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Manganese in PDB 3ito: Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant D327N in Complex with D-Psicose

Enzymatic activity of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant D327N in Complex with D-Psicose

All present enzymatic activity of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant D327N in Complex with D-Psicose:
5.3.1.14;

Protein crystallography data

The structure of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant D327N in Complex with D-Psicose, PDB code: 3ito 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) 42.15 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.762, 104.732, 115.035, 90.00, 108.24, 90.00
R / Rfree (%) 17.6 / 21.1

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant D327N in Complex with D-Psicose (pdb code 3ito). 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 D327N in Complex with D-Psicose, PDB code: 3ito:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3ito

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Manganese binding site 1 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant D327N 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 D327N in Complex with D-Psicose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:13.7
occ:1.00
 O2 A:PSV601 2.1 19.4 1.0
OE2 A:GLU219 2.1 10.1 1.0
ND1 A:HIS281 2.2 11.0 1.0
OD1 A:ASP254 2.2 7.1 1.0
O3 A:PSV601 2.5 16.2 1.0
ND2 A:ASN327 2.6 12.1 1.0
CE1 A:HIS281 3.0 13.0 1.0
CD A:GLU219 3.1 11.2 1.0
C2 A:PSV601 3.2 19.1 1.0
CG A:ASP254 3.3 6.2 1.0
CG A:HIS281 3.3 12.9 1.0
OE1 A:GLU219 3.3 11.8 1.0
C3 A:PSV601 3.4 19.1 1.0
CG A:ASN327 3.5 14.1 1.0
CE1 A:HIS257 3.7 5.8 1.0
CB A:ASP254 3.7 5.1 1.0
CB A:HIS281 3.7 11.0 1.0
O5 A:PSV601 3.9 20.0 1.0
MN A:MN502 3.9 13.6 1.0
NE2 A:HIS257 4.0 7.2 1.0
O A:HOH530 4.0 11.4 1.0
CB A:ASN327 4.1 9.7 1.0
NE2 A:HIS281 4.2 13.3 1.0
CD2 A:HIS281 4.3 14.2 1.0
OD2 A:ASP254 4.3 5.7 1.0
C1 A:PSV601 4.4 17.1 1.0
OD1 A:ASN327 4.4 14.5 1.0
CG A:GLU219 4.5 8.2 1.0
C5 A:PSV601 4.5 22.4 1.0
C4 A:PSV601 4.6 19.4 1.0
ND1 A:HIS257 4.6 7.8 1.0
O1 A:PSV601 4.9 12.2 1.0
O4 A:PSV601 5.0 20.1 1.0
CA A:ASP254 5.0 6.4 1.0

Manganese binding site 2 out of 8 in 3ito

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Manganese binding site 2 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant D327N 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 D327N in Complex with D-Psicose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:13.6
occ:1.00
 O A:HOH530 2.0 11.4 1.0
NE2 A:HIS257 2.1 7.2 1.0
OD2 A:ASP289 2.3 13.0 1.0
O1 A:PSV601 2.3 12.2 1.0
O A:HOH487 2.4 10.5 1.0
O2 A:PSV601 2.4 19.4 1.0
CG A:ASP289 3.0 10.9 1.0
CE1 A:HIS257 3.0 5.8 1.0
OD1 A:ASP289 3.0 12.6 1.0
C1 A:PSV601 3.1 17.1 1.0
C2 A:PSV601 3.1 19.1 1.0
CD2 A:HIS257 3.2 6.9 1.0
O5 A:PSV601 3.4 20.0 1.0
OD1 A:ASP254 3.7 7.1 1.0
ND2 A:ASN327 3.8 12.1 1.0
OD1 A:ASP291 3.9 13.5 1.0
MN A:MN501 3.9 13.7 1.0
NZ A:LYS221 4.1 5.4 1.0
ND1 A:HIS257 4.1 7.8 1.0
CG A:ASP254 4.2 6.2 1.0
CE A:LYS221 4.2 5.2 1.0
CG A:HIS257 4.3 6.4 1.0
OD2 A:ASP291 4.3 12.6 1.0
OD2 A:ASP254 4.4 5.7 1.0
CB A:ASP289 4.4 8.7 1.0
CG A:ASP291 4.5 12.7 1.0
CD A:LYS221 4.6 6.6 1.0
C3 A:PSV601 4.6 19.1 1.0
OE2 A:GLU219 4.8 10.1 1.0
NH2 B:ARG65 4.8 9.5 1.0
C5 A:PSV601 4.9 22.4 1.0
O3 A:PSV601 5.0 16.2 1.0

