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Manganese in PDB 5nmp: Isatin Hydrolase A (Iha) From Ralstonia Solanacearum

Protein crystallography data

The structure of Isatin Hydrolase A (Iha) From Ralstonia Solanacearum, PDB code: 5nmp was solved by T.Sommer, K.Bjerregaard-Andersen, J.P.Morth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 99.20 / 2.65
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 164.840, 164.840, 275.890, 90.00, 90.00, 120.00
R / Rfree (%) 16.1 / 19.3

Manganese Binding Sites:

The binding sites of Manganese atom in the Isatin Hydrolase A (Iha) From Ralstonia Solanacearum (pdb code 5nmp). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 10 binding sites of Manganese where determined in the Isatin Hydrolase A (Iha) From Ralstonia Solanacearum, PDB code: 5nmp:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 10 in 5nmp

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Manganese binding site 1 out of 10 in the Isatin Hydrolase A (Iha) From Ralstonia Solanacearum


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Isatin Hydrolase A (Iha) From Ralstonia Solanacearum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:61.8
occ:1.00
 ND1 A:HIS74 2.1 43.6 1.0
OD1 A:ASP80 2.2 53.1 1.0
NE2 A:HIS78 2.2 58.0 1.0
O3 A:SIN302 2.4 95.9 1.0
O4 A:SIN302 2.6 93.8 1.0
C4 A:SIN302 2.8 95.5 1.0
CE1 A:HIS74 3.0 46.3 1.0
CG A:ASP80 3.0 53.8 1.0
NE2 A:GLN226 3.0 58.4 1.0
CD2 A:HIS78 3.0 54.5 1.0
OD2 A:ASP80 3.2 60.4 1.0
CG A:HIS74 3.2 46.6 1.0
CE1 A:HIS78 3.3 56.6 1.0
OE1 A:GLN226 3.4 70.9 1.0
CD A:GLN226 3.4 62.7 1.0
CB A:HIS74 3.6 45.8 1.0
NE2 A:HIS74 4.1 49.0 1.0
CG A:HIS78 4.2 51.4 1.0
CD2 A:HIS74 4.3 49.1 1.0
ND1 A:HIS78 4.3 54.9 1.0
C3 A:SIN302 4.3 91.9 1.0
NE2 A:HIS84 4.3 48.1 1.0
CB A:ASP80 4.5 43.6 1.0
CA A:HIS74 4.5 47.5 1.0
CG A:GLN226 4.5 56.0 1.0
CD2 A:HIS84 4.6 48.4 1.0
NE2 A:HIS214 4.9 65.2 1.0
CA A:ASP80 5.0 41.3 1.0

Manganese binding site 2 out of 10 in 5nmp

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Manganese binding site 2 out of 10 in the Isatin Hydrolase A (Iha) From Ralstonia Solanacearum


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Isatin Hydrolase A (Iha) From Ralstonia Solanacearum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn301

b:54.9
occ:1.00
 OD1 B:ASP80 2.2 61.5 1.0
ND1 B:HIS74 2.2 55.8 1.0
OE1 B:GLN226 2.2 74.0 1.0
NE2 B:HIS78 2.3 58.7 1.0
O1 B:SIN302 2.7 0.8 1.0
CG B:ASP80 2.9 64.7 1.0
CE1 B:HIS74 3.0 54.2 1.0
OD2 B:ASP80 3.0 72.3 1.0
CD2 B:HIS78 3.2 59.7 1.0
CD B:GLN226 3.2 71.8 1.0
CE1 B:HIS78 3.2 57.0 1.0
CG B:HIS74 3.3 59.3 1.0
CB B:HIS74 3.7 59.1 1.0
NE2 B:GLN226 3.8 78.8 1.0
C1 B:SIN302 3.9 97.1 1.0
NE2 B:HIS84 4.1 56.3 1.0
NE2 B:HIS74 4.2 53.6 1.0
CD2 B:HIS74 4.3 57.9 1.0
CD2 B:HIS84 4.3 55.3 1.0
ND1 B:HIS78 4.3 57.2 1.0
CG B:HIS78 4.3 58.7 1.0
CB B:ASP80 4.4 57.2 1.0
CG B:GLN226 4.4 62.5 1.0
O2 B:SIN302 4.7 91.5 1.0
CA B:HIS74 4.7 59.0 1.0
NE2 B:HIS214 4.7 83.6 1.0
C2 B:SIN302 4.9 91.4 1.0

