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Manganese in PDB 3rl3: Rat Metallophosphodiesterase MPPED2

Protein crystallography data

The structure of Rat Metallophosphodiesterase MPPED2, PDB code: 3rl3 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) 47.67 / 1.42
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 97.887, 69.752, 46.984, 90.00, 103.14, 90.00
R / Rfree (%) 16 / 18.7

Other elements in 3rl3:

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

Chlorine (Cl) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Rat Metallophosphodiesterase MPPED2 (pdb code 3rl3). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 9 binding sites of Manganese where determined in the Rat Metallophosphodiesterase MPPED2, PDB code: 3rl3:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Manganese binding site 1 out of 9 in 3rl3

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Manganese binding site 1 out of 9 in the Rat Metallophosphodiesterase MPPED2


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn444

b:12.2
occ:1.00
 O2P A:5GP951 2.1 12.3 0.8
OD1 A:ASP65 2.1 12.6 1.0
NE2 A:HIS67 2.2 12.4 1.0
OD2 A:ASP86 2.2 12.1 1.0
NE2 A:HIS254 2.3 13.7 1.0
O A:HOH415 2.3 15.9 1.0
CE1 A:HIS67 3.0 14.3 1.0
CE1 A:HIS254 3.1 14.4 1.0
CG A:ASP65 3.2 10.9 1.0
CG A:ASP86 3.2 11.9 1.0
P A:5GP951 3.3 14.6 0.8
CD2 A:HIS254 3.4 13.8 1.0
CD2 A:HIS67 3.4 12.5 1.0
MN A:MN555 3.5 14.4 0.9
CB A:ASP86 3.5 11.7 1.0
O1P A:5GP951 3.7 14.2 0.8
CB A:ASP65 3.7 10.6 1.0
O5' A:5GP951 4.0 14.1 0.8
ND1 A:HIS67 4.2 15.1 1.0
OD2 A:ASP65 4.3 12.1 1.0
ND1 A:HIS254 4.3 13.7 1.0
CA A:ASP65 4.4 10.7 1.0
OD1 A:ASP86 4.4 11.7 1.0
C5' A:5GP951 4.4 16.2 0.8
CG A:HIS67 4.4 12.7 1.0
CG A:HIS254 4.4 12.8 1.0
O A:GLY252 4.5 13.2 1.0
CD2 A:HIS118 4.6 11.3 1.0
NE2 A:HIS213 4.6 12.4 1.0
CE1 A:HIS213 4.6 12.0 1.0
O3P A:5GP951 4.6 14.1 0.8
NE2 A:HIS118 4.8 13.0 1.0
CE2 A:PHE277 4.9 25.0 1.0
CZ A:PHE277 4.9 22.7 1.0

Manganese binding site 2 out of 9 in 3rl3

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Manganese binding site 2 out of 9 in the Rat Metallophosphodiesterase MPPED2


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn555

b:14.4
occ:0.90
 OD1 A:ASN117 2.0 19.0 1.0
O1P A:5GP951 2.1 14.2 0.8
O A:HOH349 2.1 18.0 1.0
O A:HOH415 2.2 15.9 1.0
NE2 A:HIS213 2.3 12.4 1.0
OD2 A:ASP86 2.3 12.1 1.0
CG A:ASN117 3.1 14.8 1.0
CG A:ASP86 3.1 11.9 1.0
CD2 A:HIS213 3.2 11.9 1.0
CE1 A:HIS213 3.3 12.0 1.0
P A:5GP951 3.3 14.6 0.8
OD1 A:ASP86 3.4 11.7 1.0
MN A:MN444 3.5 12.2 1.0
ND2 A:ASN117 3.5 18.4 1.0
O2P A:5GP951 3.6 12.3 0.8
OD1 A:ASP65 3.9 12.6 1.0
O5' A:5GP951 4.1 14.1 0.8
O A:GLY252 4.2 13.2 1.0
CA A:GLY252 4.3 12.2 1.0
CD2 A:HIS118 4.3 11.3 1.0
N A:ASN117 4.3 11.6 1.0
CB A:ASN117 4.4 13.3 1.0
ND1 A:HIS213 4.4 10.7 1.0
CG A:HIS213 4.4 10.6 1.0
CB A:ASP86 4.4 11.7 1.0
O3P A:5GP951 4.5 14.1 0.8
O A:HOH371 4.6 23.4 1.0
C A:GLY252 4.7 12.1 1.0
CA A:ASN117 4.9 11.5 1.0
NE2 A:HIS118 4.9 13.0 1.0

