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Manganese in PDB 8sma: Sfbo with Di-Manganese Cofactor

Protein crystallography data

The structure of Sfbo with Di-Manganese Cofactor, PDB code: 8sma was solved by C.Liu, J.Rittle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 93.53 / 2.18
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.388, 127.408, 137.749, 90, 90, 90
R / Rfree (%) 14.9 / 19.2

Manganese Binding Sites:

The binding sites of Manganese atom in the Sfbo with Di-Manganese Cofactor (pdb code 8sma). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Sfbo with Di-Manganese Cofactor, PDB code: 8sma:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 8sma

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Manganese binding site 1 out of 8 in the Sfbo with Di-Manganese Cofactor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Sfbo with Di-Manganese Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:27.5
occ:0.86
NE2 A:HIS32 2.0 17.3 1.0
OD2 A:ASP30 2.0 22.3 1.0
OE1 A:GLU264 2.1 32.6 1.0
NE2 A:HIS207 2.2 23.4 1.0
OD1 A:ASP337 2.2 27.9 1.0
CG A:ASP30 2.8 23.5 1.0
OD1 A:ASP30 2.9 20.8 1.0
CE1 A:HIS32 3.0 22.4 1.0
CD2 A:HIS32 3.0 20.4 1.0
CD2 A:HIS207 3.1 17.7 1.0
CE1 A:HIS207 3.2 19.7 1.0
CG A:ASP337 3.3 25.7 1.0
CD A:GLU264 3.3 28.1 1.0
MN A:MN403 3.9 36.8 0.7
O A:HOH512 4.0 22.1 1.0
OD2 A:ASP337 4.0 27.7 1.0
ND1 A:HIS32 4.1 22.5 1.0
CB A:ASP337 4.1 19.2 1.0
OE2 A:GLU264 4.1 28.8 1.0
CG A:HIS32 4.1 19.5 1.0
CB A:GLU264 4.2 22.4 1.0
CB A:ASP30 4.3 20.4 1.0
CG A:HIS207 4.3 22.0 1.0
ND1 A:HIS207 4.3 20.8 1.0
CG A:GLU264 4.3 26.7 1.0
CA A:ASP337 4.3 20.5 1.0
CG2 A:ILE263 4.5 26.6 1.0
ND1 A:HIS340 4.5 27.4 1.0
CE1 A:HIS340 4.7 28.1 1.0
O A:HOH702 4.8 33.4 1.0

Manganese binding site 2 out of 8 in 8sma

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Manganese binding site 2 out of 8 in the Sfbo with Di-Manganese Cofactor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Sfbo with Di-Manganese Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:36.8
occ:0.71
O A:HOH501 2.1 33.9 1.0
OD2 A:ASP337 2.1 27.7 1.0
ND1 A:HIS340 2.4 27.4 1.0
OE2 A:GLU264 2.5 28.8 1.0
CG A:ASP337 2.8 25.7 1.0
OD1 A:ASP337 2.9 27.9 1.0
OE1 A:GLU264 3.1 32.6 1.0
CD A:GLU264 3.2 28.1 1.0
CG A:HIS340 3.3 28.2 1.0
CE1 A:HIS340 3.4 28.1 1.0
CB A:HIS340 3.5 22.3 1.0
O1 A:SO4401 3.6 24.4 0.8
OD1 A:ASP342 3.8 23.8 1.0
O A:HOH635 3.8 35.1 1.0
MN A:MN402 3.9 27.5 0.9
O4 A:SO4401 4.0 28.3 0.8
O A:HOH504 4.3 31.6 1.0
S A:SO4401 4.3 35.7 0.8
CB A:ASP337 4.3 19.2 1.0
NE2 A:HIS32 4.3 17.3 1.0
O A:HOH702 4.4 33.4 1.0
CD2 A:HIS340 4.4 25.2 1.0
OD2 A:ASP342 4.4 35.1 1.0
NE2 A:HIS340 4.5 25.9 1.0
CG A:ASP342 4.5 28.2 1.0
CD2 A:HIS32 4.6 20.4 1.0
CE2 A:PHE208 4.6 21.7 1.0
CG A:GLU264 4.7 26.7 1.0
O A:ASP337 4.7 18.6 1.0
O2 A:SO4401 4.7 39.7 0.8
CA A:HIS340 5.0 26.3 1.0
NE2 A:GLN308 5.0 16.1 1.0

