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Manganese in PDB 4zvz: Co-Crystal Structures of PP5 in Complex with 5-Methyl-7- Oxabicyclo[2.2.1]Heptane-2,3-Dicarboxylic Acid

Enzymatic activity of Co-Crystal Structures of PP5 in Complex with 5-Methyl-7- Oxabicyclo[2.2.1]Heptane-2,3-Dicarboxylic Acid

All present enzymatic activity of Co-Crystal Structures of PP5 in Complex with 5-Methyl-7- Oxabicyclo[2.2.1]Heptane-2,3-Dicarboxylic Acid:
3.1.3.16;

Protein crystallography data

The structure of Co-Crystal Structures of PP5 in Complex with 5-Methyl-7- Oxabicyclo[2.2.1]Heptane-2,3-Dicarboxylic Acid, PDB code: 4zvz was solved by D.Chattopadhyay, M.R.Swingle, E.A.Salter, A.Wierzbicki, R.E.Honkanen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 91.03 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 40.858, 80.520, 91.165, 88.15, 87.33, 86.71
R / Rfree (%) 20.4 / 23.5

Other elements in 4zvz:

The structure of Co-Crystal Structures of PP5 in Complex with 5-Methyl-7- Oxabicyclo[2.2.1]Heptane-2,3-Dicarboxylic Acid also contains other interesting chemical elements:

Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Co-Crystal Structures of PP5 in Complex with 5-Methyl-7- Oxabicyclo[2.2.1]Heptane-2,3-Dicarboxylic Acid (pdb code 4zvz). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Co-Crystal Structures of PP5 in Complex with 5-Methyl-7- Oxabicyclo[2.2.1]Heptane-2,3-Dicarboxylic Acid, PDB code: 4zvz:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4zvz

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Manganese binding site 1 out of 8 in the Co-Crystal Structures of PP5 in Complex with 5-Methyl-7- Oxabicyclo[2.2.1]Heptane-2,3-Dicarboxylic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Co-Crystal Structures of PP5 in Complex with 5-Methyl-7- Oxabicyclo[2.2.1]Heptane-2,3-Dicarboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:22.0
occ:1.00
OD2 A:ASP242 2.1 22.1 1.0
OD2 A:ASP271 2.1 18.4 1.0
NE2 A:HIS244 2.2 21.6 1.0
O08 A:4TF503 2.3 26.3 1.0
O17 A:4TF503 2.3 29.1 1.0
O10 A:4TF503 2.5 29.0 1.0
C07 A:4TF503 2.9 27.9 1.0
CD2 A:HIS244 3.1 20.3 1.0
CG A:ASP271 3.2 17.0 1.0
CE1 A:HIS244 3.2 22.1 1.0
CG A:ASP242 3.2 20.7 1.0
C16 A:4TF503 3.2 30.1 1.0
C02 A:4TF503 3.3 29.5 1.0
C05 A:4TF503 3.3 29.4 1.0
C06 A:4TF503 3.4 29.0 1.0
MN A:MN502 3.4 19.4 1.0
C01 A:4TF503 3.4 29.7 1.0
CB A:ASP271 3.6 15.9 1.0
O09 A:4TF503 3.8 28.0 1.0
CB A:ASP242 3.9 18.8 1.0
OD1 A:ASP242 4.2 21.0 1.0
OD1 A:ASP271 4.3 17.0 1.0
CG A:HIS244 4.3 19.8 1.0
ND1 A:HIS244 4.3 20.9 1.0
CD2 A:HIS304 4.3 23.4 1.0
O18 A:4TF503 4.4 31.2 1.0
NE2 A:HIS352 4.5 21.1 1.0
CE1 A:HIS352 4.5 20.1 1.0
CE1 A:PHE446 4.5 22.1 1.0
C03 A:4TF503 4.6 29.7 1.0
C04 A:4TF503 4.6 30.9 1.0
CA A:HIS427 4.8 22.8 1.0
NE2 A:HIS304 4.8 25.9 1.0
OD1 A:ASN303 4.8 20.1 1.0
O A:HIS427 4.9 27.0 1.0
C A:HIS427 5.0 25.1 1.0

