Magnesium in PDB 7wid: Crystal Structure of Staphylococcus Aureus Clpp in Complex with ZG180

Enzymatic activity of Crystal Structure of Staphylococcus Aureus Clpp in Complex with ZG180

All present enzymatic activity of Crystal Structure of Staphylococcus Aureus Clpp in Complex with ZG180:
3.4.21.92;

Protein crystallography data

The structure of Crystal Structure of Staphylococcus Aureus Clpp in Complex with ZG180, PDB code: 7wid was solved by B.Y.Wei, J.H.Gan, C.-G.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 94.178, 126.385, 145.449, 90, 94.09, 90
R / Rfree (%) 19.7 / 20.6

Other elements in 7wid:

The structure of Crystal Structure of Staphylococcus Aureus Clpp in Complex with ZG180 also contains other interesting chemical elements:

Fluorine (F) 42 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Staphylococcus Aureus Clpp in Complex with ZG180 (pdb code 7wid). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the Crystal Structure of Staphylococcus Aureus Clpp in Complex with ZG180, PDB code: 7wid:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in 7wid

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Magnesium binding site 1 out of 13 in the Crystal Structure of Staphylococcus Aureus Clpp in Complex with ZG180


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 Staphylococcus Aureus Clpp in Complex with ZG180 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:23.7
occ:1.00
 O A:HOH392 2.5 38.5 1.0
O A:ILE81 2.6 12.2 1.0
O A:PRO86 2.7 13.9 1.0
O A:HOH381 2.7 11.9 1.0
O A:ILE84 3.3 15.0 1.0
C A:ILE81 3.7 12.2 1.0
C A:PRO86 3.8 13.8 1.0
CG1 A:ILE84 3.9 14.9 1.0
O A:HOH377 4.1 25.9 1.0
CG2 A:VAL88 4.1 12.1 1.0
N A:VAL88 4.2 12.1 1.0
C A:ILE84 4.2 15.4 1.0
CG2 A:ILE81 4.2 11.8 1.0
CA A:ASP87 4.3 13.1 1.0
N A:ASP87 4.4 13.2 1.0
O A:LYS85 4.5 15.1 1.0
C A:ASP87 4.5 12.5 1.0
CA A:GLN82 4.5 13.4 1.0
N A:GLN82 4.6 12.7 1.0
CA A:ILE81 4.6 11.8 1.0
O A:HOH316 4.6 12.7 1.0
C A:LYS85 4.7 15.5 1.0
O A:GLN82 4.7 13.7 1.0
CD1 A:ILE84 4.7 15.2 1.0
C A:GLN82 4.7 13.8 1.0
CB A:VAL88 4.8 12.2 1.0
N A:ILE84 4.8 15.0 1.0
N A:PRO86 4.8 14.6 1.0
CA A:ILE84 4.9 15.1 1.0
CA A:PRO86 4.9 14.3 1.0

Magnesium binding site 2 out of 13 in 7wid

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Magnesium binding site 2 out of 13 in the Crystal Structure of Staphylococcus Aureus Clpp in Complex with ZG180


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 Staphylococcus Aureus Clpp in Complex with ZG180 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:22.5
occ:1.00
 O B:HOH347 2.4 26.4 1.0
O B:ILE81 2.6 13.5 1.0
O B:PRO86 2.8 14.0 1.0
O B:HOH399 2.8 10.9 1.0
O B:ILE84 3.2 14.2 1.0
O B:HOH382 3.5 39.8 1.0
C B:ILE81 3.7 13.4 1.0
C B:PRO86 3.9 14.0 1.0
CG1 B:ILE84 4.0 13.9 1.0
O B:HOH369 4.1 31.5 1.0
C B:ILE84 4.2 14.8 1.0
CG2 B:VAL88 4.2 12.2 1.0
N B:VAL88 4.3 12.6 1.0
CG2 B:ILE81 4.3 12.7 1.0
CA B:ASP87 4.3 13.8 1.0
O B:LYS85 4.4 15.0 1.0
CA B:GLN82 4.5 14.6 1.0
N B:ASP87 4.5 13.6 1.0
N B:GLN82 4.5 13.9 1.0
O B:GLN82 4.6 15.3 1.0
C B:LYS85 4.6 15.2 1.0
O B:HOH328 4.6 12.1 1.0
C B:ASP87 4.6 13.4 1.0
C B:GLN82 4.7 14.9 1.0
CA B:ILE81 4.7 12.8 1.0
CD1 B:ILE84 4.8 13.8 1.0
N B:ILE84 4.8 14.7 1.0
N B:PRO86 4.8 14.5 1.0
CA B:ILE84 4.9 14.5 1.0
CB B:VAL88 4.9 12.2 1.0
OE1 B:GLN82 5.0 16.2 1.0
CA B:PRO86 5.0 14.4 1.0