Manganese binding site 3 out of 8 in 3ito

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Manganese binding site 3 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant D327N 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 D327N in Complex with D-Psicose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:25.8
occ:1.00
 OE2 B:GLU219 2.2 15.4 1.0
OD2 B:ASP254 2.3 9.1 1.0
O2 B:PSV602 2.3 28.7 1.0
O3 B:PSV602 2.5 26.8 1.0
ND2 B:ASN327 2.5 20.4 1.0
ND1 B:HIS281 3.0 22.4 1.0
CD B:GLU219 3.0 13.2 1.0
OE1 B:GLU219 3.2 15.1 1.0
CG B:ASP254 3.4 9.7 1.0
C2 B:PSV602 3.4 30.6 1.0
C3 B:PSV602 3.5 30.0 1.0
CG B:ASN327 3.6 17.2 1.0
CE1 B:HIS257 3.7 12.9 1.0
CB B:ASP254 3.8 7.9 1.0
CG B:HIS281 3.9 21.1 1.0
CE1 B:HIS281 3.9 23.6 1.0
CB B:HIS281 4.0 19.0 1.0
MN B:MN504 4.1 22.7 1.0
CB B:ASN327 4.1 12.7 1.0
NE2 B:HIS257 4.1 13.4 1.0
O5 B:PSV602 4.1 31.9 1.0
CG B:GLU219 4.4 10.9 1.0
O B:HOH1435 4.4 18.5 1.0
OD1 B:ASP254 4.5 9.4 1.0
C1 B:PSV602 4.6 29.6 1.0
ND1 B:HIS257 4.6 14.0 1.0
OD1 B:ASN327 4.6 17.1 1.0
C4 B:PSV602 4.6 31.3 1.0
C5 B:PSV602 4.7 32.2 1.0
O4 B:PSV602 4.9 30.8 1.0

Manganese binding site 4 out of 8 in 3ito

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Manganese binding site 4 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant D327N 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 D327N in Complex with D-Psicose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn504

b:22.7
occ:1.00
 O B:HOH1435 2.0 18.5 1.0
NE2 B:HIS257 2.0 13.4 1.0
O1 B:PSV602 2.2 28.3 1.0
O2 B:PSV602 2.3 28.7 1.0
O B:HOH684 2.4 15.9 1.0
OD1 B:ASP289 2.4 17.9 1.0
CE1 B:HIS257 2.9 12.9 1.0
C1 B:PSV602 3.0 29.6 1.0
C2 B:PSV602 3.1 30.6 1.0
CD2 B:HIS257 3.2 11.7 1.0
CG B:ASP289 3.2 16.1 1.0
OD2 B:ASP289 3.2 20.1 1.0
O5 B:PSV602 3.5 31.9 1.0
OD2 B:ASP254 3.7 9.1 1.0
OD1 B:ASP291 3.8 16.6 1.0
NZ B:LYS221 4.0 8.7 1.0
ND2 B:ASN327 4.0 20.4 1.0
ND1 B:HIS257 4.0 14.0 1.0
MN B:MN503 4.1 25.8 1.0
CG B:HIS257 4.2 13.2 1.0
CE B:LYS221 4.2 9.3 1.0
CG B:ASP254 4.2 9.7 1.0
OD2 B:ASP291 4.3 15.6 1.0
OD1 B:ASP254 4.4 9.4 1.0
CG B:ASP291 4.5 14.9 1.0
C3 B:PSV602 4.5 30.0 1.0
OE2 B:GLU219 4.6 15.4 1.0
CB B:ASP289 4.6 13.0 1.0
CD B:LYS221 4.6 8.1 1.0
O3 B:PSV602 4.9 26.8 1.0
C5 B:PSV602 4.9 32.2 1.0
NH2 A:ARG65 4.9 11.0 1.0
CZ A:PHE66 5.0 14.0 1.0