Manganese binding site 2 out of 8 in 4zvz

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Manganese binding site 2 out of 8 in the Co-Crystal Structures of PP5 in Complex with 5-Methyl-7- Oxabicyclo[2.2.1]Heptane-2,3-Dicarboxylic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Co-Crystal Structures of PP5 in Complex with 5-Methyl-7- Oxabicyclo[2.2.1]Heptane-2,3-Dicarboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:19.4
occ:1.00
OD1 A:ASN303 2.0 20.1 1.0
O08 A:4TF503 2.1 26.3 1.0
NE2 A:HIS352 2.2 21.1 1.0
ND1 A:HIS427 2.2 23.5 1.0
OD2 A:ASP271 2.4 18.4 1.0
O09 A:4TF503 2.8 28.0 1.0
C07 A:4TF503 2.8 27.9 1.0
CE1 A:HIS427 3.0 24.9 1.0
CG A:ASN303 3.1 21.5 1.0
CD2 A:HIS352 3.1 20.5 1.0
CE1 A:HIS352 3.2 20.1 1.0
CG A:ASP271 3.2 17.0 1.0
CG A:HIS427 3.3 23.2 1.0
MN A:MN501 3.4 22.0 1.0
OD1 A:ASP271 3.5 17.0 1.0
CA A:HIS427 3.5 22.8 1.0
ND2 A:ASN303 3.6 23.4 1.0
CB A:HIS427 3.7 22.2 1.0
OD2 A:ASP242 4.0 22.1 1.0
O17 A:4TF503 4.0 29.1 1.0
O A:HIS427 4.1 27.0 1.0
NE2 A:HIS427 4.2 25.1 1.0
C A:HIS427 4.3 25.1 1.0
C06 A:4TF503 4.3 29.0 1.0
CG A:HIS352 4.3 19.1 1.0
ND1 A:HIS352 4.3 19.0 1.0
CB A:ASN303 4.4 21.2 1.0
CD2 A:HIS427 4.4 24.2 1.0
CB A:ASP271 4.5 15.9 1.0
CD2 A:HIS304 4.5 23.4 1.0
N A:ASN303 4.5 18.0 1.0
N A:HIS427 4.6 21.3 1.0
O A:LEU385 4.7 24.8 1.0
C16 A:4TF503 4.8 30.1 1.0
CG A:ASP242 4.8 20.7 1.0
C05 A:4TF503 4.8 29.4 1.0
O10 A:4TF503 5.0 29.0 1.0
CA A:ASN303 5.0 19.8 1.0
OD1 A:ASP242 5.0 21.0 1.0

Manganese binding site 3 out of 8 in 4zvz

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Manganese binding site 3 out of 8 in the Co-Crystal Structures of PP5 in Complex with 5-Methyl-7- Oxabicyclo[2.2.1]Heptane-2,3-Dicarboxylic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Co-Crystal Structures of PP5 in Complex with 5-Methyl-7- Oxabicyclo[2.2.1]Heptane-2,3-Dicarboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:24.2
occ:1.00
OD2 B:ASP271 2.0 24.4 1.0
OD2 B:ASP242 2.1 25.3 1.0
NE2 B:HIS244 2.2 25.0 1.0
O17 B:4TF503 2.3 29.2 1.0
O08 B:4TF503 2.4 27.6 1.0
O10 B:4TF503 2.5 32.0 1.0
CG B:ASP271 3.1 22.9 1.0
C07 B:4TF503 3.1 29.8 1.0
CD2 B:HIS244 3.2 23.3 1.0
CE1 B:HIS244 3.2 25.1 1.0
CG B:ASP242 3.2 23.6 1.0
C16 B:4TF503 3.3 30.4 1.0
C02 B:4TF503 3.3 31.2 1.0
C05 B:4TF503 3.4 31.3 1.0
MN B:MN502 3.4 23.8 1.0
C06 B:4TF503 3.5 30.3 1.0
CB B:ASP271 3.5 21.6 1.0
C01 B:4TF503 3.5 30.8 1.0
CB B:ASP242 3.9 21.9 1.0
O09 B:4TF503 4.1 29.6 1.0
OD1 B:ASP271 4.2 22.7 1.0
OD1 B:ASP242 4.2 23.7 1.0
CD2 B:HIS304 4.3 24.2 1.0
ND1 B:HIS244 4.3 23.3 1.0
CG B:HIS244 4.3 22.3 1.0
CE1 B:HIS352 4.4 22.9 1.0
NE2 B:HIS352 4.4 23.1 1.0
O18 B:4TF503 4.4 30.6 1.0
CE1 B:PHE446 4.5 27.6 1.0
C03 B:4TF503 4.6 31.9 1.0
C04 B:4TF503 4.7 32.3 1.0
CA B:HIS427 4.7 25.2 1.0
OD1 B:ASN303 4.7 23.9 1.0
NE2 B:HIS304 4.8 25.5 1.0
O B:HIS427 4.9 27.9 1.0
C B:HIS427 4.9 26.4 1.0
CA B:ASP271 5.0 20.4 1.0

