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Manganese in PDB 3m0m: Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329F in Complex with D-Allose

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

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

Protein crystallography data

The structure of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329F in Complex with D-Allose, PDB code: 3m0m 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) 30.10 / 1.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.625, 104.260, 111.447, 90.00, 106.20, 90.00
R / Rfree (%) 17.7 / 19.6

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant S329F in Complex with D-Allose (pdb code 3m0m). 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 D-Allose, PDB code: 3m0m:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3m0m

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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 D-Allose


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

b:12.7
occ:1.00
 OD2 A:ASP327 2.0 13.9 1.0
OE2 A:GLU219 2.1 9.0 1.0
OD2 A:ASP254 2.2 8.6 1.0
ND1 A:HIS281 2.2 15.6 1.0
O2 A:AOS3001 2.2 12.7 1.0
O3 A:AOS3001 2.4 15.5 1.0
C2 A:AOS3001 3.0 15.4 1.0
CE1 A:HIS281 3.1 14.9 1.0
CD A:GLU219 3.1 10.8 1.0
CG A:ASP327 3.2 12.3 1.0
C3 A:AOS3001 3.3 16.1 1.0
CG A:HIS281 3.3 14.7 1.0
CG A:ASP254 3.3 9.0 1.0
OE1 A:GLU219 3.4 11.6 1.0
CB A:HIS281 3.7 13.4 1.0
CB A:ASP327 3.7 10.2 1.0
CB A:ASP254 3.8 9.2 1.0
O5 A:AOS3001 3.9 14.6 1.0
CE1 A:HIS257 3.9 11.5 1.0
O A:HOH1453 4.0 11.7 1.0
MN A:MN502 4.0 10.6 1.0
NE2 A:HIS257 4.1 10.3 1.0
OD1 A:ASP327 4.2 13.4 1.0
C5 A:AOS3001 4.3 16.2 1.0
NE2 A:HIS281 4.3 13.1 1.0
C4 A:AOS3001 4.4 16.5 1.0
OD1 A:ASP254 4.4 9.2 1.0
CD2 A:HIS281 4.4 15.3 1.0
C1 A:AOS3001 4.4 15.3 1.0
CG A:GLU219 4.5 9.9 1.0
O A:HOH470 4.8 11.2 1.0
ND1 A:HIS257 4.8 9.8 1.0
CD2 A:LEU252 4.9 14.7 1.0
O1 A:AOS3001 5.0 13.0 1.0

Manganese binding site 2 out of 8 in 3m0m

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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 D-Allose


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

b:10.6
occ:1.00
 O A:HOH1453 2.0 11.7 1.0
O A:HOH470 2.1 11.2 1.0
OD2 A:ASP289 2.2 8.9 1.0
NE2 A:HIS257 2.2 10.3 1.0
O1 A:AOS3001 2.2 13.0 1.0
O2 A:AOS3001 2.2 12.7 1.0
C1 A:AOS3001 2.8 15.3 1.0
C2 A:AOS3001 2.9 15.4 1.0
CE1 A:HIS257 3.0 11.5 1.0
CG A:ASP289 3.1 8.3 1.0
CD2 A:HIS257 3.2 10.6 1.0
OD1 A:ASP289 3.3 9.6 1.0
NZ A:LYS221 3.8 11.1 1.0
OD2 A:ASP254 3.8 8.6 1.0
O5 A:AOS3001 3.9 14.6 1.0
CE A:LYS221 4.0 9.6 1.0
MN A:MN501 4.0 12.7 1.0
OD2 A:ASP291 4.1 10.1 1.0
OD1 A:ASP291 4.1 12.5 1.0
ND1 A:HIS257 4.2 9.8 1.0
OD2 A:ASP327 4.3 13.9 1.0
CG A:HIS257 4.3 9.2 1.0
C3 A:AOS3001 4.4 16.1 1.0
CG A:ASP254 4.4 9.0 1.0
CB A:ASP289 4.4 9.1 1.0
CD A:LYS221 4.5 10.0 1.0
NH2 B:ARG65 4.5 10.5 1.0
CG A:ASP291 4.5 10.8 1.0
OD1 A:ASP254 4.6 9.2 1.0
OE2 A:GLU219 4.7 9.0 1.0
CZ B:PHE66 4.9 13.7 1.0
O3 A:AOS3001 4.9 15.5 1.0
C4 A:AOS3001 5.0 16.5 1.0

