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Manganese in PDB 8fun: Enzymatically Active, Mn/Fe Metallated Form of AIBH1H2

Protein crystallography data

The structure of Enzymatically Active, Mn/Fe Metallated Form of AIBH1H2, PDB code: 8fun was solved by M.M.Powell, J.Rittle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.56 / 2.24
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 84.142, 148.923, 234.093, 90, 90, 90
R / Rfree (%) 17.7 / 19.8

Other elements in 8fun:

The structure of Enzymatically Active, Mn/Fe Metallated Form of AIBH1H2 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Enzymatically Active, Mn/Fe Metallated Form of AIBH1H2 (pdb code 8fun). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Enzymatically Active, Mn/Fe Metallated Form of AIBH1H2, PDB code: 8fun:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 8fun

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Manganese binding site 1 out of 5 in the Enzymatically Active, Mn/Fe Metallated Form of AIBH1H2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Enzymatically Active, Mn/Fe Metallated Form of AIBH1H2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:24.0
occ:1.00
 OD1 A:ASP340 2.1 21.2 1.0
OE2 A:GLU267 2.2 25.4 1.0
OD2 A:ASP36 2.2 17.1 1.0
NE2 A:HIS38 2.2 17.2 1.0
NE2 A:HIS213 2.3 18.1 1.0
CG A:ASP36 2.9 18.8 1.0
OD1 A:ASP36 3.0 16.2 1.0
CE1 A:HIS38 3.1 24.8 1.0
CE1 A:HIS213 3.1 13.9 1.0
CD A:GLU267 3.1 14.8 1.0
CG A:ASP340 3.2 23.1 1.0
CD2 A:HIS38 3.3 18.2 1.0
CB A:GLU267 3.4 13.5 1.0
CD2 A:HIS213 3.4 15.7 1.0
CG A:GLU267 3.5 16.8 1.0
OD2 A:ASP340 3.7 20.2 1.0
ND1 A:HIS38 4.2 21.4 1.0
ND1 A:HIS343 4.2 18.1 1.0
CE1 A:HIS343 4.2 19.4 1.0
OE1 A:GLU267 4.2 16.1 1.0
O A:HOH519 4.3 15.9 1.0
CB A:ASP340 4.3 17.3 1.0
ND1 A:HIS213 4.3 16.0 1.0
CG A:HIS38 4.3 23.0 1.0
CB A:ASP36 4.4 17.1 1.0
CG A:HIS213 4.5 20.4 1.0
CA A:ASP340 4.6 19.1 1.0
CA A:GLU267 4.8 17.7 1.0
O A:ASP36 5.0 14.8 1.0

Manganese binding site 2 out of 5 in 8fun

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Manganese binding site 2 out of 5 in the Enzymatically Active, Mn/Fe Metallated Form of AIBH1H2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Enzymatically Active, Mn/Fe Metallated Form of AIBH1H2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:36.0
occ:1.00
 ND1 B:HIS340 2.1 29.2 1.0
O B:HOH629 2.1 34.9 1.0
O B:HOH601 2.1 25.2 1.0
OD2 B:ASP337 2.3 25.1 1.0
OE2 B:GLU265 2.4 26.1 1.0
O B:HOH753 2.8 36.0 1.0
CE1 B:HIS340 2.9 27.8 1.0
CG B:HIS340 3.1 30.2 1.0
CG B:ASP337 3.2 25.2 1.0
CD B:GLU265 3.3 24.7 1.0
OE1 B:GLU265 3.4 22.1 1.0
OD1 B:ASP337 3.5 18.3 1.0
CB B:HIS340 3.6 25.8 1.0
FE B:FE504 3.8 33.7 1.0
NE2 B:HIS340 4.1 36.0 1.0
O B:HOH614 4.1 24.6 1.0
OD1 B:ASP342 4.2 24.7 1.0
CD2 B:HIS340 4.2 29.8 1.0
CB B:ASP337 4.6 22.2 1.0
NE2 B:HIS27 4.6 26.6 1.0
CG B:GLU265 4.7 21.8 1.0
CD2 B:HIS27 4.8 28.5 1.0
NE2 B:GLN309 5.0 26.8 1.0

