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Manganese in PDB 3itv: Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329K in Complex with D-Psicose

Enzymatic activity of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329K in Complex with D-Psicose

All present enzymatic activity of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329K in Complex with D-Psicose:
5.3.1.14;

Protein crystallography data

The structure of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329K in Complex with D-Psicose, PDB code: 3itv 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) 46.39 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.626, 104.643, 108.424, 90.00, 107.35, 90.00
R / Rfree (%) 16.3 / 18.4

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329K in Complex with D-Psicose (pdb code 3itv). 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 Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329K in Complex with D-Psicose, PDB code: 3itv:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3itv

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Manganese binding site 1 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329K in Complex with D-Psicose


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 S329K in Complex with D-Psicose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:11.6
occ:1.00
 OD2 A:ASP327 2.0 13.4 1.0
OE2 A:GLU219 2.1 7.5 1.0
OD2 A:ASP254 2.2 6.6 1.0
O2 A:PSJ601 2.2 11.1 1.0
ND1 A:HIS281 2.3 12.5 1.0
O3 A:PSJ601 2.3 13.0 1.0
C2 A:PSJ601 3.0 12.7 1.0
CD A:GLU219 3.1 9.0 1.0
CE1 A:HIS281 3.1 11.1 1.0
CG A:ASP327 3.2 10.2 1.0
C3 A:PSJ601 3.2 13.4 1.0
OE1 A:GLU219 3.3 10.7 1.0
CG A:ASP254 3.3 7.2 1.0
CG A:HIS281 3.3 9.8 1.0
CB A:HIS281 3.7 10.8 1.0
CB A:ASP327 3.7 7.5 1.0
CB A:ASP254 3.8 7.7 1.0
CE1 A:HIS257 3.8 8.0 1.0
O5 A:PSJ601 3.9 18.0 1.0
MN A:MN502 4.0 11.1 1.0
NE2 A:HIS257 4.1 6.1 1.0
O A:HOH1639 4.1 13.3 1.0
OD1 A:ASP327 4.2 12.6 1.0
NE2 A:HIS281 4.3 12.1 1.0
C5 A:PSJ601 4.3 16.6 1.0
C4 A:PSJ601 4.3 15.3 1.0
OD1 A:ASP254 4.4 6.7 1.0
CD2 A:HIS281 4.4 12.6 1.0
CG A:GLU219 4.5 6.9 1.0
C1 A:PSJ601 4.5 12.8 1.0
O A:HOH1994 4.7 30.1 1.0
ND1 A:HIS257 4.8 6.9 1.0
O1 A:PSJ601 4.8 13.2 1.0

Manganese binding site 2 out of 8 in 3itv

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Manganese binding site 2 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329K in Complex with D-Psicose


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 S329K in Complex with D-Psicose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:11.1
occ:1.00
 O A:HOH1639 1.8 13.3 1.0
O1 A:PSJ601 2.0 13.2 1.0
NE2 A:HIS257 2.0 6.1 1.0
O A:HOH1994 2.1 30.1 1.0
OD2 A:ASP289 2.2 8.5 1.0
O2 A:PSJ601 2.3 11.1 1.0
CE1 A:HIS257 2.9 8.0 1.0
CG A:ASP289 3.0 4.8 1.0
C2 A:PSJ601 3.0 12.7 1.0
C1 A:PSJ601 3.0 12.8 1.0
CD2 A:HIS257 3.1 6.6 1.0
OD1 A:ASP289 3.1 7.7 1.0
NZ A:LYS221 3.7 7.3 1.0
OD2 A:ASP254 3.8 6.6 1.0
CE A:LYS221 3.9 5.5 1.0
OD1 A:ASP291 4.0 10.2 1.0
MN A:MN501 4.0 11.6 1.0
ND1 A:HIS257 4.1 6.9 1.0
OD2 A:ASP291 4.1 10.4 1.0
O5 A:PSJ601 4.1 18.0 1.0
CG A:HIS257 4.2 6.3 1.0
CG A:ASP254 4.3 7.2 1.0
CB A:ASP289 4.3 7.3 1.0
OD2 A:ASP327 4.3 13.4 1.0
CD A:LYS221 4.3 7.3 1.0
NZ A:LYS329 4.4 21.5 1.0
OD1 A:ASP254 4.5 6.7 1.0
CG A:ASP291 4.5 10.4 1.0
C3 A:PSJ601 4.5 13.4 1.0
NH2 B:ARG65 4.5 12.2 1.0
OE2 A:GLU219 4.8 7.5 1.0
O3 A:PSJ601 4.9 13.0 1.0

