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Manganese in PDB 3uva: Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn

Enzymatic activity of Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn

All present enzymatic activity of Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn:
5.3.1.14;

Protein crystallography data

The structure of Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn, PDB code: 3uva was solved by T.T.N.Doan, P.Prabhu, M.Jeya, J.K.Kim, L.W.Kang, J.K.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.87 / 2.69
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.374, 164.779, 92.816, 90.00, 117.01, 90.00
R / Rfree (%) 18.5 / 26.6

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn (pdb code 3uva). 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 L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn, PDB code: 3uva:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3uva

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Manganese binding site 1 out of 8 in the Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn


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 L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn419

b:69.1
occ:1.00
 OE2 A:GLU225 2.3 26.6 1.0
OD2 A:ASP325 2.9 41.8 1.0
OD2 A:ASP258 3.1 29.5 1.0
CD A:GLU225 3.1 26.5 1.0
OE1 A:GLU225 3.2 25.8 1.0
ND1 A:HIS285 3.3 36.0 1.0
CG A:ASP325 3.4 37.4 1.0
O A:HOH519 3.5 34.1 1.0
MN A:MN420 3.7 81.7 1.0
CG A:ASP258 3.9 26.5 1.0
OD1 A:ASP325 3.9 40.2 1.0
CB A:ASP258 4.0 25.2 1.0
CE1 A:HIS261 4.0 29.6 1.0
NE2 A:HIS261 4.1 30.6 1.0
CB A:ASP325 4.1 34.5 1.0
CB A:HIS285 4.1 30.7 1.0
CG A:HIS285 4.1 33.3 1.0
CE1 A:HIS285 4.3 38.2 1.0
CG A:GLU225 4.5 26.7 1.0
O A:HOH513 4.6 15.7 1.0
CD2 A:LEU256 4.8 27.0 1.0
ND1 A:HIS261 4.9 28.0 1.0

Manganese binding site 2 out of 8 in 3uva

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Manganese binding site 2 out of 8 in the Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn


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 L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn420

b:81.7
occ:1.00
 NE2 A:HIS261 2.5 30.6 1.0
OD2 A:ASP293 2.6 40.6 1.0
OD1 A:ASP293 3.0 34.2 1.0
CG A:ASP293 3.2 34.9 1.0
O A:HOH513 3.2 15.7 1.0
CE1 A:HIS261 3.4 29.6 1.0
OD1 A:ASP295 3.5 35.6 1.0
CD2 A:HIS261 3.6 28.0 1.0
NZ A:LYS227 3.6 33.9 1.0
MN A:MN419 3.7 69.1 1.0
OD2 A:ASP258 3.9 29.5 1.0
OD1 A:ASP325 4.0 40.2 1.0
OD2 A:ASP295 4.2 35.2 1.0
CG A:ASP295 4.2 33.6 1.0
CG A:ASP258 4.4 26.5 1.0
ND1 A:HIS261 4.6 28.0 1.0
CG A:ASP325 4.6 37.4 1.0
CG A:HIS261 4.7 27.4 1.0
CB A:ASP293 4.7 32.6 1.0
OD1 A:ASP258 4.7 29.4 1.0
OE2 A:GLU225 4.8 26.6 1.0
OD2 A:ASP325 4.9 41.8 1.0

Manganese binding site 3 out of 8 in 3uva

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Manganese binding site 3 out of 8 in the Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn


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 L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn419

