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Manganese in PDB 3itl: Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant D327N in Complex with L-Rhamnulose

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

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

Protein crystallography data

The structure of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant D327N in Complex with L-Rhamnulose, PDB code: 3itl 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) 42.12 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.700, 104.634, 115.096, 90.00, 108.14, 90.00
R / Rfree (%) 16.5 / 18.8

Manganese Binding Sites:

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

Manganese binding site 1 out of 8 in 3itl

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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 L-Rhamnulose


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

b:8.6
occ:1.00
 OE2 A:GLU219 2.1 8.0 1.0
OD1 A:ASP254 2.1 7.6 1.0
O2 A:LRH601 2.1 8.9 1.0
O3 A:LRH601 2.2 10.4 1.0
ND1 A:HIS281 2.2 8.2 1.0
ND2 A:ASN327 2.9 14.8 1.0
CE1 A:HIS281 3.0 10.5 1.0
CD A:GLU219 3.0 9.0 1.0
CG A:ASP254 3.2 6.2 1.0
C2 A:LRH601 3.2 9.9 1.0
C3 A:LRH601 3.2 8.2 1.0
CG A:HIS281 3.3 11.6 1.0
OE1 A:GLU219 3.3 8.2 1.0
CE1 A:HIS257 3.5 7.7 1.0
CB A:ASP254 3.6 7.0 1.0
CG A:ASN327 3.7 16.6 1.0
CB A:HIS281 3.7 9.2 1.0
O A:HOH498 3.7 10.0 1.0
MN A:MN502 3.8 7.8 1.0
NE2 A:HIS257 3.8 7.1 1.0
O5 A:LRH601 4.2 10.4 1.0
C1 A:LRH601 4.2 7.9 1.0
NE2 A:HIS281 4.2 10.0 1.0
CB A:ASN327 4.2 11.7 1.0
C4 A:LRH601 4.2 9.7 1.0
OD2 A:ASP254 4.3 6.9 1.0
CD2 A:HIS281 4.3 10.9 1.0
OD1 A:ASN327 4.4 22.2 1.0
CG A:GLU219 4.4 7.1 1.0
ND1 A:HIS257 4.5 6.2 1.0
CD2 A:LEU252 4.7 13.3 1.0
O1 A:LRH601 4.7 8.7 1.0
C5 A:LRH601 4.9 10.7 1.0
CD2 A:HIS257 4.9 6.9 1.0
CA A:ASP254 4.9 6.6 1.0
O A:HOH440 5.0 9.8 1.0

Manganese binding site 2 out of 8 in 3itl

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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 L-Rhamnulose


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

b:7.8
occ:1.00
 O A:HOH498 2.1 10.0 1.0
OD2 A:ASP289 2.1 8.6 1.0
O A:HOH440 2.2 9.8 1.0
NE2 A:HIS257 2.2 7.1 1.0
O2 A:LRH601 2.3 8.9 1.0
O1 A:LRH601 2.3 8.7 1.0
CG A:ASP289 2.9 8.1 1.0
CE1 A:HIS257 3.1 7.7 1.0
OD1 A:ASP289 3.1 10.3 1.0
C2 A:LRH601 3.1 9.9 1.0
C1 A:LRH601 3.1 7.9 1.0
CD2 A:HIS257 3.2 6.9 1.0
O5 A:LRH601 3.5 10.4 1.0
OD1 A:ASP254 3.6 7.6 1.0
ND2 A:ASN327 3.7 14.8 1.0
MN A:MN501 3.8 8.6 1.0
OD1 A:ASP291 3.9 12.6 1.0
NZ A:LYS221 4.1 6.4 1.0
CG A:ASP254 4.2 6.2 1.0
OD2 A:ASP291 4.2 10.7 1.0
ND1 A:HIS257 4.2 6.2 1.0
CE A:LYS221 4.3 7.5 1.0
CG A:HIS257 4.3 6.7 1.0
CB A:ASP289 4.4 8.0 1.0
OD2 A:ASP254 4.4 6.9 1.0
CG A:ASP291 4.5 10.8 1.0
C3 A:LRH601 4.5 8.2 1.0
CD A:LYS221 4.6 8.0 1.0
NH2 B:ARG65 4.7 8.9 1.0
O3 A:LRH601 4.7 10.4 1.0
OE2 A:GLU219 4.8 8.0 1.0
C5 A:LRH601 4.9 10.7 1.0

