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

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

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

Protein crystallography data

The structure of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329K in Complex with L-Rhamnose, PDB code: 3itt 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) 47.01 / 1.96
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.018, 104.842, 109.936, 90.00, 106.92, 90.00
R / Rfree (%) 18.3 / 22.5

Manganese Binding Sites:

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

Manganese binding site 1 out of 8 in 3itt

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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 L-Rhamnose


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 L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:24.6
occ:1.00
 ND1 A:HIS281 1.9 27.0 1.0
OD2 A:ASP327 2.0 21.2 1.0
OE2 A:GLU219 2.1 18.4 1.0
OD2 A:ASP254 2.2 19.2 1.0
O2 A:RNS2001 2.5 34.8 1.0
CE1 A:HIS281 2.6 30.7 1.0
O3 A:RNS2001 2.7 31.7 1.0
CD A:GLU219 3.0 18.5 1.0
CG A:HIS281 3.0 28.5 1.0
CG A:ASP327 3.1 19.1 1.0
OE1 A:GLU219 3.2 19.6 1.0
CG A:ASP254 3.3 14.9 1.0
C2 A:RNS2001 3.3 31.7 1.0
C3 A:RNS2001 3.6 32.7 1.0
CB A:HIS281 3.6 25.6 1.0
CB A:ASP327 3.6 19.6 1.0
CB A:ASP254 3.7 16.2 1.0
NE2 A:HIS281 3.8 30.7 1.0
CE1 A:HIS257 3.8 13.9 1.0
CD2 A:HIS281 4.0 29.1 1.0
O A:HOH439 4.1 12.6 1.0
OD1 A:ASP327 4.2 21.1 1.0
NE2 A:HIS257 4.2 15.8 1.0
O4 A:RNS2001 4.3 36.7 1.0
MN A:MN502 4.3 24.9 1.0
CG A:GLU219 4.4 15.7 1.0
OD1 A:ASP254 4.4 13.4 1.0
C4 A:RNS2001 4.5 33.5 1.0
CD2 A:LEU252 4.6 21.4 1.0
C1 A:RNS2001 4.7 31.3 1.0
ND1 A:HIS257 4.8 14.8 1.0
CA A:ASP254 4.9 15.2 1.0

Manganese binding site 2 out of 8 in 3itt

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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 L-Rhamnose


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 L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:24.9
occ:1.00
 O A:HOH439 1.9 12.6 1.0
NE2 A:HIS257 2.0 15.8 1.0
OD2 A:ASP289 2.2 15.7 1.0
O A:HOH1251 2.3 38.1 1.0
O1 A:RNS2001 2.3 28.0 1.0
O2 A:RNS2001 2.4 34.8 1.0
CG A:ASP289 2.8 16.7 1.0
OD1 A:ASP289 2.8 18.9 1.0
CE1 A:HIS257 3.0 13.9 1.0
C1 A:RNS2001 3.0 31.3 1.0
CD2 A:HIS257 3.1 11.4 1.0
C2 A:RNS2001 3.1 31.7 1.0
OD1 A:ASP291 3.8 14.5 1.0
OD2 A:ASP254 3.8 19.2 1.0
NZ A:LYS221 3.9 12.4 1.0
CE A:LYS221 4.0 11.6 1.0
OD2 A:ASP291 4.1 15.8 1.0
ND1 A:HIS257 4.1 14.8 1.0
CG A:HIS257 4.2 13.5 1.0
O4 A:RNS2001 4.2 36.7 1.0
CB A:ASP289 4.3 13.6 1.0
MN A:MN501 4.3 24.6 1.0
CG A:ASP254 4.3 14.9 1.0
CG A:ASP291 4.3 14.5 1.0
CD A:LYS221 4.4 8.9 1.0
OD1 A:ASP254 4.5 13.4 1.0
C3 A:RNS2001 4.5 32.7 1.0
NH2 B:ARG65 4.5 16.3 1.0
OD2 A:ASP327 4.5 21.2 1.0
NZ A:LYS329 4.5 26.4 1.0
C4 A:RNS2001 4.9 33.5 1.0
OE2 A:GLU219 4.9 18.4 1.0

