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Manganese in PDB 1itw: Crystal Structure of the Monomeric Isocitrate Dehydrogenase in Complex with Isocitrate and Mn

Enzymatic activity of Crystal Structure of the Monomeric Isocitrate Dehydrogenase in Complex with Isocitrate and Mn

All present enzymatic activity of Crystal Structure of the Monomeric Isocitrate Dehydrogenase in Complex with Isocitrate and Mn:
1.1.1.42;

Protein crystallography data

The structure of Crystal Structure of the Monomeric Isocitrate Dehydrogenase in Complex with Isocitrate and Mn, PDB code: 1itw was solved by Y.Yasutake, S.Watanabe, M.Yao, Y.Takada, N.Fukunaga, I.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 110.405, 119.023, 128.217, 90.00, 99.01, 90.00
R / Rfree (%) 19.3 / 22.8

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the Monomeric Isocitrate Dehydrogenase in Complex with Isocitrate and Mn (pdb code 1itw). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Crystal Structure of the Monomeric Isocitrate Dehydrogenase in Complex with Isocitrate and Mn, PDB code: 1itw:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 1itw

Go back to Manganese Binding Sites List in 1itw
Manganese binding site 1 out of 5 in the Crystal Structure of the Monomeric Isocitrate Dehydrogenase in Complex with Isocitrate and Mn


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 the Monomeric Isocitrate Dehydrogenase in Complex with Isocitrate and Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn742

b:15.0
occ:1.00
 OD2 A:ASP548 2.1 12.9 1.0
OD1 A:ASP350 2.1 13.4 1.0
O7 A:ICT743 2.2 10.2 1.0
O A:HOH944 2.2 7.0 1.0
O2 A:ICT743 2.2 10.2 1.0
O A:HOH850 2.2 8.5 1.0
C1 A:ICT743 3.1 11.4 1.0
CG A:ASP548 3.3 11.7 1.0
C2 A:ICT743 3.3 12.2 1.0
CG A:ASP350 3.3 13.3 1.0
OD1 A:ASP548 3.8 10.4 1.0
CB A:ASP350 3.9 11.9 1.0
NZ A:LYS255 3.9 8.9 1.0
O A:ASP548 4.0 9.5 1.0
O A:HOH1090 4.2 30.1 1.0
O A:HOH1063 4.2 21.6 1.0
C3 A:ICT743 4.2 10.6 1.0
O1 A:ICT743 4.3 9.5 1.0
OD2 A:ASP350 4.3 16.1 1.0
C6 A:ICT743 4.3 10.9 1.0
O A:HOH1231 4.3 27.1 1.0
CB A:ASP548 4.4 9.4 1.0
O A:ALA582 4.5 13.5 1.0
NH1 A:ARG145 4.5 10.0 1.0
CA A:ASP548 4.5 9.6 1.0
O6 A:ICT743 4.6 10.4 1.0
C A:ASP548 4.6 10.4 1.0
O A:HOH1263 4.6 35.1 1.0
O A:HOH833 4.6 15.8 1.0
O5 A:ICT743 4.7 7.9 1.0
CB A:ALA582 4.9 13.3 1.0

Manganese binding site 2 out of 5 in 1itw

Go back to Manganese Binding Sites List in 1itw
Manganese binding site 2 out of 5 in the Crystal Structure of the Monomeric Isocitrate Dehydrogenase in Complex with Isocitrate and Mn


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 the Monomeric Isocitrate Dehydrogenase in Complex with Isocitrate and Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn742

b:15.4
occ:1.00
 OD2 B:ASP548 2.1 12.9 1.0
OD1 B:ASP350 2.2 15.2 1.0
O7 B:ICT744 2.2 14.2 1.0
O B:HOH881 2.2 13.2 1.0
O2 B:ICT744 2.3 15.4 1.0
O B:HOH883 2.3 16.5 1.0
C1 B:ICT744 3.1 14.6 1.0
CG B:ASP548 3.2 11.3 1.0
C2 B:ICT744 3.3 13.2 1.0
CG B:ASP350 3.3 17.1 1.0
OD1 B:ASP548 3.8 13.2 1.0
NZ B:LYS255 3.9 10.8 1.0
CB B:ASP350 3.9 15.5 1.0
O B:ASP548 4.0 12.4 1.0
C3 B:ICT744 4.2 13.5 1.0
C6 B:ICT744 4.3 9.3 1.0
O B:HOH944 4.3 25.3 1.0
O1 B:ICT744 4.3 13.9 1.0
OD2 B:ASP350 4.3 19.5 1.0
O B:HOH1022 4.4 21.7 1.0
O B:ALA582 4.4 15.1 1.0
CB B:ASP548 4.4 10.4 1.0
O6 B:ICT744 4.5 11.6 1.0
CA B:ASP548 4.5 11.5 1.0
O B:HOH929 4.5 19.8 1.0
O B:HOH890 4.5 18.6 1.0
C B:ASP548 4.5 10.9 1.0
NH1 B:ARG145 4.6 13.4 1.0
O5 B:ICT744 4.6 14.6 1.0
CB B:ALA582 4.8 15.4 1.0

Manganese binding site 3 out of 5 in 1itw

Go back to Manganese Binding Sites List in 1itw
Manganese binding site 3 out of 5 in the Crystal Structure of the Monomeric Isocitrate Dehydrogenase in Complex with Isocitrate and Mn


