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Manganese in PDB 4r1q: Crystal Structure of Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase in Complex with L-Arabitol

Enzymatic activity of Crystal Structure of Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase in Complex with L-Arabitol

All present enzymatic activity of Crystal Structure of Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase in Complex with L-Arabitol:
5.3.1.4;

Protein crystallography data

The structure of Crystal Structure of Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase in Complex with L-Arabitol, PDB code: 4r1q was solved by J.M.Choi, Y.J.Lee, D.W.Lee, S.H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.08 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 118.514, 146.263, 215.677, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 20.1

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase in Complex with L-Arabitol (pdb code 4r1q). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase in Complex with L-Arabitol, PDB code: 4r1q:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 4r1q

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Manganese binding site 1 out of 6 in the Crystal Structure of Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase in Complex with L-Arabitol


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 Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase in Complex with L-Arabitol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:27.1
occ:1.00
 O1 A:SST501 2.2 29.1 1.0
NE2 A:HIS448 2.2 20.7 1.0
OE1 A:GLU307 2.3 23.7 1.0
OE2 A:GLU332 2.4 30.4 1.0
NE2 A:HIS349 2.5 20.1 1.0
O2 A:SST501 2.5 29.5 1.0
C2 A:SST501 3.1 27.1 1.0
C1 A:SST501 3.1 27.6 1.0
CE1 A:HIS448 3.1 19.2 1.0
CD A:GLU307 3.1 25.2 1.0
CD A:GLU332 3.2 27.0 1.0
CD2 A:HIS448 3.2 18.2 1.0
CD2 A:HIS349 3.2 20.1 1.0
OE2 A:GLU307 3.3 29.7 1.0
OE1 A:GLU332 3.3 30.9 1.0
CE1 A:HIS349 3.5 20.9 1.0
O A:HOH631 4.1 23.1 1.0
NE2 A:HIS447 4.2 23.0 1.0
ND1 A:HIS448 4.3 16.4 1.0
CG A:HIS448 4.3 20.7 1.0
CD2 A:HIS447 4.3 22.1 1.0
O A:HOH890 4.3 21.6 1.0
CG A:HIS349 4.4 21.4 1.0
CG A:GLU332 4.5 23.1 1.0
ND1 A:HIS349 4.5 26.3 1.0
C3 A:SST501 4.6 28.5 1.0
CG A:GLU307 4.6 22.4 1.0
CZ A:PHE330 4.8 18.8 1.0
CB A:GLU332 4.8 20.6 1.0

Manganese binding site 2 out of 6 in 4r1q

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Manganese binding site 2 out of 6 in the Crystal Structure of Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase in Complex with L-Arabitol


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 Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase in Complex with L-Arabitol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:26.3
occ:1.00
 OE2 B:GLU332 2.2 29.0 1.0
NE2 B:HIS448 2.3 21.0 1.0
OE1 B:GLU307 2.3 28.5 1.0
NE2 B:HIS349 2.3 24.7 1.0
O1 B:SST501 2.4 31.9 1.0
O2 B:SST501 2.7 27.6 1.0
OE2 B:GLU307 3.0 35.5 1.0
CD B:GLU307 3.0 26.4 1.0
CD2 B:HIS349 3.1 17.0 1.0
CD B:GLU332 3.2 28.2 1.0
CD2 B:HIS448 3.2 19.1 1.0
CE1 B:HIS448 3.3 18.8 1.0
C2 B:SST501 3.4 31.3 1.0
C1 B:SST501 3.4 30.5 1.0
OE1 B:GLU332 3.4 34.9 1.0
CE1 B:HIS349 3.5 20.8 1.0
O B:HOH642 4.0 24.9 1.0
O B:HOH783 4.1 27.7 1.0
CD2 B:HIS447 4.2 24.4 1.0
NE2 B:HIS447 4.2 27.0 1.0
CG B:HIS349 4.3 22.0 1.0
ND1 B:HIS448 4.4 21.4 1.0
CG B:HIS448 4.4 23.0 1.0
ND1 B:HIS349 4.5 22.6 1.0
CG B:GLU307 4.5 21.0 1.0
CG B:GLU332 4.5 23.5 1.0
CZ B:PHE330 4.7 17.4 1.0
CB B:GLU332 4.8 18.2 1.0
C3 B:SST501 4.9 29.8 1.0

