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Manganese in PDB 5k8o: MN2+/5NSA-Bound 5-Nitroanthranilate Aminohydrolase

Enzymatic activity of MN2+/5NSA-Bound 5-Nitroanthranilate Aminohydrolase

All present enzymatic activity of MN2+/5NSA-Bound 5-Nitroanthranilate Aminohydrolase:
3.5.99.8;

Protein crystallography data

The structure of MN2+/5NSA-Bound 5-Nitroanthranilate Aminohydrolase, PDB code: 5k8o was solved by S.Kalyoncu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.83 / 2.89
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 186.773, 249.338, 249.184, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 21.8

Manganese Binding Sites:

The binding sites of Manganese atom in the MN2+/5NSA-Bound 5-Nitroanthranilate Aminohydrolase (pdb code 5k8o). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the MN2+/5NSA-Bound 5-Nitroanthranilate Aminohydrolase, PDB code: 5k8o:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 5k8o

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Manganese binding site 1 out of 8 in the MN2+/5NSA-Bound 5-Nitroanthranilate Aminohydrolase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of MN2+/5NSA-Bound 5-Nitroanthranilate Aminohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:37.8
occ:1.00
 OAJ A:6R7502 1.8 44.0 0.9
OE1 A:GLU196 2.1 47.6 1.0
OE2 A:GLU196 2.1 40.3 1.0
OD1 A:ASN124 2.1 39.6 1.0
NE2 A:HIS86 2.3 38.2 1.0
CD A:GLU196 2.4 41.1 1.0
CAI A:6R7502 2.6 43.5 1.0
OAA A:6R7502 2.9 44.8 0.8
CG A:ASN124 3.0 40.2 1.0
OE1 A:GLU158 3.1 44.1 1.0
CE1 A:HIS86 3.2 37.1 1.0
CD2 A:HIS86 3.2 37.1 1.0
ND2 A:ASN124 3.3 41.0 1.0
CAD A:6R7502 3.4 44.9 1.0
CAH A:6R7502 3.5 42.7 1.0
CAB A:6R7502 3.5 49.4 0.7
CD A:GLU158 3.8 38.8 1.0
CG A:GLU196 3.9 40.2 1.0
OE2 A:GLU158 4.1 41.1 1.0
ND1 A:HIS86 4.3 41.6 1.0
CG A:HIS86 4.3 35.9 1.0
CB A:ASN124 4.4 38.5 1.0
CAE A:6R7502 4.6 46.0 0.6
OAC A:6R7502 4.6 50.7 1.0
CB A:CYS125 4.6 38.1 1.0
CAG A:6R7502 4.6 41.6 0.8
CG A:GLU158 4.7 37.4 1.0
NE A:ARG373 4.8 41.1 1.0
CB A:GLU196 4.8 40.1 1.0
CA A:ASN124 4.9 38.0 1.0
SG A:CYS125 5.0 41.6 1.0

Manganese binding site 2 out of 8 in 5k8o

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Manganese binding site 2 out of 8 in the MN2+/5NSA-Bound 5-Nitroanthranilate Aminohydrolase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of MN2+/5NSA-Bound 5-Nitroanthranilate Aminohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:41.6
occ:1.00
 OAJ B:6R7502 1.8 41.4 0.7
OE2 B:GLU196 2.1 39.4 1.0
OE1 B:GLU196 2.1 43.4 1.0
OD1 B:ASN124 2.2 43.5 1.0
NE2 B:HIS86 2.3 37.5 1.0
CD B:GLU196 2.4 38.6 1.0
CAI B:6R7502 2.6 41.5 1.0
OAC B:6R7502 2.9 46.6 0.8
CG B:ASN124 3.0 39.5 1.0
CE1 B:HIS86 3.1 36.6 1.0
CD2 B:HIS86 3.2 39.2 1.0
ND2 B:ASN124 3.3 40.0 1.0
OE1 B:GLU158 3.3 38.1 1.0
CAD B:6R7502 3.4 41.4 1.0
CAH B:6R7502 3.4 40.6 1.0
CAB B:6R7502 3.5 46.6 0.7
CG B:GLU196 3.9 37.2 1.0
CD B:GLU158 4.0 39.5 1.0
ND1 B:HIS86 4.2 34.9 1.0
CG B:HIS86 4.3 35.8 1.0
CB B:ASN124 4.5 39.3 1.0
OE2 B:GLU158 4.5 53.9 1.0
CAE B:6R7502 4.5 40.0 0.4
CB B:CYS125 4.5 38.6 1.0
CAG B:6R7502 4.6 38.9 1.0
OAA B:6R7502 4.6 43.9 1.0
NE B:ARG373 4.7 38.0 1.0
CB B:GLU196 4.8 36.4 1.0
SG B:CYS125 4.9 43.2 1.0
CG B:GLU158 4.9 38.1 1.0
CA B:ASN124 5.0 38.2 1.0

