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Manganese in PDB 8jq6: Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allose

Protein crystallography data

The structure of Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allose, PDB code: 8jq6 was solved by H.Yoshida, A.Yoshihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.43 / 1.71
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.934, 140.057, 147.47, 90, 90, 90
R / Rfree (%) 14 / 18.7

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allose (pdb code 8jq6). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allose, PDB code: 8jq6:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 8jq6

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Manganese binding site 1 out of 8 in the Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:40.9
occ:1.00
 OE2 A:GLU228 2.2 19.6 1.0
OD1 A:ASP261 2.2 18.9 1.0
OD1 A:ASP328 2.3 28.7 1.0
ND1 A:HIS288 2.5 29.2 1.0
O4 A:ALL503 2.7 35.9 1.0
O3 A:ALL503 2.8 36.7 1.0
CD A:GLU228 3.1 17.6 1.0
CG A:ASP261 3.3 16.0 1.0
OE1 A:GLU228 3.3 17.9 1.0
CG A:ASP328 3.3 23.0 1.0
CE1 A:HIS288 3.3 37.8 1.0
O A:HOH610 3.4 25.9 1.0
C3 A:ALL503 3.6 35.3 1.0
CG A:HIS288 3.6 27.2 1.0
C4 A:ALL503 3.6 38.6 1.0
CB A:ASP261 3.6 16.4 1.0
CB A:ASP328 3.7 21.0 1.0
CB A:HIS288 3.9 23.1 1.0
CE1 A:HIS264 3.9 22.8 1.0
NE2 A:HIS264 4.4 22.5 1.0
C5 A:ALL503 4.4 41.5 1.0
OD2 A:ASP261 4.4 16.8 1.0
OD2 A:ASP328 4.4 26.1 1.0
CG A:GLU228 4.4 16.2 1.0
NE2 A:HIS288 4.5 36.0 1.0
CD2 A:HIS288 4.7 29.8 1.0
ND1 A:HIS264 4.8 21.6 1.0
CA A:ASP261 4.9 15.3 1.0

Manganese binding site 2 out of 8 in 8jq6

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Manganese binding site 2 out of 8 in the Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:28.4
occ:1.00
 O A:HOH601 2.0 36.0 1.0
OD1 A:ASP296 2.0 23.6 1.0
O A:HOH610 2.0 25.9 1.0
OD1 A:ASP298 2.2 27.4 1.0
O A:HOH611 2.3 28.8 1.0
NE2 A:HIS264 2.4 22.5 1.0
CG A:ASP296 2.7 24.6 1.0
OD2 A:ASP296 2.7 28.5 1.0
CD2 A:HIS264 3.1 21.4 1.0
CG A:ASP298 3.1 21.9 1.0
OD2 A:ASP298 3.3 23.2 1.0
O3 A:ALL503 3.4 36.7 1.0
CE1 A:HIS264 3.6 22.8 1.0
O A:HOH765 3.8 24.3 1.0
OD1 A:ASP261 3.9 18.9 1.0
O2 A:ALL503 3.9 27.6 1.0
OD2 A:ASP261 4.1 16.8 1.0
CB A:ASP296 4.1 23.0 1.0
CG A:ASP261 4.3 16.0 1.0
OG A:SER290 4.3 17.2 1.0
CG A:HIS264 4.4 18.3 1.0
CB A:ASP298 4.5 19.7 1.0
O A:ASP296 4.6 21.2 1.0
ND1 A:HIS264 4.6 21.6 1.0
C3 A:ALL503 4.6 35.3 1.0
CA A:ASP296 4.7 20.4 1.0
C2 A:ALL503 4.7 35.8 1.0
C A:ASP296 4.7 20.0 1.0
CA A:ASP298 4.8 17.9 1.0
N A:ASP298 4.8 17.6 1.0
C1 A:ALL503 4.9 42.6 1.0
OD1 A:ASP328 4.9 28.7 1.0

Manganese binding site 3 out of 8 in 8jq6

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Manganese binding site 3 out of 8 in the Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:40.6
occ:1.00
 OD2 B:ASP328 2.1 34.5 1.0
OE2 B:GLU228 2.2 19.0 1.0
OD1 B:ASP261 2.2 19.2 1.0
ND1 B:HIS288 2.4 29.7 1.0
O3 B:ALL503 2.7 33.9 1.0
O4 B:ALL503 2.8 31.2 1.0
CD B:GLU228 3.0 17.2 1.0
CG B:ASP328 3.2 26.1 1.0
CG B:ASP261 3.2 16.3 1.0
CE1 B:HIS288 3.3 38.4 1.0
OE1 B:GLU228 3.3 16.8 1.0
O B:HOH650 3.4 26.8 1.0
CG B:HIS288 3.5 25.5 1.0
C3 B:ALL503 3.6 36.8 1.0
CB B:ASP261 3.7 15.6 1.0
C4 B:ALL503 3.7 37.3 1.0
CB B:ASP328 3.7 21.2 1.0
CB B:HIS288 3.8 22.3 1.0
CE1 B:HIS264 4.0 20.9 1.0
OD1 B:ASP328 4.3 31.2 1.0
C5 B:ALL503 4.3 40.1 1.0
OD2 B:ASP261 4.3 16.2 1.0
CG B:GLU228 4.4 15.6 1.0
NE2 B:HIS264 4.4 21.6 1.0
NE2 B:HIS288 4.5 35.6 1.0
CD2 B:HIS288 4.6 28.9 1.0
ND1 B:HIS264 4.8 21.1 1.0
CA B:ASP261 4.9 14.3 1.0
C2 B:ALL503 5.0 35.9 1.0