Manganese binding site 3 out of 8 in 3itv

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Manganese binding site 3 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329K in Complex with D-Psicose


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 S329K in Complex with D-Psicose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:13.1
occ:1.00
 OD2 B:ASP327 2.0 13.9 1.0
OE2 B:GLU219 2.2 7.0 1.0
ND1 B:HIS281 2.2 16.6 1.0
OD2 B:ASP254 2.2 6.0 1.0
O2 B:PSJ602 2.3 11.1 1.0
O3 B:PSJ602 2.4 13.8 1.0
CE1 B:HIS281 3.0 13.7 1.0
CD B:GLU219 3.1 8.7 1.0
CG B:ASP327 3.1 10.8 1.0
C2 B:PSJ602 3.2 14.6 1.0
C3 B:PSJ602 3.3 14.4 1.0
CG B:HIS281 3.3 11.4 1.0
OE1 B:GLU219 3.3 11.7 1.0
CG B:ASP254 3.4 8.2 1.0
CB B:ASP327 3.7 9.3 1.0
CB B:HIS281 3.7 12.1 1.0
CE1 B:HIS257 3.8 6.0 1.0
CB B:ASP254 3.9 7.8 1.0
O5 B:PSJ602 4.0 17.3 1.0
MN B:MN504 4.1 12.6 1.0
NE2 B:HIS257 4.1 7.8 1.0
OD1 B:ASP327 4.2 12.5 1.0
NE2 B:HIS281 4.2 15.6 1.0
CD2 B:HIS281 4.3 14.5 1.0
C5 B:PSJ602 4.4 16.6 1.0
OD1 B:ASP254 4.4 6.9 1.0
C4 B:PSJ602 4.4 16.4 1.0
CG B:GLU219 4.5 6.5 1.0
O B:HOH1998 4.5 4.9 1.0
C1 B:PSJ602 4.6 14.0 1.0
ND1 B:HIS257 4.8 7.0 1.0
O B:HOH1999 4.8 19.0 1.0
O1 B:PSJ602 5.0 14.4 1.0
CD2 B:LEU252 5.0 12.6 1.0

Manganese binding site 4 out of 8 in 3itv

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Manganese binding site 4 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329K in Complex with D-Psicose


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 S329K in Complex with D-Psicose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn504

b:12.6
occ:1.00
 O B:HOH1998 1.8 4.9 1.0
NE2 B:HIS257 2.1 7.8 1.0
O B:HOH1999 2.1 19.0 1.0
O1 B:PSJ602 2.1 14.4 1.0
O2 B:PSJ602 2.3 11.1 1.0
OD2 B:ASP289 2.3 8.9 1.0
CE1 B:HIS257 2.8 6.0 1.0
C2 B:PSJ602 3.0 14.6 1.0
C1 B:PSJ602 3.0 14.0 1.0
CG B:ASP289 3.1 9.1 1.0
CD2 B:HIS257 3.2 7.0 1.0
OD1 B:ASP289 3.3 9.8 1.0
NZ B:LYS221 3.8 9.9 1.0
OD2 B:ASP254 3.8 6.0 1.0
CE B:LYS221 3.9 9.5 1.0
OD1 B:ASP291 4.0 12.2 1.0
ND1 B:HIS257 4.0 7.0 1.0
MN B:MN503 4.1 13.1 1.0
OD2 B:ASP291 4.1 10.3 1.0
O5 B:PSJ602 4.1 17.3 1.0
CG B:HIS257 4.2 6.2 1.0
OD2 B:ASP327 4.3 13.9 1.0
CG B:ASP254 4.4 8.2 1.0
CD B:LYS221 4.4 7.5 1.0
CB B:ASP289 4.5 8.6 1.0
C3 B:PSJ602 4.5 14.4 1.0
CG B:ASP291 4.5 12.1 1.0
NH2 A:ARG65 4.6 14.1 1.0
OD1 B:ASP254 4.6 6.9 1.0
OE2 B:GLU219 4.7 7.0 1.0
CZ A:PHE66 4.9 11.7 1.0
O3 B:PSJ602 4.9 13.8 1.0

