Atomistry » Manganese » PDB 3hw6-3ki9 » 3itl
Atomistry »
  Manganese »
    PDB 3hw6-3ki9 »
      3itl »

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

Go back to Manganese Binding Sites List in 3itl
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

Go back to Manganese Binding Sites List in 3itl
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

Go back to Manganese Binding Sites List in 3itl
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

Go back to Manganese Binding Sites List in 3itl
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

Go back to Manganese Binding Sites List in 3itl
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

Go back to Manganese Binding Sites List in 3itl
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

Go back to Manganese Binding Sites List in 3itl
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

Go back to Manganese Binding Sites List in 3itl
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy