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Manganese in PDB 6v0t: Crystal Structure of Catalytic Subunit of Bovine Pyruvate Dehydrogenase Phosphatase 1 - Catalytic Domain

Enzymatic activity of Crystal Structure of Catalytic Subunit of Bovine Pyruvate Dehydrogenase Phosphatase 1 - Catalytic Domain

All present enzymatic activity of Crystal Structure of Catalytic Subunit of Bovine Pyruvate Dehydrogenase Phosphatase 1 - Catalytic Domain:
3.1.3.43;

Protein crystallography data

The structure of Crystal Structure of Catalytic Subunit of Bovine Pyruvate Dehydrogenase Phosphatase 1 - Catalytic Domain, PDB code: 6v0t was solved by Y.Guo, W.Qiu, S.R.Ernst, D.W.Carroll, M.L.Hackert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.12 / 2.10
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 75.339, 75.339, 173.255, 90.00, 90.00, 120.00
R / Rfree (%) 21.9 / 24.7

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Catalytic Subunit of Bovine Pyruvate Dehydrogenase Phosphatase 1 - Catalytic Domain (pdb code 6v0t). 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 Catalytic Subunit of Bovine Pyruvate Dehydrogenase Phosphatase 1 - Catalytic Domain, PDB code: 6v0t:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 6v0t

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Manganese binding site 1 out of 5 in the Crystal Structure of Catalytic Subunit of Bovine Pyruvate Dehydrogenase Phosphatase 1 - Catalytic Domain


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 Catalytic Subunit of Bovine Pyruvate Dehydrogenase Phosphatase 1 - Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:30.7
occ:1.00
 OD1 A:ASP73 2.1 25.8 1.0
O A:HOH740 2.1 28.6 1.0
O A:GLY74 2.2 25.9 1.0
O A:HOH685 2.3 31.1 1.0
O A:HOH613 2.3 26.8 1.0
O A:HOH601 2.4 32.5 1.0
CG A:ASP73 3.3 21.7 1.0
C A:GLY74 3.3 25.0 1.0
O A:HOH812 3.4 32.0 1.0
OD2 A:ASP73 3.8 27.9 1.0
MN A:MN502 3.8 29.9 1.0
N A:GLY74 3.9 29.0 1.0
OE1 A:GLU53 4.0 42.1 1.0
O A:HOH655 4.1 27.8 1.0
C A:ASP73 4.2 31.9 1.0
OD1 A:ASP54 4.2 31.2 1.0
CA A:GLY74 4.2 25.7 1.0
N A:HIS75 4.3 27.8 1.0
O A:HOH667 4.3 25.2 1.0
CB A:GLU53 4.3 31.8 1.0
O A:HOH610 4.3 29.7 1.0
CA A:HIS75 4.4 28.6 1.0
CB A:ASP73 4.5 29.9 1.0
CB A:HIS75 4.5 29.5 1.0
OD2 A:ASP446 4.6 27.9 1.0
O A:ASP73 4.6 28.1 1.0
CA A:ASP73 4.6 26.5 1.0
OD1 A:ASP445 4.6 29.4 1.0
OD2 A:ASP445 5.0 32.5 1.0

Manganese binding site 2 out of 5 in 6v0t

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Manganese binding site 2 out of 5 in the Crystal Structure of Catalytic Subunit of Bovine Pyruvate Dehydrogenase Phosphatase 1 - Catalytic Domain


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 Catalytic Subunit of Bovine Pyruvate Dehydrogenase Phosphatase 1 - Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:29.9
occ:1.00
 O A:HOH610 2.0 29.7 1.0
OD2 A:ASP73 2.1 27.9 1.0
OD2 A:ASP445 2.1 32.5 1.0
OD1 A:ASP347 2.2 26.4 1.0
O A:HOH685 2.2 31.1 1.0
O A:HOH667 2.2 25.2 1.0
CG A:ASP73 3.1 21.7 1.0
CG A:ASP347 3.1 33.5 1.0
CG A:ASP445 3.2 33.6 1.0
OD2 A:ASP347 3.3 32.1 1.0
OD1 A:ASP73 3.3 25.8 1.0
OD1 A:ASP445 3.6 29.4 1.0
MN A:MN501 3.8 30.7 1.0
O A:HOH812 3.9 32.0 1.0
O A:HOH740 4.1 28.6 1.0
O A:HOH691 4.2 26.8 1.0
N A:GLY348 4.3 26.5 1.0
O A:HOH613 4.4 26.8 1.0
CB A:ASP73 4.4 29.9 1.0
CB A:ASP445 4.5 38.8 1.0
CB A:ASP347 4.5 32.7 1.0
N A:ASP347 4.6 30.0 1.0
O A:ASP446 4.6 25.7 1.0
O A:HOH636 4.6 37.6 1.0
OD1 A:ASP54 4.6 31.2 1.0
C A:ASP347 4.8 30.2 1.0
CA A:ASP347 4.8 32.9 1.0
CB A:THR346 4.8 29.1 1.0
CA A:GLY348 4.9 33.4 1.0
O A:HOH802 5.0 59.3 1.0

