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Manganese in PDB 3m0y: Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329A in Complex with L-Rhamnose

Enzymatic activity of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329A in Complex with L-Rhamnose

All present enzymatic activity of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329A in Complex with L-Rhamnose:
5.3.1.14;

Protein crystallography data

The structure of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329A in Complex with L-Rhamnose, PDB code: 3m0y was solved by H.Yoshida, K.Takeda, K.Izumori, S.Kamitori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.21 / 1.96
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.723, 104.943, 114.992, 90.00, 108.06, 90.00
R / Rfree (%) 18.3 / 21.6

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329A in Complex with L-Rhamnose (pdb code 3m0y). 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 S329A in Complex with L-Rhamnose, PDB code: 3m0y:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3m0y

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Manganese binding site 1 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329A 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 S329A in Complex with L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:18.6
occ:1.00
 OD2 A:ASP327 2.1 16.7 1.0
OE2 A:GLU219 2.2 14.6 1.0
ND1 A:HIS281 2.2 19.0 1.0
OD1 A:ASP254 2.2 14.4 1.0
O2 A:RNS2001 2.2 20.6 1.0
O3 A:RNS2001 2.5 18.4 1.0
CE1 A:HIS281 3.0 20.9 1.0
C2 A:RNS2001 3.0 21.1 1.0
CD A:GLU219 3.1 14.7 1.0
CG A:ASP327 3.2 17.8 1.0
CG A:ASP254 3.3 14.2 1.0
CG A:HIS281 3.3 19.8 1.0
C3 A:RNS2001 3.3 21.0 1.0
OE1 A:GLU219 3.3 15.8 1.0
CB A:HIS281 3.7 18.2 1.0
CB A:ASP254 3.7 13.3 1.0
CB A:ASP327 3.7 16.2 1.0
CE1 A:HIS257 3.9 10.5 1.0
O A:HOH439 3.9 9.8 1.0
O4 A:RNS2001 4.0 25.1 1.0
NE2 A:HIS257 4.0 10.6 1.0
MN A:MN502 4.1 20.0 1.0
NE2 A:HIS281 4.2 19.7 1.0
C4 A:RNS2001 4.2 23.7 1.0
OD1 A:ASP327 4.3 15.5 1.0
CD2 A:HIS281 4.3 20.1 1.0
OD2 A:ASP254 4.4 14.0 1.0
C1 A:RNS2001 4.4 19.8 1.0
CG A:GLU219 4.5 12.7 1.0
ND1 A:HIS257 4.8 12.6 1.0
O1 A:RNS2001 4.9 18.6 1.0
C5 A:RNS2001 4.9 25.1 1.0
CD2 A:LEU252 5.0 20.6 1.0
O A:HOH527 5.0 23.4 1.0

Manganese binding site 2 out of 8 in 3m0y

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Manganese binding site 2 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329A 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 S329A in Complex with L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:20.0
occ:1.00
 O A:HOH439 2.1 9.8 1.0
OD2 A:ASP289 2.1 18.1 1.0
O1 A:RNS2001 2.2 18.6 1.0
NE2 A:HIS257 2.2 10.6 1.0
O A:HOH527 2.2 23.4 1.0
O2 A:RNS2001 2.3 20.6 1.0
C1 A:RNS2001 2.8 19.8 1.0
CG A:ASP289 3.0 16.6 1.0
C2 A:RNS2001 3.0 21.1 1.0
CE1 A:HIS257 3.1 10.5 1.0
OD1 A:ASP289 3.2 17.3 1.0
CD2 A:HIS257 3.2 11.2 1.0
OD1 A:ASP254 3.8 14.4 1.0
NZ A:LYS221 3.8 14.0 1.0
CE A:LYS221 3.9 13.5 1.0
O4 A:RNS2001 4.0 25.1 1.0
OD2 A:ASP291 4.0 17.9 1.0
MN A:MN501 4.1 18.6 1.0
OD1 A:ASP291 4.1 20.4 1.0
ND1 A:HIS257 4.2 12.6 1.0
OD2 A:ASP327 4.3 16.7 1.0
CB A:ASP289 4.3 13.4 1.0
CG A:HIS257 4.3 9.5 1.0
NH2 B:ARG65 4.4 14.8 1.0
C3 A:RNS2001 4.4 21.0 1.0
CG A:ASP254 4.4 14.2 1.0
CD A:LYS221 4.4 13.0 1.0
CG A:ASP291 4.5 17.8 1.0
C4 A:RNS2001 4.7 23.7 1.0
OD2 A:ASP254 4.7 14.0 1.0
CZ B:PHE66 4.7 17.8 1.0
OE2 A:GLU219 4.8 14.6 1.0
O3 A:RNS2001 5.0 18.4 1.0