Manganese binding site 3 out of 9 in 3rl3

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Manganese binding site 3 out of 9 in the Rat Metallophosphodiesterase MPPED2


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn666

b:16.6
occ:1.00
 OE1 A:GLU147 1.9 18.7 0.5
O A:HOH541 2.0 24.5 1.0
OD1 A:ASP150 2.1 17.4 1.0
O A:GLU147 2.1 18.0 1.0
CD A:GLU147 2.9 18.8 0.5
CG A:ASP150 3.1 16.4 1.0
C A:GLU147 3.2 18.8 1.0
OD2 A:ASP150 3.5 15.4 1.0
CG A:GLU147 3.5 20.1 0.5
OD1 A:ASN151 3.7 21.2 1.0
OE2 A:GLU147 3.8 19.1 0.5
CA A:GLU147 3.9 20.2 1.0
CG A:ASN151 4.0 19.9 1.0
O A:HOH514 4.2 31.9 1.0
CB A:GLU147 4.3 20.1 1.0
N A:ASN151 4.3 18.3 1.0
N A:ASP148 4.4 18.3 1.0
ND2 A:ASN151 4.4 19.3 1.0
N A:ASP150 4.4 15.4 1.0
CB A:ASP150 4.4 16.4 1.0
CB A:ASN151 4.5 20.0 1.0
C A:ASP148 4.6 17.6 1.0
CA A:ASP148 4.7 18.3 1.0
CA A:ASP150 4.8 16.3 1.0
N A:PHE149 4.8 16.7 1.0
O A:ASP148 4.9 16.8 1.0
C A:ASP150 4.9 17.5 1.0

Manganese binding site 4 out of 9 in 3rl3

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Manganese binding site 4 out of 9 in the Rat Metallophosphodiesterase MPPED2


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn771

b:13.7
occ:0.30
 O A:HOH520 1.9 39.6 1.0
O A:HOH326 2.0 16.9 1.0
O A:VAL243 2.1 14.1 1.0
O A:HOH523 2.2 32.4 1.0
O A:GLU205 2.2 22.4 1.0
C A:GLU205 3.2 20.6 1.0
C A:VAL243 3.2 13.9 1.0
O A:HOH473 3.4 43.4 1.0
CA A:GLY206 3.8 16.8 1.0
N A:GLY206 3.8 19.0 1.0
O A:HOH585 4.0 40.1 1.0
CA A:VAL243 4.0 13.5 1.0
O A:ARG244 4.0 14.1 1.0
O A:HOH554 4.3 41.2 1.0
CA A:GLU205 4.3 19.3 1.0
N A:ARG244 4.3 13.9 1.0
C A:ARG244 4.3 13.5 1.0
O A:ARG242 4.4 14.9 1.0
C A:GLY206 4.4 15.3 1.0
CB A:ARG244 4.5 15.1 1.0
O A:THR207 4.5 13.5 1.0
O A:HOH547 4.5 42.5 1.0
CA A:ARG244 4.5 14.9 1.0
CG1 A:VAL243 4.6 14.0 1.0
N A:THR207 4.6 13.8 1.0
CB A:GLU205 4.7 20.0 1.0
O A:HOH583 4.8 27.1 1.0
CB A:VAL243 4.9 12.4 1.0

Manganese binding site 5 out of 9 in 3rl3

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Manganese binding site 5 out of 9 in the Rat Metallophosphodiesterase MPPED2