Manganese binding site 4 out of 8 in 8jq6

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Manganese binding site 4 out of 8 in the Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:27.0
occ:1.00
 O B:HOH601 1.8 40.3 1.0
O B:HOH650 2.0 26.8 1.0
OD1 B:ASP296 2.1 24.2 1.0
OD1 B:ASP298 2.1 23.8 1.0
O B:HOH604 2.2 26.8 1.0
NE2 B:HIS264 2.4 21.6 1.0
CG B:ASP296 2.8 24.1 1.0
OD2 B:ASP296 2.8 27.2 1.0
CD2 B:HIS264 3.1 19.0 1.0
CG B:ASP298 3.1 20.4 1.0
OD2 B:ASP298 3.4 21.2 1.0
CE1 B:HIS264 3.6 20.9 1.0
O3 B:ALL503 3.6 33.9 1.0
O B:HOH764 3.8 19.3 1.0
OD2 B:ASP261 4.0 16.2 1.0
OD1 B:ASP261 4.0 19.2 1.0
O2 B:ALL503 4.0 27.1 1.0
OG B:SER290 4.2 15.2 1.0
CB B:ASP296 4.2 23.4 1.0
CG B:ASP261 4.2 16.3 1.0
CG B:HIS264 4.3 18.3 1.0
CB B:ASP298 4.4 19.7 1.0
O B:ASP296 4.5 22.4 1.0
ND1 B:HIS264 4.5 21.1 1.0
C B:ASP296 4.7 21.0 1.0
CA B:ASP296 4.7 21.7 1.0
C2 B:ALL503 4.8 35.9 1.0
CA B:ASP298 4.8 16.9 1.0
C3 B:ALL503 4.8 36.8 1.0
C1 B:ALL503 4.8 42.2 1.0
N B:ASP298 4.9 17.1 1.0
OD2 B:ASP328 4.9 34.5 1.0
CB B:SER290 5.0 15.8 1.0

Manganese binding site 5 out of 8 in 8jq6

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Manganese binding site 5 out of 8 in the Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn501

b:42.2
occ:1.00
 OD1 C:ASP261 2.2 19.4 1.0
OD2 C:ASP328 2.2 36.8 1.0
OE2 C:GLU228 2.2 23.3 1.0
ND1 C:HIS288 2.5 26.8 1.0
O3 C:AFD503 2.7 34.5 1.0
O4 C:AFD503 2.8 34.2 1.0
CD C:GLU228 3.1 19.2 1.0
CG C:ASP328 3.3 26.4 1.0
CG C:ASP261 3.3 17.2 1.0
OE1 C:GLU228 3.3 18.7 1.0
CE1 C:HIS288 3.3 33.0 1.0
O C:HOH611 3.4 28.6 1.0
CG C:HIS288 3.6 25.4 1.0
C3 C:AFD503 3.7 32.8 1.0
CB C:ASP328 3.7 22.1 1.0
CB C:ASP261 3.7 16.9 1.0
C4 C:AFD503 3.7 35.9 1.0
CB C:HIS288 3.9 21.1 1.0
CE1 C:HIS264 3.9 18.4 1.0
OD1 C:ASP328 4.4 30.1 1.0
OD2 C:ASP261 4.4 18.2 1.0
C5 C:AFD503 4.4 35.0 1.0
CG C:GLU228 4.4 17.3 1.0
NE2 C:HIS264 4.5 20.5 1.0
NE2 C:HIS288 4.5 35.4 1.0
CD2 C:HIS288 4.7 28.9 1.0
ND1 C:HIS264 4.7 19.7 1.0
CA C:ASP261 4.9 14.7 1.0

Manganese binding site 6 out of 8 in 8jq6

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Manganese binding site 6 out of 8 in the Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn502