Manganese binding site 3 out of 8 in 3itl

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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 L-Rhamnulose


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

b:13.6
occ:1.00
 OE2 B:GLU219 2.0 11.4 1.0
ND1 B:HIS281 2.1 15.6 1.0
O2 B:LRH602 2.2 13.4 1.0
O3 B:LRH602 2.2 15.0 1.0
OD2 B:ASP254 2.2 7.9 1.0
CE1 B:HIS281 2.9 16.0 1.0
ND2 B:ASN327 3.0 17.7 1.0
CD B:GLU219 3.0 9.2 1.0
C2 B:LRH602 3.2 16.7 1.0
C3 B:LRH602 3.2 15.6 1.0
CG B:ASP254 3.3 7.1 1.0
OE1 B:GLU219 3.3 12.8 1.0
CG B:HIS281 3.3 15.5 1.0
CE1 B:HIS257 3.5 10.5 1.0
CG B:ASN327 3.6 16.3 1.0
CB B:ASP254 3.7 8.2 1.0
O B:HOH464 3.7 12.9 1.0
CB B:HIS281 3.8 13.2 1.0
MN B:MN504 3.8 12.2 1.0
NE2 B:HIS257 3.9 8.8 1.0
NE2 B:HIS281 4.1 15.7 1.0
CB B:ASN327 4.2 12.0 1.0
C1 B:LRH602 4.2 14.6 1.0
O5 B:LRH602 4.2 15.9 1.0
C4 B:LRH602 4.2 15.3 1.0
CD2 B:HIS281 4.3 14.9 1.0
OD1 B:ASN327 4.3 21.8 1.0
OD1 B:ASP254 4.3 7.0 1.0
CG B:GLU219 4.4 8.3 1.0
ND1 B:HIS257 4.4 11.4 1.0
CD2 B:LEU252 4.7 15.9 1.0
O1 B:LRH602 4.8 12.7 1.0
C5 B:LRH602 4.9 17.5 1.0
CD2 B:HIS257 4.9 9.9 1.0
CA B:ASP254 5.0 8.1 1.0

Manganese binding site 4 out of 8 in 3itl

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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 L-Rhamnulose


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

b:12.2
occ:1.00
 NE2 B:HIS257 2.1 8.8 1.0
O B:HOH851 2.2 11.7 1.0
O B:HOH464 2.2 12.9 1.0
O1 B:LRH602 2.2 12.7 1.0
O2 B:LRH602 2.3 13.4 1.0
OD1 B:ASP289 2.3 11.4 1.0
CE1 B:HIS257 3.0 10.5 1.0
CG B:ASP289 3.0 9.7 1.0
C1 B:LRH602 3.1 14.6 1.0
C2 B:LRH602 3.1 16.7 1.0
OD2 B:ASP289 3.1 13.9 1.0
CD2 B:HIS257 3.2 9.9 1.0
O5 B:LRH602 3.5 15.9 1.0
OD2 B:ASP254 3.7 7.9 1.0
ND2 B:ASN327 3.8 17.7 1.0
MN B:MN503 3.8 13.6 1.0
OD1 B:ASP291 3.9 12.5 1.0
NZ B:LYS221 4.0 7.4 1.0
ND1 B:HIS257 4.2 11.4 1.0
CG B:ASP254 4.2 7.1 1.0
OD2 B:ASP291 4.2 12.8 1.0
CE B:LYS221 4.2 8.2 1.0
CG B:HIS257 4.3 8.9 1.0
OD1 B:ASP254 4.4 7.0 1.0
CG B:ASP291 4.5 12.5 1.0
C3 B:LRH602 4.5 15.6 1.0
CB B:ASP289 4.5 9.5 1.0
CD B:LYS221 4.6 7.2 1.0
O3 B:LRH602 4.7 15.0 1.0
OE2 B:GLU219 4.8 11.4 1.0
NH2 A:ARG65 4.8 10.2 1.0
C5 B:LRH602 4.9 17.5 1.0
CZ A:PHE66 5.0 13.5 1.0

