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Manganese in PDB 3m0h: Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329F in Complex with L-Rhamnose

Enzymatic activity of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329F in Complex with L-Rhamnose

All present enzymatic activity of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329F in Complex with L-Rhamnose:
5.3.1.14;

Protein crystallography data

The structure of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329F in Complex with L-Rhamnose, PDB code: 3m0h 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) 32.71 / 1.58
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.476, 104.457, 108.200, 90.00, 107.26, 90.00
R / Rfree (%) 16.1 / 18.1

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329F in Complex with L-Rhamnose (pdb code 3m0h). 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 S329F in Complex with L-Rhamnose, PDB code: 3m0h:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3m0h

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Manganese binding site 1 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329F 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 S329F in Complex with L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:12.7
occ:1.00
 OD2 A:ASP327 2.0 15.3 1.0
OE2 A:GLU219 2.1 9.8 1.0
OD2 A:ASP254 2.2 8.0 1.0
O2 A:RNS2001 2.2 13.2 1.0
ND1 A:HIS281 2.2 13.6 1.0
O3 A:RNS2001 2.3 14.8 1.0
C2 A:RNS2001 3.0 14.5 1.0
CD A:GLU219 3.1 11.4 1.0
CE1 A:HIS281 3.1 13.9 1.0
CG A:ASP327 3.1 12.0 1.0
C3 A:RNS2001 3.2 13.9 1.0
CG A:ASP254 3.3 9.6 1.0
CG A:HIS281 3.3 11.5 1.0
OE1 A:GLU219 3.3 11.5 1.0
CB A:HIS281 3.7 12.2 1.0
CB A:ASP327 3.7 10.5 1.0
O4 A:RNS2001 3.8 13.0 1.0
CB A:ASP254 3.8 9.0 1.0
CE1 A:HIS257 3.9 8.9 1.0
MN A:MN502 4.0 12.0 1.0
C4 A:RNS2001 4.0 14.6 1.0
O A:HOH1643 4.1 10.5 1.0
NE2 A:HIS257 4.1 8.6 1.0
OD1 A:ASP327 4.2 13.5 1.0
NE2 A:HIS281 4.3 14.1 1.0
OD1 A:ASP254 4.4 8.3 1.0
CD2 A:HIS281 4.4 14.9 1.0
C1 A:RNS2001 4.4 14.9 1.0
CG A:GLU219 4.5 9.5 1.0
O A:HOH1638 4.6 12.2 1.0
C5 A:RNS2001 4.7 15.5 1.0
ND1 A:HIS257 4.8 9.1 1.0
O1 A:RNS2001 4.9 14.2 1.0

Manganese binding site 2 out of 8 in 3m0h

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Manganese binding site 2 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329F 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 S329F in Complex with L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:12.0
occ:1.00
 O A:HOH1643 1.9 10.5 1.0
O2 A:RNS2001 2.1 13.2 1.0
NE2 A:HIS257 2.1 8.6 1.0
O A:HOH1638 2.1 12.2 1.0
OD2 A:ASP289 2.2 10.8 1.0
O1 A:RNS2001 2.2 14.2 1.0
C1 A:RNS2001 2.9 14.9 1.0
CE1 A:HIS257 2.9 8.9 1.0
C2 A:RNS2001 3.0 14.5 1.0
CG A:ASP289 3.1 7.4 1.0
CD2 A:HIS257 3.2 8.1 1.0
OD1 A:ASP289 3.3 9.8 1.0
NZ A:LYS221 3.8 9.0 1.0
OD2 A:ASP254 3.8 8.0 1.0
O4 A:RNS2001 3.9 13.0 1.0
CE A:LYS221 3.9 7.7 1.0
MN A:MN501 4.0 12.7 1.0
OD2 A:ASP291 4.1 9.7 1.0
OD1 A:ASP291 4.1 12.0 1.0
ND1 A:HIS257 4.1 9.1 1.0
OD2 A:ASP327 4.2 15.3 1.0
C3 A:RNS2001 4.2 13.9 1.0
CG A:HIS257 4.3 8.0 1.0
CG A:ASP254 4.4 9.6 1.0
CD A:LYS221 4.4 8.8 1.0
CB A:ASP289 4.4 8.5 1.0
CG A:ASP291 4.5 10.9 1.0
C4 A:RNS2001 4.5 14.6 1.0
NH2 B:ARG65 4.6 10.5 1.0
OD1 A:ASP254 4.6 8.3 1.0
OE2 A:GLU219 4.7 9.8 1.0
O3 A:RNS2001 4.8 14.8 1.0
CZ B:PHE66 4.8 11.5 1.0