Manganese binding site 3 out of 8 in 3itt

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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 L-Rhamnose


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 L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:23.5
occ:1.00
 ND1 B:HIS281 1.9 27.6 1.0
OD2 B:ASP327 2.0 17.9 1.0
OE2 B:GLU219 2.0 12.9 1.0
OD2 B:ASP254 2.2 18.9 1.0
CE1 B:HIS281 2.8 29.1 1.0
CD B:GLU219 2.9 12.2 1.0
O2 B:RNS2002 2.9 40.3 1.0
CG B:HIS281 3.0 26.7 1.0
CG B:ASP327 3.0 17.1 1.0
OE1 B:GLU219 3.1 16.1 1.0
CG B:ASP254 3.2 16.1 1.0
O3 B:RNS2002 3.2 38.5 1.0
CB B:HIS281 3.4 24.2 1.0
CB B:ASP327 3.5 16.1 1.0
CB B:ASP254 3.5 18.1 1.0
C2 B:RNS2002 3.8 39.6 1.0
NE2 B:HIS281 4.0 28.4 1.0
CE1 B:HIS257 4.0 15.7 1.0
CD2 B:HIS281 4.1 27.9 1.0
C3 B:RNS2002 4.1 39.9 1.0
OD1 B:ASP327 4.1 17.8 1.0
CG B:GLU219 4.3 9.7 1.0
OD1 B:ASP254 4.3 18.1 1.0
CD2 B:LEU252 4.3 27.1 1.0
O B:HOH439 4.4 20.0 1.0
NE2 B:HIS257 4.4 17.2 1.0
O4 B:RNS2002 4.5 41.4 1.0
MN B:MN504 4.7 38.3 1.0
CA B:ASP254 4.7 16.6 1.0
ND1 B:HIS257 4.8 15.3 1.0
CA B:HIS281 4.9 22.8 1.0
C4 B:RNS2002 4.9 40.4 1.0

Manganese binding site 4 out of 8 in 3itt

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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 L-Rhamnose


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 L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn504

b:38.3
occ:1.00
 O B:HOH439 1.8 20.0 1.0
NE2 B:HIS257 2.1 17.2 1.0
O B:HOH1096 2.2 37.1 1.0
O1 B:RNS2002 2.4 38.0 1.0
OD2 B:ASP289 2.4 17.7 1.0
O2 B:RNS2002 2.4 40.3 1.0
OD1 B:ASP289 2.9 23.2 1.0
CG B:ASP289 3.0 18.0 1.0
CE1 B:HIS257 3.0 15.7 1.0
C1 B:RNS2002 3.0 39.9 1.0
CD2 B:HIS257 3.2 16.6 1.0
C2 B:RNS2002 3.2 39.6 1.0
OD1 B:ASP291 3.5 15.3 1.0
OD2 B:ASP291 3.9 13.4 1.0
NZ B:LYS221 4.0 10.6 1.0
OD2 B:ASP254 4.1 18.9 1.0
CG B:ASP291 4.1 15.1 1.0
ND1 B:HIS257 4.1 15.3 1.0
O4 B:RNS2002 4.2 41.4 1.0
CE B:LYS221 4.2 10.4 1.0
CG B:HIS257 4.2 17.1 1.0
OD1 B:ASP254 4.4 18.1 1.0
CG B:ASP254 4.4 16.1 1.0
OD2 B:ASP327 4.4 17.9 1.0
CB B:ASP289 4.4 16.0 1.0
C3 B:RNS2002 4.5 39.9 1.0
CD B:LYS221 4.6 10.6 1.0
NH2 A:ARG65 4.6 18.1 1.0
MN B:MN503 4.7 23.5 1.0
C4 B:RNS2002 4.8 40.4 1.0
CG B:ASP327 4.9 17.1 1.0
CZ A:PHE66 5.0 20.2 1.0
OE2 B:GLU219 5.0 12.9 1.0

