Manganese in PDB 8dge: BOGH13ASUS From Bacteroides Ovatus

Protein crystallography data

The structure of BOGH13ASUS From Bacteroides Ovatus, PDB code: 8dge 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) 62.00 / 1.89
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 100.387, 148.443, 112.77, 90, 91, 90
R / Rfree (%) 20.9 / 27.1

Other elements in 8dge:

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

Calcium (Ca) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the BOGH13ASUS From Bacteroides Ovatus (pdb code 8dge). 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, PDB code: 8dge:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 8dge

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn802

b:35.0
occ:1.00
 OD1 A:ASP446 2.1 24.5 1.0
O A:HOH960 2.1 23.7 1.0
O A:GLY481 2.2 27.1 1.0
O A:HOH926 2.2 29.3 1.0
NE2 A:HIS437 2.3 23.0 1.0
OD1 A:ASN404 2.3 24.0 1.0
CG A:ASP446 3.0 24.5 1.0
C A:GLY481 3.2 26.9 1.0
CE1 A:HIS437 3.2 23.8 1.0
CD2 A:HIS437 3.3 23.9 1.0
OD2 A:ASP446 3.3 26.3 1.0
CG A:ASN404 3.5 21.1 1.0
CA A:GLY481 3.8 26.4 1.0
O A:ASN404 3.8 23.4 1.0
O A:PHE447 4.0 25.1 1.0
ND2 A:ASN404 4.2 19.9 1.0
N A:PHE482 4.3 26.6 1.0
ND1 A:HIS437 4.4 24.4 1.0
CB A:ASP446 4.4 25.8 1.0
O A:THR483 4.4 23.3 1.0
CG A:HIS437 4.4 24.4 1.0
CB A:ASN404 4.5 23.8 1.0
C A:ASN404 4.5 23.4 1.0
CA A:ASN404 4.5 23.4 1.0
N A:THR483 4.5 23.4 1.0
CA A:PHE482 4.6 26.4 1.0
O A:HOH1019 4.6 25.6 1.0
N A:PHE447 4.8 24.6 1.0
CA A:ASP446 4.9 25.4 1.0

Manganese binding site 2 out of 4 in 8dge

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Manganese binding site 2 out of 4 in the BOGH13ASUS From Bacteroides Ovatus


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn802

b:33.3
occ:1.00
 O B:GLY481 2.0 25.2 1.0
OD1 B:ASP446 2.1 25.4 1.0
NE2 B:HIS437 2.2 25.3 1.0
OD1 B:ASN404 2.2 23.6 1.0
O B:HOH934 2.2 27.1 1.0
O B:HOH951 2.3 29.4 1.0
C B:GLY481 3.0 25.2 1.0
CG B:ASP446 3.0 24.6 1.0
CD2 B:HIS437 3.1 27.0 1.0
CE1 B:HIS437 3.3 26.8 1.0
OD2 B:ASP446 3.3 27.7 1.0
CG B:ASN404 3.3 23.0 1.0
CA B:GLY481 3.5 23.9 1.0
O B:ASN404 3.7 26.4 1.0
ND2 B:ASN404 3.9 26.0 1.0
O B:PHE447 4.1 24.4 1.0
N B:PHE482 4.2 25.5 1.0
CG B:HIS437 4.3 27.1 1.0
ND1 B:HIS437 4.3 26.5 1.0
O B:THR483 4.4 24.2 1.0
CB B:ASP446 4.4 24.5 1.0
CB B:ASN404 4.4 22.5 1.0
C B:ASN404 4.5 23.6 1.0
N B:THR483 4.5 25.4 1.0
CA B:ASN404 4.5 24.5 1.0
CA B:PHE482 4.6 25.6 1.0
O B:HOH1162 4.7 26.8 1.0
N B:GLY481 5.0 25.3 1.0
N B:PHE447 5.0 25.5 1.0

Manganese binding site 3 out of 4 in 8dge

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn802

b:33.2
occ:1.00
 OD1 C:ASN404 2.1 25.5 1.0
O C:GLY481 2.1 24.7 1.0
OD1 C:ASP446 2.2 23.4 1.0
O C:HOH935 2.3 24.3 1.0
NE2 C:HIS437 2.3 22.6 1.0
O C:HOH923 2.3 26.4 1.0
CG C:ASP446 3.0 24.4 1.0
C C:GLY481 3.2 25.5 1.0
CE1 C:HIS437 3.2 23.5 1.0
CG C:ASN404 3.2 22.9 1.0
OD2 C:ASP446 3.2 25.4 1.0
CD2 C:HIS437 3.3 22.8 1.0
O C:ASN404 3.6 22.6 1.0
CA C:GLY481 3.7 25.8 1.0
ND2 C:ASN404 3.9 24.1 1.0
O C:PHE447 4.1 21.2 1.0
N C:PHE482 4.2 26.1 1.0
ND1 C:HIS437 4.3 21.8 1.0
CB C:ASN404 4.4 22.2 1.0
O C:THR483 4.4 27.2 1.0
C C:ASN404 4.4 22.1 1.0
CG C:HIS437 4.4 22.0 1.0
CB C:ASP446 4.4 24.4 1.0
O C:HOH1178 4.5 26.4 1.0
CA C:ASN404 4.5 22.8 1.0
N C:THR483 4.6 25.3 1.0
CA C:PHE482 4.6 26.3 1.0
N C:PHE447 5.0 23.9 1.0

Manganese binding site 4 out of 4 in 8dge

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn802

b:31.0
occ:1.00
 O D:HOH938 2.0 24.9 1.0
O D:GLY481 2.1 24.2 1.0
OD1 D:ASP446 2.1 23.0 1.0
O D:HOH972 2.2 23.6 1.0
NE2 D:HIS437 2.2 23.9 1.0
OD1 D:ASN404 2.2 24.0 1.0
CG D:ASP446 3.0 23.8 1.0
CE1 D:HIS437 3.1 26.1 1.0
C D:GLY481 3.2 25.7 1.0
CD2 D:HIS437 3.2 25.2 1.0
OD2 D:ASP446 3.3 24.9 1.0
CG D:ASN404 3.3 23.4 1.0
CA D:GLY481 3.6 26.5 1.0
O D:ASN404 3.8 27.9 1.0
ND2 D:ASN404 4.0 23.6 1.0
O D:PHE447 4.1 25.0 1.0
N D:PHE482 4.3 26.2 1.0
ND1 D:HIS437 4.3 23.3 1.0
CG D:HIS437 4.3 25.0 1.0
CB D:ASP446 4.4 23.8 1.0
O D:THR483 4.4 25.9 1.0
CB D:ASN404 4.5 22.7 1.0
C D:ASN404 4.5 24.8 1.0
CA D:ASN404 4.6 25.1 1.0
N D:THR483 4.6 27.6 1.0
CA D:PHE482 4.6 24.9 1.0
O D:HOH1127 4.6 26.3 1.0
N D:PHE447 4.9 26.7 1.0

Reference:

H.A.Brown, A.L.Deveaux, N.M.Koropatkin. BOGH13ASUS From Bacteroides Ovatus To Be Published.
Page generated: Fri Jul 28 02:16:47 2023

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