Manganese binding site 3 out of 5 in 8fun

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Manganese binding site 3 out of 5 in the Enzymatically Active, Mn/Fe Metallated Form of AIBH1H2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Enzymatically Active, Mn/Fe Metallated Form of AIBH1H2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:25.5
occ:1.00
 NE2 C:HIS38 2.1 21.3 1.0
OD1 C:ASP340 2.2 22.3 1.0
OE2 C:GLU267 2.2 15.6 1.0
OD2 C:ASP36 2.2 20.6 1.0
NE2 C:HIS213 2.3 19.7 1.0
CE1 C:HIS38 2.9 22.6 1.0
CG C:ASP36 2.9 25.7 1.0
OD1 C:ASP36 3.0 20.1 1.0
CE1 C:HIS213 3.2 20.1 1.0
CD2 C:HIS38 3.2 18.0 1.0
CD C:GLU267 3.2 18.2 1.0
CG C:ASP340 3.3 22.9 1.0
CD2 C:HIS213 3.4 22.0 1.0
CB C:GLU267 3.4 18.9 1.0
CG C:GLU267 3.6 16.7 1.0
OD2 C:ASP340 3.8 18.6 1.0
ND1 C:HIS38 4.1 21.0 1.0
ND1 C:HIS343 4.1 17.4 1.0
CE1 C:HIS343 4.2 18.3 1.0
O C:HOH506 4.2 22.9 1.0
CG C:HIS38 4.2 16.5 1.0
ND1 C:HIS213 4.3 22.5 1.0
OE1 C:GLU267 4.4 19.2 1.0
CB C:ASP36 4.4 21.3 1.0
CB C:ASP340 4.4 24.6 1.0
CG C:HIS213 4.5 18.2 1.0
CA C:ASP340 4.6 21.7 1.0
CA C:GLU267 4.8 26.4 1.0

Manganese binding site 4 out of 5 in 8fun

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Manganese binding site 4 out of 5 in the Enzymatically Active, Mn/Fe Metallated Form of AIBH1H2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Enzymatically Active, Mn/Fe Metallated Form of AIBH1H2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:35.1
occ:1.00
 OD2 D:ASP25 2.0 29.6 1.0
NE2 D:HIS27 2.1 32.1 1.0
NE2 D:HIS211 2.1 26.8 1.0
OE1 D:GLU265 2.1 28.5 1.0
OD1 D:ASP337 2.3 29.7 1.0
CG D:ASP25 2.7 26.0 1.0
OD1 D:ASP25 2.7 31.6 1.0
CE1 D:HIS27 2.8 33.4 1.0
CD2 D:HIS211 3.0 23.7 1.0
CE1 D:HIS211 3.1 23.4 1.0
CD2 D:HIS27 3.2 31.4 1.0
CG D:ASP337 3.2 28.5 1.0
CD D:GLU265 3.4 32.0 1.0
OD2 D:ASP337 3.9 27.5 1.0
ND1 D:HIS27 4.0 25.8 1.0
CB D:ASP25 4.1 23.1 1.0
OE2 D:GLU265 4.2 37.4 1.0
CG D:HIS211 4.2 25.6 1.0
MN D:MN402 4.2 46.1 0.8
CB D:ASP337 4.2 30.6 1.0
ND1 D:HIS211 4.2 27.5 1.0
CG D:HIS27 4.2 27.2 1.0
CB D:GLU265 4.3 25.7 1.0
CG D:GLU265 4.4 29.9 1.0
CA D:ASP337 4.6 29.1 1.0
CG1 D:VAL264 4.7 29.2 1.0
ND1 D:HIS340 4.7 51.4 1.0
CE1 D:HIS340 4.7 47.9 1.0

Manganese binding site 5 out of 5 in 8fun

Go back to Manganese Binding Sites List in 8fun
Manganese binding site 5 out of 5 in the Enzymatically Active, Mn/Fe Metallated Form of AIBH1H2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Enzymatically Active, Mn/Fe Metallated Form of AIBH1H2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn402

b:46.1
occ:0.75
 ND1 D:HIS340 2.1 51.4 1.0
OD2 D:ASP337 2.2 27.5 1.0
O D:HOH593 2.3 47.6 1.0
O D:HOH599 2.3 49.1 1.0
OE2 D:GLU265 2.3 37.4 1.0
CE1 D:HIS340 3.1 47.9 1.0
CD D:GLU265 3.1 32.0 1.0
CG D:HIS340 3.1 53.0 1.0
CG D:ASP337 3.1 28.5 1.0
OE1 D:GLU265 3.2 28.5 1.0
CB D:HIS340 3.4 51.9 1.0
OD1 D:ASP337 3.4 29.7 1.0
OD1 D:ASP342 3.9 57.6 1.0
MN D:MN401 4.2 35.1 1.0
NE2 D:HIS340 4.2 54.4 1.0
CD2 D:HIS340 4.2 47.8 1.0
O D:HOH539 4.3 43.0 1.0
CB D:ASP337 4.5 30.6 1.0
CG D:GLU265 4.5 29.9 1.0
NE2 D:HIS27 4.7 32.1 1.0
OE1 D:GLN309 4.7 49.0 1.0
CD2 D:HIS27 4.8 31.4 1.0
CG D:ASP342 4.9 64.8 1.0
CA D:HIS340 4.9 54.6 1.0
OD2 D:ASP342 5.0 60.1 1.0
NE2 D:GLN309 5.0 45.5 1.0

Reference:

M.M.Powell, G.Rao, R.D.Britt, J.Rittle. Enzymatic Hydroxylation of Aliphatic C-H Bonds By A Mn/Fe Cofactor. Biorxiv 2023.
ISSN: ISSN 2692-8205
PubMed: 36945426
DOI: 10.1101/2023.03.10.532131
Page generated: Sun Oct 6 12:08:14 2024

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