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Manganese in PDB 4rpa: Crystal Structure of Inorganic Pyrophosphatase From Staphylococcus Aureus in Complex with MN2+

Enzymatic activity of Crystal Structure of Inorganic Pyrophosphatase From Staphylococcus Aureus in Complex with MN2+

All present enzymatic activity of Crystal Structure of Inorganic Pyrophosphatase From Staphylococcus Aureus in Complex with MN2+:
3.6.1.1;

Protein crystallography data

The structure of Crystal Structure of Inorganic Pyrophosphatase From Staphylococcus Aureus in Complex with MN2+, PDB code: 4rpa was solved by C.S.Gajadeera, O.V.Tsodikov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.10
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 99.406, 99.406, 425.285, 90.00, 90.00, 120.00
R / Rfree (%) 22 / 24.9

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Inorganic Pyrophosphatase From Staphylococcus Aureus in Complex with MN2+ (pdb code 4rpa). 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 Inorganic Pyrophosphatase From Staphylococcus Aureus in Complex with MN2+, PDB code: 4rpa:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4rpa

Go back to Manganese Binding Sites List in 4rpa
Manganese binding site 1 out of 4 in the Crystal Structure of Inorganic Pyrophosphatase From Staphylococcus Aureus in Complex with MN2+


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 Inorganic Pyrophosphatase From Staphylococcus Aureus in Complex with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn500

b:30.2
occ:0.50
 OD2 A:ASP15 1.9 31.2 1.0
OD1 A:ASP75 1.9 28.5 1.0
O A:HOH792 1.9 33.0 1.0
OD2 A:ASP149 1.9 38.0 1.0
NE2 A:HIS97 2.0 29.6 1.0
CE1 A:HIS97 2.9 29.0 1.0
CG A:ASP75 2.9 27.2 1.0
CG A:ASP15 3.0 30.8 1.0
CG A:ASP149 3.1 35.9 1.0
CD2 A:HIS97 3.1 28.7 1.0
OD2 A:ASP75 3.3 28.8 1.0
CB A:ASP15 3.4 29.3 1.0
OD1 A:ASP149 3.5 38.3 1.0
O A:HOH692 3.5 43.9 1.0
CE1 A:HIS98 3.7 27.5 1.0
MN A:MN501 3.8 30.1 0.5
NE2 A:HIS98 4.0 27.4 1.0
OG1 A:THR119 4.0 31.4 1.0
O A:HOH794 4.0 57.3 1.0
ND1 A:HIS97 4.0 28.7 1.0
OD1 A:ASP15 4.1 31.6 1.0
CG A:HIS97 4.2 28.1 1.0
N A:THR119 4.2 30.0 1.0
CB A:ASP75 4.3 26.8 1.0
CB A:ASP149 4.4 35.1 1.0
OD2 A:ASP13 4.6 32.3 1.0
CA A:CYS118 4.6 31.9 1.0
O A:HOH793 4.7 68.7 1.0
CB A:THR119 4.7 30.5 1.0
ND1 A:HIS98 4.8 27.3 1.0
CA A:ASP15 4.9 28.5 1.0
CA A:ASP75 4.9 26.4 1.0
C A:CYS118 4.9 31.3 1.0
O A:ASP75 5.0 26.4 1.0
OD1 A:ASP13 5.0 30.1 1.0

Manganese binding site 2 out of 4 in 4rpa

Go back to Manganese Binding Sites List in 4rpa
Manganese binding site 2 out of 4 in the Crystal Structure of Inorganic Pyrophosphatase From Staphylococcus Aureus in Complex with MN2+


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 Inorganic Pyrophosphatase From Staphylococcus Aureus in Complex with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:30.1
occ:0.50
 OD2 A:ASP75 1.9 28.8 1.0
O A:HOH792 1.9 33.0 1.0
OD1 A:ASP13 1.9 30.1 1.0
NE2 A:HIS9 2.0 27.8 1.0
O A:HOH794 2.3 57.3 1.0
OD2 A:ASP13 2.6 32.3 1.0
CG A:ASP13 2.6 29.3 1.0
CE1 A:HIS9 3.0 27.2 1.0
CG A:ASP75 3.0 27.2 1.0
CD2 A:HIS9 3.0 27.2 1.0
O A:HOH628 3.4 53.5 1.0
OD1 A:ASP75 3.5 28.5 1.0
MN A:MN500 3.8 30.2 0.5
CB A:ALA16 4.0 28.0 1.0
N A:ALA16 4.0 28.2 1.0
CB A:ASP13 4.1 29.0 1.0
ND1 A:HIS9 4.1 27.4 1.0
CG A:HIS9 4.2 27.1 1.0
CB A:ASP15 4.2 29.3 1.0
CB A:ASP75 4.3 26.8 1.0
O A:ASP75 4.4 26.4 1.0
CA A:ALA16 4.5 27.7 1.0
O A:HOH692 4.5 43.9 1.0
N A:ASP13 4.5 28.2 1.0
OD2 A:ASP15 4.7 31.2 1.0
NZ A:LYS205 4.7 40.1 1.0
OD1 A:ASP149 4.7 38.3 1.0
CE1 A:HIS98 4.8 27.5 1.0
CA A:ASP13 4.8 28.4 1.0
C A:ASP15 4.8 28.4 1.0
O A:HOH689 4.9 24.1 1.0
CG A:ASP15 4.9 30.8 1.0
OD2 A:ASP149 4.9 38.0 1.0
O A:HOH603 4.9 30.8 1.0
CA A:ASP15 5.0 28.5 1.0