Magnesium binding site 3 out of 13 in 7wid

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Magnesium binding site 3 out of 13 in the Crystal Structure of Staphylococcus Aureus Clpp in Complex with ZG180


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 Staphylococcus Aureus Clpp in Complex with ZG180 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:24.3
occ:1.00
 O C:HOH384 2.6 36.5 1.0
O C:PRO86 2.6 18.4 1.0
O C:ILE81 2.7 15.9 1.0
O C:HOH378 2.7 15.1 1.0
O C:ILE84 3.3 20.7 1.0
C C:PRO86 3.7 18.2 1.0
C C:ILE81 3.8 16.4 1.0
CG1 C:ILE84 4.0 20.1 1.0
O C:HOH335 4.0 25.0 1.0
CG2 C:VAL88 4.1 16.1 1.0
N C:VAL88 4.1 16.5 1.0
CA C:ASP87 4.2 17.2 1.0
C C:ILE84 4.2 21.2 1.0
CG2 C:ILE81 4.3 15.5 1.0
N C:ASP87 4.4 17.5 1.0
O C:LYS85 4.4 19.9 1.0
C C:ASP87 4.5 16.6 1.0
C C:LYS85 4.6 20.8 1.0
CA C:GLN82 4.6 18.7 1.0
O C:HOH327 4.6 16.6 1.0
N C:GLN82 4.7 17.3 1.0
CA C:ILE81 4.7 15.5 1.0
O C:GLN82 4.7 19.4 1.0
CD1 C:ILE84 4.7 20.3 1.0
CB C:VAL88 4.8 16.2 1.0
C C:GLN82 4.8 19.6 1.0
N C:PRO86 4.8 19.1 1.0
CA C:PRO86 4.9 18.9 1.0
N C:ILE84 4.9 20.7 1.0
CA C:ILE84 4.9 20.7 1.0

Magnesium binding site 4 out of 13 in 7wid

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Magnesium binding site 4 out of 13 in the Crystal Structure of Staphylococcus Aureus Clpp in Complex with ZG180


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 Staphylococcus Aureus Clpp in Complex with ZG180 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg202

b:28.2
occ:1.00
 O E:HOH369 2.5 33.4 1.0
O E:PRO86 2.6 22.8 1.0
O E:HOH363 2.7 19.4 1.0
O E:ILE81 2.7 20.3 1.0
O E:ILE84 3.3 22.4 1.0
C E:PRO86 3.7 22.5 1.0
C E:ILE81 3.8 20.1 1.0
O E:HOH353 4.0 38.4 1.0
CG1 E:ILE84 4.0 21.9 1.0
N E:VAL88 4.1 19.0 1.0
CG2 E:VAL88 4.1 18.8 1.0
CA E:ASP87 4.2 20.4 1.0
C E:ILE84 4.3 22.9 1.0
CG2 E:ILE81 4.3 18.7 1.0
N E:ASP87 4.3 21.4 1.0
O E:LYS85 4.4 23.6 1.0
C E:ASP87 4.5 20.0 1.0
O E:HOH326 4.6 19.4 1.0
C E:LYS85 4.6 23.4 1.0
CA E:GLN82 4.6 21.6 1.0
N E:GLN82 4.7 20.6 1.0
CA E:ILE81 4.7 19.3 1.0
O E:GLN82 4.7 22.9 1.0
CB E:VAL88 4.8 18.7 1.0
CD1 E:ILE84 4.8 22.0 1.0
N E:PRO86 4.8 23.0 1.0
C E:GLN82 4.8 21.9 1.0
CA E:PRO86 4.9 23.0 1.0
N E:ILE84 4.9 21.5 1.0
CA E:ILE84 5.0 21.9 1.0