Manganese binding site 3 out of 8 in 5k8o

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Manganese binding site 3 out of 8 in the MN2+/5NSA-Bound 5-Nitroanthranilate Aminohydrolase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of MN2+/5NSA-Bound 5-Nitroanthranilate Aminohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn501

b:38.5
occ:1.00
 OD1 C:ASN124 2.1 39.4 1.0
OE1 C:GLU196 2.1 43.7 1.0
OE2 C:GLU196 2.1 49.2 1.0
NE2 C:HIS86 2.1 37.1 1.0
OAJ C:6R7502 2.3 51.1 0.7
OAA C:6R7502 2.3 41.7 1.0
CD C:GLU196 2.4 40.6 1.0
CAB C:6R7502 3.0 41.4 1.0
CAI C:6R7502 3.0 42.4 1.0
CG C:ASN124 3.1 39.2 1.0
CE1 C:HIS86 3.1 36.7 1.0
CD2 C:HIS86 3.2 36.4 1.0
CAD C:6R7502 3.3 40.6 1.0
OE1 C:GLU158 3.4 44.2 1.0
ND2 C:ASN124 3.4 49.5 1.0
CG C:GLU196 3.9 38.4 1.0
CD C:GLU158 4.0 36.6 1.0
OAC C:6R7502 4.1 42.2 1.0
CAH C:6R7502 4.1 39.8 1.0
ND1 C:HIS86 4.2 35.0 1.0
CG C:HIS86 4.3 34.8 1.0
CB C:CYS125 4.3 37.0 1.0
CB C:ASN124 4.4 37.2 1.0
OE2 C:GLU158 4.4 39.9 1.0
CAE C:6R7502 4.5 39.7 1.0
SG C:CYS125 4.6 44.6 1.0
CB C:GLU196 4.8 38.6 1.0
NE C:ARG373 4.8 39.9 1.0
CA C:ASN124 4.8 36.9 1.0
CG C:GLU158 4.9 35.5 1.0

Manganese binding site 4 out of 8 in 5k8o

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Manganese binding site 4 out of 8 in the MN2+/5NSA-Bound 5-Nitroanthranilate Aminohydrolase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of MN2+/5NSA-Bound 5-Nitroanthranilate Aminohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn501

b:38.3
occ:1.00
 OAJ D:6R7502 2.0 43.2 0.8
OD1 D:ASN124 2.1 38.6 1.0
OE1 D:GLU196 2.2 38.0 1.0
OE2 D:GLU196 2.2 37.9 1.0
NE2 D:HIS86 2.2 37.3 1.0
OAA D:6R7502 2.3 40.8 0.9
CD D:GLU196 2.5 37.6 1.0
CAI D:6R7502 2.8 40.9 1.0
CAB D:6R7502 2.9 41.3 0.9
CG D:ASN124 3.1 39.6 1.0
CE1 D:HIS86 3.1 36.9 1.0
CAD D:6R7502 3.1 41.5 1.0
OE1 D:GLU158 3.2 45.8 1.0
CD2 D:HIS86 3.3 35.6 1.0
ND2 D:ASN124 3.4 39.5 1.0
CAH D:6R7502 3.9 39.6 1.0
OAC D:6R7502 3.9 49.2 1.0
CG D:GLU196 4.0 37.2 1.0
CD D:GLU158 4.0 36.8 1.0
ND1 D:HIS86 4.2 35.3 1.0
CG D:HIS86 4.3 35.2 1.0
CAE D:6R7502 4.4 41.8 1.0
CB D:ASN124 4.4 40.7 1.0
OE2 D:GLU158 4.5 44.9 1.0
CB D:CYS125 4.5 37.5 1.0
CB D:GLU196 4.8 38.1 1.0
SG D:CYS125 4.8 38.9 1.0
CA D:ASN124 4.9 40.6 1.0
NE D:ARG373 4.9 41.6 1.0
CAG D:6R7502 4.9 43.1 0.0