Manganese binding site 3 out of 8 in 3m0m

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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 D-Allose


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 D-Allose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:12.6
occ:1.00
 OD2 B:ASP327 2.0 14.4 1.0
OE2 B:GLU219 2.1 9.6 1.0
ND1 B:HIS281 2.1 12.9 1.0
OD2 B:ASP254 2.2 10.1 1.0
O2 B:AOS3002 2.3 13.2 1.0
O3 B:AOS3002 2.3 12.9 1.0
CE1 B:HIS281 3.0 14.3 1.0
CD B:GLU219 3.1 11.1 1.0
C2 B:AOS3002 3.1 16.0 1.0
CG B:ASP327 3.2 9.4 1.0
CG B:HIS281 3.2 11.3 1.0
C3 B:AOS3002 3.3 14.8 1.0
CG B:ASP254 3.3 10.1 1.0
OE1 B:GLU219 3.4 12.1 1.0
CB B:HIS281 3.6 12.3 1.0
CB B:ASP327 3.7 10.8 1.0
CB B:ASP254 3.8 9.9 1.0
O5 B:AOS3002 3.9 15.3 1.0
CE1 B:HIS257 3.9 10.7 1.0
O B:HOH461 3.9 13.8 1.0
MN B:MN504 4.0 10.5 1.0
NE2 B:HIS257 4.1 10.3 1.0
NE2 B:HIS281 4.2 14.1 1.0
OD1 B:ASP327 4.2 11.6 1.0
C5 B:AOS3002 4.2 17.8 1.0
CD2 B:HIS281 4.3 14.2 1.0
C4 B:AOS3002 4.3 16.6 1.0
OD1 B:ASP254 4.4 9.8 1.0
CG B:GLU219 4.5 10.7 1.0
C1 B:AOS3002 4.5 14.3 1.0
ND1 B:HIS257 4.8 10.0 1.0
CD2 B:LEU252 4.9 15.3 1.0
O B:HOH1454 5.0 15.1 1.0

Manganese binding site 4 out of 8 in 3m0m

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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 D-Allose


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 D-Allose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn504

b:10.5
occ:1.00
 O B:HOH461 2.0 13.8 1.0
NE2 B:HIS257 2.2 10.3 1.0
OD2 B:ASP289 2.2 9.0 1.0
O2 B:AOS3002 2.2 13.2 1.0
O B:HOH1454 2.2 15.1 1.0
O1 B:AOS3002 2.3 17.9 1.0
C1 B:AOS3002 2.9 14.3 1.0
C2 B:AOS3002 3.0 16.0 1.0
CE1 B:HIS257 3.0 10.7 1.0
CG B:ASP289 3.1 7.9 1.0
CD2 B:HIS257 3.3 9.6 1.0
OD1 B:ASP289 3.3 10.0 1.0
O5 B:AOS3002 3.8 15.3 1.0
OD2 B:ASP254 3.8 10.1 1.0
NZ B:LYS221 3.9 10.6 1.0
CE B:LYS221 4.0 9.7 1.0
MN B:MN503 4.0 12.6 1.0
OD2 B:ASP291 4.1 11.2 1.0
OD1 B:ASP291 4.2 13.3 1.0
OD2 B:ASP327 4.2 14.4 1.0
ND1 B:HIS257 4.2 10.0 1.0
CG B:HIS257 4.3 8.8 1.0
C3 B:AOS3002 4.4 14.8 1.0
CG B:ASP254 4.4 10.1 1.0
CB B:ASP289 4.4 9.1 1.0
CD B:LYS221 4.5 9.4 1.0
NH2 A:ARG65 4.6 11.1 1.0
CG B:ASP291 4.6 11.5 1.0
OD1 B:ASP254 4.6 9.8 1.0
OE2 B:GLU219 4.7 9.6 1.0
CZ A:PHE66 4.8 12.9 1.0
O3 B:AOS3002 4.8 12.9 1.0
C5 B:AOS3002 5.0 17.8 1.0

