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Magnesium in PDB 3p2l: Crystal Structure of Atp-Dependent Clp Protease Subunit P From Francisella Tularensis

Enzymatic activity of Crystal Structure of Atp-Dependent Clp Protease Subunit P From Francisella Tularensis

All present enzymatic activity of Crystal Structure of Atp-Dependent Clp Protease Subunit P From Francisella Tularensis:
3.4.21.92;

Protein crystallography data

The structure of Crystal Structure of Atp-Dependent Clp Protease Subunit P From Francisella Tularensis, PDB code: 3p2l was solved by Y.Kim, M.Zhou, M.Gu, W.F.Anderson, A.Joachimiak, Center For Structuralgenomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.45 / 2.29
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 120.523, 128.823, 98.030, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 22.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Atp-Dependent Clp Protease Subunit P From Francisella Tularensis (pdb code 3p2l). 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 Atp-Dependent Clp Protease Subunit P From Francisella Tularensis, PDB code: 3p2l:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 3p2l

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Magnesium binding site 1 out of 7 in the Crystal Structure of Atp-Dependent Clp Protease Subunit P From Francisella Tularensis


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 Atp-Dependent Clp Protease Subunit P From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:44.7
occ:1.00
 O A:MSE84 2.6 44.4 1.0
O A:ILE87 2.7 59.0 1.0
O A:PRO89 2.7 58.7 1.0
O A:HOH259 2.8 61.1 1.0
O3 A:PO4212 2.9 0.4 1.0
O4 A:PO4212 2.9 0.6 1.0
P A:PO4212 3.1 0.7 1.0
O1 A:PO4212 3.3 0.6 1.0
O A:GLN85 3.7 62.2 1.0
C A:PRO89 3.8 57.0 1.0
C A:MSE84 3.8 45.5 1.0
C A:ILE87 3.8 59.7 1.0
C A:GLN85 4.0 55.2 1.0
CG1 A:ILE87 4.0 51.7 1.0
CA A:GLN85 4.1 51.8 1.0
O A:LYS88 4.2 69.2 1.0
O A:HOH248 4.3 75.7 1.0
C A:LYS88 4.4 65.0 1.0
CA A:ASP90 4.4 55.4 1.0
N A:ASP90 4.4 50.7 1.0
N A:ILE87 4.4 53.8 1.0
N A:GLN85 4.5 44.4 1.0
N A:PRO89 4.6 55.9 1.0
N A:VAL91 4.6 49.2 1.0
CA A:ILE87 4.6 59.1 1.0
O2 A:PO4212 4.6 0.7 1.0
N A:PHE86 4.7 54.5 1.0
CG2 A:VAL91 4.7 43.3 1.0
CA A:PRO89 4.8 57.0 1.0
N A:LYS88 4.8 60.4 1.0
C A:ASP90 4.8 53.7 1.0
C A:PHE86 4.8 53.9 1.0
CA A:MSE84 4.9 43.1 1.0
CA A:LYS88 5.0 63.4 1.0
CB A:ILE87 5.0 53.3 1.0

Magnesium binding site 2 out of 7 in 3p2l

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Magnesium binding site 2 out of 7 in the Crystal Structure of Atp-Dependent Clp Protease Subunit P From Francisella Tularensis