Manganese binding site 3 out of 8 in 3m0y

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Manganese binding site 3 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329A 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 S329A in Complex with L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:23.4
occ:1.00
 OD2 B:ASP327 2.0 21.2 1.0
ND1 B:HIS281 2.1 23.8 1.0
OE2 B:GLU219 2.1 16.0 1.0
OD2 B:ASP254 2.2 17.7 1.0
O2 B:RNS2002 2.2 19.4 1.0
O3 B:RNS2002 2.5 19.7 1.0
CE1 B:HIS281 3.0 24.2 1.0
CD B:GLU219 3.1 17.7 1.0
CG B:ASP327 3.1 21.7 1.0
C2 B:RNS2002 3.2 23.3 1.0
CG B:HIS281 3.2 23.3 1.0
CG B:ASP254 3.3 16.5 1.0
OE1 B:GLU219 3.3 20.4 1.0
C3 B:RNS2002 3.4 23.0 1.0
CB B:HIS281 3.7 22.4 1.0
CB B:ASP327 3.7 18.7 1.0
CB B:ASP254 3.8 16.4 1.0
CE1 B:HIS257 3.8 21.1 1.0
O4 B:RNS2002 4.0 25.6 1.0
MN B:MN504 4.1 23.8 1.0
NE2 B:HIS281 4.1 23.5 1.0
NE2 B:HIS257 4.1 20.9 1.0
OD1 B:ASP327 4.2 21.9 1.0
O B:HOH439 4.2 14.3 1.0
C4 B:RNS2002 4.2 26.5 1.0
CD2 B:HIS281 4.3 22.6 1.0
OD1 B:ASP254 4.4 17.6 1.0
CG B:GLU219 4.5 15.7 1.0
C1 B:RNS2002 4.5 24.2 1.0
ND1 B:HIS257 4.8 20.3 1.0
C5 B:RNS2002 4.9 26.9 1.0

Manganese binding site 4 out of 8 in 3m0y

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Manganese binding site 4 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329A 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 S329A in Complex with L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn504

b:23.8
occ:1.00
 O B:HOH439 2.0 14.3 1.0
O B:HOH562 2.1 24.2 1.0
O1 B:RNS2002 2.2 22.8 1.0
OD1 B:ASP289 2.2 15.5 1.0
NE2 B:HIS257 2.2 20.9 1.0
O2 B:RNS2002 2.3 19.4 1.0
C1 B:RNS2002 2.8 24.2 1.0
C2 B:RNS2002 3.0 23.3 1.0
CE1 B:HIS257 3.1 21.1 1.0
CG B:ASP289 3.1 15.1 1.0
CD2 B:HIS257 3.3 18.3 1.0
OD2 B:ASP289 3.5 16.5 1.0
OD2 B:ASP254 3.7 17.7 1.0
NZ B:LYS221 3.9 14.3 1.0
O4 B:RNS2002 3.9 25.6 1.0
CE B:LYS221 3.9 14.6 1.0
OD1 B:ASP291 4.0 23.5 1.0
OD2 B:ASP291 4.1 21.7 1.0
MN B:MN503 4.1 23.4 1.0
ND1 B:HIS257 4.2 20.3 1.0
OD2 B:ASP327 4.3 21.2 1.0
C3 B:RNS2002 4.3 23.0 1.0
CG B:ASP254 4.4 16.5 1.0
CG B:HIS257 4.4 18.6 1.0
CB B:ASP289 4.5 14.0 1.0
CD B:LYS221 4.5 11.8 1.0
CG B:ASP291 4.5 22.1 1.0
NH2 A:ARG65 4.6 16.1 1.0
C4 B:RNS2002 4.6 26.5 1.0
OD1 B:ASP254 4.7 17.6 1.0
CZ A:PHE66 4.8 19.1 1.0
OE2 B:GLU219 4.8 16.0 1.0
O3 B:RNS2002 4.9 19.7 1.0

