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Manganese in PDB 4gjj: Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with D-Allopyranose

Enzymatic activity of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with D-Allopyranose

All present enzymatic activity of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with D-Allopyranose:
5.3.1.14;

Protein crystallography data

The structure of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with D-Allopyranose, PDB code: 4gjj was solved by H.Yoshida, S.Kamitori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.60 / 2.38
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.650, 104.381, 113.972, 90.00, 107.91, 90.00
R / Rfree (%) 19.6 / 24.9

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with D-Allopyranose (pdb code 4gjj). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 10 binding sites of Manganese where determined in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with D-Allopyranose, PDB code: 4gjj:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 10 in 4gjj

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Manganese binding site 1 out of 10 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with D-Allopyranose


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 Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with D-Allopyranose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:27.9
occ:1.00
 OE2 A:GLU219 2.0 20.5 1.0
OD1 A:ASP327 2.1 21.8 1.0
O2 A:AOS503 2.2 34.2 1.0
OD1 A:ASP254 2.2 24.3 1.0
ND1 A:HIS281 2.2 31.7 1.0
O3 A:AOS503 2.5 37.2 1.0
C2 A:AOS503 2.8 35.6 1.0
CD A:GLU219 2.9 22.5 1.0
OE1 A:GLU219 3.0 20.4 1.0
CE1 A:HIS281 3.0 31.4 1.0
C3 A:AOS503 3.2 38.7 1.0
CG A:ASP254 3.3 22.9 1.0
CG A:ASP327 3.3 21.9 1.0
CG A:HIS281 3.3 31.6 1.0
CB A:HIS281 3.7 29.8 1.0
CB A:ASP254 3.7 20.7 1.0
CE1 A:HIS257 3.8 22.8 1.0
CB A:ASP327 3.9 21.6 1.0
NE2 A:HIS257 4.1 21.6 1.0
C5 A:AOS503 4.1 44.1 1.0
MN A:MN502 4.1 45.3 1.0
NE2 A:HIS281 4.2 32.5 1.0
O5 A:AOS503 4.2 47.5 1.0
C1 A:AOS503 4.2 35.5 1.0
C4 A:AOS503 4.3 41.6 1.0
CG A:GLU219 4.3 22.8 1.0
OD2 A:ASP327 4.3 23.0 1.0
CD2 A:HIS281 4.4 31.8 1.0
OD2 A:ASP254 4.4 20.6 1.0
ND1 A:HIS257 4.7 22.1 1.0
O1 A:AOS503 4.7 31.8 1.0
CD2 A:LEU252 4.9 27.8 1.0

Manganese binding site 2 out of 10 in 4gjj

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Manganese binding site 2 out of 10 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with D-Allopyranose


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 Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with D-Allopyranose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:45.3
occ:1.00
 OD1 A:ASP289 2.2 36.5 1.0
NE2 A:HIS257 2.4 21.6 1.0
O1 A:AOS503 2.6 31.8 1.0
O2 A:AOS503 2.7 34.2 1.0
OD2 A:ASP289 2.7 33.5 1.0
CG A:ASP289 2.8 33.2 1.0
OD1 A:ASP291 3.1 20.4 1.0
C1 A:AOS503 3.2 35.5 1.0
CD2 A:HIS257 3.3 21.3 1.0
C2 A:AOS503 3.4 35.6 1.0
CE1 A:HIS257 3.5 22.8 1.0
OD1 A:ASP254 3.6 24.3 1.0
OD2 A:ASP291 3.8 16.8 1.0
CG A:ASP291 3.9 18.9 1.0
CG A:ASP254 4.1 22.9 1.0
O5 A:AOS503 4.1 47.5 1.0
MN A:MN501 4.1 27.9 1.0
OD2 A:ASP254 4.2 20.6 1.0
CB A:ASP289 4.3 31.0 1.0
NZ A:LYS221 4.3 14.0 1.0
OD1 A:ASP327 4.3 21.8 1.0
CE A:LYS221 4.5 16.9 1.0
CG A:HIS257 4.5 21.8 1.0
NH2 B:ARG65 4.5 29.6 1.0
ND1 A:HIS257 4.5 22.1 1.0
C3 A:AOS503 4.8 38.7 1.0
CG A:ASP327 4.9 21.9 1.0
O A:HOH620 4.9 10.8 1.0

Manganese binding site 3 out of 10 in 4gjj

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Manganese binding site 3 out of 10 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with D-Allopyranose


