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Manganese in PDB 8jq4: Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with L-Rhamnose

Protein crystallography data

The structure of Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with L-Rhamnose, PDB code: 8jq4 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) 45.10 / 1.61
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 90.116, 140.786, 147.345, 90, 90, 90
R / Rfree (%) 16.5 / 20.8

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Lactobacillus Rhamnosus L-Rhamnose Isomerase in Complex with L-Rhamnose (pdb code 8jq4). 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 L-Rhamnose, PDB code: 8jq4:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 8jq4

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


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 L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:36.9
occ:1.00
 OE2 A:GLU228 2.4 22.3 1.0
OD1 A:ASP261 2.4 19.7 1.0
OD1 A:ASP328 2.4 28.7 1.0
O2 A:RM4503 2.6 20.7 1.0
ND1 A:HIS288 2.7 29.0 1.0
O3 A:RM4503 2.8 23.9 1.0
CD A:GLU228 3.2 19.1 1.0
OE1 A:GLU228 3.3 20.8 1.0
O A:HOH822 3.3 35.1 1.0
CG A:ASP261 3.3 17.1 1.0
CG A:ASP328 3.5 25.1 1.0
C2 A:RM4503 3.5 23.8 1.0
O A:HOH676 3.5 24.1 1.0
CE1 A:HIS288 3.6 32.3 1.0
CB A:ASP261 3.6 16.6 1.0
C3 A:RM4503 3.7 23.5 1.0
CG A:HIS288 3.7 24.9 1.0
CB A:ASP328 3.8 21.6 1.0
CE1 A:HIS264 3.9 23.8 1.0
CB A:HIS288 4.0 21.6 1.0
C4 A:RM4503 4.5 24.2 1.0
OD2 A:ASP261 4.5 19.0 1.0
CG A:GLU228 4.6 18.3 1.0
NE2 A:HIS264 4.6 23.7 1.0
OD2 A:ASP328 4.6 27.4 1.0
ND1 A:HIS264 4.7 23.8 1.0
O A:HOH748 4.8 50.6 1.0
NE2 A:HIS288 4.8 30.8 1.0
CD2 A:HIS288 4.9 27.4 1.0
C1 A:RM4503 4.9 23.3 1.0
CA A:ASP261 4.9 16.0 1.0

Manganese binding site 2 out of 8 in 8jq4

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


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 L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:22.8
occ:1.00
 OD1 A:ASP296 1.9 21.8 1.0
O A:HOH676 2.0 24.1 1.0
OD1 A:ASP298 2.1 27.5 1.0
O A:HOH605 2.1 24.8 1.0
O A:HOH623 2.2 26.4 1.0
NE2 A:HIS264 2.4 23.7 1.0
CG A:ASP296 2.7 22.4 1.0
OD2 A:ASP296 2.8 26.4 1.0
CG A:ASP298 3.0 21.2 1.0
CD2 A:HIS264 3.1 20.8 1.0
OD2 A:ASP298 3.3 23.2 1.0
CE1 A:HIS264 3.5 23.8 1.0
O A:HOH823 3.7 22.3 1.0
OD2 A:ASP261 4.0 19.0 1.0
OD1 A:ASP261 4.0 19.7 1.0
O2 A:RM4503 4.1 20.7 1.0
CB A:ASP296 4.1 19.6 1.0
O A:HOH748 4.2 50.6 1.0
OG A:SER290 4.2 16.9 1.0
CG A:ASP261 4.3 17.1 1.0
O1 A:RM4503 4.3 21.2 1.0
CG A:HIS264 4.3 20.4 1.0
CB A:ASP298 4.4 19.7 1.0
ND1 A:HIS264 4.5 23.8 1.0
O A:ASP296 4.6 19.8 1.0
CA A:ASP296 4.7 18.4 1.0
C A:ASP296 4.7 18.5 1.0
CA A:ASP298 4.7 18.6 1.0
N A:ASP298 4.7 17.4 1.0
CB A:SER290 4.9 16.1 1.0
CA A:GLY263 4.9 15.5 1.0