Manganese binding site 3 out of 5 in 6v0t

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Manganese binding site 3 out of 5 in the Crystal Structure of Catalytic Subunit of Bovine Pyruvate Dehydrogenase Phosphatase 1 - Catalytic Domain


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 Catalytic Subunit of Bovine Pyruvate Dehydrogenase Phosphatase 1 - Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn505

b:69.6
occ:1.00
 NE2 A:HIS414 2.2 59.0 1.0
NE2 A:HIS410 2.3 70.1 1.0
CE1 A:HIS410 2.5 73.4 1.0
O A:HOH622 2.7 54.2 1.0
CD2 A:HIS414 2.9 51.8 1.0
CE1 A:HIS414 3.3 62.2 1.0
CD2 A:HIS410 3.6 62.5 1.0
ND1 A:HIS410 3.8 60.6 1.0
CB A:ALA423 4.1 68.9 1.0
CG A:HIS414 4.2 56.3 1.0
ND1 A:HIS414 4.3 65.8 1.0
CG A:HIS410 4.3 55.0 1.0

Manganese binding site 4 out of 5 in 6v0t

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Manganese binding site 4 out of 5 in the Crystal Structure of Catalytic Subunit of Bovine Pyruvate Dehydrogenase Phosphatase 1 - Catalytic Domain


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 Catalytic Subunit of Bovine Pyruvate Dehydrogenase Phosphatase 1 - Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn506

b:36.3
occ:0.33
 O1 A:SO4503 1.7 37.9 0.3
O A:HOH626 2.6 49.0 1.0
O A:HOH779 2.9 37.6 1.0
S A:SO4503 3.0 26.8 0.3
N A:ILE291 3.1 34.4 1.0
O2 A:SO4503 3.5 38.0 0.3
CG A:PRO321 3.6 42.5 1.0
CA A:SER290 3.7 34.5 1.0
CG1 A:ILE291 3.7 39.1 1.0
CB A:SER290 3.8 35.3 1.0
O A:HOH604 3.9 42.8 1.0
O4 A:SO4503 3.9 37.5 0.3
C A:SER290 3.9 33.7 1.0
O3 A:SO4503 3.9 41.4 0.3
CB A:ILE291 3.9 38.3 1.0
CD1 A:ILE291 4.0 37.6 1.0
CD A:PRO321 4.1 40.3 1.0
CA A:ILE291 4.1 36.6 1.0
O A:TYR318 4.7 43.1 1.0
CD2 A:TYR318 4.8 35.0 1.0
CE2 A:TYR318 4.8 39.0 1.0
OG A:SER290 4.9 34.9 1.0
O A:TYR319 4.9 47.6 1.0
CB A:PRO321 4.9 41.9 1.0
N A:ASP292 5.0 34.9 1.0
N A:SER290 5.0 39.8 1.0

Manganese binding site 5 out of 5 in 6v0t

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Manganese binding site 5 out of 5 in the Crystal Structure of Catalytic Subunit of Bovine Pyruvate Dehydrogenase Phosphatase 1 - Catalytic Domain


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 Catalytic Subunit of Bovine Pyruvate Dehydrogenase Phosphatase 1 - Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn507

b:54.0
occ:0.27
 O2 A:SO4504 1.7 45.3 0.3
S A:SO4504 3.1 54.3 0.3
O A:HOH794 3.2 56.8 1.0
O1 A:SO4504 3.8 48.4 0.3
O4 A:SO4504 3.9 41.8 0.3
O3 A:SO4504 3.9 47.5 0.3
CG2 A:ILE291 4.4 41.3 1.0
CD1 A:ILE291 4.4 37.6 1.0
CB A:ILE291 4.9 38.3 1.0
O3 A:SO4503 5.0 41.4 0.3

Reference:

W.Qiu, S.R.Ernst, D.W.Carroll, T.E.Roche, M.L.Hackert, Y.Guo. Crystal Structure of Catalytic Subunit of Bovine Pyruvate Dehydrogenase Phosphatase 1 To Be Published.
Page generated: Sat Aug 16 21:44:49 2025

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