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 Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with D-Allopyranose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:24.9
occ:1.00
 OD1 B:ASP327 2.0 27.2 1.0
ND1 B:HIS281 2.0 32.1 1.0
O2 B:AFD504 2.2 38.7 1.0
OE2 B:GLU219 2.2 14.3 1.0
O3 B:AFD504 2.3 38.8 1.0
OD2 B:ASP254 2.4 22.4 1.0
CE1 B:HIS281 2.9 31.5 1.0
CD B:GLU219 3.0 15.8 1.0
CG B:ASP327 3.1 28.3 1.0
CG B:HIS281 3.1 30.7 1.0
C2 B:AFD504 3.2 42.2 1.0
OE1 B:GLU219 3.2 17.9 1.0
C3 B:AFD504 3.3 41.8 1.0
CG B:ASP254 3.4 22.2 1.0
CB B:HIS281 3.6 29.1 1.0
CB B:ASP327 3.7 27.6 1.0
CB B:ASP254 3.9 22.8 1.0
NE2 B:HIS281 4.0 31.2 1.0
CE1 B:HIS257 4.1 20.5 1.0
OD2 B:ASP327 4.1 27.9 1.0
CD2 B:HIS281 4.2 30.8 1.0
NE2 B:HIS257 4.4 19.5 1.0
C4 B:AFD504 4.4 43.4 1.0
CG B:GLU219 4.4 17.4 1.0
C1 B:AFD504 4.5 43.2 1.0
OD1 B:ASP254 4.5 23.8 1.0
C5 B:AFD504 4.5 44.1 1.0
MN B:MN502 4.6 41.0 1.0
O5 B:AFD504 4.6 44.6 1.0
CD2 B:LEU252 4.8 32.9 1.0
O4 B:AFD504 4.9 41.3 1.0
O1 B:AFD504 5.0 40.0 1.0

Manganese binding site 4 out of 10 in 4gjj

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Manganese binding site 4 out of 10 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with D-Allopyranose


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 Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with D-Allopyranose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:41.0
occ:1.00
 OD2 B:ASP289 1.9 32.7 1.0
NE2 B:HIS257 2.4 19.5 1.0
CG B:ASP289 2.5 28.5 1.0
OD1 B:ASP289 2.5 28.1 1.0
O1 B:AFD504 2.5 40.0 1.0
O2 B:AFD504 3.0 38.7 1.0
OD1 B:ASP291 3.0 29.5 1.0
CD2 B:HIS257 3.3 19.8 1.0
CE1 B:HIS257 3.4 20.5 1.0
OD2 B:ASP254 3.4 22.4 1.0
OD2 B:ASP291 3.4 30.8 1.0
C1 B:AFD504 3.5 43.2 1.0
CG B:ASP291 3.6 29.5 1.0
O5 B:AFD504 3.7 44.6 1.0
C2 B:AFD504 3.7 42.2 1.0
CB B:ASP289 3.9 25.7 1.0
NZ B:LYS221 4.0 24.1 1.0
CG B:ASP254 4.1 22.2 1.0
CE B:LYS221 4.2 25.4 1.0
OD1 B:ASP254 4.3 23.8 1.0
OD1 B:ASP327 4.4 27.2 1.0
CG B:HIS257 4.5 19.9 1.0
ND1 B:HIS257 4.5 20.4 1.0
NH2 A:ARG65 4.6 29.4 1.0
MN B:MN501 4.6 24.9 1.0
C5 B:AFD504 4.9 44.1 1.0
CD B:LYS221 4.9 23.9 1.0
CG B:ASP327 5.0 28.3 1.0

Manganese binding site 5 out of 10 in 4gjj

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Manganese binding site 5 out of 10 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with D-Allopyranose


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 Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with D-Allopyranose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:76.6
occ:1.00
 OE2 B:GLU298 2.1 36.4 1.0
OE2 C:GLU298 2.4 38.4 1.0
CD B:GLU298 3.1 35.8 1.0
CD C:GLU298 3.3 35.4 1.0
OE1 B:GLU298 3.5 35.5 1.0
OE1 C:GLU298 3.6 35.1 1.0
CG B:GLU298 4.3 33.0 1.0
CG C:GLU298 4.6 33.3 1.0
OD1 C:ASN261 4.8 24.3 1.0
NH1 B:ARG301 4.9 43.8 1.0
NH1 C:ARG301 5.0 31.0 1.0

Manganese binding site 6 out of 10 in 4gjj

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Manganese binding site 6 out of 10 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with D-Allopyranose


