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Manganese in PDB 3rl4: Rat Metallophosphodiesterase MPPED2 G252H Mutant

Protein crystallography data

The structure of Rat Metallophosphodiesterase MPPED2 G252H Mutant, PDB code: 3rl4 was solved by M.Podobnik, U.Dermol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.68 / 1.29
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 98.060, 69.385, 47.234, 90.00, 102.96, 90.00
R / Rfree (%) 16.5 / 19.1

Other elements in 3rl4:

The structure of Rat Metallophosphodiesterase MPPED2 G252H Mutant also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Rat Metallophosphodiesterase MPPED2 G252H Mutant (pdb code 3rl4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Rat Metallophosphodiesterase MPPED2 G252H Mutant, PDB code: 3rl4:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3rl4

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Manganese binding site 1 out of 8 in the Rat Metallophosphodiesterase MPPED2 G252H Mutant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Rat Metallophosphodiesterase MPPED2 G252H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn444

b:15.0
occ:1.00
 OD1 A:ASP65 2.1 16.2 1.0
O A:HOH467 2.1 19.6 1.0
O2P A:5GP951 2.1 17.3 0.9
NE2 A:HIS67 2.2 14.7 1.0
NE2 A:HIS254 2.2 16.1 1.0
OD2 A:ASP86 2.2 14.6 1.0
CE1 A:HIS67 3.0 16.2 1.0
CE1 A:HIS254 3.1 15.3 1.0
CG A:ASP65 3.2 14.4 1.0
CG A:ASP86 3.3 13.2 1.0
CD2 A:HIS254 3.3 15.4 1.0
CD2 A:HIS67 3.3 15.1 1.0
P A:5GP951 3.3 18.4 0.9
MN A:MN555 3.4 14.3 1.0
CB A:ASP86 3.5 14.0 1.0
CB A:ASP65 3.7 13.9 1.0
O1P A:5GP951 3.7 16.1 0.9
O5' A:5GP951 3.9 16.7 0.9
ND1 A:HIS67 4.2 18.4 1.0
OD2 A:ASP65 4.2 15.7 1.0
ND1 A:HIS254 4.3 15.7 1.0
O A:HIS252 4.3 14.6 1.0
CG A:HIS67 4.4 16.4 1.0
CA A:ASP65 4.4 13.5 1.0
CG A:HIS254 4.4 14.8 1.0
OD1 A:ASP86 4.4 13.9 1.0
C5' A:5GP951 4.5 17.6 0.9
NE2 A:HIS213 4.6 13.8 1.0
O3P A:5GP951 4.6 18.6 0.9
CE1 A:HIS213 4.6 12.9 1.0
CD2 A:HIS118 4.6 14.6 1.0
CA A:HIS252 4.7 13.1 1.0
NE2 A:HIS118 4.8 15.2 1.0
CZ A:PHE277 4.9 22.8 1.0
C A:HIS252 4.9 13.8 1.0
CE2 A:PHE277 4.9 23.6 1.0

Manganese binding site 2 out of 8 in 3rl4

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Manganese binding site 2 out of 8 in the Rat Metallophosphodiesterase MPPED2 G252H Mutant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Rat Metallophosphodiesterase MPPED2 G252H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn555

b:14.3
occ:1.00
 O A:HOH467 1.9 19.6 1.0
OD1 A:ASN117 2.1 15.8 1.0
O1P A:5GP951 2.2 16.1 0.9
NE2 A:HIS213 2.2 13.8 1.0
OD2 A:ASP86 2.3 14.6 1.0
ND1 A:HIS252 2.3 15.0 1.0
CE1 A:HIS252 3.1 16.0 1.0
CG A:ASN117 3.2 14.3 1.0
CG A:ASP86 3.2 13.2 1.0
CD2 A:HIS213 3.2 12.7 1.0
CE1 A:HIS213 3.2 12.9 1.0
P A:5GP951 3.3 18.4 0.9
MN A:MN444 3.4 15.0 1.0
CG A:HIS252 3.4 13.6 1.0
OD1 A:ASP86 3.5 13.9 1.0
ND2 A:ASN117 3.6 17.2 1.0
O2P A:5GP951 3.6 17.3 0.9
CA A:HIS252 3.7 13.1 1.0
OD1 A:ASP65 3.8 16.2 1.0
CB A:HIS252 3.9 13.4 1.0
O5' A:5GP951 4.1 16.7 0.9
O A:HIS252 4.1 14.6 1.0
NE2 A:HIS252 4.3 15.5 1.0
ND1 A:HIS213 4.3 13.2 1.0
CG A:HIS213 4.4 13.5 1.0
C A:HIS252 4.4 13.8 1.0
CB A:ASP86 4.4 14.0 1.0
N A:ASN117 4.4 13.9 1.0
CD2 A:HIS118 4.5 14.6 1.0
CD2 A:HIS252 4.5 15.3 1.0
CB A:ASN117 4.5 14.8 1.0
O3P A:5GP951 4.5 18.6 0.9
N A:HIS252 4.7 13.1 1.0
CG A:ASP65 4.9 14.4 1.0
CA A:ASN117 5.0 14.1 1.0