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 Atp-Dependent Clp Protease Subunit P From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:34.9
occ:1.00
 O B:ILE87 2.6 45.3 1.0
O2 B:PO4204 2.7 0.1 1.0
O B:MSE84 2.7 47.5 1.0
O B:PRO89 2.7 44.3 1.0
O B:HOH220 2.9 45.9 1.0
O3 B:PO4204 2.9 0.3 1.0
P B:PO4204 3.2 0.5 1.0
O1 B:PO4204 3.5 0.3 1.0
C B:ILE87 3.7 44.5 1.0
C B:PRO89 3.7 43.0 1.0
C B:MSE84 3.9 46.7 1.0
O B:GLN85 4.0 47.6 1.0
O B:LYS88 4.0 45.5 1.0
CG1 B:ILE87 4.1 36.6 1.0
C B:GLN85 4.1 44.4 1.0
C B:LYS88 4.2 42.6 1.0
CA B:GLN85 4.3 47.8 1.0
CA B:ASP90 4.3 44.0 1.0
N B:ASP90 4.4 43.6 1.0
N B:ILE87 4.4 45.7 1.0
CA B:ILE87 4.5 44.2 1.0
N B:PRO89 4.6 38.7 1.0
N B:GLN85 4.6 48.1 1.0
CG2 B:VAL91 4.6 38.1 1.0
O4 B:PO4204 4.6 0.0 1.0
N B:VAL91 4.6 49.5 1.0
N B:LYS88 4.7 44.0 1.0
O B:HOH317 4.7 65.7 1.0
CA B:LYS88 4.8 45.9 1.0
N B:PHE86 4.8 44.7 1.0
CA B:PRO89 4.8 43.2 1.0
C B:PHE86 4.8 46.5 1.0
C B:ASP90 4.8 48.6 1.0
CB B:ILE87 5.0 37.3 1.0
CA B:MSE84 5.0 42.6 1.0

Magnesium binding site 3 out of 7 in 3p2l

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Magnesium binding site 3 out of 7 in the Crystal Structure of Atp-Dependent Clp Protease Subunit P From Francisella Tularensis


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 Atp-Dependent Clp Protease Subunit P From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:46.8
occ:1.00
 O C:PRO89 2.6 59.7 1.0
O C:ILE87 2.7 64.1 1.0
O C:HOH233 2.7 93.9 1.0
O C:MSE84 2.7 48.7 1.0
O3 C:PO4209 3.0 1.0 1.0
O C:HOH232 3.1 67.8 1.0
O1 C:PO4209 3.5 0.8 1.0
P C:PO4209 3.6 0.4 1.0
O4 C:PO4209 3.7 0.1 1.0
C C:PRO89 3.7 60.1 1.0
C C:ILE87 3.8 61.4 1.0
O C:GLN85 3.8 57.0 1.0
C C:MSE84 3.9 49.8 1.0
O C:LYS88 4.0 59.8 1.0
CG1 C:ILE87 4.0 54.5 1.0
C C:GLN85 4.1 56.2 1.0
CA C:GLN85 4.2 57.5 1.0
C C:LYS88 4.2 59.1 1.0
N C:ILE87 4.4 59.0 1.0
CA C:ASP90 4.4 60.3 1.0
N C:ASP90 4.5 59.9 1.0
N C:VAL91 4.5 58.9 1.0
CA C:ILE87 4.5 57.4 1.0
N C:GLN85 4.6 54.7 1.0
N C:PRO89 4.6 56.2 1.0
CG2 C:VAL91 4.7 53.6 1.0
N C:LYS88 4.7 62.9 1.0
N C:PHE86 4.8 55.2 1.0
CA C:PRO89 4.8 61.7 1.0
CA C:LYS88 4.8 63.7 1.0
C C:ASP90 4.9 62.0 1.0
C C:PHE86 4.9 61.4 1.0
CB C:ILE87 4.9 52.5 1.0
CA C:MSE84 5.0 50.6 1.0
OD1 C:ASP90 5.0 67.7 1.0

Magnesium binding site 4 out of 7 in 3p2l

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Magnesium binding site 4 out of 7 in the Crystal Structure of Atp-Dependent Clp Protease Subunit P From Francisella Tularensis


