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Manganese in PDB 4xkm: Crystal Structure of Xylose Isomerase From An Human Intestinal Tract Microbe Bacteroides Thetaiotaomicron

Enzymatic activity of Crystal Structure of Xylose Isomerase From An Human Intestinal Tract Microbe Bacteroides Thetaiotaomicron

All present enzymatic activity of Crystal Structure of Xylose Isomerase From An Human Intestinal Tract Microbe Bacteroides Thetaiotaomicron:
5.3.1.5;

Protein crystallography data

The structure of Crystal Structure of Xylose Isomerase From An Human Intestinal Tract Microbe Bacteroides Thetaiotaomicron, PDB code: 4xkm was solved by B.G.Han, S.M.Bong, J.W.Cho, B.I.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.21 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 96.268, 101.658, 108.307, 82.76, 68.24, 82.98
R / Rfree (%) 18.6 / 21.1

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of Xylose Isomerase From An Human Intestinal Tract Microbe Bacteroides Thetaiotaomicron (pdb code 4xkm). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 16 binding sites of Manganese where determined in the Crystal Structure of Xylose Isomerase From An Human Intestinal Tract Microbe Bacteroides Thetaiotaomicron, PDB code: 4xkm:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 16 in 4xkm

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Manganese binding site 1 out of 16 in the Crystal Structure of Xylose Isomerase From An Human Intestinal Tract Microbe Bacteroides Thetaiotaomicron


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Xylose Isomerase From An Human Intestinal Tract Microbe Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:28.4
occ:1.00
 OD2 A:ASP341 2.1 20.0 1.0
OE2 A:GLU234 2.1 21.3 1.0
OD2 A:ASP298 2.2 18.7 1.0
OE1 A:GLU270 2.2 19.6 1.0
O A:HOH761 2.7 29.3 1.0
O A:HOH873 2.7 27.3 1.0
CD A:GLU234 3.0 21.0 1.0
CG A:ASP341 3.2 19.8 1.0
OE1 A:GLU234 3.2 21.1 1.0
CG A:ASP298 3.3 18.5 1.0
CD A:GLU270 3.4 19.6 1.0
CB A:ASP341 3.8 19.7 1.0
CB A:ASP298 3.9 18.4 1.0
CE1 A:HIS273 4.1 19.2 1.0
OD1 A:ASP341 4.2 19.8 1.0
CG A:GLU270 4.3 19.4 1.0
OE2 A:GLU270 4.3 19.7 1.0
CB A:GLU270 4.3 19.2 1.0
OD1 A:ASP298 4.3 18.5 1.0
CG A:GLU234 4.4 20.8 1.0
MN A:MN502 4.6 66.2 1.0
NE2 A:HIS273 4.7 19.2 1.0
ND2 A:ASN268 4.8 19.5 1.0
ND1 A:HIS273 4.8 19.2 1.0
CZ2 A:TRP51 5.0 20.0 1.0

Manganese binding site 2 out of 16 in 4xkm

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Manganese binding site 2 out of 16 in the Crystal Structure of Xylose Isomerase From An Human Intestinal Tract Microbe Bacteroides Thetaiotaomicron


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Xylose Isomerase From An Human Intestinal Tract Microbe Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:66.2
occ:1.00
 OE2 A:GLU270 2.2 19.7 1.0
OD2 A:ASP309 2.5 25.2 1.0
OD1 A:ASP311 2.6 22.3 1.0
CD A:GLU270 3.1 19.6 1.0
NE2 A:HIS273 3.2 19.2 1.0
OE1 A:GLU270 3.2 19.6 1.0
CG A:ASP309 3.5 24.9 1.0
CG A:ASP311 3.5 22.0 1.0
OD2 A:ASP311 3.7 22.4 1.0
CD2 A:HIS273 3.9 19.2 1.0
CE1 A:HIS273 4.0 19.2 1.0
O A:HOH873 4.1 27.3 1.0
OD2 A:ASP341 4.2 20.0 1.0
ND2 A:ASN300 4.2 18.8 1.0
CB A:ASP309 4.3 24.2 1.0
OD1 A:ASP309 4.3 25.3 1.0
CG A:ASP341 4.4 19.8 1.0
OD1 A:ASP341 4.4 19.8 1.0
CG A:GLU270 4.5 19.4 1.0
MN A:MN501 4.6 28.4 1.0
O A:ASP341 4.8 19.6 1.0
CB A:ASP311 4.9 21.5 1.0