Manganese binding site 3 out of 8 in 3rl4

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Manganese binding site 3 out of 8 in the Rat Metallophosphodiesterase MPPED2 G252H Mutant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Rat Metallophosphodiesterase MPPED2 G252H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn666

b:19.3
occ:1.00
 O A:HOH532 2.0 26.0 1.0
OE1 A:GLU147 2.0 20.6 0.5
OD1 A:ASP150 2.1 18.1 1.0
O A:GLU147 2.2 20.8 1.0
CD A:GLU147 3.0 21.8 0.5
CG A:ASP150 3.2 17.3 1.0
C A:GLU147 3.3 21.7 1.0
OD2 A:ASP150 3.5 18.2 1.0
CG A:GLU147 3.6 22.3 0.5
OD1 A:ASN151 3.7 22.5 1.0
CA A:GLU147 3.9 23.1 1.0
CG A:ASN151 3.9 21.7 1.0
OE2 A:GLU147 4.0 21.7 0.5
O A:HOH533 4.2 38.4 1.0
CB A:GLU147 4.3 23.1 1.0
ND2 A:ASN151 4.4 21.6 1.0
N A:ASP148 4.4 21.4 1.0
N A:ASN151 4.4 20.0 1.0
N A:ASP150 4.5 17.8 1.0
CB A:ASN151 4.5 21.7 1.0
CB A:ASP150 4.5 17.8 1.0
C A:ASP148 4.6 20.7 1.0
CA A:ASP148 4.7 21.5 1.0
N A:PHE149 4.8 19.4 1.0
CA A:ASP150 4.8 18.1 1.0
O A:ASP148 4.9 20.8 1.0
C A:ASP150 5.0 19.2 1.0

Manganese binding site 4 out of 8 in 3rl4

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Manganese binding site 4 out of 8 in the Rat Metallophosphodiesterase MPPED2 G252H Mutant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Rat Metallophosphodiesterase MPPED2 G252H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn771

b:28.4
occ:0.30
 O A:HOH499 2.0 54.1 1.0
O A:HOH564 2.1 41.1 1.0
O A:HOH500 2.2 28.9 1.0
O A:HOH498 2.2 45.7 1.0
OE2 A:GLU109 2.3 27.1 1.0
CD A:GLU109 3.2 22.4 1.0
OE1 A:GLU109 3.4 25.8 1.0
O A:HOH465 3.8 49.4 1.0
O A:HOH543 4.2 43.4 1.0
OH A:TYR110 4.4 23.4 1.0
CG A:GLU109 4.6 21.6 1.0

Manganese binding site 5 out of 8 in 3rl4

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Manganese binding site 5 out of 8 in the Rat Metallophosphodiesterase MPPED2 G252H Mutant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Rat Metallophosphodiesterase MPPED2 G252H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn772

b:23.6
occ:0.30
 O A:HOH509 2.0 31.8 1.0
OD2 A:ASP45 2.4 26.0 1.0
O A:HOH508 2.6 41.2 1.0
CG A:ASP45 3.4 24.1 1.0
OD1 A:ASP45 3.6 27.6 1.0
CB A:ASP45 4.7 21.8 1.0
O A:HOH376 4.9 27.2 1.0

