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Manganese in PDB 3itx: MN2+ Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase

Enzymatic activity of MN2+ Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase

All present enzymatic activity of MN2+ Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase:
5.3.1.14;

Protein crystallography data

The structure of MN2+ Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase, PDB code: 3itx was solved by H.Yoshida, M.Yamaji, T.Ishii, K.Izumori, S.Kamitori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.36 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.647, 105.115, 102.526, 90.00, 102.80, 90.00
R / Rfree (%) 16.5 / 19.7

Manganese Binding Sites:

The binding sites of Manganese atom in the MN2+ Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase (pdb code 3itx). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the MN2+ Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase, PDB code: 3itx:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3itx

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Manganese binding site 1 out of 8 in the MN2+ Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of MN2+ Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:14.6
occ:1.00
 ND1 A:HIS281 2.0 14.3 1.0
OE2 A:GLU219 2.1 7.9 1.0
OD2 A:ASP327 2.1 13.9 1.0
OD2 A:ASP254 2.2 9.2 1.0
O A:HOH1760 2.4 18.3 1.0
O A:HOH1769 2.6 25.1 1.0
CE1 A:HIS281 2.7 17.3 1.0
CD A:GLU219 3.0 10.2 1.0
CG A:HIS281 3.1 13.8 1.0
CG A:ASP327 3.2 12.7 1.0
OE1 A:GLU219 3.3 12.3 1.0
CG A:ASP254 3.3 7.6 1.0
CB A:HIS281 3.6 11.7 1.0
CB A:ASP327 3.7 10.8 1.0
CB A:ASP254 3.8 7.9 1.0
CE1 A:HIS257 3.9 7.9 1.0
NE2 A:HIS281 3.9 16.8 1.0
O A:HOH1759 4.1 10.7 1.0
CD2 A:HIS281 4.1 16.1 1.0
NE2 A:HIS257 4.1 7.5 1.0
MN A:MN502 4.2 30.3 1.0
OD1 A:ASP327 4.3 13.9 1.0
CG A:GLU219 4.4 7.7 1.0
OD1 A:ASP254 4.4 5.8 1.0
CD2 A:LEU252 4.8 15.6 1.0
ND1 A:HIS257 4.8 7.2 1.0

Manganese binding site 2 out of 8 in 3itx

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Manganese binding site 2 out of 8 in the MN2+ Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of MN2+ Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:30.3
occ:1.00
 O A:HOH1759 2.1 10.7 1.0
NE2 A:HIS257 2.1 7.5 1.0
O A:HOH1062 2.2 11.7 1.0
OD2 A:ASP289 2.2 11.1 1.0
O A:HOH1037 2.3 13.5 1.0
O A:HOH1760 2.3 18.3 1.0
CE1 A:HIS257 2.9 7.9 1.0
CG A:ASP289 3.0 9.0 1.0
OD1 A:ASP289 3.2 13.2 1.0
CD2 A:HIS257 3.2 7.5 1.0
NZ A:LYS221 3.8 7.7 1.0
OD2 A:ASP254 4.0 9.2 1.0
CE A:LYS221 4.0 7.0 1.0
OD1 A:ASP291 4.0 9.6 1.0
ND1 A:HIS257 4.1 7.2 1.0
OD2 A:ASP291 4.1 7.7 1.0
MN A:MN501 4.2 14.6 1.0
CG A:HIS257 4.2 5.5 1.0
OD2 A:ASP327 4.3 13.9 1.0
CD A:LYS221 4.4 7.1 1.0
CG A:ASP254 4.4 7.6 1.0
CB A:ASP289 4.4 8.3 1.0
CG A:ASP291 4.5 8.0 1.0
OD1 A:ASP254 4.6 5.8 1.0
OE2 A:GLU219 4.6 7.9 1.0
NH2 B:ARG65 4.7 8.3 1.0
O A:HOH1769 4.8 25.1 1.0
CZ B:PHE66 4.9 11.8 1.0

Manganese binding site 3 out of 8 in 3itx

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Manganese binding site 3 out of 8 in the MN2+ Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of MN2+ Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:17.7
occ:1.00
 OE2 B:GLU219 2.1 11.7 1.0
OD2 B:ASP254 2.2 8.5 1.0
OD2 B:ASP327 2.2 16.6 1.0
ND1 B:HIS281 2.3 17.0 1.0
O B:HOH1757 2.5 33.7 1.0
O B:HOH1756 2.8 25.0 1.0
CD B:GLU219 2.9 14.2 1.0
OE1 B:GLU219 3.2 15.9 1.0
CG B:ASP254 3.2 7.8 1.0
CG B:ASP327 3.3 13.6 1.0
CE1 B:HIS281 3.3 18.6 1.0
CG B:HIS281 3.3 15.4 1.0
CB B:HIS281 3.6 12.4 1.0
CB B:ASP254 3.6 8.0 1.0
CB B:ASP327 3.7 11.5 1.0
O B:HOH1134 3.7 15.9 1.0
CE1 B:HIS257 4.0 9.4 1.0
CG B:GLU219 4.3 10.0 1.0
OD1 B:ASP254 4.3 8.7 1.0
NE2 B:HIS257 4.4 11.6 1.0
OD1 B:ASP327 4.4 11.6 1.0
NE2 B:HIS281 4.4 18.6 1.0
CD2 B:HIS281 4.5 16.9 1.0
O B:HOH1078 4.6 8.8 1.0
ND1 B:HIS257 4.8 9.9 1.0
CA B:ASP254 4.8 7.8 1.0