Magnesium binding site 5 out of 13 in 7wid

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Magnesium binding site 5 out of 13 in the Crystal Structure of Staphylococcus Aureus Clpp in Complex with ZG180


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 Staphylococcus Aureus Clpp in Complex with ZG180 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg202

b:30.6
occ:1.00
 O F:HOH396 2.6 37.6 1.0
O F:PRO86 2.7 20.3 1.0
O F:ILE81 2.7 17.4 1.0
O F:HOH380 2.7 19.0 1.0
O F:ILE84 3.2 19.8 1.0
C F:PRO86 3.8 20.1 1.0
C F:ILE81 3.8 16.9 1.0
O F:HOH361 3.9 34.9 1.0
CG1 F:ILE84 4.0 18.4 1.0
C F:ILE84 4.2 19.9 1.0
CG2 F:VAL88 4.2 18.1 1.0
N F:VAL88 4.2 18.1 1.0
CA F:ASP87 4.2 19.6 1.0
CG2 F:ILE81 4.4 16.0 1.0
O F:LYS85 4.4 21.6 1.0
N F:ASP87 4.4 19.8 1.0
C F:ASP87 4.5 18.9 1.0
C F:LYS85 4.6 21.4 1.0
CA F:GLN82 4.6 18.2 1.0
O F:HOH338 4.6 19.5 1.0
N F:GLN82 4.6 17.3 1.0
O F:GLN82 4.7 19.0 1.0
CA F:ILE81 4.7 16.1 1.0
C F:GLN82 4.7 18.6 1.0
CD1 F:ILE84 4.8 18.4 1.0
N F:PRO86 4.8 20.3 1.0
CB F:VAL88 4.9 18.1 1.0
N F:ILE84 4.9 18.4 1.0
CA F:ILE84 4.9 19.1 1.0
CA F:PRO86 4.9 20.2 1.0

Magnesium binding site 6 out of 13 in 7wid

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Magnesium binding site 6 out of 13 in the Crystal Structure of Staphylococcus Aureus Clpp in Complex with ZG180


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 Staphylococcus Aureus Clpp in Complex with ZG180 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg202

b:25.8
occ:1.00
 O G:HOH368 2.4 37.5 1.0
O G:ILE81 2.6 14.0 1.0
O G:HOH392 2.7 14.3 1.0
O G:PRO86 2.7 16.6 1.0
O G:ILE84 3.2 16.7 1.0
O G:HOH353 3.5 41.2 1.0
C G:ILE81 3.7 14.0 1.0
C G:PRO86 3.9 17.2 1.0
CG1 G:ILE84 3.9 16.1 1.0
O G:HOH342 4.1 28.8 1.0
C G:ILE84 4.2 17.4 1.0
CG2 G:VAL88 4.2 14.2 1.0
N G:VAL88 4.3 14.8 1.0
CG2 G:ILE81 4.3 13.4 1.0
CA G:ASP87 4.3 16.4 1.0
O G:LYS85 4.5 18.2 1.0
CA G:GLN82 4.5 15.5 1.0
N G:ASP87 4.5 16.7 1.0
N G:GLN82 4.5 14.9 1.0
O G:HOH345 4.6 12.5 1.0
O G:GLN82 4.6 14.9 1.0
C G:ASP87 4.6 15.7 1.0
CA G:ILE81 4.6 13.3 1.0
C G:LYS85 4.6 18.4 1.0
C G:GLN82 4.6 15.8 1.0
CD1 G:ILE84 4.8 16.1 1.0
N G:ILE84 4.8 16.7 1.0
CA G:ILE84 4.8 16.9 1.0
CB G:VAL88 4.8 14.2 1.0
N G:PRO86 4.9 17.7 1.0
NE2 G:GLN82 4.9 17.1 1.0
CA G:PRO86 5.0 17.3 1.0