Manganese binding site 5 out of 8 in 3ito

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Manganese binding site 5 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant D327N 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 D327N in Complex with D-Psicose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn505

b:21.0
occ:1.00
 O2 C:PSV603 2.2 30.8 1.0
OE2 C:GLU219 2.2 13.4 1.0
OD2 C:ASP254 2.3 10.5 1.0
ND1 C:HIS281 2.4 17.0 1.0
ND2 C:ASN327 2.5 18.3 1.0
O3 C:PSV603 2.6 28.3 1.0
CD C:GLU219 3.0 14.6 1.0
OE1 C:GLU219 3.2 17.3 1.0
C2 C:PSV603 3.3 31.0 1.0
CE1 C:HIS281 3.3 19.5 1.0
CG C:ASP254 3.3 9.6 1.0
C3 C:PSV603 3.4 31.3 1.0
CG C:HIS281 3.5 17.8 1.0
CG C:ASN327 3.6 17.3 1.0
CE1 C:HIS257 3.6 11.1 1.0
CB C:ASP254 3.8 9.4 1.0
CB C:HIS281 3.8 15.6 1.0
MN C:MN506 4.0 18.1 1.0
NE2 C:HIS257 4.0 13.5 1.0
O5 C:PSV603 4.1 31.2 1.0
O C:HOH1436 4.1 17.9 1.0
CB C:ASN327 4.1 13.0 1.0
CG C:GLU219 4.4 10.7 1.0
C1 C:PSV603 4.4 30.5 1.0
OD1 C:ASP254 4.4 9.8 1.0
NE2 C:HIS281 4.5 19.2 1.0
ND1 C:HIS257 4.5 11.1 1.0
CD2 C:HIS281 4.6 18.5 1.0
OD1 C:ASN327 4.6 17.2 1.0
C4 C:PSV603 4.7 31.6 1.0
C5 C:PSV603 4.8 32.8 1.0
O1 C:PSV603 4.8 26.5 1.0

Manganese binding site 6 out of 8 in 3ito

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Manganese binding site 6 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant D327N 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 D327N in Complex with D-Psicose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn506

b:18.1
occ:1.00
 NE2 C:HIS257 2.0 13.5 1.0
O C:HOH1436 2.0 17.9 1.0
O1 C:PSV603 2.2 26.5 1.0
O C:HOH1421 2.4 38.2 1.0
O2 C:PSV603 2.5 30.8 1.0
OD2 C:ASP289 2.5 19.9 1.0
CE1 C:HIS257 2.8 11.1 1.0
OD1 C:ASP289 3.0 19.9 1.0
CG C:ASP289 3.1 17.0 1.0
CD2 C:HIS257 3.1 11.3 1.0
C1 C:PSV603 3.2 30.5 1.0
C2 C:PSV603 3.2 31.0 1.0
O5 C:PSV603 3.6 31.2 1.0
OD2 C:ASP254 3.7 10.5 1.0
OD1 C:ASP291 3.8 18.0 1.0
MN C:MN505 4.0 21.0 1.0
ND1 C:HIS257 4.0 11.1 1.0
NZ C:LYS221 4.1 8.2 1.0
ND2 C:ASN327 4.1 18.3 1.0
CG C:ASP254 4.1 9.6 1.0
CG C:HIS257 4.2 9.8 1.0
CE C:LYS221 4.3 6.8 1.0
OD1 C:ASP254 4.3 9.8 1.0
OD2 C:ASP291 4.4 17.0 1.0
CG C:ASP291 4.5 16.6 1.0
CB C:ASP289 4.5 14.9 1.0
OE2 C:GLU219 4.6 13.4 1.0
CD C:LYS221 4.6 5.3 1.0
C3 C:PSV603 4.7 31.3 1.0
NH1 D:ARG65 4.9 12.4 1.0