Manganese binding site 3 out of 8 in 3m0h

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Manganese binding site 3 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329F 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 S329F in Complex with L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:12.4
occ:1.00
 OD2 B:ASP327 2.1 13.7 1.0
OE2 B:GLU219 2.1 8.5 1.0
ND1 B:HIS281 2.2 13.6 1.0
OD2 B:ASP254 2.2 8.0 1.0
O2 B:RNS2002 2.3 13.8 1.0
O3 B:RNS2002 2.4 14.4 1.0
CE1 B:HIS281 3.0 12.6 1.0
CD B:GLU219 3.1 9.6 1.0
C2 B:RNS2002 3.1 15.1 1.0
CG B:ASP327 3.2 11.2 1.0
CG B:HIS281 3.3 9.4 1.0
C3 B:RNS2002 3.3 14.2 1.0
CG B:ASP254 3.3 8.9 1.0
OE1 B:GLU219 3.4 11.5 1.0
CB B:HIS281 3.7 11.0 1.0
CB B:ASP327 3.7 9.8 1.0
CB B:ASP254 3.8 7.2 1.0
O4 B:RNS2002 3.8 14.5 1.0
CE1 B:HIS257 3.9 8.0 1.0
MN B:MN504 4.1 11.6 1.0
C4 B:RNS2002 4.1 14.4 1.0
NE2 B:HIS257 4.2 9.0 1.0
O B:HOH1640 4.2 10.7 1.0
NE2 B:HIS281 4.2 12.5 1.0
OD1 B:ASP327 4.3 11.8 1.0
CD2 B:HIS281 4.3 11.7 1.0
OD1 B:ASP254 4.4 9.2 1.0
CG B:GLU219 4.4 8.4 1.0
C1 B:RNS2002 4.6 14.2 1.0
C5 B:RNS2002 4.8 15.9 1.0
ND1 B:HIS257 4.8 9.7 1.0
O B:HOH1639 4.8 11.8 1.0
CD2 B:LEU252 5.0 13.1 1.0

Manganese binding site 4 out of 8 in 3m0h

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Manganese binding site 4 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329F 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 S329F in Complex with L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn504

b:11.6
occ:1.00
 O B:HOH1640 1.9 10.7 1.0
O2 B:RNS2002 2.1 13.8 1.0
O B:HOH1639 2.1 11.8 1.0
NE2 B:HIS257 2.1 9.0 1.0
OD2 B:ASP289 2.2 10.0 1.0
O1 B:RNS2002 2.2 12.2 1.0
C1 B:RNS2002 2.9 14.2 1.0
C2 B:RNS2002 2.9 15.1 1.0
CE1 B:HIS257 2.9 8.0 1.0
CG B:ASP289 3.1 9.7 1.0
OD1 B:ASP289 3.3 11.2 1.0
CD2 B:HIS257 3.3 7.8 1.0
O4 B:RNS2002 3.8 14.5 1.0
OD2 B:ASP254 3.8 8.0 1.0
NZ B:LYS221 3.8 10.0 1.0
CE B:LYS221 4.0 9.4 1.0
OD2 B:ASP291 4.0 9.5 1.0
MN B:MN503 4.1 12.4 1.0
OD1 B:ASP291 4.1 11.6 1.0
ND1 B:HIS257 4.1 9.7 1.0
C3 B:RNS2002 4.2 14.2 1.0
OD2 B:ASP327 4.2 13.7 1.0
CG B:HIS257 4.3 8.5 1.0
CG B:ASP254 4.4 8.9 1.0
CB B:ASP289 4.4 9.1 1.0
CD B:LYS221 4.4 7.8 1.0
CG B:ASP291 4.5 12.6 1.0
C4 B:RNS2002 4.5 14.4 1.0
NH2 A:ARG65 4.5 11.7 1.0
OD1 B:ASP254 4.6 9.2 1.0
OE2 B:GLU219 4.8 8.5 1.0
CZ A:PHE66 4.8 13.2 1.0
O3 B:RNS2002 4.8 14.4 1.0