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn772

b:22.2
occ:0.40
 MN A:MN773 1.9 23.2 0.3
O A:HOH585 2.4 40.1 1.0
O A:GLY206 2.5 15.2 1.0
OD1 A:ASP208 2.6 16.8 1.0
CG A:ASP208 3.4 14.9 1.0
C A:GLY206 3.4 15.3 1.0
OD2 A:ASP208 3.6 14.9 1.0
CA A:GLY206 3.9 16.8 1.0
O A:HOH350 4.3 20.6 1.0
O A:HOH326 4.3 16.9 1.0
O A:HOH584 4.4 25.6 1.0
N A:ASP208 4.4 11.5 1.0
C A:THR207 4.5 12.8 1.0
N A:THR207 4.6 13.8 1.0
O A:THR207 4.6 13.5 1.0
CB A:ASP208 4.6 12.4 1.0
CA A:ASP208 4.7 11.9 1.0
CD A:ARG173 4.8 11.8 1.0
CA A:THR207 5.0 13.1 1.0
O A:HOH523 5.0 32.4 1.0

Manganese binding site 6 out of 9 in 3rl3

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Manganese binding site 6 out of 9 in the Rat Metallophosphodiesterase MPPED2


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn773

b:23.2
occ:0.30
 MN A:MN772 1.9 22.2 0.4
OD1 A:ASP208 2.3 16.8 1.0
O A:HOH585 3.1 40.1 1.0
CG A:ASP208 3.3 14.9 1.0
OD2 A:ASP208 3.5 14.9 1.0
O A:HOH584 3.9 25.6 1.0
O A:GLY206 4.3 15.2 1.0
CB A:ASP208 4.6 12.4 1.0
CB A:PRO291 4.8 22.4 1.0
CG A:PRO291 5.0 22.2 1.0

Manganese binding site 7 out of 9 in 3rl3

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Manganese binding site 7 out of 9 in the Rat Metallophosphodiesterase MPPED2


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn774

b:26.4
occ:0.30
 O A:HOH557 1.8 23.4 1.0
O A:HOH556 2.0 43.7 1.0
OD2 A:ASP45 2.2 28.0 1.0
CG A:ASP45 3.2 22.9 1.0
OD1 A:ASP45 3.5 26.6 1.0
CB A:ASP45 4.6 20.1 1.0
O A:HOH381 4.6 24.0 1.0
O A:HOH475 4.9 40.1 1.0

Manganese binding site 8 out of 9 in 3rl3

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Manganese binding site 8 out of 9 in the Rat Metallophosphodiesterase MPPED2


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn775

b:22.6
occ:0.35
 O A:HOH494 2.2 21.8 1.0
NE2 A:HIS42 2.3 22.6 1.0
O A:HOH566 2.5 40.7 1.0
CD2 A:HIS42 3.2 20.7 1.0
CE1 A:HIS42 3.4 20.7 1.0
O A:HOH450 4.0 34.1 1.0
O A:PRO39 4.2 22.2 1.0
CG2 A:THR261 4.3 14.9 1.0
CG A:HIS42 4.4 18.4 1.0
ND1 A:HIS42 4.4 18.8 1.0
O A:HOH299 4.5 50.5 1.0
O A:HIS40 4.6 17.9 1.0
O A:HOH477 4.9 36.5 1.0

Manganese binding site 9 out of 9 in 3rl3

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Manganese binding site 9 out of 9 in the Rat Metallophosphodiesterase MPPED2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Rat Metallophosphodiesterase MPPED2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn776

b:18.8
occ:0.30
 O A:HOH297 1.7 27.8 1.0
O3P A:5GP951 2.1 14.1 0.8
O A:HOH298 2.4 19.1 0.5
P A:5GP951 3.5 14.6 0.8
O5' A:5GP951 3.7 14.1 0.8
NE1 A:TRP186 3.9 17.3 0.4
ND2 A:ASN184 4.0 29.7 1.0
NE2 A:HIS118 4.1 13.0 1.0
C5' A:5GP951 4.1 16.2 0.8
O4' A:5GP951 4.2 16.9 0.8
O1P A:5GP951 4.2 14.2 0.8
CE2 A:TRP186 4.3 22.0 0.4
CE2 A:PHE183 4.3 27.7 1.0
CZ2 A:TRP186 4.4 19.1 0.4
O A:HOH582 4.5 47.4 1.0
O2P A:5GP951 4.6 12.3 0.8
CE1 A:HIS118 4.7 12.9 1.0
CD1 A:TRP186 4.7 19.5 0.4
C4' A:5GP951 4.8 16.7 0.8
ND2 A:ASN117 4.9 18.4 1.0
CD2 A:PHE183 4.9 27.2 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 17:45:37 2024

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