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 Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with D-Allopyranose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn501

b:31.5
occ:1.00
 ND1 C:HIS281 2.0 28.1 1.0
OD1 C:ASP327 2.1 34.9 1.0
OE2 C:GLU219 2.2 32.5 1.0
O2 C:AOS503 2.3 40.4 1.0
OD2 C:ASP254 2.3 28.4 1.0
O3 C:AOS503 2.4 34.9 1.0
CE1 C:HIS281 2.8 28.2 1.0
C2 C:AOS503 2.9 40.0 1.0
CD C:GLU219 3.1 34.4 1.0
CG C:HIS281 3.1 28.9 1.0
OE1 C:GLU219 3.2 35.7 1.0
C3 C:AOS503 3.2 40.6 1.0
CG C:ASP327 3.2 34.5 1.0
CG C:ASP254 3.3 28.9 1.0
CB C:HIS281 3.6 29.3 1.0
CB C:ASP254 3.7 27.8 1.0
CB C:ASP327 3.8 32.7 1.0
CE1 C:HIS257 4.0 36.1 1.0
NE2 C:HIS281 4.0 27.2 1.0
CD2 C:HIS281 4.1 27.6 1.0
OD2 C:ASP327 4.2 35.8 1.0
MN C:MN502 4.3 47.6 1.0
C1 C:AOS503 4.4 38.6 1.0
C4 C:AOS503 4.4 43.4 1.0
NE2 C:HIS257 4.4 36.9 1.0
C5 C:AOS503 4.4 44.8 1.0
OD1 C:ASP254 4.4 31.0 1.0
CG C:GLU219 4.5 32.5 1.0
O5 C:AOS503 4.6 46.7 1.0
ND1 C:HIS257 4.8 35.4 1.0
O1 C:AOS503 4.9 37.8 1.0
CA C:ASP254 4.9 28.4 1.0

Manganese binding site 7 out of 10 in 4gjj

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Manganese binding site 7 out of 10 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with D-Allopyranose


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 Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with D-Allopyranose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn502

b:47.6
occ:1.00
 OD1 C:ASP289 2.3 27.0 1.0
NE2 C:HIS257 2.3 36.9 1.0
OD2 C:ASP289 2.6 26.6 1.0
O2 C:AOS503 2.8 40.4 1.0
CG C:ASP289 2.8 26.0 1.0
O1 C:AOS503 2.8 37.8 1.0
OD1 C:ASP291 3.0 33.2 1.0
CE1 C:HIS257 3.2 36.1 1.0
CD2 C:HIS257 3.4 34.6 1.0
OD2 C:ASP254 3.5 28.4 1.0
C1 C:AOS503 3.6 38.6 1.0
C2 C:AOS503 3.6 40.0 1.0
OD2 C:ASP291 3.7 29.9 1.0
CG C:ASP291 3.8 30.6 1.0
OD1 C:ASP254 3.9 31.0 1.0
CG C:ASP254 4.0 28.9 1.0
O5 C:AOS503 4.3 46.7 1.0
CB C:ASP289 4.3 26.6 1.0
MN C:MN501 4.3 31.5 1.0
ND1 C:HIS257 4.4 35.4 1.0
NZ C:LYS221 4.4 29.7 1.0
CG C:HIS257 4.5 35.1 1.0
CE C:LYS221 4.6 29.4 1.0
OD1 C:ASP327 4.6 34.9 1.0
NH1 D:ARG65 4.7 27.1 1.0
CG C:ASP327 4.9 34.5 1.0
OD2 C:ASP327 5.0 35.8 1.0
CD C:LYS221 5.0 31.5 1.0

Manganese binding site 8 out of 10 in 4gjj

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Manganese binding site 8 out of 10 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with D-Allopyranose


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 Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with D-Allopyranose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn501