Manganese binding site 3 out of 8 in 8sma

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Manganese binding site 3 out of 8 in the Sfbo with Di-Manganese Cofactor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Sfbo with Di-Manganese Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:23.8
occ:0.82
OD2 B:ASP30 2.0 20.5 1.0
OE1 B:GLU264 2.0 24.7 1.0
NE2 B:HIS32 2.2 25.0 1.0
OD1 B:ASP337 2.2 28.6 1.0
NE2 B:HIS207 2.2 22.8 1.0
CG B:ASP30 2.9 22.8 1.0
OD1 B:ASP30 3.0 18.6 1.0
CD2 B:HIS32 3.1 22.8 1.0
CE1 B:HIS32 3.1 25.5 1.0
CG B:ASP337 3.2 24.8 1.0
CE1 B:HIS207 3.2 22.2 1.0
CD2 B:HIS207 3.3 20.0 1.0
CD B:GLU264 3.3 21.0 1.0
MN B:MN403 3.8 35.8 0.6
OD2 B:ASP337 3.8 29.0 1.0
OE2 B:GLU264 3.9 26.1 1.0
O B:HOH531 4.1 18.3 1.0
CB B:ASP337 4.1 23.2 1.0
ND1 B:HIS32 4.2 24.4 1.0
CG B:HIS32 4.3 21.4 1.0
CB B:GLU264 4.3 19.3 1.0
CB B:ASP30 4.3 21.1 1.0
ND1 B:HIS207 4.3 22.1 1.0
CG B:GLU264 4.3 23.2 1.0
ND1 B:HIS340 4.4 29.4 1.0
CG B:HIS207 4.4 20.8 1.0
CA B:ASP337 4.4 22.2 1.0
CE1 B:HIS340 4.5 27.6 1.0
O B:HOH507 4.5 30.8 0.8
CG2 B:ILE263 4.6 28.0 1.0
OE1 B:GLN308 4.9 19.9 1.0

Manganese binding site 4 out of 8 in 8sma

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Manganese binding site 4 out of 8 in the Sfbo with Di-Manganese Cofactor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Sfbo with Di-Manganese Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn403

b:35.8
occ:0.57
O B:HOH501 2.1 33.6 1.0
OD2 B:ASP337 2.1 29.0 1.0
O B:HOH507 2.2 30.8 0.8
ND1 B:HIS340 2.3 29.4 1.0
OE2 B:GLU264 2.3 26.1 1.0
CG B:ASP337 2.9 24.8 1.0
OD1 B:ASP337 3.0 28.6 1.0
CD B:GLU264 3.1 21.0 1.0
OE1 B:GLU264 3.2 24.7 1.0
CE1 B:HIS340 3.2 27.6 1.0
CG B:HIS340 3.3 23.7 1.0
CB B:HIS340 3.6 26.3 1.0
O2 B:SO4401 3.8 23.5 0.8
MN B:MN402 3.8 23.8 0.8
OD1 B:ASP342 3.9 24.1 1.0
O3 B:SO4401 3.9 24.4 0.8
O B:HOH651 4.1 34.6 1.0
O B:HOH511 4.2 25.5 1.0
NE2 B:HIS340 4.3 30.2 1.0
S B:SO4401 4.4 29.1 0.8
NE2 B:HIS32 4.4 25.0 1.0
CB B:ASP337 4.4 23.2 1.0
CD2 B:HIS340 4.4 26.2 1.0
CE2 B:PHE208 4.5 21.4 1.0
CG B:GLU264 4.6 23.2 1.0
OD2 B:ASP342 4.6 30.5 1.0
CG B:ASP342 4.7 30.4 1.0
CD2 B:HIS32 4.7 22.8 1.0
O4 B:SO4401 4.8 31.2 0.8
O B:ASP337 4.9 22.7 1.0

