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Manganese in PDB 4zda: Crystal Structure of Isocitrate Dehydrogenase in Complex with Isocitrate and Mn From M. Smegmatis

Enzymatic activity of Crystal Structure of Isocitrate Dehydrogenase in Complex with Isocitrate and Mn From M. Smegmatis

All present enzymatic activity of Crystal Structure of Isocitrate Dehydrogenase in Complex with Isocitrate and Mn From M. Smegmatis:
1.1.1.42;

Protein crystallography data

The structure of Crystal Structure of Isocitrate Dehydrogenase in Complex with Isocitrate and Mn From M. Smegmatis, PDB code: 4zda was solved by F.Pojer, P.Murima, J.D.Mckinney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.59 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 201.774, 206.162, 145.598, 90.00, 90.97, 90.00
R / Rfree (%) 21.4 / 25.7

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Isocitrate Dehydrogenase in Complex with Isocitrate and Mn From M. Smegmatis (pdb code 4zda). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of Isocitrate Dehydrogenase in Complex with Isocitrate and Mn From M. Smegmatis, PDB code: 4zda:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 4zda

Go back to Manganese Binding Sites List in 4zda
Manganese binding site 1 out of 6 in the Crystal Structure of Isocitrate Dehydrogenase in Complex with Isocitrate and Mn From M. Smegmatis


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 Isocitrate Dehydrogenase in Complex with Isocitrate and Mn From M. Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn801

b:66.4
occ:1.00
 O1 A:ICT802 2.0 61.2 1.0
OD1 A:ASP551 2.2 45.1 1.0
OD2 A:ASP352 2.4 53.3 1.0
OD2 A:ASP555 2.6 55.8 1.0
O7 A:ICT802 2.7 59.1 1.0
C1 A:ICT802 2.9 60.1 1.0
C2 A:ICT802 3.4 59.4 1.0
CG A:ASP551 3.5 45.8 1.0
CG A:ASP352 3.6 51.6 1.0
O A:ASP551 3.8 46.4 1.0
CG A:ASP555 3.8 54.6 1.0
O2 A:ICT802 3.8 60.2 1.0
NZ A:LYS257 4.1 44.3 1.0
CB A:ASP352 4.1 49.4 1.0
OD2 A:ASP551 4.2 48.9 1.0
C A:ASP551 4.4 45.0 1.0
O A:ALA585 4.4 52.8 1.0
CA A:ASP551 4.4 44.2 1.0
CB A:ASP551 4.5 44.4 1.0
OD1 A:ASP555 4.5 56.2 1.0
C6 A:ICT802 4.5 58.4 1.0
C3 A:ICT802 4.6 58.9 1.0
O6 A:ICT802 4.6 58.7 1.0
OD1 A:ASP352 4.6 53.0 1.0
CB A:ASP555 4.8 50.5 1.0
CB A:ALA585 4.9 50.0 1.0
O5 A:ICT802 4.9 57.5 1.0

Manganese binding site 2 out of 6 in 4zda

Go back to Manganese Binding Sites List in 4zda
Manganese binding site 2 out of 6 in the Crystal Structure of Isocitrate Dehydrogenase in Complex with Isocitrate and Mn From M. Smegmatis


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 Isocitrate Dehydrogenase in Complex with Isocitrate and Mn From M. Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn801

b:65.9
occ:1.00
 OD1 B:ASP551 2.3 52.7 1.0
OD2 B:ASP555 2.5 57.6 1.0
OD2 B:ASP352 2.5 52.9 1.0
O7 B:ICT802 2.5 60.4 1.0
O1 B:ICT802 3.0 60.2 1.0
C1 B:ICT802 3.4 58.7 1.0
C2 B:ICT802 3.5 58.7 1.0
CG B:ASP551 3.5 53.8 1.0
CG B:ASP555 3.6 57.1 1.0
CG B:ASP352 3.7 53.0 1.0
O B:ASP551 3.9 47.8 1.0
OD1 B:ASP555 4.1 60.7 1.0
NZ B:LYS257 4.1 59.1 1.0
O2 B:ICT802 4.2 59.2 1.0
OD2 B:ASP551 4.2 55.6 1.0
CB B:ASP352 4.2 51.7 1.0
CA B:ASP551 4.5 49.2 1.0
C B:ASP551 4.5 48.6 1.0
O6 B:ICT802 4.5 59.8 1.0
C6 B:ICT802 4.5 58.6 1.0
CB B:ASP551 4.6 51.5 1.0
C3 B:ICT802 4.6 58.4 1.0
OD1 B:ASP352 4.7 53.2 1.0
CB B:ALA585 4.7 58.9 1.0
O B:ALA585 4.8 58.0 1.0
CB B:ASP555 4.8 53.5 1.0
NH1 B:ARG147 4.9 54.4 1.0
O5 B:ICT802 5.0 57.7 1.0