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 Atp-Dependent Clp Protease Subunit P From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:49.4
occ:1.00
 O D:MSE84 2.6 58.9 1.0
O D:ILE87 2.8 60.2 1.0
O D:HOH210 2.8 54.0 1.0
O D:PRO89 2.9 59.6 1.0
O4 D:PO4209 2.9 0.3 1.0
O1 D:PO4209 3.1 0.2 1.0
P D:PO4209 3.5 0.7 1.0
C D:MSE84 3.8 56.8 1.0
C D:PRO89 3.9 60.4 1.0
O3 D:PO4209 3.9 0.6 1.0
O D:GLN85 3.9 62.0 1.0
C D:ILE87 4.0 59.5 1.0
C D:GLN85 4.0 60.7 1.0
O D:LYS88 4.1 59.0 1.0
CG1 D:ILE87 4.1 53.7 1.0
CA D:GLN85 4.2 56.0 1.0
CA D:ASP90 4.2 61.4 1.0
N D:VAL91 4.4 60.2 1.0
N D:ASP90 4.4 57.7 1.0
C D:LYS88 4.4 62.1 1.0
N D:GLN85 4.5 53.3 1.0
N D:ILE87 4.5 59.5 1.0
CG2 D:VAL91 4.6 54.1 1.0
N D:PHE86 4.6 60.3 1.0
O D:HOH272 4.7 61.5 1.0
CA D:ILE87 4.7 60.7 1.0
C D:ASP90 4.7 63.4 1.0
OD1 D:ASP90 4.8 72.2 1.0
N D:PRO89 4.8 62.2 1.0
CA D:MSE84 4.9 53.2 1.0
C D:PHE86 4.9 63.3 1.0
O2 D:PO4209 4.9 0.0 1.0
CA D:PRO89 5.0 64.5 1.0
N D:LYS88 5.0 60.4 1.0

Magnesium binding site 5 out of 7 in 3p2l

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Magnesium binding site 5 out of 7 in the Crystal Structure of Atp-Dependent Clp Protease Subunit P From Francisella Tularensis


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 Atp-Dependent Clp Protease Subunit P From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg202

b:50.6
occ:1.00
 O E:PRO89 2.7 62.4 1.0
O4 E:PO4210 2.7 0.7 1.0
O E:ILE87 2.8 75.5 1.0
O E:HOH223 2.8 57.0 1.0
O E:MSE84 2.8 69.6 1.0
O3 E:PO4210 3.2 0.1 1.0
P E:PO4210 3.3 0.3 1.0
O1 E:PO4210 3.5 0.2 1.0
C E:PRO89 3.7 69.2 1.0
C E:ILE87 3.9 72.1 1.0
O E:HOH283 3.9 70.2 1.0
C E:MSE84 4.0 63.5 1.0
O E:LYS88 4.0 73.2 1.0
O E:GLN85 4.0 75.1 1.0
CG1 E:ILE87 4.1 63.8 1.0
C E:GLN85 4.2 71.7 1.0
C E:LYS88 4.3 70.0 1.0
CA E:ASP90 4.3 69.3 1.0
N E:ASP90 4.4 66.9 1.0
N E:ILE87 4.5 69.3 1.0
CA E:GLN85 4.5 67.3 1.0
N E:VAL91 4.5 68.5 1.0
O E:HOH211 4.6 0.9 1.0
N E:PRO89 4.6 64.5 1.0
N E:PHE86 4.6 66.4 1.0
CA E:ILE87 4.7 68.6 1.0
OD1 E:ASP90 4.7 79.0 1.0
CG2 E:VAL91 4.7 54.3 1.0
CA E:PRO89 4.7 69.7 1.0
O2 E:PO4210 4.7 0.5 1.0
C E:ASP90 4.8 69.1 1.0
N E:GLN85 4.8 60.2 1.0
N E:LYS88 4.8 72.0 1.0
CA E:LYS88 4.9 74.2 1.0
C E:PHE86 4.9 68.1 1.0

Magnesium binding site 6 out of 7 in 3p2l

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Magnesium binding site 6 out of 7 in the Crystal Structure of Atp-Dependent Clp Protease Subunit P From Francisella Tularensis