Manganese binding site 5 out of 8 in 8sma

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Manganese binding site 5 out of 8 in the Sfbo with Di-Manganese Cofactor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Sfbo with Di-Manganese Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn402

b:24.1
occ:0.79
NE2 G:HIS32 2.0 20.7 1.0
OD2 G:ASP30 2.0 16.5 1.0
OE1 G:GLU264 2.1 31.8 1.0
NE2 G:HIS207 2.2 19.3 1.0
OD1 G:ASP337 2.2 27.1 1.0
CG G:ASP30 2.9 22.1 1.0
CE1 G:HIS32 2.9 21.1 1.0
CD2 G:HIS32 3.0 21.8 1.0
CE1 G:HIS207 3.1 18.0 1.0
OD1 G:ASP30 3.1 20.0 1.0
CG G:ASP337 3.2 25.6 1.0
CD2 G:HIS207 3.2 19.3 1.0
CD G:GLU264 3.3 23.4 1.0
MN G:MN403 3.6 34.1 0.6
OD2 G:ASP337 3.9 23.4 1.0
OE2 G:GLU264 4.0 27.4 1.0
O G:HOH540 4.1 21.3 1.0
ND1 G:HIS32 4.1 21.3 1.0
CB G:ASP337 4.1 20.2 1.0
CG G:HIS32 4.1 25.6 1.0
ND1 G:HIS207 4.2 16.3 1.0
CB G:GLU264 4.3 19.8 1.0
CB G:ASP30 4.3 17.6 1.0
CG G:HIS207 4.3 23.0 1.0
O G:HOH523 4.3 32.6 0.7
ND1 G:HIS340 4.3 32.8 1.0
CG G:GLU264 4.4 24.8 1.0
CA G:ASP337 4.4 21.8 1.0
CE1 G:HIS340 4.5 34.6 1.0
CG2 G:ILE263 4.7 27.8 1.0
O G:HOH704 4.8 33.3 1.0
OE1 G:GLN308 5.0 23.9 1.0

Manganese binding site 6 out of 8 in 8sma

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Manganese binding site 6 out of 8 in the Sfbo with Di-Manganese Cofactor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Sfbo with Di-Manganese Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn403

b:34.1
occ:0.61
O G:HOH517 1.8 26.9 1.0
O G:HOH523 2.1 32.6 0.7
OD2 G:ASP337 2.1 23.4 1.0
OE2 G:GLU264 2.2 27.4 1.0
ND1 G:HIS340 2.3 32.8 1.0
CG G:ASP337 2.8 25.6 1.0
OD1 G:ASP337 2.8 27.1 1.0
OE1 G:GLU264 2.9 31.8 1.0
CD G:GLU264 2.9 23.4 1.0
CE1 G:HIS340 3.2 34.6 1.0
CG G:HIS340 3.3 33.2 1.0
MN G:MN402 3.6 24.1 0.8
CB G:HIS340 3.7 24.7 1.0
O4 G:SO4401 3.9 25.9 0.9
OD1 G:ASP342 4.0 32.8 1.0
O1 G:SO4401 4.1 31.1 0.9
NE2 G:HIS32 4.2 20.7 1.0
CB G:ASP337 4.3 20.2 1.0
O G:HOH519 4.3 24.4 1.0
O G:HOH657 4.4 40.0 1.0
CE2 G:PHE208 4.4 21.4 1.0
NE2 G:HIS340 4.4 30.4 1.0
CG G:GLU264 4.4 24.8 1.0
CD2 G:HIS340 4.5 34.9 1.0
O G:HOH704 4.5 33.3 1.0
CD2 G:HIS32 4.6 21.8 1.0
S G:SO4401 4.6 40.6 0.9
OD2 G:ASP342 4.7 29.7 1.0
CG G:ASP342 4.8 33.4 1.0
CZ G:PHE208 4.8 19.9 1.0
O G:ASP337 4.8 22.0 1.0
CE1 G:HIS207 4.9 18.0 1.0
NE2 G:HIS207 4.9 19.3 1.0
NE2 G:GLN308 4.9 24.9 1.0