Manganese binding site 3 out of 8 in 8jq4

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


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 L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:36.4
occ:1.00
 OD1 B:ASP261 2.3 16.8 1.0
OE2 B:GLU228 2.4 19.6 1.0
OD2 B:ASP328 2.4 31.0 1.0
O2 B:RM4503 2.6 20.2 1.0
ND1 B:HIS288 2.7 26.5 1.0
O3 B:RM4503 2.7 22.5 1.0
CD B:GLU228 3.2 17.6 1.0
OE1 B:GLU228 3.3 17.9 1.0
CG B:ASP261 3.4 15.7 1.0
CG B:ASP328 3.4 26.7 1.0
O B:HOH810 3.5 33.3 1.0
C2 B:RM4503 3.5 21.4 1.0
O B:HOH668 3.5 24.3 1.0
CE1 B:HIS288 3.6 29.4 1.0
C3 B:RM4503 3.7 22.2 1.0
CB B:ASP261 3.7 14.8 1.0
CG B:HIS288 3.7 23.9 1.0
CB B:ASP328 3.8 20.6 1.0
CB B:HIS288 3.9 21.2 1.0
CE1 B:HIS264 3.9 20.6 1.0
C4 B:RM4503 4.4 23.6 1.0
OD2 B:ASP261 4.5 16.8 1.0
NE2 B:HIS264 4.5 22.1 1.0
OD1 B:ASP328 4.5 25.8 1.0
CG B:GLU228 4.6 15.5 1.0
ND1 B:HIS264 4.7 20.4 1.0
NE2 B:HIS288 4.8 29.3 1.0
C1 B:RM4503 4.8 21.6 1.0
CD2 B:HIS288 4.9 26.5 1.0
CA B:ASP261 5.0 13.8 1.0

Manganese binding site 4 out of 8 in 8jq4

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


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 L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:23.3
occ:1.00
 OD1 B:ASP296 2.0 20.0 1.0
O B:HOH668 2.0 24.3 1.0
O B:HOH602 2.1 30.4 1.0
OD1 B:ASP298 2.1 22.9 1.0
O B:HOH629 2.1 26.7 1.0
NE2 B:HIS264 2.4 22.1 1.0
CG B:ASP296 2.7 20.2 1.0
OD2 B:ASP296 2.9 28.0 1.0
CG B:ASP298 3.0 19.9 1.0
CD2 B:HIS264 3.1 20.0 1.0
OD2 B:ASP298 3.4 21.1 1.0
CE1 B:HIS264 3.5 20.6 1.0
O B:HOH816 3.7 18.2 1.0
OD2 B:ASP261 3.9 16.8 1.0
OD1 B:ASP261 4.0 16.8 1.0
O2 B:RM4503 4.1 20.2 1.0
OG B:SER290 4.2 17.1 1.0
CB B:ASP296 4.2 20.2 1.0
CG B:ASP261 4.2 15.7 1.0
O1 B:RM4503 4.2 21.3 1.0
CG B:HIS264 4.3 18.5 1.0
CB B:ASP298 4.4 19.7 1.0
ND1 B:HIS264 4.5 20.4 1.0
O B:ASP296 4.5 20.8 1.0
CA B:ASP296 4.7 18.3 1.0
C B:ASP296 4.7 18.1 1.0
CA B:ASP298 4.7 17.4 1.0
N B:ASP298 4.8 17.8 1.0
CB B:SER290 4.9 16.1 1.0
CA B:GLY263 4.9 14.3 1.0

Manganese binding site 5 out of 8 in 8jq4

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


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 L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn501

b:36.2
occ:1.00
 OE2 C:GLU228 2.3 22.5 1.0
OD1 C:ASP261 2.4 17.8 1.0
OD2 C:ASP328 2.5 39.0 1.0
O2 C:RM4503 2.6 21.9 1.0
ND1 C:HIS288 2.6 24.1 1.0
O3 C:RM4503 2.9 24.7 1.0
CD C:GLU228 3.1 20.1 1.0
OE1 C:GLU228 3.2 22.1 1.0
CG C:ASP261 3.3 15.8 1.0
O C:HOH879 3.5 30.9 1.0
CG C:ASP328 3.5 30.1 1.0
CE1 C:HIS288 3.5 29.7 1.0
C2 C:RM4503 3.5 23.7 1.0
O C:HOH761 3.6 26.7 1.0
CG C:HIS288 3.6 24.2 1.0
CB C:ASP261 3.6 16.0 1.0
C3 C:RM4503 3.8 24.2 1.0
CB C:ASP328 3.8 22.8 1.0
CB C:HIS288 3.9 21.1 1.0
CE1 C:HIS264 3.9 23.0 1.0
NE2 C:HIS264 4.5 23.2 1.0
OD2 C:ASP261 4.5 17.2 1.0
CG C:GLU228 4.5 19.0 1.0
C4 C:RM4503 4.5 24.8 1.0
ND1 C:HIS264 4.6 21.1 1.0
OD1 C:ASP328 4.6 32.1 1.0
NE2 C:HIS288 4.7 31.1 1.0
CD2 C:HIS288 4.8 26.5 1.0
CA C:ASP261 4.9 15.5 1.0
C1 C:RM4503 4.9 23.5 1.0