Manganese binding site 3 out of 6 in 4zda

Go back to Manganese Binding Sites List in 4zda
Manganese binding site 3 out of 6 in the Crystal Structure of Isocitrate Dehydrogenase in Complex with Isocitrate and Mn From M. Smegmatis


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 Isocitrate Dehydrogenase in Complex with Isocitrate and Mn From M. Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn801

b:68.5
occ:1.00
 OD2 C:ASP555 2.3 59.0 1.0
OD1 C:ASP551 2.5 51.1 1.0
OD2 C:ASP352 2.5 50.9 1.0
O7 C:ICT802 2.7 58.9 1.0
O2 C:ICT802 2.7 63.5 1.0
CG C:ASP555 3.4 57.6 1.0
C1 C:ICT802 3.4 59.5 1.0
CG C:ASP352 3.6 50.2 1.0
C2 C:ICT802 3.6 58.8 1.0
CG C:ASP551 3.7 50.8 1.0
O C:ASP551 3.8 51.4 1.0
OD1 C:ASP555 4.0 58.8 1.0
CB C:ASP352 4.1 49.9 1.0
CB C:ALA585 4.4 52.7 1.0
OD2 C:ASP551 4.4 49.8 1.0
NZ C:LYS257 4.4 52.1 1.0
C C:ASP551 4.5 50.9 1.0
CB C:ASP555 4.5 54.2 1.0
O1 C:ICT802 4.5 60.6 1.0
OD1 C:ASP352 4.5 50.7 1.0
CA C:ASP551 4.6 50.5 1.0
O C:ALA585 4.6 54.1 1.0
CB C:ASP551 4.7 50.1 1.0
C3 C:ICT802 4.8 59.0 1.0
C6 C:ICT802 4.9 59.1 1.0
NH1 C:ARG147 4.9 62.5 1.0
OG1 C:THR554 4.9 56.5 1.0

Manganese binding site 4 out of 6 in 4zda

Go back to Manganese Binding Sites List in 4zda
Manganese binding site 4 out of 6 in the Crystal Structure of Isocitrate Dehydrogenase in Complex with Isocitrate and Mn From M. Smegmatis


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 Isocitrate Dehydrogenase in Complex with Isocitrate and Mn From M. Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn801

b:70.5
occ:1.00
 OD1 D:ASP551 2.2 47.6 1.0
OD2 D:ASP352 2.4 54.9 1.0
OD2 D:ASP555 2.5 61.2 1.0
O7 D:ICT802 2.5 61.2 1.0
O1 D:ICT802 2.8 60.4 1.0
CG D:ASP551 3.4 49.0 1.0
CG D:ASP352 3.5 53.2 1.0
C2 D:ICT802 3.5 62.3 1.0
C1 D:ICT802 3.6 61.2 1.0
CG D:ASP555 3.6 59.4 1.0
O D:ASP551 3.6 52.2 1.0
CB D:ASP352 4.0 51.4 1.0
OD2 D:ASP551 4.1 49.0 1.0
NZ D:LYS257 4.2 49.6 1.0
C D:ASP551 4.3 50.2 1.0
OD1 D:ASP555 4.3 59.8 1.0
CB D:ASP551 4.5 50.1 1.0
CA D:ASP551 4.5 49.6 1.0
CB D:ASP555 4.5 55.7 1.0
OD1 D:ASP352 4.6 54.4 1.0
O2 D:ICT802 4.7 61.0 1.0
O5 D:ICT802 4.8 69.5 1.0
C3 D:ICT802 4.8 65.2 1.0
C6 D:ICT802 4.8 67.2 1.0
O D:ALA585 4.9 58.7 1.0

