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Magnesium in PDB 8k32: The Complex Structure of Slkari with Nadh at 2.12-Angstrom Resolution

Enzymatic activity of The Complex Structure of Slkari with Nadh at 2.12-Angstrom Resolution

All present enzymatic activity of The Complex Structure of Slkari with Nadh at 2.12-Angstrom Resolution:
1.1.1.86;

Protein crystallography data

The structure of The Complex Structure of Slkari with Nadh at 2.12-Angstrom Resolution, PDB code: 8k32 was solved by C.Y.Chen, C.H.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.09 / 2.12
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 131.557, 131.557, 297.906, 90, 90, 120
R / Rfree (%) 17.9 / 21.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Complex Structure of Slkari with Nadh at 2.12-Angstrom Resolution (pdb code 8k32). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the The Complex Structure of Slkari with Nadh at 2.12-Angstrom Resolution, PDB code: 8k32:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8k32

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Magnesium binding site 1 out of 8 in the The Complex Structure of Slkari with Nadh at 2.12-Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Complex Structure of Slkari with Nadh at 2.12-Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg408

b:41.9
occ:1.00
 O A:HOH721 1.9 29.4 1.0
OE1 A:GLU200 2.0 26.9 1.0
O A:HOH603 2.1 21.4 1.0
OD1 A:ASP196 2.2 23.2 1.0
O A:HOH516 2.3 35.0 1.0
O A:HOH518 2.4 33.1 1.0
CD A:GLU200 3.0 19.3 1.0
CG A:ASP196 3.2 20.5 1.0
OE2 A:GLU200 3.5 17.2 1.0
OD2 A:ASP196 3.5 26.1 1.0
O A:HOH704 3.8 43.4 1.0
O A:HOH696 3.8 29.5 1.0
O A:HOH566 4.0 20.7 1.0
O A:HOH619 4.1 20.0 1.0
NE2 A:HIS113 4.2 19.4 1.0
CG A:GLU200 4.2 24.0 1.0
O A:HOH735 4.3 30.9 1.0
OG B:SER257 4.3 20.4 1.0
CE1 A:HIS113 4.3 18.3 1.0
CB A:ASP196 4.5 17.1 1.0
O B:HOH601 4.7 26.3 1.0
CD2 A:HIS113 4.8 16.2 1.0
O A:ASP196 4.8 15.0 1.0
CB B:ALA260 4.9 18.7 1.0
ND1 A:HIS113 4.9 15.7 1.0
C A:ASP196 5.0 16.9 1.0

Magnesium binding site 2 out of 8 in 8k32

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Magnesium binding site 2 out of 8 in the The Complex Structure of Slkari with Nadh at 2.12-Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Complex Structure of Slkari with Nadh at 2.12-Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg409

b:50.2
occ:1.00
 OD1 B:ASP196 2.5 37.7 1.0
OE1 A:GLU232 2.5 36.5 1.0
OE2 A:GLU236 2.8 51.5 1.0
OE1 A:GLU236 2.9 50.9 1.0
O A:HOH732 2.9 43.1 1.0
CD A:GLU236 3.1 49.7 1.0
O B:HOH543 3.2 39.8 1.0
CD A:GLU232 3.4 37.1 1.0
O A:HOH517 3.4 33.1 1.0
NZ B:LYS136 3.5 48.4 1.0
O B:HOH608 3.5 40.2 1.0
OE2 A:GLU232 3.6 41.3 1.0
CG B:ASP196 3.7 36.8 1.0
O B:HOH595 4.3 60.9 1.0
CG A:GLU236 4.4 37.8 1.0
CB B:ASP196 4.5 34.0 1.0
OD2 B:ASP196 4.5 37.2 1.0
CA B:ASP196 4.7 31.8 1.0
CE B:LYS136 4.8 54.3 1.0
CG A:GLU232 4.8 33.9 1.0

