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Manganese in PDB 2enx: Structure of the Family II Inorganic Pyrophosphatase From Streptococcus Agalactiae at 2.8 Resolution

Enzymatic activity of Structure of the Family II Inorganic Pyrophosphatase From Streptococcus Agalactiae at 2.8 Resolution

All present enzymatic activity of Structure of the Family II Inorganic Pyrophosphatase From Streptococcus Agalactiae at 2.8 Resolution:
3.6.1.1;

Protein crystallography data

The structure of Structure of the Family II Inorganic Pyrophosphatase From Streptococcus Agalactiae at 2.8 Resolution, PDB code: 2enx was solved by M.K.Rantanen, L.Lehtio, L.Rajagopal, C.E.Rubens, A.Goldman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.50 / 2.80
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.960, 181.960, 132.610, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 26.7

Other elements in 2enx:

The structure of Structure of the Family II Inorganic Pyrophosphatase From Streptococcus Agalactiae at 2.8 Resolution also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of the Family II Inorganic Pyrophosphatase From Streptococcus Agalactiae at 2.8 Resolution (pdb code 2enx). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Structure of the Family II Inorganic Pyrophosphatase From Streptococcus Agalactiae at 2.8 Resolution, PDB code: 2enx:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 2enx

Go back to Manganese Binding Sites List in 2enx
Manganese binding site 1 out of 4 in the Structure of the Family II Inorganic Pyrophosphatase From Streptococcus Agalactiae at 2.8 Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of the Family II Inorganic Pyrophosphatase From Streptococcus Agalactiae at 2.8 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:17.9
occ:1.00
 OD1 A:ASP77 1.8 17.7 1.0
OD2 A:ASP13 2.5 17.7 1.0
NE2 A:HIS9 2.5 18.0 1.0
O5 A:2PN1001 2.7 18.1 1.0
CG A:ASP77 2.8 17.9 1.0
MN A:MN402 3.1 18.2 1.0
CG A:ASP13 3.2 18.6 1.0
OD2 A:ASP77 3.3 17.9 1.0
OD1 A:ASP13 3.3 18.1 1.0
P2 A:2PN1001 3.4 18.2 1.0
CD2 A:HIS9 3.4 17.7 1.0
CE1 A:HIS9 3.4 17.9 1.0
O4 A:2PN1001 3.6 18.1 1.0
O6 A:2PN1001 3.7 17.8 1.0
CB A:ALA16 3.9 18.0 1.0
N A:ALA16 4.0 18.3 1.0
CB A:ASP77 4.1 18.2 1.0
CA A:ALA16 4.3 17.8 1.0
CB A:ASP15 4.4 18.2 1.0
OD2 A:ASP15 4.4 18.0 1.0
NZ A:LYS207 4.4 18.1 1.0
O A:ASP77 4.4 17.7 1.0
ND1 A:HIS9 4.6 18.6 1.0
CG A:HIS9 4.6 18.1 1.0
OD1 A:ASP151 4.6 17.9 1.0
CB A:ASP13 4.7 18.3 1.0
CE1 A:HIS100 4.7 18.4 1.0
C A:ASP15 4.8 17.8 1.0
CG A:ASP15 4.9 18.6 1.0
N1 A:2PN1001 4.9 18.5 1.0
OD2 A:ASP151 5.0 18.4 1.0
MG A:MG501 5.0 17.7 1.0

Manganese binding site 2 out of 4 in 2enx

Go back to Manganese Binding Sites List in 2enx
Manganese binding site 2 out of 4 in the Structure of the Family II Inorganic Pyrophosphatase From Streptococcus Agalactiae at 2.8 Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of the Family II Inorganic Pyrophosphatase From Streptococcus Agalactiae at 2.8 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:18.2
occ:1.00
 O4 A:2PN1001 2.0 18.1 1.0
OD2 A:ASP15 2.1 18.0 1.0
OD2 A:ASP77 2.3 17.9 1.0
OD2 A:ASP151 2.4 18.4 1.0
NE2 A:HIS99 2.5 18.1 1.0
P2 A:2PN1001 3.1 18.2 1.0
MN A:MN401 3.1 17.9 1.0
CG A:ASP15 3.1 18.6 1.0
CE1 A:HIS99 3.1 18.4 1.0
CG A:ASP77 3.1 17.9 1.0
CG A:ASP151 3.2 18.6 1.0
OD1 A:ASP77 3.3 17.7 1.0
OD1 A:ASP151 3.4 17.9 1.0
O6 A:2PN1001 3.4 17.8 1.0
CB A:ASP15 3.4 18.2 1.0
CD2 A:HIS99 3.7 18.5 1.0
O5 A:2PN1001 3.8 18.1 1.0
CE1 A:HIS100 4.3 18.4 1.0
OD1 A:ASP15 4.3 17.9 1.0
ND1 A:HIS99 4.4 18.3 1.0
N A:ALA121 4.4 18.5 1.0
CB A:ASP77 4.5 18.2 1.0
N1 A:2PN1001 4.5 18.5 1.0
CB A:ASP151 4.5 17.9 1.0
CG A:HIS99 4.7 18.0 1.0
OD1 A:ASP13 4.7 18.1 1.0
CA A:SER120 4.7 17.8 1.0
CA A:ASP15 4.8 17.9 1.0
NE2 A:HIS100 4.8 17.8 1.0
CB A:ALA121 4.9 17.7 1.0
CB A:SER120 4.9 18.4 1.0
C A:ASP15 5.0 17.8 1.0

