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Manganese in PDB 8dl2: BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose

Protein crystallography data

The structure of BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose, PDB code: 8dl2 was solved by H.A.Brown, A.L.Deveaux, N.M.Koropatkin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.60 / 1.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 100.08, 125.31, 150.78, 90, 102.11, 90
R / Rfree (%) 17.5 / 21.9

Other elements in 8dl2:

The structure of BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose also contains other interesting chemical elements:

Calcium (Ca) 4 atoms
Chlorine (Cl) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose (pdb code 8dl2). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose, PDB code: 8dl2:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 8dl2

Go back to Manganese Binding Sites List in 8dl2
Manganese binding site 1 out of 4 in the BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn807

b:21.8
occ:1.00
 OD1 A:ASN404 2.1 9.5 1.0
O A:GLY481 2.2 8.4 1.0
OD1 A:ASP446 2.2 9.7 1.0
O A:HOH982 2.2 10.2 1.0
NE2 A:HIS437 2.2 7.5 1.0
O A:HOH949 2.3 5.2 1.0
CG A:ASP446 3.0 9.3 1.0
CD2 A:HIS437 3.1 7.9 1.0
C A:GLY481 3.2 9.4 1.0
CG A:ASN404 3.2 8.9 1.0
CE1 A:HIS437 3.3 8.3 1.0
OD2 A:ASP446 3.3 10.1 1.0
CA A:GLY481 3.6 9.6 1.0
O A:ASN404 3.8 8.5 1.0
ND2 A:ASN404 3.9 9.0 1.0
O A:PHE447 4.2 10.0 1.0
N A:PHE482 4.3 9.9 1.0
CG A:HIS437 4.3 8.7 1.0
ND1 A:HIS437 4.3 8.1 1.0
CB A:ASN404 4.4 9.0 1.0
CB A:ASP446 4.4 9.2 1.0
O A:THR483 4.5 10.4 1.0
C A:ASN404 4.6 8.8 1.0
CA A:ASN404 4.6 9.0 1.0
N A:THR483 4.6 11.6 1.0
O A:HOH1112 4.6 8.9 1.0
CA A:PHE482 4.6 10.9 1.0
N A:PHE447 4.9 8.7 1.0

Manganese binding site 2 out of 4 in 8dl2

Go back to Manganese Binding Sites List in 8dl2
Manganese binding site 2 out of 4 in the BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn809

b:20.7
occ:1.00
 OD1 B:ASP446 2.1 8.9 1.0
O B:GLY481 2.2 9.1 1.0
O B:HOH978 2.2 6.8 1.0
OD1 B:ASN404 2.2 6.9 1.0
O B:HOH928 2.3 6.6 1.0
NE2 B:HIS437 2.3 8.9 1.0
CG B:ASP446 3.0 9.4 1.0
OD2 B:ASP446 3.1 10.0 1.0
C B:GLY481 3.1 8.6 1.0
CD2 B:HIS437 3.3 9.3 1.0
CG B:ASN404 3.3 7.6 1.0
CE1 B:HIS437 3.3 8.9 1.0
CA B:GLY481 3.6 8.2 1.0
O B:ASN404 3.8 8.1 1.0
ND2 B:ASN404 3.9 7.8 1.0
O B:PHE447 4.0 9.0 1.0
N B:PHE482 4.3 9.1 1.0
CB B:ASP446 4.4 9.7 1.0
CB B:ASN404 4.4 7.6 1.0
O B:THR483 4.4 8.7 1.0
ND1 B:HIS437 4.4 9.3 1.0
CG B:HIS437 4.4 9.7 1.0
CA B:ASN404 4.5 7.7 1.0
C B:ASN404 4.5 8.4 1.0
CA B:PHE482 4.6 9.1 1.0
N B:THR483 4.6 10.3 1.0
O B:HOH1061 4.7 11.9 1.0
N B:PHE447 4.9 8.8 1.0

Manganese binding site 3 out of 4 in 8dl2

Go back to Manganese Binding Sites List in 8dl2
Manganese binding site 3 out of 4 in the BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn805

b:31.4
occ:1.00
 OD1 C:ASN404 2.1 14.7 1.0
OD1 C:ASP446 2.2 16.6 1.0
O C:HOH937 2.2 14.8 1.0
O C:HOH964 2.2 13.0 1.0
O C:GLY481 2.3 14.8 1.0
NE2 C:HIS437 2.3 17.1 1.0
CG C:ASP446 3.1 15.3 1.0
CD2 C:HIS437 3.2 19.2 1.0
C C:GLY481 3.2 14.3 1.0
CG C:ASN404 3.2 14.3 1.0
OD2 C:ASP446 3.3 16.1 1.0
CE1 C:HIS437 3.4 17.3 1.0
CA C:GLY481 3.6 14.5 1.0
O C:ASN404 3.8 14.4 1.0
ND2 C:ASN404 3.9 14.7 1.0
O C:PHE447 4.1 16.4 1.0
N C:PHE482 4.3 15.3 1.0
CG C:HIS437 4.4 18.1 1.0
CB C:ASN404 4.4 14.8 1.0
O C:THR483 4.4 19.1 1.0
ND1 C:HIS437 4.4 17.7 1.0
CB C:ASP446 4.5 14.8 1.0
CA C:ASN404 4.5 15.1 1.0
C C:ASN404 4.5 15.3 1.0
N C:THR483 4.6 16.8 1.0
CA C:PHE482 4.6 16.1 1.0
O C:HOH917 4.6 19.2 1.0
N C:PHE447 5.0 14.9 1.0

Manganese binding site 4 out of 4 in 8dl2

Go back to Manganese Binding Sites List in 8dl2
Manganese binding site 4 out of 4 in the BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn805

b:36.1
occ:1.00
 OD1 D:ASP446 2.0 21.3 1.0
O D:GLY481 2.1 21.0 1.0
O D:HOH962 2.2 21.4 1.0
OD1 D:ASN404 2.2 19.9 1.0
NE2 D:HIS437 2.3 25.2 1.0
O D:HOH904 2.3 21.1 1.0
CG D:ASP446 3.0 22.7 1.0
C D:GLY481 3.1 22.7 1.0
CE1 D:HIS437 3.2 27.2 1.0
CG D:ASN404 3.2 20.8 1.0
CD2 D:HIS437 3.3 28.6 1.0
OD2 D:ASP446 3.3 25.6 1.0
CA D:GLY481 3.6 22.0 1.0
ND2 D:ASN404 3.8 19.8 1.0
O D:ASN404 3.8 21.4 1.0
O D:PHE447 4.1 23.2 1.0
N D:PHE482 4.2 22.1 1.0
ND1 D:HIS437 4.3 25.3 1.0
CB D:ASP446 4.4 21.0 1.0
CG D:HIS437 4.4 26.9 1.0
CB D:ASN404 4.4 20.2 1.0
O D:THR483 4.5 25.9 1.0
CA D:ASN404 4.5 19.9 1.0
C D:ASN404 4.5 18.5 1.0
CA D:PHE482 4.6 23.5 1.0
N D:THR483 4.6 25.2 1.0
O D:HOH946 4.7 26.9 1.0
N D:PHE447 5.0 19.7 1.0
CA D:ASP446 5.0 20.6 1.0

Reference:

H.A.Brown, A.L.Deveaux, N.M.Koropatkin. BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose To Be Published.
Page generated: Sun Oct 6 11:33:39 2024

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