Magnesium binding site 3 out of 8 in 8k32

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Magnesium binding site 3 out of 8 in the The Complex Structure of Slkari with Nadh at 2.12-Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Complex Structure of Slkari with Nadh at 2.12-Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg406

b:43.5
occ:1.00
 OD2 A:ASP196 2.6 26.1 1.0
OE1 B:GLU236 2.6 41.4 1.0
OE1 B:GLU232 2.7 23.9 1.0
OE2 B:GLU236 3.1 39.7 1.0
CD B:GLU236 3.1 39.4 1.0
O A:HOH591 3.3 19.4 1.0
O B:HOH572 3.4 22.5 1.0
O A:HOH735 3.4 30.9 1.0
NZ A:LYS136 3.4 26.2 1.0
CD B:GLU232 3.5 23.9 1.0
OE2 B:GLU232 3.5 26.2 1.0
O A:HOH518 3.6 33.1 1.0
CG A:ASP196 3.7 20.5 1.0
O A:HOH705 3.8 29.6 1.0
O B:HOH586 3.9 33.8 1.0
O B:HOH651 4.4 54.0 1.0
CB A:ASP196 4.4 17.1 1.0
OD1 A:ASP196 4.5 23.2 1.0
CG B:GLU236 4.5 29.6 1.0
CE A:LYS136 4.7 26.1 1.0
CA A:ASP196 4.7 16.7 1.0
O A:HOH696 4.8 29.5 1.0
CG B:GLU232 4.9 20.1 1.0
O A:HOH602 4.9 19.9 1.0

Magnesium binding site 4 out of 8 in 8k32

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Magnesium binding site 4 out of 8 in the The Complex Structure of Slkari with Nadh at 2.12-Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Complex Structure of Slkari with Nadh at 2.12-Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg407

b:51.0
occ:1.00
 OE1 B:GLU200 1.9 36.9 1.0
O B:HOH530 2.1 33.6 1.0
O B:HOH560 2.3 37.7 1.0
OD2 B:ASP196 2.5 37.2 1.0
O B:HOH543 2.6 39.8 1.0
CD B:GLU200 3.1 32.0 1.0
CG B:ASP196 3.5 36.8 1.0
OE2 B:GLU200 3.6 30.5 1.0
OD1 B:ASP196 3.8 37.7 1.0
OG A:SER257 3.9 33.8 1.0
CG B:GLU200 4.2 33.3 1.0
O B:HOH523 4.3 38.7 1.0
O A:HOH604 4.4 31.1 1.0
O A:HOH732 4.4 43.1 1.0
NE2 B:HIS113 4.5 41.2 1.0
CE1 B:HIS113 4.6 40.1 1.0
CB A:ALA260 4.7 28.4 1.0
CB B:ASP196 4.9 34.0 1.0
CD2 B:HIS113 4.9 44.8 1.0
CB A:SER257 5.0 30.5 1.0

Magnesium binding site 5 out of 8 in 8k32

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Magnesium binding site 5 out of 8 in the The Complex Structure of Slkari with Nadh at 2.12-Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Complex Structure of Slkari with Nadh at 2.12-Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg407

b:38.6
occ:1.00
 O C:HOH623 1.8 32.7 1.0
OE2 C:GLU200 2.0 33.6 1.0
O C:HOH534 2.0 31.0 1.0
O C:HOH508 2.1 36.1 1.0
O D:HOH528 2.2 45.0 1.0
OD1 C:ASP196 2.4 29.0 1.0
CD C:GLU200 3.0 28.6 1.0
CG C:ASP196 3.3 30.2 1.0
OD2 C:ASP196 3.4 35.1 1.0
OE1 C:GLU200 3.5 26.8 1.0
O C:HOH551 4.0 30.2 1.0
O C:HOH637 4.0 33.3 1.0
O C:HOH638 4.1 34.8 1.0
OG D:SER257 4.2 29.5 1.0
CG C:GLU200 4.3 30.2 1.0
O D:HOH689 4.3 33.2 1.0
O C:HOH617 4.4 28.5 1.0
NE2 C:HIS113 4.5 31.6 1.0
CE1 C:HIS113 4.5 29.3 1.0
CB C:ASP196 4.7 28.6 1.0
CB D:ALA260 4.7 26.1 1.0
O C:ASP196 4.9 25.6 1.0
CD2 C:HIS113 5.0 27.6 1.0