Manganese binding site 3 out of 4 in 2enx

Go back to Manganese Binding Sites List in 2enx
Manganese binding site 3 out of 4 in the Structure of the Family II Inorganic Pyrophosphatase From Streptococcus Agalactiae at 2.8 Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of the Family II Inorganic Pyrophosphatase From Streptococcus Agalactiae at 2.8 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn403

b:18.6
occ:1.00
 O5 B:2PN1002 1.9 18.0 1.0
OD1 B:ASP77 2.0 18.6 1.0
OD2 B:ASP13 2.0 17.8 1.0
NE2 B:HIS9 2.6 18.1 1.0
CG B:ASP13 2.7 17.7 1.0
OD1 B:ASP13 2.8 17.9 1.0
CG B:ASP77 2.9 18.1 1.0
P2 B:2PN1002 3.0 18.3 1.0
OD2 B:ASP77 3.2 18.6 1.0
MN B:MN404 3.3 18.1 1.0
O4 B:2PN1002 3.3 18.6 1.0
CD2 B:HIS9 3.5 18.5 1.0
CE1 B:HIS9 3.7 18.5 1.0
O6 B:2PN1002 3.8 18.3 1.0
NZ B:LYS207 4.0 18.2 1.0
CB B:ASP13 4.1 18.0 1.0
CB B:ASP77 4.2 18.4 1.0
CB B:ALA16 4.3 18.4 1.0
CB B:ASP15 4.4 17.9 1.0
N B:ALA16 4.4 18.0 1.0
N1 B:2PN1002 4.4 17.8 1.0
OD1 B:ASP151 4.5 18.0 1.0
OD2 B:ASP15 4.5 17.7 1.0
CE1 B:HIS100 4.5 18.2 1.0
OD2 B:ASP151 4.6 18.5 1.0
CE B:LYS207 4.7 18.2 1.0
O B:ASP77 4.7 18.0 1.0
CG B:HIS9 4.7 18.1 1.0
ND1 B:HIS9 4.8 17.7 1.0
CA B:ALA16 4.9 17.7 1.0
NE2 B:HIS100 4.9 18.6 1.0
O B:HOH2099 4.9 18.2 1.0
CG B:ASP151 5.0 18.5 1.0
O B:HOH2105 5.0 18.2 1.0
CG B:ASP15 5.0 18.4 1.0

Manganese binding site 4 out of 4 in 2enx

Go back to Manganese Binding Sites List in 2enx
Manganese binding site 4 out of 4 in the Structure of the Family II Inorganic Pyrophosphatase From Streptococcus Agalactiae at 2.8 Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of the Family II Inorganic Pyrophosphatase From Streptococcus Agalactiae at 2.8 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn404

b:18.1
occ:1.00
 OD2 B:ASP151 2.1 18.5 1.0
OD2 B:ASP15 2.1 17.7 1.0
O4 B:2PN1002 2.3 18.6 1.0
NE2 B:HIS99 2.3 17.9 1.0
OD2 B:ASP77 2.5 18.6 1.0
OD1 B:ASP77 2.9 18.6 1.0
CG B:ASP77 3.0 18.1 1.0
CG B:ASP15 3.0 18.4 1.0
CE1 B:HIS99 3.1 17.7 1.0
CG B:ASP151 3.1 18.5 1.0
MN B:MN403 3.3 18.6 1.0
CD2 B:HIS99 3.4 18.1 1.0
CB B:ASP15 3.4 17.9 1.0
P2 B:2PN1002 3.4 18.3 1.0
OD1 B:ASP151 3.6 18.0 1.0
O5 B:2PN1002 3.8 18.0 1.0
OD2 B:ASP13 4.1 17.8 1.0
O6 B:2PN1002 4.1 18.3 1.0
OD1 B:ASP15 4.1 18.0 1.0
CE1 B:HIS100 4.2 18.2 1.0
ND1 B:HIS99 4.3 18.2 1.0
CB B:ASP77 4.3 18.4 1.0
CG B:HIS99 4.4 18.4 1.0
N B:ALA121 4.4 17.9 1.0
CB B:ASP151 4.4 17.7 1.0
CA B:SER120 4.7 17.7 1.0
NZ B:LYS298 4.8 18.6 1.0
N1 B:2PN1002 4.8 17.8 1.0
NE2 B:HIS100 4.8 18.6 1.0
CA B:ASP15 4.8 17.7 1.0
CB B:SER120 4.9 17.8 1.0
CB B:ALA121 4.9 18.2 1.0

Reference:

M.K.Rantanen, L.Lehtio, L.Rajagopal, C.E.Rubens, A.Goldman. Structure of the Streptococcus Agalactiae Family II Inorganic Pyrophosphatase at 2.80 A Resolution Acta Crystallogr.,Sect.D V. 63 738 2007.
ISSN: ISSN 0907-4449
PubMed: 17505113
DOI: 10.1107/S0907444907019695
Page generated: Sat Oct 5 13:58:46 2024

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