Manganese binding site 6 out of 8 in 3rl4

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Manganese binding site 6 out of 8 in the Rat Metallophosphodiesterase MPPED2 G252H Mutant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Rat Metallophosphodiesterase MPPED2 G252H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn773

b:27.8
occ:0.40
 O A:HOH563 2.0 47.3 1.0
MN A:MN774 2.2 24.7 0.4
OD1 A:ASP208 2.2 19.4 1.0
O A:HOH590 2.5 27.4 1.0
CG A:ASP208 3.2 16.6 1.0
OD2 A:ASP208 3.5 16.6 1.0
O A:HOH406 3.7 29.8 1.0
O A:GLY206 4.4 17.9 1.0
CB A:ASP208 4.5 15.1 1.0
CB A:PRO291 4.9 25.6 1.0
CG A:PRO291 5.0 25.1 1.0

Manganese binding site 7 out of 8 in 3rl4

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Manganese binding site 7 out of 8 in the Rat Metallophosphodiesterase MPPED2 G252H Mutant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Rat Metallophosphodiesterase MPPED2 G252H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn774

b:24.7
occ:0.40
 MN A:MN773 2.2 27.8 0.4
O A:GLY206 2.4 17.9 1.0
OD1 A:ASP208 2.7 19.4 1.0
O A:HOH590 2.8 27.4 1.0
C A:GLY206 3.4 17.6 1.0
CG A:ASP208 3.5 16.6 1.0
OD2 A:ASP208 3.7 16.6 1.0
CA A:GLY206 3.8 19.4 1.0
O A:HOH332 4.0 23.3 1.0
O A:HOH563 4.0 47.3 1.0
O A:HOH510 4.3 19.1 1.0
N A:ASP208 4.5 14.1 1.0
O A:HOH406 4.5 29.8 1.0
C A:THR207 4.5 14.6 1.0
N A:THR207 4.5 15.8 1.0
O A:THR207 4.7 15.3 1.0
CD A:ARG173 4.7 14.8 1.0
CB A:ASP208 4.7 15.1 1.0
CA A:ASP208 4.8 14.2 1.0
O A:HOH517 4.9 33.2 1.0
CA A:THR207 5.0 14.7 1.0
CG A:ARG173 5.0 14.1 1.0

Manganese binding site 8 out of 8 in 3rl4

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Manganese binding site 8 out of 8 in the Rat Metallophosphodiesterase MPPED2 G252H Mutant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Rat Metallophosphodiesterase MPPED2 G252H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn775

b:17.3
occ:0.35
 O A:HOH510 2.0 19.1 1.0
O A:HOH511 2.1 40.7 1.0
O A:VAL243 2.1 16.2 1.0
O A:GLU205 2.2 24.6 1.0
O A:HOH517 2.3 33.2 1.0
O A:HOH413 2.6 35.9 1.0
C A:GLU205 3.2 22.8 1.0
C A:VAL243 3.2 15.4 1.0
CA A:GLY206 3.8 19.4 1.0
N A:GLY206 3.9 20.9 1.0
CA A:VAL243 4.0 16.0 1.0
O A:ARG244 4.0 15.8 1.0
C A:ARG244 4.3 15.4 1.0
N A:ARG244 4.3 15.4 1.0
CA A:GLU205 4.3 21.8 1.0
O A:ARG242 4.4 17.1 1.0
C A:GLY206 4.4 17.6 1.0
CB A:ARG244 4.5 17.0 1.0
O A:THR207 4.5 15.3 1.0
CG1 A:VAL243 4.5 17.0 1.0
CA A:ARG244 4.5 16.3 1.0
N A:THR207 4.7 15.8 1.0
O A:HOH393 4.8 31.2 1.0
CB A:GLU205 4.8 22.5 1.0
CB A:VAL243 4.9 15.5 1.0
N A:PRO245 5.0 15.2 1.0

Reference:

U.Dermol, V.Janardan, R.Tyagi, S.S.Visweswariah, M.Podobnik. Unique Utilization of A Phosphoprotein Phosphatase Fold By A Mammalian Phosphodiesterase Associated with Wagr Syndrome. J.Mol.Biol. V. 412 481 2011.
ISSN: ISSN 0022-2836
PubMed: 21824479
DOI: 10.1016/J.JMB.2011.07.060
Page generated: Sat Oct 5 17:46:10 2024

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