Manganese binding site 4 out of 8 in 3itx

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Manganese binding site 4 out of 8 in the MN2+ Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of MN2+ Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn504

b:26.9
occ:1.00
 OD1 B:ASP289 1.9 13.3 1.0
O B:HOH1078 2.0 8.8 1.0
O B:HOH1134 2.0 15.9 1.0
OD1 B:ASP291 2.3 12.4 1.0
OD2 B:ASP289 2.3 15.8 1.0
CG B:ASP289 2.4 13.0 1.0
NE2 B:HIS257 2.6 11.6 1.0
O B:HOH1768 2.9 30.6 1.0
CG B:ASP291 3.1 11.2 1.0
CD2 B:HIS257 3.2 9.9 1.0
OD2 B:ASP291 3.3 10.9 1.0
CE1 B:HIS257 3.8 9.4 1.0
CB B:ASP289 3.9 11.5 1.0
OD1 B:ASP254 3.9 8.7 1.0
O B:HOH1757 3.9 33.7 1.0
OD2 B:ASP254 4.0 8.5 1.0
O B:HOH1758 4.2 16.3 1.0
CG B:ASP254 4.2 7.8 1.0
O B:HOH498 4.2 14.4 1.0
O B:ASP289 4.4 9.3 1.0
OD1 B:ASN283 4.5 11.5 1.0
CG B:HIS257 4.5 8.7 1.0
CB B:ASP291 4.5 7.4 1.0
NH2 A:ARG65 4.6 8.2 1.0
CA B:ASP289 4.6 9.9 1.0
C B:ASP289 4.7 7.7 1.0
OD2 B:ASP327 4.7 16.6 1.0
ND1 B:HIS257 4.8 9.9 1.0
O B:HOH1708 4.8 32.4 1.0
O B:ASP327 4.9 8.0 1.0
CA B:ASP291 4.9 7.5 1.0
N B:ASP291 4.9 7.0 1.0

Manganese binding site 5 out of 8 in 3itx

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Manganese binding site 5 out of 8 in the MN2+ Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of MN2+ Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn505

b:22.2
occ:1.00
 OD2 C:ASP327 2.1 19.2 1.0
OE2 C:GLU219 2.1 10.1 1.0
OD2 C:ASP254 2.2 10.4 1.0
ND1 C:HIS281 2.2 19.1 1.0
O C:HOH1397 2.5 28.4 1.0
O C:HOH1751 2.9 36.2 1.0
CD C:GLU219 3.0 12.9 1.0
CG C:ASP327 3.2 18.4 1.0
OE1 C:GLU219 3.2 15.2 1.0
CE1 C:HIS281 3.2 19.8 1.0
CG C:ASP254 3.3 10.6 1.0
CG C:HIS281 3.3 18.4 1.0
CB C:ASP327 3.6 14.6 1.0
O C:HOH1638 3.6 17.9 1.0
CB C:HIS281 3.6 15.9 1.0
CB C:ASP254 3.7 6.9 1.0
CE1 C:HIS257 4.0 10.2 1.0
OD1 C:ASP327 4.3 18.4 1.0
NE2 C:HIS281 4.3 20.9 1.0
CG C:GLU219 4.3 9.0 1.0
OD1 C:ASP254 4.4 10.9 1.0
CD2 C:HIS281 4.4 19.7 1.0
NE2 C:HIS257 4.4 11.5 1.0
O C:HOH1038 4.5 13.1 1.0
CA C:ASP254 4.8 8.1 1.0
ND1 C:HIS257 4.8 9.1 1.0

Manganese binding site 6 out of 8 in 3itx

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Manganese binding site 6 out of 8 in the MN2+ Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of MN2+ Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn506