Manganese binding site 5 out of 8 in 3m0h

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Manganese binding site 5 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329F 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 S329F in Complex with L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn505

b:13.6
occ:1.00
 OD2 C:ASP327 2.0 15.0 1.0
OE2 C:GLU219 2.1 10.7 1.0
O2 C:RNS2003 2.2 13.2 1.0
ND1 C:HIS281 2.2 16.1 1.0
OD2 C:ASP254 2.2 8.5 1.0
O3 C:RNS2003 2.4 14.9 1.0
C2 C:RNS2003 3.0 13.6 1.0
CE1 C:HIS281 3.1 14.6 1.0
CD C:GLU219 3.1 11.8 1.0
CG C:ASP327 3.2 12.0 1.0
C3 C:RNS2003 3.2 15.6 1.0
CG C:HIS281 3.3 12.8 1.0
CG C:ASP254 3.3 10.1 1.0
OE1 C:GLU219 3.4 13.4 1.0
CB C:HIS281 3.7 14.0 1.0
CB C:ASP327 3.7 10.2 1.0
O4 C:RNS2003 3.8 16.0 1.0
CE1 C:HIS257 3.8 10.4 1.0
CB C:ASP254 3.9 9.6 1.0
MN C:MN506 4.0 12.1 1.0
C4 C:RNS2003 4.1 17.2 1.0
NE2 C:HIS257 4.1 10.4 1.0
O C:HOH1644 4.1 7.9 1.0
OD1 C:ASP327 4.2 14.0 1.0
NE2 C:HIS281 4.2 15.5 1.0
CD2 C:HIS281 4.4 15.2 1.0
OD1 C:ASP254 4.4 9.1 1.0
C1 C:RNS2003 4.4 16.0 1.0
CG C:GLU219 4.5 9.7 1.0
O C:HOH1641 4.7 12.0 1.0
C5 C:RNS2003 4.8 17.2 1.0
ND1 C:HIS257 4.8 10.0 1.0
O1 C:RNS2003 4.9 12.5 1.0
CD2 C:LEU252 5.0 13.8 1.0

Manganese binding site 6 out of 8 in 3m0h

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Manganese binding site 6 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329F 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 S329F in Complex with L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn506

b:12.1
occ:1.00
 O C:HOH1644 1.9 7.9 1.0
O C:HOH1641 2.1 12.0 1.0
NE2 C:HIS257 2.1 10.4 1.0
O2 C:RNS2003 2.1 13.2 1.0
O1 C:RNS2003 2.1 12.5 1.0
OD2 C:ASP289 2.2 8.7 1.0
C1 C:RNS2003 2.8 16.0 1.0
C2 C:RNS2003 3.0 13.6 1.0
CE1 C:HIS257 3.0 10.4 1.0
CG C:ASP289 3.1 7.9 1.0
CD2 C:HIS257 3.3 10.5 1.0
OD1 C:ASP289 3.3 10.1 1.0
NZ C:LYS221 3.8 9.6 1.0
OD2 C:ASP254 3.9 8.5 1.0
O4 C:RNS2003 3.9 16.0 1.0
MN C:MN505 4.0 13.6 1.0
CE C:LYS221 4.0 10.0 1.0
OD2 C:ASP291 4.0 9.8 1.0
OD1 C:ASP291 4.1 12.5 1.0
ND1 C:HIS257 4.1 10.0 1.0
OD2 C:ASP327 4.2 15.0 1.0
C3 C:RNS2003 4.2 15.6 1.0
CG C:HIS257 4.3 9.6 1.0
CG C:ASP254 4.4 10.1 1.0
CB C:ASP289 4.4 8.4 1.0
CD C:LYS221 4.5 7.8 1.0
CG C:ASP291 4.5 12.1 1.0
NH2 D:ARG65 4.5 9.4 1.0
C4 C:RNS2003 4.5 17.2 1.0
OD1 C:ASP254 4.7 9.1 1.0
OE2 C:GLU219 4.7 10.7 1.0
CZ D:PHE66 4.8 12.4 1.0
O3 C:RNS2003 4.8 14.9 1.0