Manganese binding site 3 out of 16 in 4xkm

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Manganese binding site 3 out of 16 in the Crystal Structure of Xylose Isomerase From An Human Intestinal Tract Microbe Bacteroides Thetaiotaomicron


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 Xylose Isomerase From An Human Intestinal Tract Microbe Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:22.9
occ:1.00
 OD1 B:ASP341 2.0 19.2 1.0
OE2 B:GLU234 2.1 18.1 1.0
OE1 B:GLU270 2.2 18.2 1.0
OD2 B:ASP298 2.2 17.4 1.0
O B:HOH859 2.4 20.6 1.0
O B:HOH769 2.7 26.3 1.0
CD B:GLU234 3.0 17.9 1.0
CG B:ASP341 3.1 19.1 1.0
OE1 B:GLU234 3.3 18.0 1.0
CG B:ASP298 3.4 17.3 1.0
CD B:GLU270 3.4 18.1 1.0
CB B:ASP341 3.7 19.0 1.0
CB B:ASP298 3.9 17.2 1.0
CE1 B:HIS273 4.1 17.4 1.0
OD2 B:ASP341 4.2 19.1 1.0
OE2 B:GLU270 4.3 18.4 1.0
CG B:GLU270 4.3 17.8 1.0
CB B:GLU270 4.3 17.4 1.0
OD1 B:ASP298 4.4 17.3 1.0
CG B:GLU234 4.4 17.7 1.0
NE2 B:HIS273 4.6 17.4 1.0
MN B:MN502 4.8 56.9 1.0
ND2 B:ASN268 4.8 17.2 1.0
ND1 B:HIS273 4.9 17.4 1.0

Manganese binding site 4 out of 16 in 4xkm

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Manganese binding site 4 out of 16 in the Crystal Structure of Xylose Isomerase From An Human Intestinal Tract Microbe Bacteroides Thetaiotaomicron


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 Xylose Isomerase From An Human Intestinal Tract Microbe Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:56.9
occ:1.00
 OE2 B:GLU270 2.1 18.4 1.0
OD2 B:ASP309 2.3 25.3 1.0
OD1 B:ASP311 2.4 22.2 1.0
CD B:GLU270 3.1 18.1 1.0
CG B:ASP309 3.3 24.6 1.0
OE1 B:GLU270 3.4 18.2 1.0
CG B:ASP311 3.4 22.1 1.0
NE2 B:HIS273 3.4 17.4 1.0
OD2 B:ASP311 3.7 22.3 1.0
ND2 B:ASN300 3.9 18.0 1.0
CD2 B:HIS273 4.0 17.4 1.0
CB B:ASP309 4.1 24.0 1.0
OD1 B:ASP309 4.2 24.9 1.0
OD1 B:ASP341 4.3 19.2 1.0
CE1 B:HIS273 4.3 17.4 1.0
O B:HOH859 4.3 20.6 1.0
CG B:GLU270 4.5 17.8 1.0
CG B:ASP341 4.5 19.1 1.0
OD2 B:ASP341 4.6 19.1 1.0
O B:ASP341 4.6 19.1 1.0
CB B:ASN272 4.7 17.6 1.0
CB B:ASP311 4.7 21.6 1.0
MN B:MN501 4.8 22.9 1.0

Manganese binding site 5 out of 16 in 4xkm

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Manganese binding site 5 out of 16 in the Crystal Structure of Xylose Isomerase From An Human Intestinal Tract Microbe Bacteroides Thetaiotaomicron


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 Xylose Isomerase From An Human Intestinal Tract Microbe Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn501

b:27.3
occ:1.00
 OD2 C:ASP341 2.0 22.7 1.0
OE1 C:GLU270 2.1 21.1 1.0
OE2 C:GLU234 2.1 21.6 1.0
OD2 C:ASP298 2.2 23.0 1.0
O C:HOH752 2.5 20.7 1.0
CD C:GLU234 3.0 21.6 1.0
CG C:ASP341 3.2 22.6 1.0
OE1 C:GLU234 3.3 21.7 1.0
CD C:GLU270 3.3 21.1 1.0
CG C:ASP298 3.3 22.8 1.0
CB C:ASP341 3.8 22.5 1.0
CB C:ASP298 3.9 22.6 1.0
CE1 C:HIS273 4.1 20.6 1.0
OE2 C:GLU270 4.2 21.2 1.0
OD1 C:ASP341 4.2 22.8 1.0
CG C:GLU270 4.3 20.8 1.0
CB C:GLU270 4.4 20.6 1.0
OD1 C:ASP298 4.4 23.1 1.0
CG C:GLU234 4.4 21.4 1.0
NE2 C:HIS273 4.7 20.7 1.0
MN C:MN502 4.8 70.7 1.0
ND1 C:HIS273 4.8 20.6 1.0
ND2 C:ASN268 4.9 20.2 1.0
CZ2 C:TRP51 5.0 21.1 1.0