b:30.0
occ:1.00
 O C:HOH1038 1.9 13.1 1.0
OD1 C:ASP289 2.0 12.7 1.0
O C:HOH1638 2.0 17.9 1.0
OD1 C:ASP291 2.3 15.4 1.0
OD2 C:ASP289 2.4 13.7 1.0
CG C:ASP289 2.5 11.3 1.0
NE2 C:HIS257 2.7 11.5 1.0
O C:HOH1752 2.9 27.7 1.0
CG C:ASP291 3.1 11.7 1.0
CD2 C:HIS257 3.2 10.1 1.0
OD2 C:ASP291 3.2 13.0 1.0
OD1 C:ASP254 3.8 10.9 1.0
OD2 C:ASP254 3.8 10.4 1.0
CE1 C:HIS257 3.9 10.2 1.0
CB C:ASP289 4.0 12.4 1.0
O C:HOH1751 4.0 36.2 1.0
CG C:ASP254 4.1 10.6 1.0
O C:HOH480 4.1 10.5 1.0
O C:HOH1111 4.2 20.6 1.0
ND2 C:ASN283 4.4 11.5 1.0
CB C:ASP291 4.5 11.3 1.0
CG C:HIS257 4.5 9.0 1.0
O C:ASP289 4.5 11.8 1.0
CA C:ASP289 4.6 11.5 1.0
NH2 D:ARG65 4.7 10.7 1.0
O C:HOH1635 4.7 38.7 1.0
OD2 C:ASP327 4.8 19.2 1.0
ND1 C:HIS257 4.8 9.1 1.0
C C:ASP289 4.8 11.2 1.0
O C:ASP327 4.9 9.5 1.0
CA C:ASP291 4.9 9.3 1.0
NZ C:LYS221 4.9 9.4 1.0
CE C:LYS221 5.0 7.5 1.0
N C:ASP291 5.0 8.3 1.0

Manganese binding site 7 out of 8 in 3itx

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Manganese binding site 7 out of 8 in the MN2+ Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of MN2+ Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn507

b:15.5
occ:1.00
 ND1 D:HIS281 2.0 16.7 1.0
OD2 D:ASP327 2.0 16.7 1.0
OE2 D:GLU219 2.1 11.3 1.0
OD2 D:ASP254 2.2 8.5 1.0
O D:HOH1753 2.3 23.3 1.0
O D:HOH1754 2.7 22.8 1.0
CE1 D:HIS281 2.8 19.0 1.0
CD D:GLU219 3.0 13.1 1.0
CG D:HIS281 3.1 16.4 1.0
CG D:ASP327 3.2 15.1 1.0
OE1 D:GLU219 3.3 13.8 1.0
CG D:ASP254 3.3 8.7 1.0
CB D:HIS281 3.6 13.6 1.0
CB D:ASP327 3.7 12.7 1.0
CB D:ASP254 3.8 7.4 1.0
CE1 D:HIS257 3.9 7.6 1.0
NE2 D:HIS281 4.0 18.3 1.0
CD2 D:HIS281 4.1 17.8 1.0
MN D:MN508 4.2 30.1 1.0
NE2 D:HIS257 4.2 7.9 1.0
OD1 D:ASP327 4.2 16.4 1.0
O D:HOH1755 4.3 12.0 1.0
OD1 D:ASP254 4.4 9.8 1.0
CG D:GLU219 4.4 9.0 1.0
ND1 D:HIS257 4.8 7.8 1.0

Manganese binding site 8 out of 8 in 3itx

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Manganese binding site 8 out of 8 in the MN2+ Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of MN2+ Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn508

b:30.1
occ:1.00
 O D:HOH1755 1.9 12.0 1.0
NE2 D:HIS257 2.1 7.9 1.0
O D:HOH1065 2.2 17.0 1.0
O D:HOH1753 2.3 23.3 1.0
OD2 D:ASP289 2.3 13.7 1.0
O D:HOH1069 2.4 20.8 1.0
CE1 D:HIS257 2.9 7.6 1.0
CG D:ASP289 3.1 12.4 1.0
OD1 D:ASP289 3.1 14.6 1.0
CD2 D:HIS257 3.2 9.0 1.0
OD2 D:ASP254 3.8 8.5 1.0
NZ D:LYS221 4.0 7.0 1.0
OD1 D:ASP291 4.0 12.9 1.0
CE D:LYS221 4.1 6.4 1.0
ND1 D:HIS257 4.1 7.8 1.0
OD2 D:ASP291 4.1 9.8 1.0
MN D:MN507 4.2 15.5 1.0
CG D:HIS257 4.3 7.4 1.0
OD2 D:ASP327 4.3 16.7 1.0
CG D:ASP254 4.4 8.7 1.0
CD D:LYS221 4.5 6.7 1.0
CB D:ASP289 4.5 11.0 1.0
CG D:ASP291 4.5 9.8 1.0
OD1 D:ASP254 4.6 9.8 1.0
OE2 D:GLU219 4.7 11.3 1.0
NH2 C:ARG65 4.7 10.4 1.0
O D:HOH1754 4.8 22.8 1.0
CZ C:PHE66 4.9 11.6 1.0

Reference:

H.Yoshida, M.Yamaji, T.Ishii, K.Izumori, S.Kamitori. Catalytic Reaction Mechanism of Pseudomonas Stutzeri L-Rhamnose Isomerase Deduced From X-Ray Structures Febs J. V. 277 1045 2010.
ISSN: ISSN 1742-464X
PubMed: 20088877
DOI: 10.1111/J.1742-4658.2009.07548.X
Page generated: Sat Oct 5 16:38:49 2024

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