b:26.5
occ:1.00
 OD1 C:ASP296 2.0 26.6 1.0
O C:HOH611 2.0 28.6 1.0
O C:HOH601 2.0 31.3 1.0
OD1 C:ASP298 2.2 22.9 1.0
O C:HOH615 2.3 27.7 1.0
NE2 C:HIS264 2.3 20.5 1.0
CG C:ASP296 2.8 26.2 1.0
OD2 C:ASP296 2.9 32.4 1.0
CD2 C:HIS264 3.1 18.4 1.0
CG C:ASP298 3.1 22.8 1.0
OD2 C:ASP298 3.4 23.0 1.0
CE1 C:HIS264 3.5 18.4 1.0
O3 C:AFD503 3.6 34.5 1.0
O C:HOH765 3.8 20.0 1.0
O1 C:AFD503 3.8 35.5 1.0
OD2 C:ASP261 4.0 18.2 1.0
OD1 C:ASP261 4.0 19.4 1.0
O2 C:AFD503 4.1 25.4 1.0
CB C:ASP296 4.2 25.3 1.0
CG C:ASP261 4.3 17.2 1.0
OG C:SER290 4.3 17.4 1.0
CG C:HIS264 4.3 16.8 1.0
ND1 C:HIS264 4.5 19.7 1.0
CB C:ASP298 4.5 20.1 1.0
O C:ASP296 4.5 24.7 1.0
C C:ASP296 4.7 21.4 1.0
CA C:ASP296 4.7 21.7 1.0
CA C:ASP298 4.8 18.1 1.0
C3 C:AFD503 4.8 32.8 1.0
C2 C:AFD503 4.8 31.3 1.0
N C:ASP298 4.9 18.0 1.0
C1 C:AFD503 4.9 33.3 1.0
CA C:GLY263 5.0 13.9 1.0
OD2 C:ASP328 5.0 36.8 1.0

Manganese binding site 7 out of 8 in 8jq6

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Manganese binding site 7 out of 8 in the Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn501

b:37.6
occ:1.00
 OD1 D:ASP328 2.2 30.3 1.0
OD1 D:ASP261 2.3 16.5 1.0
OE2 D:GLU228 2.3 17.9 1.0
ND1 D:HIS288 2.5 28.7 1.0
O3 D:AFD503 2.7 31.5 1.0
O4 D:AFD503 2.7 30.9 1.0
CD D:GLU228 3.1 16.2 1.0
OE1 D:GLU228 3.2 16.5 1.0
CG D:ASP328 3.3 25.2 1.0
CG D:ASP261 3.3 15.2 1.0
CE1 D:HIS288 3.3 37.1 1.0
O D:HOH688 3.5 24.2 1.0
C3 D:AFD503 3.6 31.4 1.0
CG D:HIS288 3.6 27.3 1.0
C4 D:AFD503 3.6 33.7 1.0
CB D:ASP328 3.7 21.5 1.0
CB D:ASP261 3.7 14.8 1.0
CB D:HIS288 4.0 22.9 1.0
CE1 D:HIS264 4.0 21.2 1.0
C5 D:AFD503 4.3 34.7 1.0
OD2 D:ASP261 4.4 15.7 1.0
OD2 D:ASP328 4.4 24.6 1.0
CG D:GLU228 4.4 14.9 1.0
NE2 D:HIS288 4.5 37.5 1.0
NE2 D:HIS264 4.6 21.2 1.0
CD2 D:HIS288 4.7 31.9 1.0
ND1 D:HIS264 4.7 20.4 1.0
CA D:ASP261 4.9 14.1 1.0

Manganese binding site 8 out of 8 in 8jq6

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Manganese binding site 8 out of 8 in the Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with D-Allose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn502

b:25.0
occ:1.00
 OD1 D:ASP296 2.0 23.2 1.0
O D:HOH688 2.0 24.2 1.0
O D:HOH603 2.0 33.0 1.0
OD1 D:ASP298 2.1 22.3 1.0
O D:HOH638 2.2 28.5 1.0
NE2 D:HIS264 2.4 21.2 1.0
CG D:ASP296 2.8 24.9 1.0
OD2 D:ASP296 2.9 29.2 1.0
CG D:ASP298 3.0 20.2 1.0
CD2 D:HIS264 3.1 20.4 1.0
OD2 D:ASP298 3.3 22.7 1.0
CE1 D:HIS264 3.6 21.2 1.0
O D:HOH751 3.8 20.6 1.0
O3 D:AFD503 3.8 31.5 1.0
O1 D:AFD503 3.9 37.9 1.0
OD2 D:ASP261 4.0 15.7 1.0
OD1 D:ASP261 4.0 16.5 1.0
O2 D:AFD503 4.1 26.5 1.0
CB D:ASP296 4.2 23.6 1.0
OG D:SER290 4.3 15.9 1.0
CG D:ASP261 4.3 15.2 1.0
CG D:HIS264 4.4 18.2 1.0
CB D:ASP298 4.4 18.1 1.0
O D:ASP296 4.5 22.9 1.0
ND1 D:HIS264 4.5 20.4 1.0
C D:ASP296 4.7 22.6 1.0
CA D:ASP296 4.7 22.6 1.0
CA D:ASP298 4.7 16.9 1.0
N D:ASP298 4.8 16.8 1.0
C2 D:AFD503 4.9 31.7 1.0
C3 D:AFD503 4.9 31.4 1.0
OD1 D:ASP328 4.9 30.3 1.0
C1 D:AFD503 5.0 33.5 1.0

Reference:

H.Yoshida, N.Yamamoto, L.H.Kurahara, K.Izumori, A.Yoshihara. X-Ray Structure and Characterization of A Probiotic Lactobacillus Rhamnosus Probio-M9 L-Rhamnose Isomerase. Appl.Microbiol.Biotechnol. V. 108 249 2024.
ISSN: ESSN 1432-0614
PubMed: 38430263
DOI: 10.1007/S00253-024-13075-9
Page generated: Sun Oct 6 13:20:49 2024

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