O F:HOH491 4.2 35.5 1.0
OD2 F:ASP37 4.2 24.6 1.0
O1B F:ANP302 4.2 21.4 1.0
O2A F:ANP302 4.3 22.6 1.0
NZ F:LYS117 4.3 30.1 1.0
CG F:ASP37 4.4 26.1 1.0
O3A F:ANP302 4.4 34.6 1.0
O3G F:ANP302 4.4 29.0 1.0
OG F:SER80 4.5 28.9 1.0
PA F:ANP302 4.7 27.1 1.0
O1A F:ANP302 4.7 31.7 1.0
O3' F:ADX301 4.8 31.5 1.0
NZ F:LYS15 4.9 21.7 1.0
CE F:LYS15 4.9 22.8 1.0

Reference:

T.Kawakami, T.Teramoto, Y.Kakuta. Crystal Structure of Adenosine 5'-Phosphosulfate Kinase Isolated From Archaeoglobus Fulgidus. Biochem.Biophys.Res.Commun. V. 643 105 2022.
ISSN: ESSN 1090-2104
PubMed: 36592583
DOI: 10.1016/J.BBRC.2022.12.081
Page generated: Fri Apr 7 03:03:00 2023

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