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 the Monomeric Isocitrate Dehydrogenase in Complex with Isocitrate and Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn743

b:28.5
occ:1.00
 OE2 B:GLU239 2.1 19.8 1.0
O B:HOH1350 2.1 28.1 1.0
O B:HOH1349 2.2 25.8 1.0
O B:HOH1093 2.3 23.8 1.0
O B:HOH1348 2.3 29.7 1.0
CD B:GLU239 3.2 19.7 1.0
OE1 B:GLU239 3.5 21.8 1.0
O B:HOH1234 3.6 32.9 1.0
O B:HOH941 4.3 24.2 1.0
O B:HOH1196 4.3 27.4 1.0
O B:HIS175 4.4 15.1 1.0
OD2 B:ASP177 4.5 23.7 1.0
CG B:GLU239 4.5 18.3 1.0
CE2 B:PHE235 4.7 14.3 1.0
CB B:ALA174 5.0 14.4 1.0

Manganese binding site 4 out of 5 in 1itw

Go back to Manganese Binding Sites List in 1itw
Manganese binding site 4 out of 5 in the Crystal Structure of the Monomeric Isocitrate Dehydrogenase in Complex with Isocitrate and Mn


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 the Monomeric Isocitrate Dehydrogenase in Complex with Isocitrate and Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn742

b:24.1
occ:1.00
 OD2 C:ASP548 2.1 16.8 1.0
O7 C:ICT743 2.2 22.1 1.0
O C:HOH1065 2.2 16.6 1.0
O C:HOH772 2.2 19.8 1.0
O2 C:ICT743 2.2 22.8 1.0
OD1 C:ASP350 2.3 24.7 1.0
C1 C:ICT743 3.1 23.7 1.0
CG C:ASP548 3.3 18.3 1.0
C2 C:ICT743 3.3 22.8 1.0
CG C:ASP350 3.4 25.7 1.0
CB C:ASP350 3.9 24.2 1.0
OD1 C:ASP548 3.9 17.8 1.0
O C:ASP548 4.0 21.0 1.0
NZ C:LYS255 4.0 15.2 1.0
O C:HOH1003 4.1 37.2 1.0
OD1 C:ASP552 4.1 31.4 1.0
C3 C:ICT743 4.3 23.2 1.0
O1 C:ICT743 4.3 23.5 1.0
C6 C:ICT743 4.4 22.7 1.0
CB C:ASP548 4.4 18.1 1.0
OD2 C:ASP350 4.4 26.0 1.0
NH1 C:ARG145 4.4 21.9 1.0
CA C:ASP548 4.5 20.1 1.0
C C:ASP548 4.5 20.3 1.0
O C:ALA582 4.5 22.2 1.0
O C:HOH1045 4.6 40.2 1.0
CG C:ASP552 4.6 30.0 1.0
O6 C:ICT743 4.6 24.0 1.0
O C:HOH1048 4.7 33.8 1.0
O C:HOH859 4.7 31.6 1.0
O5 C:ICT743 4.8 23.8 1.0
CB C:ALA582 4.8 24.6 1.0

Manganese binding site 5 out of 5 in 1itw

Go back to Manganese Binding Sites List in 1itw
Manganese binding site 5 out of 5 in the Crystal Structure of the Monomeric Isocitrate Dehydrogenase in Complex with Isocitrate and Mn


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 the Monomeric Isocitrate Dehydrogenase in Complex with Isocitrate and Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn742

b:16.8
occ:1.00
 OD2 D:ASP548 2.0 9.8 1.0
OD1 D:ASP350 2.1 18.7 1.0
O7 D:ICT743 2.2 11.6 1.0
O2 D:ICT743 2.2 12.7 1.0
O D:HOH809 2.2 14.9 1.0
O D:HOH896 2.3 12.2 1.0
C1 D:ICT743 3.1 12.8 1.0
CG D:ASP548 3.2 12.5 1.0
CG D:ASP350 3.3 15.5 1.0
C2 D:ICT743 3.3 13.1 1.0
OD1 D:ASP548 3.8 11.2 1.0
CB D:ASP350 3.9 16.8 1.0
NZ D:LYS255 4.0 10.6 1.0
O D:ASP548 4.0 11.9 1.0
O D:HOH1123 4.1 25.5 1.0
C3 D:ICT743 4.2 13.3 1.0
OD2 D:ASP350 4.3 16.4 1.0
C6 D:ICT743 4.3 13.6 1.0
O1 D:ICT743 4.3 10.6 1.0
CB D:ASP548 4.4 11.0 1.0
O D:ALA582 4.4 14.4 1.0
NH1 D:ARG145 4.4 15.2 1.0
O6 D:ICT743 4.5 13.8 1.0
CA D:ASP548 4.5 11.3 1.0
O D:HOH1082 4.5 24.2 1.0
C D:ASP548 4.5 12.7 1.0
O D:HOH848 4.6 19.3 1.0
O5 D:ICT743 4.7 12.8 1.0
CB D:ALA582 4.8 16.1 1.0

Reference:

Y.Yasutake, S.Watanabe, M.Yao, Y.Takada, N.Fukunaga, I.Tanaka. Structure of the Monomeric Isocitrate Dehydrogenase: Evidence of A Protein Monomerization By A Domain Duplication Structure V. 10 1637 2002.
ISSN: ISSN 0969-2126
PubMed: 12467571
DOI: 10.1016/S0969-2126(02)00904-8
Page generated: Sat Oct 5 11:04:26 2024

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