Manganese binding site 5 out of 8 in 3m0y

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Manganese binding site 5 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329A 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 S329A in Complex with L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn505

b:22.7
occ:1.00
 OD2 C:ASP327 2.1 20.6 1.0
ND1 C:HIS281 2.1 21.0 1.0
OE2 C:GLU219 2.2 21.0 1.0
O2 C:RNS2003 2.2 27.6 1.0
OD2 C:ASP254 2.2 16.6 1.0
O3 C:RNS2003 2.6 26.0 1.0
CE1 C:HIS281 2.9 22.9 1.0
C2 C:RNS2003 3.1 28.2 1.0
CD C:GLU219 3.1 23.4 1.0
CG C:ASP327 3.2 22.1 1.0
CG C:HIS281 3.2 21.7 1.0
CG C:ASP254 3.3 18.3 1.0
OE1 C:GLU219 3.3 24.8 1.0
C3 C:RNS2003 3.4 29.4 1.0
CB C:HIS281 3.7 22.0 1.0
CB C:ASP254 3.7 18.0 1.0
CB C:ASP327 3.8 19.3 1.0
O4 C:RNS2003 3.9 31.6 1.0
CE1 C:HIS257 3.9 16.7 1.0
O C:HOH500 4.1 12.5 1.0
MN C:MN506 4.1 23.4 1.0
NE2 C:HIS281 4.1 22.2 1.0
C4 C:RNS2003 4.2 30.6 1.0
NE2 C:HIS257 4.2 19.0 1.0
CD2 C:HIS281 4.3 21.6 1.0
OD1 C:ASP327 4.3 21.4 1.0
OD1 C:ASP254 4.4 18.1 1.0
C1 C:RNS2003 4.5 28.0 1.0
CG C:GLU219 4.5 21.0 1.0
O C:HOH524 4.7 24.3 1.0
ND1 C:HIS257 4.8 17.7 1.0
CD2 C:LEU252 4.9 20.4 1.0
C5 C:RNS2003 4.9 32.6 1.0
O1 C:RNS2003 5.0 28.5 1.0
CA C:ASP254 5.0 17.2 1.0

Manganese binding site 6 out of 8 in 3m0y

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Manganese binding site 6 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329A 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 S329A in Complex with L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn506

b:23.4
occ:1.00
 O C:HOH500 2.0 12.5 1.0
O C:HOH524 2.1 24.3 1.0
NE2 C:HIS257 2.1 19.0 1.0
O1 C:RNS2003 2.1 28.5 1.0
OD2 C:ASP289 2.2 19.5 1.0
O2 C:RNS2003 2.3 27.6 1.0
C1 C:RNS2003 2.8 28.0 1.0
CG C:ASP289 2.9 19.4 1.0
C2 C:RNS2003 3.0 28.2 1.0
CE1 C:HIS257 3.0 16.7 1.0
OD1 C:ASP289 3.0 17.7 1.0
CD2 C:HIS257 3.2 17.7 1.0
OD2 C:ASP254 3.8 16.6 1.0
NZ C:LYS221 3.9 16.1 1.0
O4 C:RNS2003 4.0 31.6 1.0
OD2 C:ASP291 4.0 20.4 1.0
CE C:LYS221 4.0 15.7 1.0
OD1 C:ASP291 4.1 24.0 1.0
MN C:MN505 4.1 22.7 1.0
ND1 C:HIS257 4.2 17.7 1.0
CG C:ASP254 4.3 18.3 1.0
CB C:ASP289 4.3 16.5 1.0
CG C:HIS257 4.3 18.2 1.0
C3 C:RNS2003 4.3 29.4 1.0
NH1 D:ARG65 4.4 18.7 1.0
OD2 C:ASP327 4.4 20.6 1.0
CD C:LYS221 4.4 14.3 1.0
CG C:ASP291 4.5 21.8 1.0
OD1 C:ASP254 4.5 18.1 1.0
C4 C:RNS2003 4.6 30.6 1.0
CZ D:PHE66 4.8 19.7 1.0
OE2 C:GLU219 4.9 21.0 1.0
O3 C:RNS2003 5.0 26.0 1.0

Manganese binding site 7 out of 8 in 3m0y

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Manganese binding site 7 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329A 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 S329A in Complex with L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn507

b:19.6
occ:1.00
 O2 D:RNS2004 2.1 19.1 1.0
ND1 D:HIS281 2.1 16.4 1.0
OE2 D:GLU219 2.1 17.6 1.0
OD2 D:ASP327 2.2 13.7 1.0
OD2 D:ASP254 2.2 17.8 1.0
O3 D:RNS2004 2.5 21.7 1.0
CE1 D:HIS281 3.0 17.9 1.0
C2 D:RNS2004 3.0 23.9 1.0
CD D:GLU219 3.1 19.8 1.0
CG D:HIS281 3.2 18.2 1.0
CG D:ASP254 3.3 16.0 1.0
CG D:ASP327 3.3 16.9 1.0
C3 D:RNS2004 3.3 24.7 1.0
OE1 D:GLU219 3.3 19.4 1.0
CB D:HIS281 3.7 17.2 1.0
CB D:ASP254 3.7 14.4 1.0
CB D:ASP327 3.8 15.5 1.0
CE1 D:HIS257 3.8 18.4 1.0
O4 D:RNS2004 3.8 29.6 1.0
MN D:MN508 4.1 21.0 1.0
C4 D:RNS2004 4.1 27.5 1.0
O D:HOH487 4.1 9.6 1.0
NE2 D:HIS281 4.1 16.1 1.0
NE2 D:HIS257 4.2 17.5 1.0
CD2 D:HIS281 4.3 16.8 1.0
OD1 D:ASP327 4.4 16.8 1.0
OD1 D:ASP254 4.4 15.0 1.0
C1 D:RNS2004 4.4 23.0 1.0
CG D:GLU219 4.5 15.4 1.0
ND1 D:HIS257 4.7 17.5 1.0
C5 D:RNS2004 4.8 28.4 1.0
O1 D:RNS2004 4.9 23.2 1.0
O D:HOH486 4.9 22.1 1.0
CA D:ASP254 5.0 14.9 1.0

Manganese binding site 8 out of 8 in 3m0y

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Manganese binding site 8 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329A 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 S329A in Complex with L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn508

b:21.0
occ:1.00
 O D:HOH487 2.0 9.6 1.0
O1 D:RNS2004 2.1 23.2 1.0
OD2 D:ASP289 2.1 16.0 1.0
NE2 D:HIS257 2.2 17.5 1.0
O D:HOH486 2.2 22.1 1.0
O2 D:RNS2004 2.3 19.1 1.0
C1 D:RNS2004 2.7 23.0 1.0
C2 D:RNS2004 3.0 23.9 1.0
CG D:ASP289 3.0 15.5 1.0
CE1 D:HIS257 3.0 18.4 1.0
OD1 D:ASP289 3.2 16.7 1.0
CD2 D:HIS257 3.3 16.1 1.0
OD2 D:ASP254 3.8 17.8 1.0
O4 D:RNS2004 3.8 29.6 1.0
NZ D:LYS221 3.9 19.6 1.0
OD1 D:ASP291 4.0 19.4 1.0
MN D:MN507 4.1 19.6 1.0
CE D:LYS221 4.1 17.9 1.0
OD2 D:ASP291 4.1 18.5 1.0
OD2 D:ASP327 4.2 13.7 1.0
ND1 D:HIS257 4.2 17.5 1.0
C3 D:RNS2004 4.3 24.7 1.0
CG D:ASP254 4.3 16.0 1.0
CG D:HIS257 4.3 17.2 1.0
CB D:ASP289 4.4 14.8 1.0
CD D:LYS221 4.5 15.1 1.0
NH2 C:ARG65 4.5 17.6 1.0
CG D:ASP291 4.5 18.5 1.0
C4 D:RNS2004 4.5 27.5 1.0
OD1 D:ASP254 4.6 15.0 1.0
CZ C:PHE66 4.7 20.8 1.0
OE2 D:GLU219 4.9 17.6 1.0
O3 D:RNS2004 4.9 21.7 1.0

Reference:

H.Yoshida, K.Takeda, K.Izumori, S.Kamitori. Elucidation of the Role of SER329 and the C-Terminal Region in the Catalytic Activity of Pseudomonas Stutzeri L-Rhamnose Isomerase Protein Eng.Des.Sel. V. 23 919 2010.
ISSN: ISSN 1741-0126
PubMed: 20977999
DOI: 10.1093/PROTEIN/GZQ077
Page generated: Sat Oct 5 17:01:55 2024

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