b:82.2
occ:1.00
 OE2 B:GLU225 2.6 27.6 1.0
OD2 B:ASP258 2.7 28.4 1.0
OD2 B:ASP325 3.2 36.1 1.0
ND1 B:HIS285 3.2 32.3 1.0
CG B:ASP325 3.3 34.3 1.0
O B:HOH488 3.4 29.0 1.0
O B:HOH465 3.5 26.2 1.0
CD B:GLU225 3.6 27.3 1.0
CG B:ASP258 3.6 26.7 1.0
OD1 B:ASP325 3.7 36.9 1.0
CB B:ASP325 3.8 32.3 1.0
O B:HOH479 3.8 29.7 1.0
CB B:ASP258 3.8 26.1 1.0
OE1 B:GLU225 3.9 28.3 1.0
NE2 B:HIS261 4.0 34.9 1.0
MN B:MN420 4.0 75.0 1.0
CE1 B:HIS261 4.1 34.6 1.0
CG B:HIS285 4.1 31.0 1.0
CE1 B:HIS285 4.2 32.9 1.0
CB B:HIS285 4.2 29.1 1.0
OD1 B:ASP258 4.8 28.0 1.0
CG B:GLU225 4.9 27.9 1.0
CD2 B:HIS261 5.0 32.1 1.0

Manganese binding site 4 out of 8 in 3uva

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Manganese binding site 4 out of 8 in the Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn


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 L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn420

b:75.0
occ:1.00
 O B:HOH488 2.4 29.0 1.0
NE2 B:HIS261 3.1 34.9 1.0
OD1 B:ASP293 3.2 39.6 1.0
OD2 B:ASP295 3.5 44.8 1.0
OD1 B:ASP295 3.6 43.1 1.0
CG B:ASP293 3.8 36.5 1.0
OD2 B:ASP293 3.9 42.6 1.0
CE1 B:HIS261 4.0 34.6 1.0
CG B:ASP295 4.0 40.3 1.0
OD1 B:ASP325 4.0 36.9 1.0
MN B:MN419 4.0 82.2 1.0
CD2 B:HIS261 4.0 32.1 1.0
NZ B:LYS227 4.3 30.0 1.0
OD2 B:ASP258 4.3 28.4 1.0
O B:HOH465 4.5 26.2 1.0
CG B:ASP325 4.7 34.3 1.0
OD2 B:ASP325 4.7 36.1 1.0
CE B:LYS227 4.9 27.9 1.0
CB B:ASP293 5.0 34.0 1.0

Manganese binding site 5 out of 8 in 3uva

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Manganese binding site 5 out of 8 in the Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn


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 L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn419

b:81.8
occ:1.00
 OD2 C:ASP258 2.6 31.6 1.0
OE2 C:GLU225 2.6 31.1 1.0
OD2 C:ASP325 2.9 37.0 1.0
ND1 C:HIS285 3.2 35.4 1.0
OE1 C:GLU225 3.2 24.8 1.0
CD C:GLU225 3.3 26.4 1.0
CG C:ASP258 3.7 26.6 1.0
CG C:ASP325 3.8 36.5 1.0
O C:HOH509 3.9 38.4 1.0
NE2 C:HIS261 4.0 24.5 1.0
CE1 C:HIS285 4.0 36.8 1.0
CE1 C:HIS261 4.1 25.0 1.0
CG C:HIS285 4.1 33.7 1.0
MN C:MN420 4.2 67.8 1.0
CB C:HIS285 4.3 30.9 1.0
CB C:ASP325 4.3 34.3 1.0
CB C:ASP258 4.3 24.3 1.0
CG C:GLU225 4.7 24.9 1.0
OD1 C:ASP325 4.7 40.3 1.0
OD1 C:ASP258 4.7 24.9 1.0
CD2 C:HIS261 5.0 24.4 1.0

Manganese binding site 6 out of 8 in 3uva

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Manganese binding site 6 out of 8 in the Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn


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 L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn420

b:67.8
occ:1.00
 OD2 C:ASP293 2.7 37.3 1.0
OD1 C:ASP293 2.7 34.1 1.0
NE2 C:HIS261 2.9 24.5 1.0
OD1 C:ASP295 3.0 38.2 1.0
CG C:ASP293 3.1 33.3 1.0
O C:HOH509 3.1 38.4 1.0
CD2 C:HIS261 3.5 24.4 1.0
OD2 C:ASP295 3.5 37.4 1.0
OD2 C:ASP258 3.5 31.6 1.0
CG C:ASP295 3.6 35.9 1.0
OD1 C:ASP258 3.8 24.9 1.0
CG C:ASP258 3.9 26.6 1.0
CE1 C:HIS261 4.1 25.0 1.0
OD1 C:ASP325 4.1 40.3 1.0
MN C:MN419 4.2 81.8 1.0
OD2 C:ASP325 4.3 37.0 1.0
CG C:ASP325 4.3 36.5 1.0
OG C:SER287 4.5 26.8 1.0
CB C:ASP293 4.6 31.7 1.0
CG C:HIS261 4.8 24.9 1.0
NZ C:LYS227 4.8 25.9 1.0
O C:ASP293 5.0 32.0 1.0

