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Manganese in PDB 1wpn: Crystal Structure of the N-Terminal Core of Bacillus Subtilis Inorganic Pyrophosphatase

Enzymatic activity of Crystal Structure of the N-Terminal Core of Bacillus Subtilis Inorganic Pyrophosphatase

All present enzymatic activity of Crystal Structure of the N-Terminal Core of Bacillus Subtilis Inorganic Pyrophosphatase:
3.6.1.1;

Protein crystallography data

The structure of Crystal Structure of the N-Terminal Core of Bacillus Subtilis Inorganic Pyrophosphatase, PDB code: 1wpn was solved by I.P.Fabrichniy, L.Lehtio, A.Salminen, A.A.Baykov, R.Lahti, A.Goldman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.57 / 1.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.140, 60.970, 74.060, 90.00, 99.99, 90.00
R / Rfree (%) 13.9 / 16.6

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the N-Terminal Core of Bacillus Subtilis Inorganic Pyrophosphatase (pdb code 1wpn). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of the N-Terminal Core of Bacillus Subtilis Inorganic Pyrophosphatase, PDB code: 1wpn:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1wpn

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Manganese binding site 1 out of 4 in the Crystal Structure of the N-Terminal Core of Bacillus Subtilis Inorganic Pyrophosphatase


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 the N-Terminal Core of Bacillus Subtilis Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:9.7
occ:1.00
 O A:HOH704 2.1 10.4 1.0
OD1 A:ASP13 2.1 11.0 1.0
O A:HOH772 2.2 15.9 1.0
OD1 A:ASP75 2.2 7.4 1.0
NE2 A:HIS9 2.3 8.0 1.0
OD2 A:ASP13 2.7 10.0 1.0
CG A:ASP13 2.8 8.7 1.0
CG A:ASP75 3.1 7.4 1.0
CD2 A:HIS9 3.2 8.9 1.0
CE1 A:HIS9 3.3 8.1 1.0
OD2 A:ASP75 3.4 7.8 1.0
MN A:MN602 3.7 8.1 1.0
O A:HOH730 4.0 16.7 1.0
OG1 A:THR16 4.1 8.9 1.0
O A:HOH858 4.2 31.7 1.0
CB A:ASP13 4.3 9.2 1.0
O A:HOH800 4.3 35.8 1.0
O A:ASP75 4.4 8.3 1.0
CG A:HIS9 4.4 7.7 1.0
ND1 A:HIS9 4.4 8.5 1.0
CB A:ASP75 4.5 7.8 1.0
OD1 A:ASP149 4.5 11.5 1.0
CB A:THR16 4.5 8.4 1.0
O A:HOH755 4.6 14.1 1.0
CB A:ASP15 4.6 9.2 1.0
N A:THR16 4.6 7.6 1.0
CE1 A:HIS98 4.7 9.3 1.0
O A:HOH712 4.9 10.3 1.0
OD2 A:ASP15 4.9 8.5 1.0
NE2 A:HIS98 4.9 11.1 1.0

Manganese binding site 2 out of 4 in 1wpn

Go back to Manganese Binding Sites List in 1wpn
Manganese binding site 2 out of 4 in the Crystal Structure of the N-Terminal Core of Bacillus Subtilis Inorganic Pyrophosphatase


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 the N-Terminal Core of Bacillus Subtilis Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:8.1
occ:1.00
 O A:HOH704 2.0 10.4 1.0
OD2 A:ASP15 2.1 8.5 1.0
OD2 A:ASP75 2.2 7.8 1.0
OD2 A:ASP149 2.2 10.1 1.0
NE2 A:HIS97 2.2 8.7 1.0
CG A:ASP15 3.1 8.8 1.0
CG A:ASP75 3.1 7.4 1.0
CE1 A:HIS97 3.1 10.2 1.0
CG A:ASP149 3.2 10.6 1.0
CD2 A:HIS97 3.2 8.0 1.0
CB A:ASP15 3.4 9.2 1.0
OD1 A:ASP149 3.5 11.5 1.0
OD1 A:ASP75 3.5 7.4 1.0
O A:HOH730 3.6 16.7 1.0
MN A:MN601 3.7 9.7 1.0
OG1 A:THR119 4.0 8.7 1.0
CE1 A:HIS98 4.0 9.3 1.0
N A:THR119 4.1 7.4 1.0
OD1 A:ASP15 4.2 9.5 1.0
ND1 A:HIS97 4.3 11.0 1.0
O A:HOH772 4.3 15.9 1.0
CB A:ASP75 4.3 7.8 1.0
CG A:HIS97 4.4 7.3 1.0
NE2 A:HIS98 4.4 11.1 1.0
CA A:CYS118 4.4 9.0 1.0
CB A:ASP149 4.5 10.1 1.0
O A:GLY117 4.8 13.0 1.0
C A:CYS118 4.8 9.2 1.0
CA A:ASP15 4.8 7.9 1.0
CB A:THR119 4.9 7.8 1.0
CA A:ASP75 5.0 7.2 1.0
SG A:CYS118 5.0 11.0 1.0