Magnesium binding site 7 out of 13 in 7wid

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Magnesium binding site 7 out of 13 in the Crystal Structure of Staphylococcus Aureus Clpp in Complex with ZG180


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 Staphylococcus Aureus Clpp in Complex with ZG180 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg202

b:21.6
occ:1.00
 O H:ILE81 2.6 11.6 1.0
O H:HOH384 2.6 33.2 1.0
O H:PRO86 2.7 13.9 1.0
O H:HOH383 2.8 11.5 1.0
O H:ILE84 3.3 14.2 1.0
O H:HOH385 3.5 40.0 1.0
C H:ILE81 3.7 11.8 1.0
C H:PRO86 3.8 14.1 1.0
CG1 H:ILE84 3.9 13.9 1.0
CG2 H:VAL88 4.1 13.3 1.0
O H:HOH377 4.1 27.2 1.0
N H:VAL88 4.2 13.6 1.0
C H:ILE84 4.2 14.9 1.0
CG2 H:ILE81 4.2 11.4 1.0
CA H:ASP87 4.3 14.1 1.0
N H:ASP87 4.4 13.9 1.0
O H:LYS85 4.5 14.8 1.0
C H:ASP87 4.5 13.9 1.0
CA H:GLN82 4.5 13.2 1.0
N H:GLN82 4.6 12.5 1.0
O H:HOH344 4.6 11.6 1.0
CA H:ILE81 4.6 11.3 1.0
C H:LYS85 4.6 15.1 1.0
O H:GLN82 4.7 13.9 1.0
C H:GLN82 4.7 13.6 1.0
CD1 H:ILE84 4.7 14.0 1.0
CB H:VAL88 4.8 13.4 1.0
N H:PRO86 4.9 14.6 1.0
N H:ILE84 4.9 14.3 1.0
CA H:ILE84 4.9 14.3 1.0
CA H:PRO86 4.9 14.1 1.0

Magnesium binding site 8 out of 13 in 7wid

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Magnesium binding site 8 out of 13 in the Crystal Structure of Staphylococcus Aureus Clpp in Complex with ZG180


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Staphylococcus Aureus Clpp in Complex with ZG180 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg202

b:19.8
occ:1.00
 O I:HOH388 2.5 36.8 1.0
O I:PRO86 2.6 12.6 1.0
O I:ILE81 2.7 12.6 1.0
O I:HOH398 2.7 11.7 1.0
O I:ILE84 3.2 13.5 1.0
O I:HOH351 3.5 35.3 1.0
C I:PRO86 3.7 13.0 1.0
C I:ILE81 3.8 12.8 1.0
O I:HOH353 3.9 22.2 1.0
CG1 I:ILE84 3.9 13.0 1.0
CG2 I:VAL88 4.1 11.5 1.0
C I:ILE84 4.2 14.1 1.0
N I:VAL88 4.2 11.5 1.0
CA I:ASP87 4.2 12.6 1.0
CG2 I:ILE81 4.3 11.9 1.0
N I:ASP87 4.4 12.6 1.0
O I:LYS85 4.4 14.7 1.0
C I:ASP87 4.5 11.9 1.0
C I:LYS85 4.5 14.4 1.0
CA I:GLN82 4.6 13.8 1.0
O I:HOH335 4.6 9.5 1.0
N I:GLN82 4.6 13.3 1.0
CA I:ILE81 4.7 12.0 1.0
O I:GLN82 4.7 13.8 1.0
CD1 I:ILE84 4.7 12.9 1.0
N I:PRO86 4.7 13.4 1.0
C I:GLN82 4.8 14.0 1.0
CB I:VAL88 4.8 11.3 1.0
CA I:PRO86 4.8 13.3 1.0
N I:ILE84 4.9 13.6 1.0
CA I:ILE84 4.9 13.6 1.0
NE2 I:GLN82 4.9 15.0 1.0

Magnesium binding site 9 out of 13 in 7wid

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Magnesium binding site 9 out of 13 in the Crystal Structure of Staphylococcus Aureus Clpp in Complex with ZG180