Manganese binding site 4 out of 8 in 4zvz

Go back to Manganese Binding Sites List in 4zvz
Manganese binding site 4 out of 8 in the Co-Crystal Structures of PP5 in Complex with 5-Methyl-7- Oxabicyclo[2.2.1]Heptane-2,3-Dicarboxylic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Co-Crystal Structures of PP5 in Complex with 5-Methyl-7- Oxabicyclo[2.2.1]Heptane-2,3-Dicarboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:23.8
occ:1.00
OD1 B:ASN303 2.0 23.9 1.0
NE2 B:HIS352 2.1 23.1 1.0
O08 B:4TF503 2.1 27.6 1.0
ND1 B:HIS427 2.2 27.4 1.0
OD2 B:ASP271 2.4 24.4 1.0
C07 B:4TF503 2.9 29.8 1.0
CE1 B:HIS427 3.0 29.2 1.0
CG B:ASN303 3.0 25.1 1.0
O09 B:4TF503 3.0 29.6 1.0
CD2 B:HIS352 3.1 23.0 1.0
CE1 B:HIS352 3.1 22.9 1.0
CG B:ASP271 3.2 22.9 1.0
CG B:HIS427 3.3 26.8 1.0
MN B:MN501 3.4 24.2 1.0
OD1 B:ASP271 3.4 22.7 1.0
ND2 B:ASN303 3.6 26.1 1.0
CA B:HIS427 3.6 25.2 1.0
CB B:HIS427 3.8 25.4 1.0
O17 B:4TF503 3.9 29.2 1.0
OD2 B:ASP242 4.1 25.3 1.0
ND1 B:HIS352 4.2 22.6 1.0
O B:HIS427 4.2 27.9 1.0
NE2 B:HIS427 4.2 29.4 1.0
CG B:HIS352 4.2 22.7 1.0
CB B:ASN303 4.3 25.4 1.0
C06 B:4TF503 4.4 30.3 1.0
CD2 B:HIS427 4.4 27.9 1.0
C B:HIS427 4.4 26.4 1.0
N B:ASN303 4.4 23.0 1.0
CB B:ASP271 4.5 21.6 1.0
CD2 B:HIS304 4.5 24.2 1.0
O B:LEU385 4.6 27.0 1.0
N B:HIS427 4.6 23.7 1.0
C16 B:4TF503 4.7 30.4 1.0
CA B:ASN303 4.9 24.3 1.0
C05 B:4TF503 4.9 31.3 1.0
CG B:ASP242 4.9 23.6 1.0
O10 B:4TF503 5.0 32.0 1.0

Manganese binding site 5 out of 8 in 4zvz

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Manganese binding site 5 out of 8 in the Co-Crystal Structures of PP5 in Complex with 5-Methyl-7- Oxabicyclo[2.2.1]Heptane-2,3-Dicarboxylic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Co-Crystal Structures of PP5 in Complex with 5-Methyl-7- Oxabicyclo[2.2.1]Heptane-2,3-Dicarboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn501

b:23.8
occ:1.00
OD2 C:ASP242 2.1 26.5 1.0
OD2 C:ASP271 2.1 24.5 1.0
NE2 C:HIS244 2.2 26.6 1.0
O18 C:4TF503 2.2 27.3 1.0
O09 C:4TF503 2.4 27.2 1.0
O10 C:4TF503 2.4 28.8 1.0
C07 C:4TF503 3.0 28.4 1.0
CD2 C:HIS244 3.1 25.6 1.0
CE1 C:HIS244 3.2 26.6 1.0
CG C:ASP271 3.2 23.0 1.0
C16 C:4TF503 3.2 28.4 1.0
CG C:ASP242 3.2 25.5 1.0
C05 C:4TF503 3.3 29.1 1.0
C02 C:4TF503 3.3 29.0 1.0
MN C:MN502 3.4 21.9 1.0
C06 C:4TF503 3.5 28.6 1.0
C01 C:4TF503 3.5 28.6 1.0
CB C:ASP271 3.5 21.8 1.0
CB C:ASP242 3.9 24.3 1.0
O08 C:4TF503 3.9 28.1 1.0
OD1 C:ASP242 4.2 25.4 1.0
ND1 C:HIS244 4.3 25.5 1.0
OD1 C:ASP271 4.3 22.7 1.0
CD2 C:HIS304 4.3 25.0 1.0
CG C:HIS244 4.3 25.0 1.0
O17 C:4TF503 4.3 28.4 1.0
CE1 C:HIS352 4.5 19.5 1.0
CE1 C:PHE446 4.5 27.1 1.0
NE2 C:HIS352 4.6 19.7 1.0
C04 C:4TF503 4.6 30.5 1.0
C03 C:4TF503 4.6 29.6 1.0
CA C:HIS427 4.8 27.4 1.0
NE2 C:HIS304 4.8 26.8 1.0
OD1 C:ASN303 4.9 22.8 1.0
O C:HIS427 4.9 30.2 1.0
C C:HIS427 5.0 28.7 1.0