Manganese binding site 5 out of 8 in 3m0m

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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 D-Allose


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

b:15.2
occ:1.00
 OD2 C:ASP327 2.0 18.6 1.0
OD2 C:ASP254 2.2 10.8 1.0
ND1 C:HIS281 2.2 18.6 1.0
O2 C:AOS3003 2.2 17.0 1.0
OE2 C:GLU219 2.2 13.2 1.0
O3 C:AOS3003 2.4 18.3 1.0
CE1 C:HIS281 3.0 18.3 1.0
C2 C:AOS3003 3.1 18.6 1.0
CG C:ASP327 3.1 14.3 1.0
CD C:GLU219 3.2 12.3 1.0
C3 C:AOS3003 3.3 20.2 1.0
CG C:HIS281 3.3 17.4 1.0
CG C:ASP254 3.3 10.8 1.0
OE1 C:GLU219 3.4 14.9 1.0
CB C:HIS281 3.7 17.5 1.0
CB C:ASP327 3.7 14.1 1.0
CB C:ASP254 3.8 10.6 1.0
O5 C:AOS3003 3.9 20.2 1.0
CE1 C:HIS257 3.9 11.8 1.0
O C:HOH1483 4.0 14.8 1.0
MN C:MN506 4.0 12.4 1.0
NE2 C:HIS257 4.1 11.8 1.0
OD1 C:ASP327 4.2 16.8 1.0
NE2 C:HIS281 4.2 18.3 1.0
C5 C:AOS3003 4.2 21.4 1.0
C4 C:AOS3003 4.3 21.3 1.0
OD1 C:ASP254 4.3 10.4 1.0
CD2 C:HIS281 4.4 18.8 1.0
C1 C:AOS3003 4.5 19.1 1.0
CG C:GLU219 4.5 11.7 1.0
ND1 C:HIS257 4.8 10.3 1.0
O C:HOH1466 4.8 14.5 1.0
CD2 C:LEU252 5.0 17.6 1.0

Manganese binding site 6 out of 8 in 3m0m

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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 D-Allose


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

b:12.4
occ:1.00
 O C:HOH1483 2.0 14.8 1.0
OD2 C:ASP289 2.2 12.2 1.0
O C:HOH1466 2.2 14.5 1.0
NE2 C:HIS257 2.2 11.8 1.0
O2 C:AOS3003 2.2 17.0 1.0
O1 C:AOS3003 2.2 16.5 1.0
C1 C:AOS3003 2.8 19.1 1.0
C2 C:AOS3003 2.9 18.6 1.0
CG C:ASP289 3.0 11.2 1.0
CE1 C:HIS257 3.1 11.8 1.0
CD2 C:HIS257 3.3 10.2 1.0
OD1 C:ASP289 3.3 11.4 1.0
OD2 C:ASP254 3.8 10.8 1.0
O5 C:AOS3003 3.8 20.2 1.0
NZ C:LYS221 3.8 12.6 1.0
OD2 C:ASP291 4.0 12.7 1.0
MN C:MN505 4.0 15.2 1.0
CE C:LYS221 4.0 11.8 1.0
OD1 C:ASP291 4.1 13.0 1.0
ND1 C:HIS257 4.2 10.3 1.0
OD2 C:ASP327 4.2 18.6 1.0
C3 C:AOS3003 4.3 20.2 1.0
CG C:HIS257 4.4 10.0 1.0
CG C:ASP254 4.4 10.8 1.0
CB C:ASP289 4.4 11.3 1.0
CD C:LYS221 4.4 10.2 1.0
CG C:ASP291 4.5 13.0 1.0
NH1 D:ARG65 4.5 13.1 1.0
OD1 C:ASP254 4.7 10.4 1.0
OE2 C:GLU219 4.8 13.2 1.0
O3 C:AOS3003 4.8 18.3 1.0
CZ D:PHE66 4.8 15.7 1.0
C4 C:AOS3003 5.0 21.3 1.0
C5 C:AOS3003 5.0 21.4 1.0