Manganese binding site 3 out of 6 in 4r1q

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Manganese binding site 3 out of 6 in the Crystal Structure of Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase in Complex with L-Arabitol


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 Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase in Complex with L-Arabitol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn503

b:26.5
occ:1.00
 NE2 C:HIS448 2.2 20.6 1.0
O1 C:SST501 2.3 31.1 1.0
OE2 C:GLU332 2.3 27.6 1.0
OE1 C:GLU307 2.3 23.4 1.0
NE2 C:HIS349 2.5 22.4 1.0
O2 C:SST501 2.6 28.1 1.0
OE2 C:GLU307 3.0 36.9 1.0
CD C:GLU307 3.0 26.3 1.0
C1 C:SST501 3.2 25.8 1.0
CE1 C:HIS448 3.2 16.4 1.0
CD2 C:HIS448 3.2 16.6 1.0
C2 C:SST501 3.2 29.4 1.0
CD C:GLU332 3.2 31.1 1.0
CD2 C:HIS349 3.3 20.2 1.0
CE1 C:HIS349 3.5 20.5 1.0
OE1 C:GLU332 3.5 37.9 1.0
O C:HOH620 4.0 25.0 1.0
NE2 C:HIS447 4.1 22.0 1.0
CD2 C:HIS447 4.3 20.0 1.0
O C:HOH687 4.3 20.6 1.0
ND1 C:HIS448 4.3 17.8 1.0
CG C:HIS448 4.3 18.7 1.0
CG C:HIS349 4.5 21.4 1.0
CG C:GLU307 4.5 19.2 1.0
ND1 C:HIS349 4.5 23.2 1.0
CG C:GLU332 4.6 22.2 1.0
C3 C:SST501 4.7 30.2 1.0
CZ C:PHE330 4.8 17.1 1.0
CB C:GLU332 4.9 19.2 1.0

Manganese binding site 4 out of 6 in 4r1q

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Manganese binding site 4 out of 6 in the Crystal Structure of Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase in Complex with L-Arabitol


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 Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase in Complex with L-Arabitol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn501

b:28.7
occ:1.00
 NE2 D:HIS448 2.1 19.2 1.0
O1 A:SST502 2.2 28.1 1.0
OE1 D:GLU332 2.4 26.0 1.0
OE1 D:GLU307 2.4 28.3 1.0
NE2 D:HIS349 2.4 22.3 1.0
O2 A:SST502 2.7 29.6 1.0
CE1 D:HIS448 3.1 18.1 1.0
OE2 D:GLU307 3.2 32.8 1.0
CD D:GLU307 3.2 26.9 1.0
CD2 D:HIS448 3.2 18.2 1.0
C1 A:SST502 3.2 28.2 1.0
CD2 D:HIS349 3.2 19.4 1.0
C2 A:SST502 3.2 27.3 1.0
CD D:GLU332 3.3 26.9 1.0
CE1 D:HIS349 3.5 21.0 1.0
OE2 D:GLU332 3.6 34.4 1.0
O A:HOH689 3.9 25.4 1.0
ND1 D:HIS448 4.2 16.4 1.0
CG D:HIS448 4.3 17.4 1.0
O A:HOH718 4.3 21.8 1.0
CD2 D:HIS447 4.3 23.3 1.0
NE2 D:HIS447 4.3 24.0 1.0
CG D:HIS349 4.4 23.2 1.0
ND1 D:HIS349 4.6 19.9 1.0
CG D:GLU332 4.6 19.3 1.0
CG D:GLU307 4.6 19.6 1.0
C3 A:SST502 4.7 32.4 1.0
CZ D:PHE330 4.7 17.0 1.0
CB D:GLU332 4.8 17.1 1.0