Manganese binding site 6 out of 8 in 8jq4

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


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 L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn502

b:23.5
occ:1.00
 OD1 C:ASP296 1.9 20.9 1.0
O C:HOH610 2.0 28.0 1.0
O C:HOH761 2.0 26.7 1.0
OD1 C:ASP298 2.1 21.6 1.0
O C:HOH617 2.2 22.9 1.0
NE2 C:HIS264 2.5 23.2 1.0
CG C:ASP296 2.8 21.8 1.0
OD2 C:ASP296 3.0 24.3 1.0
CG C:ASP298 3.1 18.9 1.0
CD2 C:HIS264 3.1 19.8 1.0
OD2 C:ASP298 3.4 22.4 1.0
CE1 C:HIS264 3.6 23.0 1.0
O C:HOH834 3.7 20.1 1.0
OD2 C:ASP261 4.0 17.2 1.0
OD1 C:ASP261 4.0 17.8 1.0
O2 C:RM4503 4.1 21.9 1.0
CB C:ASP296 4.2 19.1 1.0
O1 C:RM4503 4.2 22.9 1.0
OG C:SER290 4.2 17.4 1.0
CG C:ASP261 4.3 15.8 1.0
CG C:HIS264 4.3 18.0 1.0
CB C:ASP298 4.4 18.4 1.0
O C:ASP296 4.6 21.6 1.0
ND1 C:HIS264 4.6 21.1 1.0
CA C:ASP298 4.7 17.3 1.0
C C:ASP296 4.7 19.5 1.0
CA C:ASP296 4.7 18.2 1.0
N C:ASP298 4.8 17.5 1.0
CA C:GLY263 5.0 14.8 1.0
CB C:SER290 5.0 16.4 1.0

Manganese binding site 7 out of 8 in 8jq4

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


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 L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn501

b:35.3
occ:1.00
 OE2 D:GLU228 2.4 22.4 1.0
OD1 D:ASP328 2.4 35.1 1.0
OD1 D:ASP261 2.4 19.2 1.0
O2 D:RM4503 2.5 25.1 1.0
O3 D:RM4503 2.7 25.8 1.0
ND1 D:HIS288 2.8 25.2 1.0
CD D:GLU228 3.1 17.5 1.0
OE1 D:GLU228 3.3 17.8 1.0
C2 D:RM4503 3.4 23.0 1.0
CG D:ASP261 3.4 17.1 1.0
CG D:ASP328 3.4 29.8 1.0
O D:HOH839 3.5 33.4 1.0
O D:HOH757 3.6 23.3 1.0
C3 D:RM4503 3.6 24.2 1.0
CE1 D:HIS288 3.7 32.1 1.0
CB D:ASP261 3.7 17.1 1.0
CB D:ASP328 3.8 23.5 1.0
CG D:HIS288 3.8 24.8 1.0
CE1 D:HIS264 3.9 23.1 1.0
CB D:HIS288 4.0 21.5 1.0
C4 D:RM4503 4.4 24.2 1.0
NE2 D:HIS264 4.5 22.8 1.0
CG D:GLU228 4.5 16.6 1.0
OD2 D:ASP261 4.6 17.0 1.0
OD2 D:ASP328 4.6 26.9 1.0
ND1 D:HIS264 4.6 21.2 1.0
C1 D:RM4503 4.8 23.6 1.0
NE2 D:HIS288 4.8 31.7 1.0
CD2 D:HIS288 4.9 29.4 1.0
CA D:ASP261 5.0 15.6 1.0

Manganese binding site 8 out of 8 in 8jq4

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


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 L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn502

b:22.6
occ:1.00
 OD1 D:ASP296 2.0 21.2 1.0
O D:HOH757 2.0 23.3 1.0
OD1 D:ASP298 2.1 23.2 1.0
O D:HOH610 2.1 25.0 1.0
O D:HOH626 2.1 25.5 1.0
NE2 D:HIS264 2.4 22.8 1.0
CG D:ASP296 2.8 21.2 1.0
OD2 D:ASP296 2.9 26.2 1.0
CG D:ASP298 3.0 19.3 1.0
CD2 D:HIS264 3.1 20.4 1.0
OD2 D:ASP298 3.3 23.9 1.0
CE1 D:HIS264 3.5 23.1 1.0
O D:HOH782 3.7 21.1 1.0
OD2 D:ASP261 3.9 17.0 1.0
OD1 D:ASP261 4.0 19.2 1.0
O2 D:RM4503 4.1 25.1 1.0
OG D:SER290 4.2 17.5 1.0
CB D:ASP296 4.2 20.1 1.0
CG D:ASP261 4.2 17.1 1.0
O1 D:RM4503 4.3 24.4 1.0
CG D:HIS264 4.3 19.3 1.0
CB D:ASP298 4.4 17.7 1.0
ND1 D:HIS264 4.5 21.2 1.0
O D:ASP296 4.6 19.6 1.0
CA D:ASP298 4.7 16.6 1.0
C D:ASP296 4.7 18.1 1.0
CA D:ASP296 4.7 18.9 1.0
N D:ASP298 4.8 16.2 1.0
CB D:SER290 4.9 17.4 1.0
CA D:GLY263 5.0 15.3 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 13:20:47 2024

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