Manganese binding site 5 out of 8 in 3itv

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Manganese binding site 5 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329K in Complex with D-Psicose


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 S329K in Complex with D-Psicose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn505

b:15.6
occ:1.00
 OD2 C:ASP327 1.9 15.2 1.0
ND1 C:HIS281 2.1 19.8 1.0
OE2 C:GLU219 2.2 8.4 1.0
OD2 C:ASP254 2.2 7.4 1.0
O2 C:PSJ603 2.3 14.4 1.0
O3 C:PSJ603 2.4 15.3 1.0
CE1 C:HIS281 2.9 18.7 1.0
CG C:ASP327 3.1 11.7 1.0
CD C:GLU219 3.1 11.4 1.0
C2 C:PSJ603 3.2 15.3 1.0
CG C:HIS281 3.3 15.8 1.0
C3 C:PSJ603 3.3 16.4 1.0
OE1 C:GLU219 3.3 12.4 1.0
CG C:ASP254 3.4 10.0 1.0
CB C:ASP327 3.7 8.1 1.0
CB C:HIS281 3.8 16.2 1.0
CE1 C:HIS257 3.8 8.4 1.0
CB C:ASP254 3.9 8.7 1.0
O5 C:PSJ603 3.9 20.0 1.0
MN C:MN506 4.1 13.8 1.0
NE2 C:HIS281 4.1 18.9 1.0
OD1 C:ASP327 4.1 13.3 1.0
NE2 C:HIS257 4.1 9.2 1.0
CD2 C:HIS281 4.3 19.5 1.0
C5 C:PSJ603 4.3 19.2 1.0
O C:HOH1996 4.4 4.6 1.0
OD1 C:ASP254 4.4 7.5 1.0
C4 C:PSJ603 4.4 17.5 1.0
CG C:GLU219 4.5 8.8 1.0
C1 C:PSJ603 4.6 14.9 1.0
ND1 C:HIS257 4.7 8.6 1.0
O C:HOH1273 4.8 22.8 1.0
CD2 C:LEU252 4.9 14.2 1.0
O1 C:PSJ603 4.9 13.0 1.0

Manganese binding site 6 out of 8 in 3itv

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Manganese binding site 6 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329K in Complex with D-Psicose


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 S329K in Complex with D-Psicose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn506

b:13.8
occ:1.00
 O C:HOH1996 1.8 4.6 1.0
NE2 C:HIS257 2.0 9.2 1.0
O1 C:PSJ603 2.1 13.0 1.0
O C:HOH1273 2.1 22.8 1.0
OD2 C:ASP289 2.2 9.0 1.0
O2 C:PSJ603 2.3 14.4 1.0
CE1 C:HIS257 2.8 8.4 1.0
C2 C:PSJ603 3.0 15.3 1.0
CG C:ASP289 3.0 8.1 1.0
C1 C:PSJ603 3.0 14.9 1.0
CD2 C:HIS257 3.2 8.6 1.0
OD1 C:ASP289 3.2 8.7 1.0
NZ C:LYS221 3.8 8.0 1.0
OD2 C:ASP254 3.9 7.4 1.0
OD1 C:ASP291 4.0 11.0 1.0
CE C:LYS221 4.0 9.1 1.0
ND1 C:HIS257 4.0 8.6 1.0
MN C:MN505 4.1 15.6 1.0
O5 C:PSJ603 4.1 20.0 1.0
OD2 C:ASP291 4.1 10.2 1.0
CG C:HIS257 4.2 6.8 1.0
CD C:LYS221 4.4 8.1 1.0
CG C:ASP254 4.4 10.0 1.0
CB C:ASP289 4.4 7.9 1.0
OD2 C:ASP327 4.5 15.2 1.0
CG C:ASP291 4.5 10.6 1.0
C3 C:PSJ603 4.5 16.4 1.0
OD1 C:ASP254 4.6 7.5 1.0
NH2 D:ARG65 4.6 11.3 1.0
OE2 C:GLU219 4.7 8.4 1.0
O3 C:PSJ603 4.9 15.3 1.0
CZ D:PHE66 4.9 12.0 1.0