Manganese binding site 3 out of 10 in 5nmp

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Manganese binding site 3 out of 10 in the Isatin Hydrolase A (Iha) From Ralstonia Solanacearum


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Isatin Hydrolase A (Iha) From Ralstonia Solanacearum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn301

b:43.6
occ:1.00
 ND1 C:HIS74 2.1 49.2 1.0
OD1 C:ASP80 2.1 60.8 1.0
NE2 C:HIS78 2.2 50.9 1.0
O2 C:SIN302 2.4 0.6 1.0
CG C:ASP80 2.9 55.8 1.0
OD2 C:ASP80 2.9 56.8 1.0
CE1 C:HIS74 3.0 48.5 1.0
NE2 C:GLN226 3.1 68.4 1.0
C1 C:SIN302 3.1 0.7 1.0
CD2 C:HIS78 3.1 51.0 1.0
CE1 C:HIS78 3.2 43.6 1.0
CG C:HIS74 3.2 50.5 1.0
O1 C:SIN302 3.4 0.5 1.0
CD C:GLN226 3.4 64.4 1.0
OE1 C:GLN226 3.5 67.2 1.0
CB C:HIS74 3.7 50.5 1.0
NE2 C:HIS74 4.1 49.0 1.0
NE2 C:HIS84 4.2 50.8 1.0
CD2 C:HIS74 4.3 50.6 1.0
ND1 C:HIS78 4.3 48.1 1.0
CG C:HIS78 4.3 50.9 1.0
CB C:ASP80 4.3 46.8 1.0
C2 C:SIN302 4.4 0.9 1.0
CG C:GLN226 4.4 55.7 1.0
CD2 C:HIS84 4.4 45.8 1.0
CA C:HIS74 4.6 54.1 1.0
NE2 C:HIS214 4.8 68.4 1.0
CE1 C:HIS84 4.9 51.1 1.0
CA C:ASP80 5.0 44.2 1.0

Manganese binding site 4 out of 10 in 5nmp

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Manganese binding site 4 out of 10 in the Isatin Hydrolase A (Iha) From Ralstonia Solanacearum


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Isatin Hydrolase A (Iha) From Ralstonia Solanacearum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn301

b:57.6
occ:1.00
 O3 D:SIN302 2.1 80.9 1.0
OD1 D:ASP80 2.2 73.6 1.0
O4 D:SIN302 2.2 87.1 1.0
ND1 D:HIS74 2.2 56.7 1.0
OD2 D:ASP80 2.2 69.3 1.0
NE2 D:HIS78 2.2 59.3 1.0
C4 D:SIN302 2.5 87.8 1.0
CG D:ASP80 2.5 66.2 1.0
CD2 D:HIS78 3.0 58.1 1.0
CE1 D:HIS74 3.0 56.1 1.0
NE2 D:GLN226 3.2 76.5 1.0
CG D:HIS74 3.3 55.1 1.0
CE1 D:HIS78 3.3 57.3 1.0
CD D:GLN226 3.4 74.8 1.0
OE1 D:GLN226 3.5 76.3 1.0
CB D:HIS74 3.8 52.2 1.0
C3 D:SIN302 4.0 91.8 1.0
CB D:ASP80 4.0 56.2 1.0
NE2 D:HIS74 4.2 55.0 1.0
CG D:HIS78 4.2 55.0 1.0
ND1 D:HIS78 4.3 55.6 1.0
CD2 D:HIS74 4.4 55.1 1.0
CG D:GLN226 4.4 69.3 1.0
NE2 D:HIS84 4.5 54.1 1.0
CD2 D:HIS84 4.6 53.9 1.0
CA D:HIS74 4.7 53.0 1.0
C2 D:SIN302 4.8 92.2 1.0
CA D:ASP80 4.8 53.8 1.0
NE2 D:HIS214 4.8 71.2 1.0