Manganese binding site 6 out of 8 in 4zvz

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Manganese binding site 6 out of 8 in the Co-Crystal Structures of PP5 in Complex with 5-Methyl-7- Oxabicyclo[2.2.1]Heptane-2,3-Dicarboxylic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Co-Crystal Structures of PP5 in Complex with 5-Methyl-7- Oxabicyclo[2.2.1]Heptane-2,3-Dicarboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn502

b:21.9
occ:1.00
OD1 C:ASN303 2.1 22.8 1.0
NE2 C:HIS352 2.1 19.7 1.0
ND1 C:HIS427 2.1 29.2 1.0
O09 C:4TF503 2.2 27.2 1.0
OD2 C:ASP271 2.3 24.5 1.0
CE1 C:HIS427 2.9 30.6 1.0
C07 C:4TF503 3.0 28.4 1.0
O08 C:4TF503 3.0 28.1 1.0
CE1 C:HIS352 3.0 19.5 1.0
CD2 C:HIS352 3.1 19.8 1.0
CG C:ASN303 3.1 23.7 1.0
CG C:ASP271 3.1 23.0 1.0
CG C:HIS427 3.3 28.6 1.0
OD1 C:ASP271 3.4 22.7 1.0
MN C:MN501 3.4 23.8 1.0
CA C:HIS427 3.6 27.4 1.0
ND2 C:ASN303 3.7 25.0 1.0
CB C:HIS427 3.8 27.4 1.0
O18 C:4TF503 3.9 27.3 1.0
OD2 C:ASP242 4.0 26.5 1.0
NE2 C:HIS427 4.1 30.8 1.0
ND1 C:HIS352 4.2 19.3 1.0
O C:HIS427 4.3 30.2 1.0
CG C:HIS352 4.3 19.6 1.0
CD2 C:HIS427 4.3 29.7 1.0
CB C:ASN303 4.4 23.3 1.0
C C:HIS427 4.4 28.7 1.0
C06 C:4TF503 4.4 28.6 1.0
N C:ASN303 4.4 21.0 1.0
CB C:ASP271 4.4 21.8 1.0
CD2 C:HIS304 4.5 25.0 1.0
N C:HIS427 4.6 25.9 1.0
O C:LEU385 4.6 29.8 1.0
C16 C:4TF503 4.7 28.4 1.0
CG C:ASP242 4.9 25.5 1.0
C05 C:4TF503 4.9 29.1 1.0
CA C:ASN303 4.9 21.9 1.0

Manganese binding site 7 out of 8 in 4zvz

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Manganese binding site 7 out of 8 in the Co-Crystal Structures of PP5 in Complex with 5-Methyl-7- Oxabicyclo[2.2.1]Heptane-2,3-Dicarboxylic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Co-Crystal Structures of PP5 in Complex with 5-Methyl-7- Oxabicyclo[2.2.1]Heptane-2,3-Dicarboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn501

