Atomistry » Manganese » PDB 1w2c-1xie » 1wpn
Atomistry »
  Manganese »
    PDB 1w2c-1xie »
      1wpn »

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

Go back to Manganese Binding Sites List in 1wpn
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

Go back to Manganese Binding Sites List in 1wpn
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy