Atomistry » Manganese » PDB 4qsh-4u3o » 4r1q
Atomistry »
  Manganese »
    PDB 4qsh-4u3o »
      4r1q »

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

Go back to Manganese Binding Sites List in 4r1q
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

Go back to Manganese Binding Sites List in 4r1q
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

Go back to Manganese Binding Sites List in 4r1q
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

Go back to Manganese Binding Sites List in 4r1q
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

Go back to Manganese Binding Sites List in 4r1q
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

Last articles

Cl in 3TXI
Cl in 3TXJ
Cl in 3TXH
Cl in 3TXF
Cl in 3TXE
Cl in 3TXD
Cl in 3TXB
Cl in 3TW9
Cl in 3TX8
Cl in 3TX3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy