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Zinc in PDB 5k8p: ZN2+/Tetrahedral Intermediate-Bound R289A 5-Nitroanthranilate Aminohydrolase

Enzymatic activity of ZN2+/Tetrahedral Intermediate-Bound R289A 5-Nitroanthranilate Aminohydrolase

All present enzymatic activity of ZN2+/Tetrahedral Intermediate-Bound R289A 5-Nitroanthranilate Aminohydrolase:
3.5.99.8;

Protein crystallography data

The structure of ZN2+/Tetrahedral Intermediate-Bound R289A 5-Nitroanthranilate Aminohydrolase, PDB code: 5k8p was solved by S.Kalyoncu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.16 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 185.884, 247.634, 247.870, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 20.4

Zinc Binding Sites:

The binding sites of Zinc atom in the ZN2+/Tetrahedral Intermediate-Bound R289A 5-Nitroanthranilate Aminohydrolase (pdb code 5k8p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the ZN2+/Tetrahedral Intermediate-Bound R289A 5-Nitroanthranilate Aminohydrolase, PDB code: 5k8p:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5k8p

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Zinc binding site 1 out of 8 in the ZN2+/Tetrahedral Intermediate-Bound R289A 5-Nitroanthranilate Aminohydrolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of ZN2+/Tetrahedral Intermediate-Bound R289A 5-Nitroanthranilate Aminohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:38.9
occ:0.68
 OD1 A:ASN124 2.1 43.1 1.0
OE1 A:GLU196 2.1 43.6 1.0
OE2 A:GLU196 2.1 39.5 1.0
NE2 A:HIS86 2.1 30.6 1.0
O14 A:6R8502 2.4 45.0 1.0
CD A:GLU196 2.4 35.6 1.0
O11 A:6R8502 2.6 56.0 1.0
CD2 A:HIS86 3.1 23.3 1.0
CE1 A:HIS86 3.1 27.5 1.0
CG A:ASN124 3.1 43.0 1.0
C10 A:6R8502 3.2 49.8 1.0
ND2 A:ASN124 3.6 42.8 1.0
OE1 A:GLU158 3.6 33.1 1.0
C01 A:6R8502 3.7 46.9 1.0
C06 A:6R8502 3.9 46.1 1.0
O12 A:6R8502 3.9 52.0 1.0
CG A:GLU196 4.0 35.2 1.0
NH1 A:ARG373 4.0 40.6 1.0
CD A:GLU158 4.1 32.4 1.0
N13 A:6R8502 4.2 45.0 1.0
ND1 A:HIS86 4.2 27.0 1.0
CB A:CYS125 4.2 34.8 1.0
CG A:HIS86 4.3 24.1 1.0
OE2 A:GLU158 4.3 33.5 1.0
CB A:ASN124 4.5 35.8 1.0
SG A:CYS125 4.6 33.8 1.0
CB A:GLU196 4.8 30.1 1.0
CA A:ASN124 4.9 36.3 1.0
C02 A:6R8502 4.9 41.8 1.0
O A:HOH672 4.9 26.2 1.0
C05 A:6R8502 4.9 48.6 1.0

Zinc binding site 2 out of 8 in 5k8p

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Zinc binding site 2 out of 8 in the ZN2+/Tetrahedral Intermediate-Bound R289A 5-Nitroanthranilate Aminohydrolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of ZN2+/Tetrahedral Intermediate-Bound R289A 5-Nitroanthranilate Aminohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:33.1
occ:0.72
 OD1 B:ASN124 2.1 35.9 1.0
OE1 B:GLU196 2.1 34.2 1.0
NE2 B:HIS86 2.1 25.9 1.0
OE2 B:GLU196 2.1 34.7 1.0
O14 B:6R8502 2.3 42.2 1.0
O11 B:6R8502 2.4 54.0 1.0
CD B:GLU196 2.4 29.5 1.0
CE1 B:HIS86 3.0 22.8 1.0
CG B:ASN124 3.1 34.4 1.0
CD2 B:HIS86 3.1 22.0 1.0
C10 B:6R8502 3.5 52.2 1.0
ND2 B:ASN124 3.6 37.4 1.0
C01 B:6R8502 3.6 45.5 1.0
OE1 B:GLU158 3.9 27.7 1.0
CG B:GLU196 4.0 28.8 1.0
C06 B:6R8502 4.0 46.8 1.0
O B:HOH671 4.0 29.7 1.0
OE2 B:GLU158 4.0 32.1 1.0
N13 B:6R8502 4.1 45.9 1.0
CD B:GLU158 4.2 28.3 1.0
ND1 B:HIS86 4.2 24.9 1.0
CB B:CYS125 4.2 23.9 1.0
CG B:HIS86 4.2 22.5 1.0
NH1 B:ARG373 4.3 32.3 1.0
CB B:ASN124 4.4 27.1 1.0
SG B:CYS125 4.4 30.6 1.0
O12 B:6R8502 4.5 56.9 1.0
CB B:GLU196 4.8 24.8 1.0
CA B:ASN124 4.8 26.4 1.0
C02 B:6R8502 4.8 40.6 1.0
O B:HOH760 4.9 25.3 1.0