Manganese binding site 5 out of 10 in 5nmp

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Manganese binding site 5 out of 10 in the Isatin Hydrolase A (Iha) From Ralstonia Solanacearum


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Isatin Hydrolase A (Iha) From Ralstonia Solanacearum within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn301

b:56.4
occ:1.00
 O1 E:SIN302 2.0 0.7 1.0
ND1 E:HIS74 2.2 56.9 1.0
OD1 E:ASP80 2.2 65.3 1.0
NE2 E:HIS78 2.2 55.5 1.0
C1 E:SIN302 2.5 0.8 1.0
O2 E:SIN302 2.6 0.1 1.0
CD2 E:HIS78 3.0 56.7 1.0
CG E:ASP80 3.0 66.4 1.0
CE1 E:HIS74 3.1 57.4 1.0
NE2 E:GLN226 3.1 78.2 1.0
CG E:HIS74 3.2 56.9 1.0
OD2 E:ASP80 3.2 68.0 1.0
CE1 E:HIS78 3.3 55.3 1.0
CD E:GLN226 3.5 79.0 1.0
CB E:HIS74 3.5 56.6 1.0
OE1 E:GLN226 3.6 86.0 1.0
C2 E:SIN302 3.9 0.8 1.0
NE2 E:HIS74 4.2 57.6 1.0
CG E:HIS78 4.2 55.9 1.0
CD2 E:HIS74 4.3 57.5 1.0
ND1 E:HIS78 4.3 55.7 1.0
NE2 E:HIS84 4.4 60.3 1.0
CB E:ASP80 4.5 64.3 1.0
CG E:GLN226 4.5 72.4 1.0
CA E:HIS74 4.5 55.5 1.0
CD2 E:HIS84 4.6 64.8 1.0
NE2 E:HIS214 4.8 83.6 1.0
C3 E:SIN302 5.0 0.3 1.0

Manganese binding site 6 out of 10 in 5nmp

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Manganese binding site 6 out of 10 in the Isatin Hydrolase A (Iha) From Ralstonia Solanacearum


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Isatin Hydrolase A (Iha) From Ralstonia Solanacearum within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn301

b:48.0
occ:1.00
 O3 F:SIN302 2.0 80.9 1.0
O4 F:SIN302 2.0 81.9 1.0
OD1 F:ASP80 2.1 61.7 1.0
NE2 F:HIS78 2.2 46.5 1.0
ND1 F:HIS74 2.2 53.0 1.0
C4 F:SIN302 2.3 86.2 1.0
CD2 F:HIS78 3.0 45.9 1.0
CG F:ASP80 3.0 56.9 1.0
CE1 F:HIS74 3.1 49.4 1.0
OD2 F:ASP80 3.1 57.4 1.0
NE2 F:GLN226 3.2 63.7 1.0
CG F:HIS74 3.2 48.5 1.0
CE1 F:HIS78 3.3 51.5 1.0
CD F:GLN226 3.5 66.5 1.0
CB F:HIS74 3.6 49.0 1.0
OE1 F:GLN226 3.7 72.8 1.0
C3 F:SIN302 3.8 91.2 1.0
CG F:HIS78 4.2 48.6 1.0
NE2 F:HIS74 4.2 50.7 1.0
NE2 F:HIS84 4.3 55.3 1.0
ND1 F:HIS78 4.3 49.6 1.0
CD2 F:HIS74 4.3 49.0 1.0
CB F:ASP80 4.4 51.3 1.0
CG F:GLN226 4.4 61.5 1.0
CD2 F:HIS84 4.5 54.0 1.0
CA F:HIS74 4.5 52.4 1.0
C2 F:SIN302 4.5 95.2 1.0
NE2 F:HIS214 4.8 64.0 1.0
CA F:ASP80 5.0 48.5 1.0
CE1 F:HIS84 5.0 55.1 1.0