b:27.7
occ:1.00
NE2 D:HIS244 2.1 28.8 1.0
OD2 D:ASP271 2.1 25.7 1.0
OD2 D:ASP242 2.1 26.5 1.0
O18 D:4TF503 2.2 31.4 1.0
O09 D:4TF503 2.3 27.8 1.0
O10 D:4TF503 2.5 30.9 1.0
C07 D:4TF503 2.9 28.8 1.0
CD2 D:HIS244 3.1 26.9 1.0
CE1 D:HIS244 3.1 29.0 1.0
C16 D:4TF503 3.2 30.9 1.0
CG D:ASP271 3.2 23.8 1.0
C05 D:4TF503 3.2 30.3 1.0
CG D:ASP242 3.3 24.5 1.0
C06 D:4TF503 3.3 30.1 1.0
C02 D:4TF503 3.4 30.6 1.0
MN D:MN502 3.4 28.6 1.0
C01 D:4TF503 3.5 31.0 1.0
CB D:ASP271 3.6 22.1 1.0
O08 D:4TF503 3.9 28.3 1.0
CB D:ASP242 3.9 22.9 1.0
OD1 D:ASP242 4.2 24.4 1.0
CD2 D:HIS304 4.2 29.7 1.0
ND1 D:HIS244 4.2 27.3 1.0
CG D:HIS244 4.3 25.9 1.0
O17 D:4TF503 4.3 32.7 1.0
OD1 D:ASP271 4.3 23.9 1.0
CE1 D:PHE446 4.6 24.5 1.0
C04 D:4TF503 4.6 31.2 1.0
CE1 D:HIS352 4.6 25.5 1.0
NE2 D:HIS352 4.6 26.4 1.0
C03 D:4TF503 4.7 31.1 1.0
NE2 D:HIS304 4.7 32.2 1.0
OD1 D:ASN303 4.8 27.1 1.0
CA D:HIS427 4.9 32.2 1.0
O D:HIS427 5.0 37.0 1.0

Manganese binding site 8 out of 8 in 4zvz

Go back to Manganese Binding Sites List in 4zvz
Manganese binding site 8 out of 8 in the Co-Crystal Structures of PP5 in Complex with 5-Methyl-7- Oxabicyclo[2.2.1]Heptane-2,3-Dicarboxylic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Co-Crystal Structures of PP5 in Complex with 5-Methyl-7- Oxabicyclo[2.2.1]Heptane-2,3-Dicarboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn502

b:28.6
occ:1.00
OD1 D:ASN303 2.0 27.1 1.0
O09 D:4TF503 2.0 27.8 1.0
NE2 D:HIS352 2.2 26.4 1.0
ND1 D:HIS427 2.3 34.6 1.0
OD2 D:ASP271 2.4 25.7 1.0
C07 D:4TF503 2.8 28.8 1.0
O08 D:4TF503 2.9 28.3 1.0
CG D:ASN303 3.0 29.3 1.0
CE1 D:HIS427 3.1 37.1 1.0
CE1 D:HIS352 3.1 25.5 1.0
CD2 D:HIS352 3.2 26.4 1.0
CG D:ASP271 3.2 23.8 1.0
CG D:HIS427 3.4 33.8 1.0
OD1 D:ASP271 3.4 23.9 1.0
MN D:MN501 3.4 27.7 1.0
ND2 D:ASN303 3.5 31.2 1.0
CA D:HIS427 3.6 32.2 1.0
CB D:HIS427 3.9 31.9 1.0
OD2 D:ASP242 3.9 26.5 1.0
O D:HIS427 4.2 37.0 1.0
O18 D:4TF503 4.2 31.4 1.0
C06 D:4TF503 4.3 30.1 1.0
ND1 D:HIS352 4.3 24.8 1.0
NE2 D:HIS427 4.3 37.2 1.0
CB D:ASN303 4.3 29.4 1.0
CG D:HIS352 4.3 25.3 1.0
C D:HIS427 4.3 34.7 1.0
CB D:ASP271 4.4 22.1 1.0
N D:ASN303 4.5 25.5 1.0
CD2 D:HIS427 4.5 35.3 1.0
CD2 D:HIS304 4.5 29.7 1.0
N D:HIS427 4.6 29.7 1.0
O D:LEU385 4.7 29.2 1.0
CG D:ASP242 4.8 24.5 1.0
C05 D:4TF503 4.8 30.3 1.0
C16 D:4TF503 4.8 30.9 1.0
CA D:ASN303 4.9 27.6 1.0
OD1 D:ASP242 4.9 24.4 1.0

Reference:

D.Chattopadhyay, M.R.Swingle, E.A.Salter, E.Wood, B.D'arcy, C.Zivanov, K.Abney, A.Musiyenko, S.F.Rusin, A.Kettenbach, L.Yet, C.E.Schroeder, J.E.Golden, W.H.Dunham, A.C.Gingras, S.Banerjee, D.Forbes, A.Wierzbicki, R.E.Honkanen. Crystal Structures and Mutagenesis of Ppp-Family Ser/Thr Protein Phosphatases Elucidate the Selectivity of Cantharidin and Novel Norcantharidin-Based Inhibitors of PP5C. Biochem. Pharmacol. V. 109 14 2016.
ISSN: ISSN 1873-2968
PubMed: 27002182
DOI: 10.1016/J.BCP.2016.03.011
Page generated: Tue Dec 15 04:34:50 2020

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