Manganese binding site 6 out of 16 in 4xkm

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Manganese binding site 6 out of 16 in the Crystal Structure of Xylose Isomerase From An Human Intestinal Tract Microbe Bacteroides Thetaiotaomicron


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 Xylose Isomerase From An Human Intestinal Tract Microbe Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn502

b:70.7
occ:1.00
 OE2 C:GLU270 2.1 21.2 1.0
OD2 C:ASP309 2.4 30.1 1.0
OD1 C:ASP311 2.4 26.4 1.0
CD C:GLU270 3.1 21.1 1.0
CG C:ASP309 3.2 29.7 1.0
NE2 C:HIS273 3.3 20.7 1.0
CG C:ASP311 3.3 26.3 1.0
OE1 C:GLU270 3.5 21.1 1.0
OD2 C:ASP311 3.5 26.7 1.0
O C:HOH798 3.6 36.8 1.0
OD1 C:ASP309 3.9 30.1 1.0
ND2 C:ASN300 3.9 22.1 1.0
CD2 C:HIS273 4.0 20.6 1.0
CB C:ASP309 4.1 28.9 1.0
CE1 C:HIS273 4.2 20.6 1.0
OD2 C:ASP341 4.4 22.7 1.0
CG C:GLU270 4.4 20.8 1.0
OD1 C:ASP341 4.5 22.8 1.0
CG C:ASP341 4.5 22.6 1.0
O C:ASP341 4.7 22.5 1.0
CB C:ASN272 4.7 21.2 1.0
CB C:ASP311 4.7 25.7 1.0
MN C:MN501 4.8 27.3 1.0

Manganese binding site 7 out of 16 in 4xkm

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Manganese binding site 7 out of 16 in the Crystal Structure of Xylose Isomerase From An Human Intestinal Tract Microbe Bacteroides Thetaiotaomicron


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 Xylose Isomerase From An Human Intestinal Tract Microbe Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn501

b:32.5
occ:1.00
 OD2 D:ASP341 2.0 22.0 1.0
OE2 D:GLU234 2.1 24.9 1.0
OD2 D:ASP298 2.1 21.3 1.0
OE1 D:GLU270 2.1 23.0 1.0
O D:HOH780 2.7 25.8 1.0
CD D:GLU234 3.0 24.7 1.0
CG D:ASP341 3.1 21.8 1.0
OE1 D:GLU234 3.3 24.7 1.0
CG D:ASP298 3.3 21.1 1.0
CD D:GLU270 3.4 22.9 1.0
CB D:ASP341 3.7 21.8 1.0
CB D:ASP298 3.9 21.0 1.0
OE2 D:GLU270 4.2 23.1 1.0
OD1 D:ASP341 4.2 21.9 1.0
CE1 D:HIS273 4.3 21.6 1.0
OD1 D:ASP298 4.3 21.3 1.0
CG D:GLU270 4.3 22.6 1.0
CG D:GLU234 4.4 24.4 1.0
CB D:GLU270 4.4 22.4 1.0
MN D:MN502 4.5 71.4 1.0
NE2 D:HIS273 4.6 21.6 1.0
ND2 D:ASN268 4.9 22.7 1.0
CZ2 D:TRP51 5.0 23.0 1.0
ND1 D:HIS273 5.0 21.4 1.0

Manganese binding site 8 out of 16 in 4xkm

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Manganese binding site 8 out of 16 in the Crystal Structure of Xylose Isomerase From An Human Intestinal Tract Microbe Bacteroides Thetaiotaomicron