Manganese binding site 5 out of 8 in 3itt

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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 L-Rhamnose


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 L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn505

b:29.5
occ:1.00
 ND1 C:HIS281 1.7 26.4 1.0
OD2 C:ASP327 1.9 24.0 1.0
OD2 C:ASP254 2.2 20.1 1.0
OE2 C:GLU219 2.2 22.8 1.0
CE1 C:HIS281 2.5 29.3 1.0
O2 C:RNS2003 2.8 43.8 1.0
CG C:HIS281 2.9 29.0 1.0
CG C:ASP327 3.0 22.1 1.0
CD C:GLU219 3.0 22.8 1.0
O3 C:RNS2003 3.0 42.1 1.0
OE1 C:GLU219 3.1 23.7 1.0
CG C:ASP254 3.2 20.7 1.0
CB C:ASP327 3.5 21.2 1.0
CB C:HIS281 3.5 27.1 1.0
C2 C:RNS2003 3.6 42.4 1.0
CB C:ASP254 3.6 19.0 1.0
NE2 C:HIS281 3.6 27.1 1.0
CE1 C:HIS257 3.8 16.9 1.0
CD2 C:HIS281 3.9 28.5 1.0
C3 C:RNS2003 3.9 43.3 1.0
OD1 C:ASP327 4.1 24.8 1.0
O C:HOH912 4.1 25.6 1.0
O4 C:RNS2003 4.1 44.0 1.0
NE2 C:HIS257 4.3 18.1 1.0
OD1 C:ASP254 4.3 21.1 1.0
CG C:GLU219 4.4 20.0 1.0
MN C:MN506 4.5 35.0 1.0
C4 C:RNS2003 4.6 44.1 1.0
CD2 C:LEU252 4.6 28.2 1.0
ND1 C:HIS257 4.7 15.9 1.0
CA C:ASP254 4.8 18.3 1.0
CA C:HIS281 5.0 26.4 1.0
CA C:ASP327 5.0 21.6 1.0

Manganese binding site 6 out of 8 in 3itt

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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 L-Rhamnose


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 L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn506

b:35.0
occ:1.00
 O C:HOH912 1.8 25.6 1.0
O C:HOH1259 1.9 36.6 1.0
NE2 C:HIS257 2.1 18.1 1.0
OD2 C:ASP289 2.2 17.1 1.0
OD1 C:ASP289 2.6 20.6 1.0
O2 C:RNS2003 2.6 43.8 1.0
CG C:ASP289 2.7 19.0 1.0
O1 C:RNS2003 2.8 42.5 1.0
CE1 C:HIS257 3.0 16.9 1.0
CD2 C:HIS257 3.1 14.9 1.0
OD1 C:ASP291 3.3 22.6 1.0
C1 C:RNS2003 3.5 42.6 1.0
C2 C:RNS2003 3.6 42.4 1.0
OD2 C:ASP291 3.8 18.3 1.0
OD2 C:ASP254 3.9 20.1 1.0
CG C:ASP291 4.0 18.5 1.0
ND1 C:HIS257 4.1 15.9 1.0
OD1 C:ASP254 4.2 21.1 1.0
CB C:ASP289 4.2 18.2 1.0
NZ C:LYS221 4.2 14.1 1.0
CG C:HIS257 4.2 16.3 1.0
CG C:ASP254 4.2 20.7 1.0
NZ C:LYS329 4.2 27.0 1.0
CE C:LYS221 4.3 12.3 1.0
O4 C:RNS2003 4.3 44.0 1.0
NH2 D:ARG65 4.4 19.1 1.0
OD2 C:ASP327 4.4 24.0 1.0
MN C:MN505 4.5 29.5 1.0
CD C:LYS221 4.7 10.0 1.0
C3 C:RNS2003 4.8 43.3 1.0
O C:ASP289 5.0 19.4 1.0
CG C:ASP327 5.0 22.1 1.0