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 Atp-Dependent Clp Protease Subunit P From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg202

b:53.6
occ:1.00
 O F:MSE84 2.6 62.4 1.0
O F:ILE87 2.6 70.8 1.0
O F:PRO89 2.6 65.0 1.0
O4 F:PO4208 2.8 0.6 1.0
O1 F:PO4208 3.1 0.3 1.0
O F:HOH249 3.1 62.0 1.0
P F:PO4208 3.4 0.3 1.0
C F:PRO89 3.7 64.4 1.0
C F:ILE87 3.7 68.1 1.0
O2 F:PO4208 3.8 0.6 1.0
C F:MSE84 3.8 60.3 1.0
CG1 F:ILE87 3.8 53.3 1.0
O F:LYS88 3.9 71.7 1.0
O F:GLN85 4.0 63.8 1.0
C F:LYS88 4.2 69.3 1.0
C F:GLN85 4.2 63.9 1.0
CA F:GLN85 4.2 61.4 1.0
CA F:ASP90 4.3 63.4 1.0
N F:ASP90 4.3 63.5 1.0
N F:ILE87 4.5 70.0 1.0
N F:VAL91 4.5 59.8 1.0
N F:GLN85 4.5 62.5 1.0
CG2 F:VAL91 4.5 59.6 1.0
CA F:ILE87 4.5 65.4 1.0
N F:PRO89 4.6 61.7 1.0
N F:LYS88 4.7 68.5 1.0
CD1 F:ILE87 4.7 45.8 1.0
CA F:PRO89 4.7 63.8 1.0
CA F:LYS88 4.8 74.4 1.0
C F:ASP90 4.8 63.3 1.0
O3 F:PO4208 4.8 0.9 1.0
CB F:ILE87 4.8 57.2 1.0
OD1 F:ASP90 4.8 72.7 1.0
CA F:MSE84 4.9 56.7 1.0
N F:PHE86 4.9 69.4 1.0

Magnesium binding site 7 out of 7 in 3p2l

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Magnesium binding site 7 out of 7 in the Crystal Structure of Atp-Dependent Clp Protease Subunit P From Francisella Tularensis


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 Atp-Dependent Clp Protease Subunit P From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg202

b:38.4
occ:1.00
 O1 G:PO4211 2.6 0.7 1.0
O G:MSE84 2.7 41.4 1.0
O G:ILE87 2.7 54.0 1.0
O G:PRO89 2.7 50.1 1.0
O G:HOH233 3.0 49.5 1.0
O3 G:PO4211 3.0 0.4 1.0
P G:PO4211 3.2 0.6 1.0
O2 G:PO4211 3.6 0.7 1.0
C G:PRO89 3.8 46.9 1.0
C G:ILE87 3.8 52.2 1.0
C G:MSE84 3.9 42.6 1.0
O G:GLN85 3.9 49.1 1.0
CG1 G:ILE87 4.0 42.6 1.0
O G:LYS88 4.0 54.2 1.0
C G:GLN85 4.1 48.0 1.0
CA G:GLN85 4.3 43.7 1.0
C G:LYS88 4.3 51.3 1.0
CA G:ASP90 4.3 48.0 1.0
O A:HOH262 4.4 71.5 1.0
N G:ASP90 4.4 46.8 1.0
N G:ILE87 4.4 45.3 1.0
O G:HOH220 4.5 62.2 1.0
N G:GLN85 4.6 42.2 1.0
CA G:ILE87 4.6 43.3 1.0
O4 G:PO4211 4.6 1.0 1.0
N G:VAL91 4.6 45.9 1.0
N G:PRO89 4.6 50.0 1.0
CG2 G:VAL91 4.7 34.5 1.0
OD1 G:ASP90 4.7 57.5 1.0
N G:LYS88 4.8 47.2 1.0
N G:PHE86 4.8 50.7 1.0
C G:PHE86 4.8 50.6 1.0
CA G:PRO89 4.8 49.0 1.0
C G:ASP90 4.9 45.3 1.0
CA G:MSE84 4.9 43.0 1.0
CA G:LYS88 4.9 52.0 1.0
CB G:ILE87 4.9 42.3 1.0

Reference:

Y.Kim, M.Zhou, M.Gu, W.F.Anderson, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of Atp-Dependent Clp Protease Subunit P From Francisella Tularensis To Be Published.
Page generated: Thu Aug 15 09:06:32 2024

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