Manganese binding site 7 out of 8 in 3m0h

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Manganese binding site 7 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329F 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 S329F in Complex with L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn507

b:11.2
occ:1.00
 OD2 D:ASP327 2.0 13.1 1.0
OE2 D:GLU219 2.1 7.7 1.0
OD2 D:ASP254 2.2 6.1 1.0
ND1 D:HIS281 2.3 12.2 1.0
O2 D:RNS2004 2.3 12.2 1.0
O3 D:RNS2004 2.3 12.2 1.0
C2 D:RNS2004 3.1 13.1 1.0
CD D:GLU219 3.1 11.3 1.0
CE1 D:HIS281 3.1 10.8 1.0
CG D:ASP327 3.2 9.8 1.0
C3 D:RNS2004 3.2 12.2 1.0
CG D:ASP254 3.3 8.4 1.0
CG D:HIS281 3.3 9.1 1.0
OE1 D:GLU219 3.4 11.3 1.0
CB D:HIS281 3.7 10.6 1.0
CB D:ASP327 3.7 9.1 1.0
O4 D:RNS2004 3.8 14.2 1.0
CB D:ASP254 3.8 8.1 1.0
CE1 D:HIS257 3.9 7.7 1.0
O D:HOH440 3.9 11.2 1.0
MN D:MN508 4.0 10.3 1.0
C4 D:RNS2004 4.1 12.2 1.0
NE2 D:HIS257 4.1 8.4 1.0
OD1 D:ASP327 4.2 9.7 1.0
NE2 D:HIS281 4.3 10.4 1.0
OD1 D:ASP254 4.4 8.2 1.0
CD2 D:HIS281 4.4 11.5 1.0
CG D:GLU219 4.4 9.3 1.0
C1 D:RNS2004 4.5 13.2 1.0
C5 D:RNS2004 4.7 15.0 1.0
O D:HOH1642 4.8 9.7 1.0
ND1 D:HIS257 4.8 9.1 1.0
O1 D:RNS2004 5.0 11.5 1.0

Manganese binding site 8 out of 8 in 3m0h

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Manganese binding site 8 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329F 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 S329F in Complex with L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn508

b:10.3
occ:1.00
 O D:HOH440 2.0 11.2 1.0
O2 D:RNS2004 2.0 12.2 1.0
O D:HOH1642 2.1 9.7 1.0
OD2 D:ASP289 2.1 9.3 1.0
NE2 D:HIS257 2.1 8.4 1.0
O1 D:RNS2004 2.1 11.5 1.0
C1 D:RNS2004 2.8 13.2 1.0
C2 D:RNS2004 2.9 13.1 1.0
CE1 D:HIS257 3.0 7.7 1.0
CG D:ASP289 3.0 7.7 1.0
CD2 D:HIS257 3.3 8.2 1.0
OD1 D:ASP289 3.3 9.8 1.0
O4 D:RNS2004 3.8 14.2 1.0
OD2 D:ASP254 3.8 6.1 1.0
NZ D:LYS221 3.8 10.3 1.0
CE D:LYS221 4.0 9.0 1.0
MN D:MN507 4.0 11.2 1.0
OD2 D:ASP291 4.1 9.3 1.0
OD1 D:ASP291 4.1 11.6 1.0
ND1 D:HIS257 4.1 9.1 1.0
C3 D:RNS2004 4.2 12.2 1.0
OD2 D:ASP327 4.2 13.1 1.0
CG D:HIS257 4.3 7.6 1.0
CD D:LYS221 4.4 9.5 1.0
CG D:ASP254 4.4 8.4 1.0
CB D:ASP289 4.4 8.9 1.0
C4 D:RNS2004 4.5 12.2 1.0
NH2 C:ARG65 4.5 9.6 1.0
CG D:ASP291 4.5 10.6 1.0
OD1 D:ASP254 4.6 8.2 1.0
OE2 D:GLU219 4.7 7.7 1.0
O3 D:RNS2004 4.7 12.2 1.0
CZ C:PHE66 4.8 11.3 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 16:55:20 2024

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