Manganese binding site 5 out of 8 in 3itl

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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 L-Rhamnulose


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

b:14.2
occ:1.00
 OE2 C:GLU219 2.1 12.0 1.0
OD2 C:ASP254 2.1 11.3 1.0
O3 C:LRH603 2.2 15.3 1.0
O2 C:LRH603 2.2 16.5 1.0
ND1 C:HIS281 2.2 12.7 1.0
ND2 C:ASN327 2.9 20.7 1.0
CD C:GLU219 3.0 13.0 1.0
CE1 C:HIS281 3.0 16.0 1.0
CG C:ASP254 3.2 9.8 1.0
C2 C:LRH603 3.2 16.4 1.0
C3 C:LRH603 3.2 15.7 1.0
OE1 C:GLU219 3.3 13.2 1.0
CG C:HIS281 3.3 13.9 1.0
CE1 C:HIS257 3.5 10.3 1.0
CG C:ASN327 3.6 19.2 1.0
CB C:ASP254 3.7 9.2 1.0
O C:HOH469 3.7 13.1 1.0
CB C:HIS281 3.7 13.2 1.0
MN C:MN506 3.8 11.6 1.0
NE2 C:HIS257 3.9 10.8 1.0
CB C:ASN327 4.2 13.7 1.0
C1 C:LRH603 4.2 16.9 1.0
NE2 C:HIS281 4.2 13.2 1.0
O5 C:LRH603 4.2 16.3 1.0
C4 C:LRH603 4.3 15.8 1.0
OD1 C:ASP254 4.3 9.0 1.0
OD1 C:ASN327 4.3 22.5 1.0
CD2 C:HIS281 4.4 13.5 1.0
CG C:GLU219 4.4 10.6 1.0
ND1 C:HIS257 4.4 10.5 1.0
CD2 C:LEU252 4.8 17.6 1.0
O1 C:LRH603 4.8 14.0 1.0
C5 C:LRH603 4.9 17.4 1.0
CA C:ASP254 4.9 8.6 1.0
CD2 C:HIS257 4.9 10.6 1.0

Manganese binding site 6 out of 8 in 3itl

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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 L-Rhamnulose


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

b:11.6
occ:1.00
 O C:HOH469 2.1 13.1 1.0
NE2 C:HIS257 2.1 10.8 1.0
OD2 C:ASP289 2.2 11.8 1.0
O2 C:LRH603 2.2 16.5 1.0
O C:HOH1516 2.3 14.3 1.0
O1 C:LRH603 2.3 14.0 1.0
CG C:ASP289 2.9 9.7 1.0
CE1 C:HIS257 3.0 10.3 1.0
OD1 C:ASP289 3.0 11.3 1.0
C2 C:LRH603 3.1 16.4 1.0
C1 C:LRH603 3.1 16.9 1.0
CD2 C:HIS257 3.2 10.6 1.0
O5 C:LRH603 3.5 16.3 1.0
OD2 C:ASP254 3.6 11.3 1.0
ND2 C:ASN327 3.8 20.7 1.0
MN C:MN505 3.8 14.2 1.0
OD1 C:ASP291 3.8 14.2 1.0
NZ C:LYS221 4.1 7.2 1.0
OD2 C:ASP291 4.1 12.6 1.0
ND1 C:HIS257 4.2 10.5 1.0
CG C:ASP254 4.2 9.8 1.0
CE C:LYS221 4.2 9.1 1.0
CG C:HIS257 4.3 10.8 1.0
OD1 C:ASP254 4.3 9.0 1.0
CB C:ASP289 4.4 10.0 1.0
CG C:ASP291 4.4 14.0 1.0
C3 C:LRH603 4.5 15.7 1.0
CD C:LYS221 4.7 6.8 1.0
O3 C:LRH603 4.7 15.3 1.0
NH1 D:ARG65 4.8 10.1 1.0
OE2 C:GLU219 4.8 12.0 1.0
C5 C:LRH603 4.9 17.4 1.0