Manganese binding site 7 out of 10 in 5nmp

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Manganese binding site 7 out of 10 in the Isatin Hydrolase A (Iha) From Ralstonia Solanacearum


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Isatin Hydrolase A (Iha) From Ralstonia Solanacearum within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn301

b:61.2
occ:1.00
 OD1 G:ASP80 2.2 73.8 1.0
ND1 G:HIS74 2.2 59.8 1.0
O G:HOH417 2.2 70.6 1.0
NE2 G:HIS78 2.2 72.2 1.0
OD2 G:ASP80 2.8 76.6 1.0
CG G:ASP80 2.8 75.0 1.0
CE1 G:HIS74 3.1 63.4 1.0
CE1 G:HIS78 3.2 66.7 1.0
CD2 G:HIS78 3.2 68.5 1.0
CG G:HIS74 3.2 64.6 1.0
NE2 G:GLN226 3.3 80.7 1.0
OE1 G:GLN226 3.5 79.0 1.0
CD G:GLN226 3.5 77.0 1.0
CB G:HIS74 3.6 62.8 1.0
NE2 G:HIS84 4.1 73.0 1.0
NE2 G:HIS74 4.2 65.2 1.0
CD2 G:HIS74 4.3 65.3 1.0
ND1 G:HIS78 4.3 60.6 1.0
CG G:HIS78 4.3 64.0 1.0
CB G:ASP80 4.3 73.5 1.0
CD2 G:HIS84 4.4 72.3 1.0
CA G:HIS74 4.6 63.1 1.0
CG G:GLN226 4.6 71.3 1.0
NE2 G:HIS214 4.6 85.4 1.0
CE1 G:HIS84 5.0 74.1 1.0

Manganese binding site 8 out of 10 in 5nmp

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Manganese binding site 8 out of 10 in the Isatin Hydrolase A (Iha) From Ralstonia Solanacearum


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Isatin Hydrolase A (Iha) From Ralstonia Solanacearum within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn301

b:73.5
occ:1.00
 ND1 H:HIS74 2.1 68.5 1.0
OD1 H:ASP80 2.2 79.5 1.0
NE2 H:HIS78 2.3 75.7 1.0
O4 H:SIN302 2.4 0.2 1.0
NE2 H:GLN226 2.5 96.8 1.0
CE1 H:HIS74 3.0 68.3 1.0
CG H:ASP80 3.0 78.9 1.0
CD2 H:HIS78 3.1 73.1 1.0
OD2 H:ASP80 3.1 83.6 1.0
CG H:HIS74 3.2 69.1 1.0
CE1 H:HIS78 3.3 76.0 1.0
CD H:GLN226 3.3 96.4 1.0
CB H:HIS74 3.6 71.5 1.0
C4 H:SIN302 3.7 0.2 1.0
OE1 H:GLN226 3.7 0.4 1.0
NE2 H:HIS74 4.1 66.2 1.0
CG H:HIS78 4.2 72.6 1.0
NE2 H:HIS84 4.2 71.8 1.0
CD2 H:HIS74 4.3 67.4 1.0
ND1 H:HIS78 4.3 74.1 1.0
O3 H:SIN302 4.3 0.3 1.0
CG H:GLN226 4.4 89.5 1.0
CD2 H:HIS84 4.4 70.7 1.0
CB H:ASP80 4.4 71.0 1.0
CA H:HIS74 4.7 73.0 1.0
C3 H:SIN302 4.7 0.0 1.0
CE1 H:HIS214 4.7 93.2 1.0