Manganese binding site 5 out of 8 in 5k8o

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Manganese binding site 5 out of 8 in the MN2+/5NSA-Bound 5-Nitroanthranilate Aminohydrolase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of MN2+/5NSA-Bound 5-Nitroanthranilate Aminohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn501

b:38.8
occ:1.00
 OAJ E:6R7502 1.7 37.9 0.7
OE1 E:GLU196 2.1 43.9 1.0
OE2 E:GLU196 2.1 35.8 1.0
OD1 E:ASN124 2.1 34.5 1.0
NE2 E:HIS86 2.3 35.2 1.0
CD E:GLU196 2.4 36.0 1.0
CAI E:6R7502 2.6 37.5 1.0
OAA E:6R7502 3.0 38.3 1.0
CG E:ASN124 3.2 33.6 1.0
CE1 E:HIS86 3.2 33.5 1.0
OE1 E:GLU158 3.3 41.0 1.0
CD2 E:HIS86 3.3 35.1 1.0
CAH E:6R7502 3.4 36.6 1.0
CAD E:6R7502 3.5 37.7 1.0
ND2 E:ASN124 3.5 34.3 1.0
CAB E:6R7502 3.6 41.5 0.8
CG E:GLU196 3.9 36.4 1.0
CD E:GLU158 3.9 36.1 1.0
OE2 E:GLU158 4.2 48.1 1.0
ND1 E:HIS86 4.4 33.2 1.0
CB E:CYS125 4.4 31.2 1.0
CG E:HIS86 4.4 33.8 1.0
CB E:ASN124 4.5 32.4 1.0
CAG E:6R7502 4.6 35.2 0.9
CAE E:6R7502 4.7 36.1 0.5
SG E:CYS125 4.7 30.2 1.0
OAC E:6R7502 4.7 47.6 0.9
CB E:GLU196 4.7 36.0 1.0
NE E:ARG373 4.8 38.1 1.0
CA E:ASN124 4.9 30.6 1.0
CG E:GLU158 5.0 35.1 1.0

Manganese binding site 6 out of 8 in 5k8o

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Manganese binding site 6 out of 8 in the MN2+/5NSA-Bound 5-Nitroanthranilate Aminohydrolase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of MN2+/5NSA-Bound 5-Nitroanthranilate Aminohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn501

b:33.9
occ:1.00
 OAJ F:6R7502 2.0 33.7 0.9
OD1 F:ASN124 2.0 33.5 1.0
OE1 F:GLU196 2.1 34.5 1.0
OE2 F:GLU196 2.2 45.5 1.0
NE2 F:HIS86 2.3 32.6 1.0
OAC F:6R7502 2.4 34.2 1.0
CD F:GLU196 2.4 34.4 1.0
CAI F:6R7502 2.9 34.1 1.0
CG F:ASN124 3.0 33.0 1.0
CAB F:6R7502 3.1 34.1 0.6
CE1 F:HIS86 3.2 32.1 1.0
CD2 F:HIS86 3.3 32.9 1.0
CAD F:6R7502 3.4 33.9 1.0
ND2 F:ASN124 3.4 32.6 1.0
OE1 F:GLU158 3.5 34.2 1.0
CAH F:6R7502 3.9 33.7 1.0
CG F:GLU196 3.9 34.0 1.0
CD F:GLU158 4.1 34.1 1.0
OAA F:6R7502 4.2 38.0 1.0
CB F:ASN124 4.4 33.5 1.0
ND1 F:HIS86 4.4 31.3 1.0
CB F:CYS125 4.4 39.8 1.0
CG F:HIS86 4.4 31.7 1.0
OE2 F:GLU158 4.6 37.9 1.0
CAE F:6R7502 4.6 33.5 1.0
CB F:GLU196 4.7 34.2 1.0
NE F:ARG373 4.7 35.4 1.0
SG F:CYS125 4.8 40.5 1.0
CA F:ASN124 4.8 34.4 1.0