Manganese binding site 7 out of 8 in 3itv

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Manganese binding site 7 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329K in Complex with D-Psicose


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 S329K in Complex with D-Psicose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn507

b:14.0
occ:1.00
 OD2 D:ASP327 1.9 15.5 1.0
OE2 D:GLU219 2.1 7.0 1.0
OD2 D:ASP254 2.2 5.4 1.0
ND1 D:HIS281 2.2 16.1 1.0
O2 D:PSJ604 2.3 15.8 1.0
O3 D:PSJ604 2.3 17.0 1.0
CG D:ASP327 3.1 9.8 1.0
CE1 D:HIS281 3.1 14.2 1.0
CD D:GLU219 3.1 11.8 1.0
C2 D:PSJ604 3.1 17.1 1.0
C3 D:PSJ604 3.2 16.9 1.0
CG D:ASP254 3.3 7.9 1.0
CG D:HIS281 3.3 11.6 1.0
OE1 D:GLU219 3.4 11.6 1.0
CB D:ASP327 3.7 8.6 1.0
CB D:HIS281 3.7 12.5 1.0
CE1 D:HIS257 3.8 7.9 1.0
CB D:ASP254 3.8 7.6 1.0
O5 D:PSJ604 3.9 19.1 1.0
MN D:MN508 4.0 11.6 1.0
OD1 D:ASP327 4.1 12.4 1.0
NE2 D:HIS257 4.1 9.2 1.0
NE2 D:HIS281 4.3 14.9 1.0
C5 D:PSJ604 4.4 18.9 1.0
OD1 D:ASP254 4.4 6.3 1.0
CD2 D:HIS281 4.4 15.5 1.0
C4 D:PSJ604 4.4 18.4 1.0
O D:HOH1997 4.4 3.7 1.0
CG D:GLU219 4.5 7.5 1.0
C1 D:PSJ604 4.6 15.8 1.0
O D:HOH1616 4.6 26.6 1.0
ND1 D:HIS257 4.7 9.1 1.0
O1 D:PSJ604 4.9 13.9 1.0
CD2 D:LEU252 5.0 13.3 1.0

Manganese binding site 8 out of 8 in 3itv

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Manganese binding site 8 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329K in Complex with D-Psicose


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 S329K in Complex with D-Psicose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn508

b:11.6
occ:1.00
 O D:HOH1997 1.7 3.7 1.0
NE2 D:HIS257 2.0 9.2 1.0
O1 D:PSJ604 2.1 13.9 1.0
O D:HOH1616 2.1 26.6 1.0
OD2 D:ASP289 2.2 10.3 1.0
O2 D:PSJ604 2.3 15.8 1.0
CE1 D:HIS257 2.9 7.9 1.0
C2 D:PSJ604 3.0 17.1 1.0
C1 D:PSJ604 3.0 15.8 1.0
CG D:ASP289 3.0 9.2 1.0
CD2 D:HIS257 3.1 8.5 1.0
OD1 D:ASP289 3.2 8.8 1.0
NZ D:LYS221 3.8 8.8 1.0
OD2 D:ASP254 3.9 5.4 1.0
CE D:LYS221 3.9 7.5 1.0
OD1 D:ASP291 4.0 10.1 1.0
ND1 D:HIS257 4.0 9.1 1.0
MN D:MN507 4.0 14.0 1.0
O5 D:PSJ604 4.1 19.1 1.0
OD2 D:ASP291 4.2 9.4 1.0
CG D:HIS257 4.2 7.0 1.0
CG D:ASP254 4.3 7.9 1.0
CD D:LYS221 4.4 7.8 1.0
CB D:ASP289 4.4 8.8 1.0
NZ D:LYS329 4.4 22.0 1.0
C3 D:PSJ604 4.5 16.9 1.0
CG D:ASP291 4.5 10.6 1.0
NH2 C:ARG65 4.5 11.2 1.0
OD1 D:ASP254 4.6 6.3 1.0
OD2 D:ASP327 4.6 15.5 1.0
OE2 D:GLU219 4.8 7.0 1.0
O3 D:PSJ604 4.9 17.0 1.0
CZ C:PHE66 5.0 11.3 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 16:38:30 2024

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