Manganese binding site 7 out of 8 in 3uva

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Manganese binding site 7 out of 8 in the Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn


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 L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn419

b:71.4
occ:1.00
 OE2 D:GLU225 2.4 38.5 1.0
OD2 D:ASP258 2.6 25.1 1.0
CD D:GLU225 3.1 35.3 1.0
OE1 D:GLU225 3.2 36.4 1.0
ND1 D:HIS285 3.2 27.2 1.0
CG D:ASP258 3.5 24.9 1.0
OD2 D:ASP325 3.6 33.1 1.0
CG D:ASP325 3.7 34.9 1.0
CB D:ASP258 3.7 25.8 1.0
CE1 D:HIS261 3.7 28.3 1.0
NE2 D:HIS261 4.0 28.2 1.0
CB D:HIS285 4.0 25.9 1.0
MN D:MN420 4.0 75.3 1.0
CG D:HIS285 4.0 26.6 1.0
OD1 D:ASP325 4.1 39.2 1.0
CB D:ASP325 4.1 33.0 1.0
O D:HOH484 4.2 18.1 1.0
CE1 D:HIS285 4.3 30.5 1.0
CG D:GLU225 4.5 32.7 1.0
ND1 D:HIS261 4.6 27.0 1.0
OD1 D:ASP258 4.6 26.9 1.0
CD1 D:LEU256 4.7 32.6 1.0
CD2 D:HIS261 4.9 26.0 1.0
CA D:ASP258 5.0 26.5 1.0

Manganese binding site 8 out of 8 in 3uva

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Manganese binding site 8 out of 8 in the Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn


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 L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn420

b:75.3
occ:1.00
 OD2 D:ASP293 2.3 35.1 1.0
NE2 D:HIS261 2.7 28.2 1.0
CE1 D:HIS261 3.3 28.3 1.0
CG D:ASP293 3.4 32.7 1.0
NZ D:LYS227 3.7 25.8 1.0
O D:HOH486 3.8 30.6 1.0
CD2 D:HIS261 3.9 26.0 1.0
OD1 D:ASP293 3.9 37.2 1.0
MN D:MN419 4.0 71.4 1.0
OD1 D:ASP325 4.1 39.2 1.0
OD2 D:ASP258 4.2 25.1 1.0
OD2 D:ASP295 4.3 37.0 1.0
OD1 D:ASP295 4.3 36.6 1.0
ND1 D:HIS261 4.6 27.0 1.0
CG D:ASP295 4.7 32.4 1.0
CB D:ASP293 4.7 30.2 1.0
CG D:ASP325 4.8 34.9 1.0
CE D:LYS227 4.9 26.1 1.0
CG D:HIS261 4.9 26.1 1.0
OE2 D:GLU225 4.9 38.5 1.0
CD D:LYS227 4.9 26.9 1.0
CG D:ASP258 5.0 24.9 1.0

Reference:

P.Prabhu, T.N.Doan, M.Tiwari, R.Singh, S.C.Kim, M.K.Hong, Y.C.Kang, L.W.Kang, J.K.Lee. Structure-Based Studies on the Metal Binding of Two-Metal-Dependent Sugar Isomerases. Febs J. V. 281 3446 2014.
ISSN: ISSN 1742-464X
PubMed: 24925069
DOI: 10.1111/FEBS.12872
Page generated: Tue Dec 15 04:16:29 2020

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