Manganese binding site 7 out of 8 in 3itt

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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 L-Rhamnose


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 L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn507

b:23.6
occ:1.00
 ND1 D:HIS281 1.9 23.9 1.0
OD2 D:ASP327 2.0 24.1 1.0
OE2 D:GLU219 2.0 19.1 1.0
OD2 D:ASP254 2.2 20.7 1.0
O2 D:RNS2004 2.7 30.1 1.0
CE1 D:HIS281 2.8 24.8 1.0
CD D:GLU219 3.0 20.6 1.0
O3 D:RNS2004 3.0 34.0 1.0
CG D:HIS281 3.0 23.4 1.0
CG D:ASP327 3.1 24.3 1.0
OE1 D:GLU219 3.2 23.1 1.0
CG D:ASP254 3.3 18.4 1.0
CB D:HIS281 3.5 20.8 1.0
CB D:ASP327 3.6 21.3 1.0
C2 D:RNS2004 3.6 32.2 1.0
CB D:ASP254 3.7 17.4 1.0
CE1 D:HIS257 3.8 17.4 1.0
C3 D:RNS2004 3.9 34.5 1.0
NE2 D:HIS281 4.0 24.5 1.0
CD2 D:HIS281 4.1 23.6 1.0
OD1 D:ASP327 4.2 25.7 1.0
NE2 D:HIS257 4.3 18.4 1.0
CG D:GLU219 4.3 17.6 1.0
O4 D:RNS2004 4.4 38.0 1.0
O D:HOH440 4.4 14.6 1.0
OD1 D:ASP254 4.4 15.3 1.0
MN D:MN508 4.5 29.6 1.0
CD2 D:LEU252 4.7 25.9 1.0
ND1 D:HIS257 4.7 19.2 1.0
C4 D:RNS2004 4.7 37.7 1.0
CA D:ASP254 4.9 16.1 1.0
CA D:HIS281 4.9 21.1 1.0

Manganese binding site 8 out of 8 in 3itt

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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 L-Rhamnose


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 L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn508

b:29.6
occ:1.00
 O D:HOH440 1.8 14.6 1.0
O D:HOH1153 2.0 46.9 1.0
NE2 D:HIS257 2.1 18.4 1.0
OD2 D:ASP289 2.3 15.0 1.0
O2 D:RNS2004 2.4 30.1 1.0
O1 D:RNS2004 2.5 26.0 1.0
OD1 D:ASP289 2.9 15.8 1.0
CG D:ASP289 2.9 16.0 1.0
C1 D:RNS2004 2.9 31.1 1.0
CE1 D:HIS257 3.0 17.4 1.0
C2 D:RNS2004 3.1 32.2 1.0
CD2 D:HIS257 3.1 17.4 1.0
OD1 D:ASP291 3.6 17.1 1.0
OD2 D:ASP254 3.8 20.7 1.0
NZ D:LYS221 4.1 16.9 1.0
OD2 D:ASP291 4.1 18.9 1.0
O4 D:RNS2004 4.1 38.0 1.0
ND1 D:HIS257 4.2 19.2 1.0
CE D:LYS221 4.2 15.1 1.0
NZ D:LYS329 4.2 28.6 1.0
CG D:HIS257 4.2 17.5 1.0
CG D:ASP254 4.3 18.4 1.0
CG D:ASP291 4.3 13.8 1.0
CB D:ASP289 4.3 14.1 1.0
OD2 D:ASP327 4.4 24.1 1.0
OD1 D:ASP254 4.4 15.3 1.0
MN D:MN507 4.5 23.6 1.0
C3 D:RNS2004 4.5 34.5 1.0
CD D:LYS221 4.6 14.4 1.0
NH2 C:ARG65 4.6 21.5 1.0
C4 D:RNS2004 4.8 37.7 1.0
OE2 D:GLU219 4.9 19.1 1.0
CG D:ASP327 5.0 24.3 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 16:37:54 2024

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