Manganese binding site 7 out of 8 in 3ito

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Manganese binding site 7 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant D327N 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 D327N in Complex with D-Psicose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn507

b:13.1
occ:1.00
 O2 D:PSV604 2.0 16.4 1.0
OE2 D:GLU219 2.1 10.6 1.0
OD2 D:ASP254 2.2 11.3 1.0
ND1 D:HIS281 2.2 13.2 1.0
O3 D:PSV604 2.4 17.0 1.0
ND2 D:ASN327 2.6 12.4 1.0
CE1 D:HIS281 3.0 16.3 1.0
CD D:GLU219 3.0 11.0 1.0
C2 D:PSV604 3.1 20.2 1.0
CG D:ASP254 3.2 9.1 1.0
CG D:HIS281 3.3 14.4 1.0
OE1 D:GLU219 3.3 9.6 1.0
C3 D:PSV604 3.3 21.8 1.0
CG D:ASN327 3.5 13.6 1.0
CE1 D:HIS257 3.7 8.7 1.0
CB D:ASP254 3.7 6.3 1.0
CB D:HIS281 3.7 11.7 1.0
MN D:MN508 3.8 14.7 1.0
O5 D:PSV604 3.8 21.4 1.0
O D:HOH457 3.9 9.1 1.0
NE2 D:HIS257 4.0 8.2 1.0
CB D:ASN327 4.1 9.3 1.0
NE2 D:HIS281 4.2 16.0 1.0
OD1 D:ASP254 4.3 6.2 1.0
CD2 D:HIS281 4.3 14.7 1.0
C1 D:PSV604 4.3 18.9 1.0
OD1 D:ASN327 4.4 14.9 1.0
C5 D:PSV604 4.4 24.6 1.0
CG D:GLU219 4.4 7.8 1.0
C4 D:PSV604 4.4 23.9 1.0
ND1 D:HIS257 4.6 9.9 1.0
O4 D:PSV604 4.8 27.1 1.0
O1 D:PSV604 4.8 15.4 1.0
CD2 D:LEU252 4.9 17.1 1.0
CA D:ASP254 5.0 6.4 1.0

Manganese binding site 8 out of 8 in 3ito

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Manganese binding site 8 out of 8 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant D327N 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 D327N in Complex with D-Psicose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn508

b:14.7
occ:1.00
 O D:HOH457 2.0 9.1 1.0
NE2 D:HIS257 2.1 8.2 1.0
OD2 D:ASP289 2.2 13.0 1.0
O1 D:PSV604 2.3 15.4 1.0
O2 D:PSV604 2.3 16.4 1.0
O D:HOH536 2.4 16.0 1.0
CE1 D:HIS257 3.0 8.7 1.0
CG D:ASP289 3.0 11.0 1.0
C2 D:PSV604 3.1 20.2 1.0
C1 D:PSV604 3.1 18.9 1.0
CD2 D:HIS257 3.2 7.1 1.0
OD1 D:ASP289 3.2 11.8 1.0
O5 D:PSV604 3.5 21.4 1.0
OD2 D:ASP254 3.6 11.3 1.0
ND2 D:ASN327 3.7 12.4 1.0
MN D:MN507 3.8 13.1 1.0
OD1 D:ASP291 3.9 12.3 1.0
CG D:ASP254 4.1 9.1 1.0
ND1 D:HIS257 4.2 9.9 1.0
NZ D:LYS221 4.2 10.4 1.0
CG D:HIS257 4.3 10.3 1.0
CE D:LYS221 4.3 10.2 1.0
OD2 D:ASP291 4.3 10.7 1.0
OD1 D:ASP254 4.3 6.2 1.0
CB D:ASP289 4.5 8.6 1.0
C3 D:PSV604 4.5 21.8 1.0
CG D:ASP291 4.5 11.3 1.0
OE2 D:GLU219 4.6 10.6 1.0
CD D:LYS221 4.7 6.9 1.0
NH2 C:ARG65 4.8 8.9 1.0
C5 D:PSV604 4.9 24.6 1.0
O3 D:PSV604 4.9 17.0 1.0
CG D:ASN327 5.0 13.6 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 16:37:39 2024

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