Manganese binding site 3 out of 4 in 4rpa

Go back to Manganese Binding Sites List in 4rpa
Manganese binding site 3 out of 4 in the Crystal Structure of Inorganic Pyrophosphatase From Staphylococcus Aureus in Complex with MN2+


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 Inorganic Pyrophosphatase From Staphylococcus Aureus in Complex with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn500

b:31.6
occ:0.50
 OD2 B:ASP15 1.9 36.5 1.0
OD1 B:ASP75 1.9 29.5 1.0
O B:HOH771 1.9 31.4 1.0
OD2 B:ASP149 1.9 39.6 1.0
NE2 B:HIS97 2.0 31.2 1.0
CE1 B:HIS97 2.8 30.5 1.0
CG B:ASP15 2.9 37.4 1.0
CG B:ASP75 3.0 28.4 1.0
CG B:ASP149 3.1 39.9 1.0
O B:HOH704 3.1 41.5 1.0
CD2 B:HIS97 3.2 30.3 1.0
CB B:ASP15 3.4 36.0 1.0
OD2 B:ASP75 3.4 29.8 1.0
OD1 B:ASP149 3.5 41.3 1.0
MN B:MN501 3.8 29.6 0.5
CE1 B:HIS98 3.8 31.2 1.0
ND1 B:HIS97 4.0 30.1 1.0
OD1 B:ASP15 4.1 37.5 1.0
NE2 B:HIS98 4.1 30.9 1.0
OG1 B:THR119 4.1 35.3 1.0
CG B:HIS97 4.2 29.9 1.0
N B:THR119 4.2 35.4 1.0
CB B:ASP75 4.3 28.2 1.0
CB B:ASP149 4.4 38.6 1.0
CA B:CYS118 4.7 36.4 1.0
CB B:THR119 4.7 35.2 1.0
OD2 B:ASP13 4.8 32.1 1.0
CA B:ASP15 4.8 35.2 1.0
C B:CYS118 5.0 35.8 1.0
OD1 B:ASP13 5.0 32.0 1.0
ND1 B:HIS98 5.0 30.5 1.0
CA B:ASP75 5.0 28.0 1.0
O B:GLY117 5.0 35.2 1.0

Manganese binding site 4 out of 4 in 4rpa

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Manganese binding site 4 out of 4 in the Crystal Structure of Inorganic Pyrophosphatase From Staphylococcus Aureus in Complex with MN2+


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 Inorganic Pyrophosphatase From Staphylococcus Aureus in Complex with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:29.6
occ:0.50
 OD2 B:ASP75 1.9 29.8 1.0
O B:HOH771 1.9 31.4 1.0
OD1 B:ASP13 1.9 32.0 1.0
NE2 B:HIS9 2.0 29.1 1.0
OD2 B:ASP13 2.4 32.1 1.0
CG B:ASP13 2.5 31.8 1.0
CE1 B:HIS9 2.9 28.9 1.0
CG B:ASP75 3.0 28.4 1.0
CD2 B:HIS9 3.0 29.0 1.0
OD1 B:ASP75 3.5 29.5 1.0
MN B:MN500 3.8 31.6 0.5
CB B:ASP13 4.0 31.9 1.0
CB B:ALA16 4.0 33.6 1.0
N B:ALA16 4.1 33.7 1.0
ND1 B:HIS9 4.1 28.9 1.0
CG B:HIS9 4.2 28.7 1.0
CB B:ASP15 4.2 36.0 1.0
O B:HOH704 4.2 41.5 1.0
CB B:ASP75 4.3 28.2 1.0
O B:ASP75 4.3 27.1 1.0
N B:ASP13 4.5 30.9 1.0
CA B:ALA16 4.5 33.6 1.0
OD2 B:ASP15 4.6 36.5 1.0
CE1 B:HIS98 4.7 31.2 1.0
OD1 B:ASP149 4.8 41.3 1.0
CA B:ASP13 4.8 31.6 1.0
C B:ASP15 4.8 34.5 1.0
CG B:ASP15 4.9 37.4 1.0
O B:HOH662 4.9 21.4 1.0
OD2 B:ASP149 4.9 39.6 1.0
O B:HOH604 5.0 28.2 1.0
CA B:ASP15 5.0 35.2 1.0
NZ B:LYS205 5.0 38.9 1.0

Reference:

C.S.Gajadeera, X.Zhang, Y.Wei, O.V.Tsodikov. Structure of Inorganic Pyrophosphatase From Staphylococcus Aureus Reveals Conformational Flexibility of the Active Site. J.Struct.Biol. 2015.
ISSN: ESSN 1095-8657
PubMed: 25576794
DOI: 10.1016/J.JSB.2014.12.003
Page generated: Sat Oct 5 21:11:21 2024

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