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 Xylose Isomerase From An Human Intestinal Tract Microbe Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn502

b:71.4
occ:1.00
 OD2 D:ASP309 2.1 30.3 1.0
OE2 D:GLU270 2.2 23.1 1.0
OD1 D:ASP311 2.6 25.1 1.0
CD D:GLU270 3.1 22.9 1.0
NE2 D:HIS273 3.3 21.6 1.0
CG D:ASP309 3.3 29.9 1.0
OE1 D:GLU270 3.3 23.0 1.0
O D:HOH679 3.3 37.1 1.0
CG D:ASP311 3.4 25.0 1.0
OD2 D:ASP311 3.6 25.4 1.0
OD1 D:ASP309 3.8 30.4 1.0
OD2 D:ASP341 3.8 22.0 1.0
CD2 D:HIS273 3.9 21.4 1.0
ND2 D:ASN300 4.1 20.9 1.0
CG D:ASP341 4.2 21.8 1.0
CE1 D:HIS273 4.3 21.6 1.0
OD1 D:ASP341 4.3 21.9 1.0
MN D:MN501 4.5 32.5 1.0
CB D:ASP309 4.5 29.0 1.0
CG D:GLU270 4.5 22.6 1.0
O D:ASP341 4.6 21.5 1.0
CB D:ASP311 4.9 24.8 1.0

Manganese binding site 9 out of 16 in 4xkm

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Manganese binding site 9 out of 16 in the Crystal Structure of Xylose Isomerase From An Human Intestinal Tract Microbe Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of Xylose Isomerase From An Human Intestinal Tract Microbe Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn501

b:29.4
occ:1.00
 OD2 E:ASP341 2.0 23.9 1.0
OE2 E:GLU234 2.1 24.1 1.0
OE1 E:GLU270 2.1 22.4 1.0
OD2 E:ASP298 2.3 23.7 1.0
O E:HOH720 2.6 29.3 1.0
CD E:GLU234 3.0 24.2 1.0
CG E:ASP341 3.1 23.5 1.0
OE1 E:GLU234 3.2 24.3 1.0
CD E:GLU270 3.4 22.4 1.0
CG E:ASP298 3.4 23.5 1.0
CB E:ASP341 3.7 23.3 1.0
CB E:ASP298 3.9 23.3 1.0
OD1 E:ASP341 4.1 23.6 1.0
OE2 E:GLU270 4.2 22.5 1.0
CG E:GLU270 4.2 22.2 1.0
CB E:GLU270 4.3 22.1 1.0
CG E:GLU234 4.4 24.0 1.0
CE1 E:HIS273 4.4 22.2 1.0
OD1 E:ASP298 4.4 23.6 1.0
MN E:MN502 4.5 75.7 1.0
NE2 E:HIS273 4.6 22.2 1.0
ND2 E:ASN268 4.9 23.3 1.0

Manganese binding site 10 out of 16 in 4xkm

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Manganese binding site 10 out of 16 in the Crystal Structure of Xylose Isomerase From An Human Intestinal Tract Microbe Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of Xylose Isomerase From An Human Intestinal Tract Microbe Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn502

b:75.7
occ:1.00
 OE2 E:GLU270 2.3 22.5 1.0
OD1 E:ASP311 2.6 26.5 1.0
OD2 E:ASP309 2.7 30.5 1.0
CD E:GLU270 3.1 22.4 1.0
O E:HOH826 3.2 40.5 1.0
OE1 E:GLU270 3.2 22.4 1.0
CG E:ASP311 3.5 26.2 1.0
NE2 E:HIS273 3.5 22.2 1.0
OD2 E:ASP311 3.7 26.6 1.0
CG E:ASP309 3.7 29.9 1.0
OD2 E:ASP341 3.9 23.9 1.0
CG E:ASP341 4.1 23.5 1.0
CD2 E:HIS273 4.1 22.1 1.0
OD1 E:ASP341 4.1 23.6 1.0
ND2 E:ASN300 4.2 21.7 1.0
OD1 E:ASP309 4.4 30.4 1.0
MN E:MN501 4.5 29.4 1.0
CB E:ASP309 4.5 29.1 1.0
CE1 E:HIS273 4.5 22.2 1.0
CG E:GLU270 4.6 22.2 1.0
O E:ASP341 4.6 22.9 1.0
CB E:ASP311 4.9 25.8 1.0
NE2 E:HIS52 5.0 23.8 1.0

Reference:

B.G.Han, S.M.Bong, J.W.Cho, M.D.Kim, S.J.Kim, B.I.Lee. Crystal Structure of A Class 2 D-Xylose Isomerase From the Human Intestinal Tract Microbe Bacteroides Thetaiotaomicron Biodesign V. 3 41 2015.
ISSN: ESSN 2288-7105
Page generated: Sat Oct 5 22:55:21 2024

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