Manganese binding site 3 out of 4 in 1wpn

Go back to Manganese Binding Sites List in 1wpn
Manganese binding site 3 out of 4 in the Crystal Structure of the N-Terminal Core of Bacillus Subtilis Inorganic Pyrophosphatase


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 the N-Terminal Core of Bacillus Subtilis Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn603

b:8.0
occ:1.00
 O B:HOH605 2.1 8.6 1.0
O B:HOH665 2.1 13.6 1.0
OD1 B:ASP75 2.2 6.3 1.0
OD1 B:ASP13 2.2 9.4 1.0
NE2 B:HIS9 2.3 8.0 1.0
OD2 B:ASP13 2.6 8.3 1.0
CG B:ASP13 2.8 8.7 1.0
CG B:ASP75 3.2 6.6 1.0
CD2 B:HIS9 3.2 7.3 1.0
CE1 B:HIS9 3.3 8.2 1.0
OD2 B:ASP75 3.4 7.3 1.0
MN B:MN604 3.7 6.7 1.0
O B:HOH645 4.0 12.4 1.0
OG1 B:THR16 4.1 7.7 1.0
CB B:ASP13 4.3 7.4 1.0
O B:HOH730 4.3 29.8 1.0
O B:HOH717 4.3 28.1 1.0
O B:ASP75 4.4 7.0 1.0
CG B:HIS9 4.4 7.5 1.0
ND1 B:HIS9 4.4 7.9 1.0
CB B:ASP75 4.5 6.3 1.0
O B:HOH629 4.5 12.4 1.0
CB B:THR16 4.5 7.3 1.0
OD1 B:ASP149 4.6 8.4 1.0
N B:THR16 4.6 6.6 1.0
CB B:ASP15 4.6 7.3 1.0
CE1 B:HIS98 4.6 8.3 1.0
O B:HOH617 4.9 8.0 1.0
NE2 B:HIS98 4.9 9.6 1.0
OD1 B:ASP15 4.9 7.2 1.0

Manganese binding site 4 out of 4 in 1wpn

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Manganese binding site 4 out of 4 in the Crystal Structure of the N-Terminal Core of Bacillus Subtilis Inorganic Pyrophosphatase


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 the N-Terminal Core of Bacillus Subtilis Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn604

b:6.7
occ:1.00
 O B:HOH605 2.0 8.6 1.0
OD1 B:ASP15 2.1 7.2 1.0
OD2 B:ASP75 2.2 7.3 1.0
OD2 B:ASP149 2.2 8.7 1.0
NE2 B:HIS97 2.2 7.1 1.0
CG B:ASP15 3.1 7.0 1.0
CG B:ASP75 3.1 6.6 1.0
CE1 B:HIS97 3.1 8.9 1.0
CG B:ASP149 3.2 7.0 1.0
CD2 B:HIS97 3.2 6.3 1.0
CB B:ASP15 3.3 7.3 1.0
OD1 B:ASP75 3.4 6.3 1.0
OD1 B:ASP149 3.4 8.4 1.0
O B:HOH645 3.6 12.4 1.0
MN B:MN603 3.7 8.0 1.0
OG1 B:THR119 4.0 7.1 1.0
CE1 B:HIS98 4.0 8.3 1.0
N B:THR119 4.1 6.7 1.0
OD2 B:ASP15 4.2 7.7 1.0
ND1 B:HIS97 4.3 9.7 1.0
CG B:HIS97 4.3 6.6 1.0
CB B:ASP75 4.4 6.3 1.0
O B:HOH665 4.4 13.6 1.0
NE2 B:HIS98 4.4 9.6 1.0
CA B:CYS118 4.5 7.4 1.0
CB B:ASP149 4.5 8.5 1.0
O B:GLY117 4.8 10.0 1.0
C B:CYS118 4.8 7.3 1.0
CA B:ASP15 4.8 6.5 1.0
CB B:THR119 4.9 6.2 1.0
OD2 B:ASP13 4.9 8.3 1.0
SG B:CYS118 5.0 9.0 1.0

Reference:

I.P.Fabrichniy, L.Lehtio, A.Salminen, A.B.Zyryanov, A.A.Baykov, R.Lahti, A.Goldman. Structural Studies of Metal Ions in Family II Pyrophosphatases: the Requirement For A Janus Ion Biochemistry V. 43 14403 2004.
ISSN: ISSN 0006-2960
PubMed: 15533045
DOI: 10.1021/BI0484973
Page generated: Sat Oct 5 12:57:00 2024

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