Manganese binding site 7 out of 8 in 8sma

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Manganese binding site 7 out of 8 in the Sfbo with Di-Manganese Cofactor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Sfbo with Di-Manganese Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn402

b:26.8
occ:0.86
OD2 J:ASP30 2.1 23.5 1.0
OE1 J:GLU264 2.1 24.3 1.0
NE2 J:HIS32 2.1 22.6 1.0
OD1 J:ASP337 2.2 26.3 1.0
NE2 J:HIS207 2.3 26.8 1.0
CG J:ASP30 2.9 23.9 1.0
OD1 J:ASP30 3.0 23.5 1.0
CD2 J:HIS32 3.0 27.9 1.0
CE1 J:HIS32 3.1 30.8 1.0
CG J:ASP337 3.2 26.7 1.0
CD2 J:HIS207 3.2 22.7 1.0
CD J:GLU264 3.3 22.9 1.0
CE1 J:HIS207 3.4 25.0 1.0
MN J:MN403 3.8 31.5 0.6
OD2 J:ASP337 3.9 27.0 1.0
OE2 J:GLU264 4.1 25.7 1.0
CB J:ASP337 4.1 21.1 1.0
O J:HOH548 4.1 20.9 1.0
CG J:HIS32 4.2 23.7 1.0
ND1 J:HIS32 4.2 29.8 1.0
CB J:GLU264 4.3 19.0 1.0
CB J:ASP30 4.3 22.1 1.0
ND1 J:HIS340 4.4 28.4 1.0
CG J:GLU264 4.4 23.3 1.0
CG J:HIS207 4.4 18.2 1.0
CA J:ASP337 4.4 24.4 1.0
CE1 J:HIS340 4.4 25.6 1.0
ND1 J:HIS207 4.4 20.3 1.0
CG2 J:ILE263 4.6 28.5 1.0
O J:HOH692 4.8 30.6 1.0
O J:HOH502 4.8 30.5 1.0

Manganese binding site 8 out of 8 in 8sma

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Manganese binding site 8 out of 8 in the Sfbo with Di-Manganese Cofactor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Sfbo with Di-Manganese Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn403

b:31.5
occ:0.56
O J:HOH501 1.9 24.4 1.0
ND1 J:HIS340 2.1 28.4 1.0
OD2 J:ASP337 2.1 27.0 1.0
O J:HOH502 2.4 30.5 1.0
OE2 J:GLU264 2.4 25.7 1.0
CG J:ASP337 2.8 26.7 1.0
OD1 J:ASP337 2.9 26.3 1.0
CE1 J:HIS340 3.1 25.6 1.0
OE1 J:GLU264 3.1 24.3 1.0
CD J:GLU264 3.1 22.9 1.0
CG J:HIS340 3.1 28.4 1.0
CB J:HIS340 3.5 23.9 1.0
O2 J:SO4401 3.7 30.4 0.8
OD1 J:ASP342 3.8 26.3 1.0
MN J:MN402 3.8 26.8 0.9
O J:HOH504 4.1 25.2 1.0
O3 J:SO4401 4.2 33.5 0.8
NE2 J:HIS340 4.2 29.3 1.0
CD2 J:HIS340 4.3 29.8 1.0
O J:HOH513 4.3 33.2 1.0
CB J:ASP337 4.3 21.1 1.0
NE2 J:HIS32 4.4 22.6 1.0
S J:SO4401 4.5 35.1 0.8
CE2 J:PHE208 4.5 20.8 1.0
CG J:GLU264 4.6 23.3 1.0
CG J:ASP342 4.6 30.6 1.0
OD2 J:ASP342 4.6 35.1 1.0
O J:HOH692 4.6 30.6 1.0
CD2 J:HIS32 4.6 27.9 1.0
O J:ASP337 4.8 24.3 1.0
NE2 J:GLN308 4.8 20.7 1.0
O4 J:SO4401 4.9 32.1 0.8

Reference:

C.Liu, M.M.Powell, G.Rao, R.D.Britt, J.Rittle. Bioinformatic Discovery of A Cambialistic Monooxygenase. J.Am.Chem.Soc. V. 146 1783 2024.
ISSN: ESSN 1520-5126
PubMed: 38198693
DOI: 10.1021/JACS.3C12131
Page generated: Sun Oct 6 13:49:54 2024

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