Manganese binding site 5 out of 6 in 4r1q

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Manganese binding site 5 out of 6 in the Crystal Structure of Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase in Complex with L-Arabitol


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 Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase in Complex with L-Arabitol within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn502

b:36.1
occ:1.00
 O1 E:SST501 2.2 38.5 1.0
NE2 E:HIS448 2.2 29.0 1.0
NE2 E:HIS349 2.4 31.9 1.0
OE1 E:GLU307 2.4 35.3 1.0
OE1 E:GLU332 2.5 39.1 1.0
O2 E:SST501 2.6 36.8 1.0
C1 E:SST501 3.0 35.7 1.0
C2 E:SST501 3.0 41.0 1.0
CD2 E:HIS448 3.1 28.1 1.0
OE2 E:GLU307 3.1 41.1 1.0
CD E:GLU307 3.2 34.6 1.0
CD E:GLU332 3.2 36.8 1.0
CE1 E:HIS448 3.2 24.5 1.0
CD2 E:HIS349 3.3 28.1 1.0
OE2 E:GLU332 3.4 42.3 1.0
CE1 E:HIS349 3.5 32.3 1.0
O E:HOH649 4.0 34.5 1.0
O E:HOH791 4.1 29.1 1.0
NE2 E:HIS447 4.1 33.4 1.0
CD2 E:HIS447 4.2 27.1 1.0
CG E:HIS448 4.3 26.6 1.0
ND1 E:HIS448 4.3 25.3 1.0
CG E:HIS349 4.5 30.2 1.0
CG E:GLU332 4.5 30.1 1.0
C3 E:SST501 4.5 40.5 1.0
ND1 E:HIS349 4.5 33.0 1.0
CG E:GLU307 4.6 28.2 1.0
CB E:GLU332 4.7 26.8 1.0
CZ E:PHE330 4.9 29.9 1.0

Manganese binding site 6 out of 6 in 4r1q

Go back to Manganese Binding Sites List in 4r1q
Manganese binding site 6 out of 6 in the Crystal Structure of Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase in Complex with L-Arabitol


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 Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase in Complex with L-Arabitol within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn501

b:39.2
occ:1.00
 NE2 F:HIS448 2.1 32.0 1.0
OE2 F:GLU332 2.3 40.1 1.0
OE1 F:GLU307 2.4 36.0 1.0
O1 C:SST502 2.5 41.5 1.0
NE2 F:HIS349 2.5 34.1 1.0
O2 C:SST502 2.5 43.2 1.0
C2 C:SST502 3.0 42.8 1.0
CE1 F:HIS448 3.0 27.2 1.0
C1 C:SST502 3.1 41.3 1.0
CD2 F:HIS448 3.2 32.7 1.0
CD F:GLU332 3.2 39.2 1.0
CD F:GLU307 3.2 38.1 1.0
CD2 F:HIS349 3.2 35.4 1.0
OE2 F:GLU307 3.3 42.2 1.0
OE1 F:GLU332 3.4 47.2 1.0
CE1 F:HIS349 3.6 38.3 1.0
O F:HOH638 3.8 36.0 1.0
CE1 F:HIS447 4.1 35.5 1.0
ND1 F:HIS448 4.2 26.5 1.0
CG F:HIS448 4.3 33.4 1.0
ND1 F:HIS447 4.3 39.0 1.0
O C:HOH746 4.4 31.5 1.0
CG F:HIS349 4.5 39.5 1.0
C3 C:SST502 4.5 42.8 1.0
CG F:GLU332 4.6 34.0 1.0
ND1 F:HIS349 4.6 39.3 1.0
CG F:GLU307 4.7 30.8 1.0
CB F:GLU332 4.8 31.4 1.0
CZ F:PHE330 4.9 28.8 1.0

Reference:

J.M.Choi, Y.J.Lee, D.W.Lee, S.H.Lee. Crystal Structure of Thermophilic L-Arabinose Isomerase with L-Arabitol From Geobacillus Kaustophilus To Be Published.
Page generated: Sat Oct 5 21:05:49 2024

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