Manganese binding site 7 out of 8 in 3itl

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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 L-Rhamnulose


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

b:9.1
occ:1.00
 OE2 D:GLU219 2.1 8.8 1.0
O2 D:LRH604 2.1 10.2 1.0
OD2 D:ASP254 2.1 8.7 1.0
O3 D:LRH604 2.2 10.1 1.0
ND1 D:HIS281 2.2 9.2 1.0
ND2 D:ASN327 2.9 13.1 1.0
CE1 D:HIS281 3.0 12.2 1.0
CD D:GLU219 3.1 8.5 1.0
C2 D:LRH604 3.2 12.1 1.0
C3 D:LRH604 3.2 11.8 1.0
CG D:ASP254 3.2 8.0 1.0
CG D:HIS281 3.3 9.7 1.0
OE1 D:GLU219 3.3 8.1 1.0
CE1 D:HIS257 3.6 8.5 1.0
CG D:ASN327 3.6 13.3 1.0
CB D:ASP254 3.6 4.8 1.0
CB D:HIS281 3.7 8.7 1.0
O D:HOH458 3.7 9.1 1.0
MN D:MN508 3.8 8.4 1.0
NE2 D:HIS257 3.8 7.9 1.0
O5 D:LRH604 4.1 11.4 1.0
C4 D:LRH604 4.2 12.8 1.0
C1 D:LRH604 4.2 10.6 1.0
CB D:ASN327 4.2 8.7 1.0
NE2 D:HIS281 4.2 11.1 1.0
OD1 D:ASP254 4.3 7.3 1.0
OD1 D:ASN327 4.3 18.7 1.0
CD2 D:HIS281 4.4 9.7 1.0
CG D:GLU219 4.4 8.0 1.0
ND1 D:HIS257 4.5 8.2 1.0
O1 D:LRH604 4.7 11.2 1.0
C5 D:LRH604 4.8 14.3 1.0
CD2 D:LEU252 4.8 13.7 1.0
CD2 D:HIS257 4.9 8.0 1.0
CA D:ASP254 4.9 6.7 1.0

Manganese binding site 8 out of 8 in 3itl

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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 L-Rhamnulose


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

b:8.4
occ:1.00
 O D:HOH458 2.1 9.1 1.0
OD2 D:ASP289 2.1 8.6 1.0
NE2 D:HIS257 2.2 7.9 1.0
O D:HOH449 2.2 9.4 1.0
O2 D:LRH604 2.2 10.2 1.0
O1 D:LRH604 2.3 11.2 1.0
CG D:ASP289 2.9 9.0 1.0
OD1 D:ASP289 3.1 9.8 1.0
CE1 D:HIS257 3.1 8.5 1.0
C2 D:LRH604 3.1 12.1 1.0
C1 D:LRH604 3.1 10.6 1.0
CD2 D:HIS257 3.2 8.0 1.0
O5 D:LRH604 3.5 11.4 1.0
OD2 D:ASP254 3.5 8.7 1.0
MN D:MN507 3.8 9.1 1.0
ND2 D:ASN327 3.8 13.1 1.0
OD1 D:ASP291 3.9 13.4 1.0
NZ D:LYS221 4.1 9.3 1.0
CG D:ASP254 4.1 8.0 1.0
OD2 D:ASP291 4.2 10.4 1.0
ND1 D:HIS257 4.2 8.2 1.0
CE D:LYS221 4.3 9.6 1.0
CG D:HIS257 4.3 7.6 1.0
OD1 D:ASP254 4.3 7.3 1.0
CB D:ASP289 4.4 8.5 1.0
CG D:ASP291 4.5 10.9 1.0
C3 D:LRH604 4.5 11.8 1.0
CD D:LYS221 4.7 9.3 1.0
O3 D:LRH604 4.7 10.1 1.0
NH2 C:ARG65 4.8 10.2 1.0
OE2 D:GLU219 4.8 8.8 1.0
C5 D:LRH604 4.9 14.3 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 16:37:01 2024

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