Manganese binding site 7 out of 8 in 3m0m

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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 D-Allose


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

b:11.6
occ:1.00
 OD2 D:ASP327 2.0 12.7 1.0
OE2 D:GLU219 2.1 8.8 1.0
OD2 D:ASP254 2.2 8.5 1.0
ND1 D:HIS281 2.2 12.0 1.0
O2 D:AOS3004 2.3 14.0 1.0
O3 D:AOS3004 2.3 14.2 1.0
CD D:GLU219 3.1 12.2 1.0
C2 D:AOS3004 3.1 15.4 1.0
CE1 D:HIS281 3.1 12.4 1.0
CG D:ASP327 3.2 9.9 1.0
C3 D:AOS3004 3.3 13.7 1.0
CG D:ASP254 3.3 8.4 1.0
CG D:HIS281 3.3 9.2 1.0
OE1 D:GLU219 3.4 10.9 1.0
CB D:HIS281 3.7 12.3 1.0
CB D:ASP327 3.7 10.2 1.0
CB D:ASP254 3.8 8.2 1.0
O D:HOH443 3.8 10.0 1.0
CE1 D:HIS257 3.9 10.4 1.0
O5 D:AOS3004 4.0 15.3 1.0
MN D:MN508 4.1 9.6 1.0
NE2 D:HIS257 4.1 10.0 1.0
OD1 D:ASP327 4.2 13.4 1.0
NE2 D:HIS281 4.3 12.0 1.0
C5 D:AOS3004 4.3 15.5 1.0
C4 D:AOS3004 4.4 15.3 1.0
OD1 D:ASP254 4.4 9.4 1.0
CD2 D:HIS281 4.4 11.9 1.0
CG D:GLU219 4.4 9.1 1.0
C1 D:AOS3004 4.5 15.1 1.0
ND1 D:HIS257 4.8 10.7 1.0
O D:HOH881 4.9 12.0 1.0
CD2 D:LEU252 4.9 13.9 1.0

Manganese binding site 8 out of 8 in 3m0m

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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 D-Allose


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

b:9.6
occ:1.00
 O D:HOH443 2.0 10.0 1.0
OD2 D:ASP289 2.1 9.9 1.0
O2 D:AOS3004 2.2 14.0 1.0
NE2 D:HIS257 2.2 10.0 1.0
O1 D:AOS3004 2.2 15.5 1.0
O D:HOH881 2.2 12.0 1.0
C1 D:AOS3004 2.8 15.1 1.0
C2 D:AOS3004 2.9 15.4 1.0
CG D:ASP289 3.0 8.8 1.0
CE1 D:HIS257 3.0 10.4 1.0
CD2 D:HIS257 3.2 9.5 1.0
OD1 D:ASP289 3.3 10.2 1.0
OD2 D:ASP254 3.8 8.5 1.0
NZ D:LYS221 3.9 9.5 1.0
O5 D:AOS3004 3.9 15.3 1.0
OD2 D:ASP291 4.0 9.3 1.0
MN D:MN507 4.1 11.6 1.0
CE D:LYS221 4.1 9.3 1.0
OD1 D:ASP291 4.2 11.1 1.0
OD2 D:ASP327 4.2 12.7 1.0
ND1 D:HIS257 4.2 10.7 1.0
C3 D:AOS3004 4.3 13.7 1.0
CG D:HIS257 4.3 9.2 1.0
CB D:ASP289 4.4 8.3 1.0
CG D:ASP254 4.4 8.4 1.0
CD D:LYS221 4.5 9.5 1.0
CG D:ASP291 4.5 10.6 1.0
NH2 C:ARG65 4.5 11.6 1.0
OD1 D:ASP254 4.7 9.4 1.0
OE2 D:GLU219 4.7 8.8 1.0
O3 D:AOS3004 4.8 14.2 1.0
CZ C:PHE66 4.8 14.1 1.0
C4 D:AOS3004 5.0 15.3 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 17:01:56 2024

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