Magnesium binding site 6 out of 8 in 8k32

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Magnesium binding site 6 out of 8 in the The Complex Structure of Slkari with Nadh at 2.12-Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Complex Structure of Slkari with Nadh at 2.12-Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg408

b:51.5
occ:1.00
 OE1 C:GLU232 2.5 27.4 1.0
OD2 D:ASP196 2.7 28.8 1.0
OE1 C:GLU236 2.9 43.0 1.0
O C:HOH620 3.1 32.8 1.0
NZ D:LYS136 3.3 29.6 1.0
CD C:GLU232 3.3 27.8 1.0
O D:HOH592 3.4 23.7 1.0
OE2 C:GLU232 3.4 32.2 1.0
O D:HOH685 3.5 46.7 1.0
O D:HOH544 3.7 32.1 1.0
CD C:GLU236 3.7 43.0 1.0
CG D:ASP196 3.7 24.9 1.0
CG C:GLU236 4.2 33.6 1.0
CB D:ASP196 4.4 23.6 1.0
CE D:LYS136 4.5 30.9 1.0
OD1 D:ASP196 4.5 28.6 1.0
O D:HOH731 4.6 34.6 1.0
OE2 C:GLU236 4.6 42.3 1.0
CA D:ASP196 4.7 21.1 1.0
CG C:GLU232 4.8 25.8 1.0

Magnesium binding site 7 out of 8 in 8k32

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Magnesium binding site 7 out of 8 in the The Complex Structure of Slkari with Nadh at 2.12-Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Complex Structure of Slkari with Nadh at 2.12-Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg408

b:51.0
occ:1.00
 OE2 D:GLU236 2.6 51.1 1.0
OE2 D:GLU232 2.6 33.3 1.0
OD2 C:ASP196 2.6 35.1 1.0
OE1 D:GLU236 2.8 48.5 1.0
CD D:GLU236 3.1 46.1 1.0
O C:HOH606 3.2 32.9 1.0
OE1 D:GLU232 3.3 34.6 1.0
CD D:GLU232 3.3 32.3 1.0
O C:HOH638 3.5 34.8 1.0
O C:HOH508 3.6 36.1 1.0
NZ C:LYS136 3.7 33.7 1.0
CG C:ASP196 3.8 30.2 1.0
O D:HOH515 3.9 28.8 1.0
CB C:ASP196 4.5 28.6 1.0
CG D:GLU236 4.5 38.7 1.0
OD1 C:ASP196 4.7 29.0 1.0
O C:HOH637 4.8 33.3 1.0
CG D:GLU232 4.8 29.5 1.0
O C:HOH543 4.9 31.3 1.0
CE C:LYS136 4.9 41.2 1.0
CA C:ASP196 4.9 25.9 1.0

Magnesium binding site 8 out of 8 in 8k32

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Magnesium binding site 8 out of 8 in the The Complex Structure of Slkari with Nadh at 2.12-Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Complex Structure of Slkari with Nadh at 2.12-Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg409

b:39.2
occ:1.00
 OE1 D:GLU200 2.0 28.6 1.0
O D:HOH703 2.0 55.3 1.0
O D:HOH587 2.1 37.5 1.0
O D:HOH544 2.2 32.1 1.0
O D:HOH575 2.2 25.7 1.0
OD1 D:ASP196 2.6 28.6 1.0
CD D:GLU200 3.1 22.4 1.0
CG D:ASP196 3.5 24.9 1.0
OE2 D:GLU200 3.6 22.1 1.0
OD2 D:ASP196 3.6 28.8 1.0
O D:HOH527 3.9 25.2 1.0
O D:HOH731 3.9 34.6 1.0
O D:HOH759 4.1 38.6 1.0
OG C:SER257 4.2 23.8 1.0
O D:HOH661 4.2 24.5 1.0
CG D:GLU200 4.3 25.8 1.0
O C:HOH644 4.3 26.9 1.0
NE2 D:HIS113 4.4 23.9 1.0
CE1 D:HIS113 4.5 23.8 1.0
CB C:ALA260 4.7 22.2 1.0
CD2 D:HIS113 4.9 23.2 1.0
CB D:ASP196 4.9 23.6 1.0

Reference:

C.Y.Chen, C.H.Huang. Structural Bases of Coenzyme Specificity of Thermophilic Ketol-Acid Reductoisomerase To Be Published.
Page generated: Fri Oct 4 13:46:23 2024

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