Manganese binding site 9 out of 10 in 5nmp

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Manganese binding site 9 out of 10 in the Isatin Hydrolase A (Iha) From Ralstonia Solanacearum


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Isatin Hydrolase A (Iha) From Ralstonia Solanacearum within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn301

b:50.6
occ:1.00
 ND1 I:HIS74 2.1 50.7 1.0
OD1 I:ASP80 2.2 61.8 1.0
NE2 I:HIS78 2.2 50.3 1.0
O3 I:SIN302 2.3 0.2 1.0
O4 I:SIN302 2.5 0.5 1.0
C4 I:SIN302 2.8 0.9 1.0
CG I:ASP80 2.9 59.1 1.0
CE1 I:HIS74 3.0 51.1 1.0
OD2 I:ASP80 3.0 57.5 1.0
CD2 I:HIS78 3.1 52.6 1.0
CG I:HIS74 3.2 52.2 1.0
CE1 I:HIS78 3.2 50.6 1.0
NE2 I:GLN226 3.3 70.2 1.0
CD I:GLN226 3.6 69.4 1.0
OE1 I:GLN226 3.6 75.8 1.0
CB I:HIS74 3.6 52.5 1.0
NE2 I:HIS74 4.1 51.5 1.0
CD2 I:HIS74 4.2 54.5 1.0
CG I:HIS78 4.3 50.8 1.0
C3 I:SIN302 4.3 0.9 1.0
ND1 I:HIS78 4.3 49.5 1.0
NE2 I:HIS84 4.4 60.5 1.0
CB I:ASP80 4.4 55.4 1.0
CD2 I:HIS84 4.5 58.5 1.0
CG I:GLN226 4.6 61.6 1.0
CA I:HIS74 4.6 54.1 1.0
NE2 I:HIS214 4.8 59.7 1.0

Manganese binding site 10 out of 10 in 5nmp

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Manganese binding site 10 out of 10 in the Isatin Hydrolase A (Iha) From Ralstonia Solanacearum


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Isatin Hydrolase A (Iha) From Ralstonia Solanacearum within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn301

b:46.1
occ:1.00
 ND1 J:HIS74 2.2 56.5 1.0
OD1 J:ASP80 2.2 67.7 1.0
NE2 J:HIS78 2.2 52.0 1.0
O J:HOH428 2.2 50.2 1.0
CD2 J:HIS78 3.0 50.1 1.0
CG J:ASP80 3.0 63.2 1.0
CG J:HIS74 3.1 57.9 1.0
CE1 J:HIS74 3.1 53.0 1.0
NE2 J:GLN226 3.1 61.4 1.0
OD2 J:ASP80 3.2 63.2 1.0
CE1 J:HIS78 3.2 51.8 1.0
CB J:HIS74 3.4 46.7 1.0
CD J:GLN226 3.6 61.2 1.0
OE1 J:GLN226 3.8 66.6 1.0
NE2 J:HIS74 4.2 55.2 1.0
CD2 J:HIS74 4.2 56.2 1.0
CG J:HIS78 4.2 50.4 1.0
NE2 J:HIS84 4.3 53.0 1.0
ND1 J:HIS78 4.3 50.5 1.0
CA J:HIS74 4.4 46.2 1.0
CB J:ASP80 4.5 56.1 1.0
CD2 J:HIS84 4.5 53.6 1.0
CG J:GLN226 4.6 54.2 1.0
NE2 J:HIS214 4.8 63.6 1.0

Reference:

T.Sommer, K.Bjerregaard-Andersen, L.Uribe, M.Etzerodt, G.Diezemann, J.Gauss, M.Cascella, J.P.Morth. A Fundamental Catalytic Difference Between Zinc and Manganese Dependent Enzymes Revealed in A Bacterial Isatin Hydrolase. Sci Rep V. 8 13104 2018.
ISSN: ESSN 2045-2322
PubMed: 30166577
DOI: 10.1038/S41598-018-31259-Y
Page generated: Sun Oct 6 02:03:58 2024

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