Manganese binding site 7 out of 8 in 5k8o

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Manganese binding site 7 out of 8 in the MN2+/5NSA-Bound 5-Nitroanthranilate Aminohydrolase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of MN2+/5NSA-Bound 5-Nitroanthranilate Aminohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn501

b:41.1
occ:1.00
 OD1 G:ASN124 2.1 43.2 1.0
OE1 G:GLU196 2.1 46.9 1.0
OE2 G:GLU196 2.1 41.5 1.0
NE2 G:HIS86 2.2 40.4 1.0
OAC G:6R7502 2.2 44.1 1.0
OAJ G:6R7502 2.3 46.7 0.7
CD G:GLU196 2.4 42.0 1.0
CAB G:6R7502 2.9 43.9 1.0
CAI G:6R7502 3.0 43.8 1.0
CE1 G:HIS86 3.1 39.6 1.0
CG G:ASN124 3.1 40.9 1.0
CAD G:6R7502 3.2 43.5 1.0
CD2 G:HIS86 3.2 38.7 1.0
OE1 G:GLU158 3.3 50.3 1.0
ND2 G:ASN124 3.4 41.9 1.0
OAA G:6R7502 3.9 47.9 1.0
CG G:GLU196 3.9 41.4 1.0
CD G:GLU158 4.0 42.8 1.0
CAH G:6R7502 4.1 43.4 1.0
ND1 G:HIS86 4.2 38.0 1.0
CG G:HIS86 4.3 37.4 1.0
OE2 G:GLU158 4.4 52.3 1.0
CB G:ASN124 4.4 40.8 1.0
CAE G:6R7502 4.4 43.3 1.0
CB G:CYS125 4.5 46.0 1.0
CB G:GLU196 4.7 41.0 1.0
NE G:ARG373 4.7 43.3 1.0
CA G:ASN124 4.8 40.9 1.0
SG G:CYS125 4.9 36.9 1.0
CG G:GLU158 5.0 39.7 1.0

Manganese binding site 8 out of 8 in 5k8o

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Manganese binding site 8 out of 8 in the MN2+/5NSA-Bound 5-Nitroanthranilate Aminohydrolase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of MN2+/5NSA-Bound 5-Nitroanthranilate Aminohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn501

b:39.7
occ:1.00
 OAJ H:6R7502 1.7 39.6 0.8
OE2 H:GLU196 2.1 39.8 1.0
OE1 H:GLU196 2.1 50.2 1.0
OD1 H:ASN124 2.2 38.1 1.0
NE2 H:HIS86 2.3 39.0 1.0
CD H:GLU196 2.4 40.5 1.0
CAI H:6R7502 2.5 39.2 1.0
OAC H:6R7502 2.9 40.8 1.0
CG H:ASN124 3.2 38.1 1.0
CE1 H:HIS86 3.2 38.5 1.0
CD2 H:HIS86 3.2 39.7 1.0
OE1 H:GLU158 3.2 45.2 1.0
CAH H:6R7502 3.3 38.2 1.0
CAD H:6R7502 3.3 39.4 1.0
CAB H:6R7502 3.5 39.8 0.6
ND2 H:ASN124 3.5 37.7 1.0
CD H:GLU158 3.9 44.3 1.0
CG H:GLU196 3.9 40.0 1.0
OE2 H:GLU158 4.2 51.8 1.0
ND1 H:HIS86 4.3 38.0 1.0
CG H:HIS86 4.3 37.8 1.0
CAG H:6R7502 4.5 37.4 0.8
CAE H:6R7502 4.5 38.2 1.0
CB H:ASN124 4.5 37.7 1.0
CB H:CYS125 4.6 39.3 1.0
OAA H:6R7502 4.6 44.0 0.8
CB H:GLU196 4.7 40.5 1.0
NE H:ARG373 4.8 41.0 1.0
CG H:GLU158 4.9 38.8 1.0
SG H:CYS125 4.9 36.5 1.0
CAF H:6R7502 5.0 37.3 1.0
CA H:ASN124 5.0 39.2 1.0

Reference:

S.Kalyoncu, D.P.Heaner, Z.Kurt, C.M.Bethel, C.U.Ukachukwu, S.Chakravarthy, J.C.Spain, R.L.Lieberman. Enzymatic Hydrolysis By Transition-Metal-Dependent Nucleophilic Aromatic Substitution. Nat.Chem.Biol. V. 12 1031 2016.
ISSN: ESSN 1552-4469
PubMed: 27694799
DOI: 10.1038/NCHEMBIO.2191
Page generated: Sun Oct 6 01:36:15 2024

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