b:22.2
occ:1.00
 ND1 D:HIS281 2.0 24.6 1.0
OD1 D:ASP327 2.1 26.9 1.0
O2 D:AOS504 2.1 37.2 1.0
OE2 D:GLU219 2.2 30.4 1.0
OD2 D:ASP254 2.2 29.9 1.0
O3 D:AOS504 2.3 39.9 1.0
CE1 D:HIS281 2.8 21.2 1.0
C2 D:AOS504 2.9 40.1 1.0
CD D:GLU219 3.0 29.3 1.0
C3 D:AOS504 3.1 43.1 1.0
OE1 D:GLU219 3.2 30.2 1.0
CG D:HIS281 3.2 26.0 1.0
CG D:ASP327 3.2 24.2 1.0
CG D:ASP254 3.3 27.1 1.0
CE1 D:HIS257 3.7 29.8 1.0
CB D:HIS281 3.7 23.6 1.0
O D:HOH622 3.7 15.5 1.0
CB D:ASP327 3.8 23.3 1.0
CB D:ASP254 3.8 25.8 1.0
MN D:MN502 3.9 37.4 1.0
NE2 D:HIS257 3.9 29.6 1.0
NE2 D:HIS281 4.0 23.5 1.0
O5 D:AOS504 4.1 51.7 1.0
C5 D:AOS504 4.2 50.0 1.0
CD2 D:HIS281 4.2 25.1 1.0
OD2 D:ASP327 4.3 23.6 1.0
C4 D:AOS504 4.3 47.7 1.0
C1 D:AOS504 4.3 38.1 1.0
OD1 D:ASP254 4.4 28.9 1.0
CG D:GLU219 4.4 28.4 1.0
ND1 D:HIS257 4.7 30.0 1.0
O1 D:AOS504 4.9 35.4 1.0

Manganese binding site 9 out of 10 in 4gjj

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Manganese binding site 9 out of 10 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with D-Allopyranose


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 Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with D-Allopyranose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn502

b:37.4
occ:1.00
 OD1 D:ASP289 2.0 25.1 1.0
O D:HOH622 2.1 15.5 1.0
NE2 D:HIS257 2.1 29.6 1.0
O2 D:AOS504 2.3 37.2 1.0
O1 D:AOS504 2.5 35.4 1.0
CG D:ASP289 2.9 25.0 1.0
C1 D:AOS504 2.9 38.1 1.0
CE1 D:HIS257 3.0 29.8 1.0
C2 D:AOS504 3.0 40.1 1.0
OD2 D:ASP289 3.2 20.8 1.0
CD2 D:HIS257 3.2 28.5 1.0
OD2 D:ASP254 3.7 29.9 1.0
O5 D:AOS504 3.8 51.7 1.0
OD1 D:ASP291 3.8 23.5 1.0
MN D:MN501 3.9 22.2 1.0
NZ D:LYS221 4.0 30.5 1.0
OD1 D:ASP327 4.1 26.9 1.0
ND1 D:HIS257 4.1 30.0 1.0
CG D:ASP254 4.2 27.1 1.0
CE D:LYS221 4.2 25.4 1.0
CG D:HIS257 4.3 28.3 1.0
CB D:ASP289 4.3 25.3 1.0
OD1 D:ASP254 4.3 28.9 1.0
OD2 D:ASP291 4.4 23.9 1.0
C3 D:AOS504 4.4 43.1 1.0
CG D:ASP291 4.5 23.8 1.0
CD D:LYS221 4.5 26.6 1.0
NH2 C:ARG65 4.5 17.6 1.0
CG D:ASP327 4.8 24.2 1.0
CZ C:PHE66 4.8 33.2 1.0
C5 D:AOS504 4.9 50.0 1.0
O3 D:AOS504 4.9 39.9 1.0

Manganese binding site 10 out of 10 in 4gjj

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Manganese binding site 10 out of 10 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with D-Allopyranose


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 Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with D-Allopyranose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn503

b:62.2
occ:1.00
 OE2 D:GLU298 2.6 33.7 1.0
OE2 A:GLU298 2.6 34.3 1.0
O D:HOH663 2.8 19.4 1.0
CD D:GLU298 3.3 32.1 1.0
OE1 D:GLU298 3.3 33.6 1.0
O A:HOH655 3.3 26.1 1.0
CD A:GLU298 3.4 29.7 1.0
OE1 A:GLU298 3.6 29.4 1.0
NH2 D:ARG301 4.5 33.7 1.0
CG A:GLU298 4.5 27.3 1.0
CG D:GLU298 4.6 28.8 1.0
OD1 A:ASN261 4.9 27.4 1.0
OD1 D:ASN261 5.0 23.3 1.0

Reference:

H.Yoshida, A.Yoshihara, M.Teraoka, S.Yamashita, K.Izumori, S.Kamitori. Structure of L-Rhamnose Isomerase in Complex with L-Rhamnopyranose Demonstrates the Sugar-Ring Opening Mechanism and the Role of A Substrate Sub-Binding Site. Febs Open Bio V. 3 35 2013.
ISSN: ESSN 2211-5463
PubMed: 23772372
DOI: 10.1016/J.FOB.2012.11.008
Page generated: Sat Oct 5 19:33:03 2024

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