Manganese binding site 5 out of 6 in 4zda

Go back to Manganese Binding Sites List in 4zda
Manganese binding site 5 out of 6 in the Crystal Structure of Isocitrate Dehydrogenase in Complex with Isocitrate and Mn From M. Smegmatis


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 Isocitrate Dehydrogenase in Complex with Isocitrate and Mn From M. Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn801

b:86.8
occ:1.00
 O1 E:ICT802 2.1 70.2 1.0
OD1 E:ASP551 2.1 53.3 1.0
OD2 E:ASP555 2.4 80.0 1.0
OD2 E:ASP352 2.5 61.9 1.0
O7 E:ICT802 2.7 68.6 1.0
C1 E:ICT802 3.1 68.7 1.0
CG E:ASP551 3.4 56.0 1.0
C2 E:ICT802 3.5 68.7 1.0
CG E:ASP555 3.5 78.4 1.0
CG E:ASP352 3.6 61.1 1.0
O E:ASP551 3.9 59.2 1.0
OD1 E:ASP555 4.1 80.7 1.0
OD2 E:ASP551 4.1 56.8 1.0
CB E:ASP352 4.2 59.4 1.0
O2 E:ICT802 4.2 69.0 1.0
NZ E:LYS257 4.3 56.2 1.0
C E:ASP551 4.4 57.5 1.0
CB E:ASP551 4.4 56.6 1.0
CA E:ASP551 4.4 57.1 1.0
C6 E:ICT802 4.5 66.8 1.0
O5 E:ICT802 4.5 67.3 1.0
OD1 E:ASP352 4.6 62.8 1.0
CB E:ASP555 4.6 73.7 1.0
C3 E:ICT802 4.6 67.8 1.0
CB E:ALA585 4.7 68.6 1.0
O E:ALA585 4.7 67.6 1.0
O6 E:ICT802 4.8 64.2 1.0
NH1 E:ARG147 4.9 61.8 1.0

Manganese binding site 6 out of 6 in 4zda

Go back to Manganese Binding Sites List in 4zda
Manganese binding site 6 out of 6 in the Crystal Structure of Isocitrate Dehydrogenase in Complex with Isocitrate and Mn From M. Smegmatis


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 Isocitrate Dehydrogenase in Complex with Isocitrate and Mn From M. Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn801

b:80.5
occ:1.00
 OD1 F:ASP551 2.3 57.8 1.0
O7 F:ICT802 2.4 77.0 1.0
OD2 F:ASP555 2.4 75.0 1.0
OD2 F:ASP352 2.6 66.7 1.0
CG F:ASP551 3.6 59.5 1.0
O2 F:ICT802 3.6 74.2 1.0
CG F:ASP555 3.6 72.1 1.0
C2 F:ICT802 3.7 75.4 1.0
CG F:ASP352 3.8 65.9 1.0
O F:ASP551 3.9 65.4 1.0
C1 F:ICT802 3.9 76.4 1.0
OD1 F:ASP555 4.2 73.1 1.0
OD2 F:ASP551 4.3 59.7 1.0
CB F:ALA585 4.3 66.4 1.0
CB F:ASP352 4.4 63.8 1.0
NZ F:LYS257 4.4 67.5 1.0
C F:ASP551 4.5 62.4 1.0
O F:ALA585 4.5 64.0 1.0
NH1 F:ARG147 4.5 64.5 1.0
CA F:ASP551 4.5 61.4 1.0
CB F:ASP551 4.6 59.4 1.0
CB F:ASP555 4.7 67.8 1.0
C6 F:ICT802 4.7 73.3 1.0
C3 F:ICT802 4.8 75.5 1.0
O5 F:ICT802 4.8 72.7 1.0
OD1 F:ASP352 4.8 67.1 1.0
O1 F:ICT802 5.0 78.6 1.0
OG1 F:THR554 5.0 57.1 1.0

Reference:

F.Pojer, P.Murima, J.D.Mckinney. Crystal Structure of Isocitrate Dehydrogenase in Complex with Isocitrate and Mn From M. Smegmatis To Be Published.
Page generated: Sat Oct 5 23:13:56 2024

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