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Staphylococcus Aureus Clpp in Complex with ZG180 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg202

b:25.4
occ:1.00
 O J:PRO86 2.6 17.3 1.0
O J:HOH398 2.6 36.2 1.0
O J:ILE81 2.6 16.9 1.0
O J:HOH364 2.7 14.6 1.0
O J:ILE84 3.3 18.5 1.0
O J:HOH354 3.4 45.7 1.0
C J:PRO86 3.7 17.4 1.0
C J:ILE81 3.8 16.5 1.0
CG1 J:ILE84 3.9 18.4 1.0
O J:HOH330 4.0 28.1 1.0
CG2 J:VAL88 4.1 15.2 1.0
N J:VAL88 4.1 15.3 1.0
C J:ILE84 4.2 19.2 1.0
CA J:ASP87 4.2 16.4 1.0
CG2 J:ILE81 4.3 15.5 1.0
N J:ASP87 4.4 16.8 1.0
O J:LYS85 4.4 19.3 1.0
C J:ASP87 4.5 15.8 1.0
O J:HOH367 4.5 14.9 1.0
C J:LYS85 4.6 19.3 1.0
CA J:GLN82 4.6 18.4 1.0
N J:GLN82 4.6 17.4 1.0
CA J:ILE81 4.7 15.8 1.0
CD1 J:ILE84 4.7 18.3 1.0
O J:GLN82 4.7 18.7 1.0
CB J:VAL88 4.8 15.2 1.0
C J:GLN82 4.8 18.7 1.0
N J:PRO86 4.8 18.2 1.0
CA J:PRO86 4.9 17.9 1.0
N J:ILE84 4.9 19.3 1.0
CA J:ILE84 4.9 19.1 1.0

Magnesium binding site 10 out of 13 in 7wid

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Magnesium binding site 10 out of 13 in the Crystal Structure of Staphylococcus Aureus Clpp in Complex with ZG180


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Staphylococcus Aureus Clpp in Complex with ZG180 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg202

b:30.4
occ:1.00
 O K:ILE81 2.6 21.2 1.0
O K:HOH348 2.6 43.5 1.0
O K:HOH380 2.7 21.0 1.0
O K:PRO86 2.8 20.9 1.0
O K:HOH337 3.1 51.9 1.0
O K:ILE84 3.2 21.3 1.0
C K:ILE81 3.7 20.8 1.0
C K:PRO86 3.9 20.7 1.0
CG1 K:ILE84 4.0 20.8 1.0
O K:HOH326 4.1 33.9 1.0
C K:ILE84 4.2 21.1 1.0
CG2 K:VAL88 4.2 19.2 1.0
N K:VAL88 4.2 19.5 1.0
CG2 K:ILE81 4.3 19.7 1.0
CA K:ASP87 4.3 20.5 1.0
O K:LYS85 4.5 21.3 1.0
CA K:GLN82 4.5 22.4 1.0
N K:ASP87 4.5 20.3 1.0
N K:GLN82 4.5 21.8 1.0
O K:GLN82 4.6 23.6 1.0
C K:ASP87 4.6 20.0 1.0
O K:HOH312 4.6 21.7 1.0
C K:LYS85 4.6 20.9 1.0
CA K:ILE81 4.7 20.1 1.0
C K:GLN82 4.7 22.9 1.0
CD1 K:ILE84 4.8 20.6 1.0
N K:ILE84 4.8 22.0 1.0
CB K:VAL88 4.9 19.5 1.0
N K:PRO86 4.9 20.9 1.0
CA K:ILE84 4.9 21.3 1.0
OE1 K:GLN82 5.0 24.4 1.0
CA K:PRO86 5.0 20.9 1.0

Reference:

B.Wei, T.Zhang, P.Wang, Y.Pan, J.Li, W.Chen, M.Zhang, Q.Ji, W.Wu, L.Lan, J.Gan, C.G.Yang. Anti-Infective Therapy Using Species-Specific Activators of Staphylococcus Aureus Clpp. Nat Commun V. 13 6909 2022.
ISSN: ESSN 2041-1723
PubMed: 36376309
DOI: 10.1038/S41467-022-34753-0
Page generated: Fri Apr 7 01:50:17 2023

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