Zinc binding site 3 out of 8 in 5k8p

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Zinc binding site 3 out of 8 in the ZN2+/Tetrahedral Intermediate-Bound R289A 5-Nitroanthranilate Aminohydrolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of ZN2+/Tetrahedral Intermediate-Bound R289A 5-Nitroanthranilate Aminohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:30.6
occ:0.71
 OD1 C:ASN124 2.0 33.1 1.0
OE1 C:GLU196 2.1 32.3 1.0
OE2 C:GLU196 2.1 34.0 1.0
NE2 C:HIS86 2.1 23.5 1.0
O14 C:6R8502 2.4 34.9 1.0
CD C:GLU196 2.4 28.0 1.0
CD2 C:HIS86 3.1 20.6 1.0
CE1 C:HIS86 3.1 21.9 1.0
CG C:ASN124 3.2 35.1 1.0
O11 C:6R8502 3.4 56.4 1.0
C10 C:6R8502 3.5 51.8 1.0
C01 C:6R8502 3.6 44.6 1.0
ND2 C:ASN124 3.7 37.0 1.0
C06 C:6R8502 3.8 47.6 1.0
N13 C:6R8502 3.9 44.7 1.0
O12 C:6R8502 4.0 55.5 1.0
O C:HOH637 4.0 27.4 1.0
CG C:GLU196 4.0 25.8 1.0
OE1 C:GLU158 4.0 25.5 1.0
CB C:CYS125 4.1 22.2 1.0
OE2 C:GLU158 4.2 28.3 1.0
ND1 C:HIS86 4.2 21.9 1.0
NH1 C:ARG373 4.2 29.6 1.0
CG C:HIS86 4.3 20.7 1.0
CD C:GLU158 4.3 27.3 1.0
SG C:CYS125 4.4 28.6 1.0
CB C:ASN124 4.4 31.2 1.0
CA C:ASN124 4.7 27.4 1.0
CB C:GLU196 4.8 23.9 1.0
C02 C:6R8502 4.9 38.4 1.0
C05 C:6R8502 5.0 47.9 1.0

Zinc binding site 4 out of 8 in 5k8p

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Zinc binding site 4 out of 8 in the ZN2+/Tetrahedral Intermediate-Bound R289A 5-Nitroanthranilate Aminohydrolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of ZN2+/Tetrahedral Intermediate-Bound R289A 5-Nitroanthranilate Aminohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:38.4
occ:0.70
 OD1 D:ASN124 2.1 39.3 1.0
OE2 D:GLU196 2.1 38.2 1.0
NE2 D:HIS86 2.1 26.2 1.0
OE1 D:GLU196 2.2 33.7 1.0
CD D:GLU196 2.5 32.4 1.0
CD2 D:HIS86 3.1 25.8 1.0
CE1 D:HIS86 3.1 24.6 1.0
CG D:ASN124 3.1 40.5 1.0
ND2 D:ASN124 3.6 41.2 1.0
OE1 D:GLU158 3.8 27.8 1.0
O D:HOH689 4.0 30.5 1.0
CG D:GLU196 4.0 27.2 1.0
CB D:CYS125 4.1 30.6 1.0
ND1 D:HIS86 4.2 23.7 1.0
CG D:HIS86 4.3 25.8 1.0
CD D:GLU158 4.3 28.4 1.0
NH1 D:ARG373 4.3 27.6 1.0
CB D:ASN124 4.4 31.0 1.0
SG D:CYS125 4.4 31.7 1.0
OE2 D:GLU158 4.4 28.4 1.0
CB D:GLU196 4.8 23.3 1.0
CA D:ASN124 4.8 31.1 1.0
O D:HOH721 4.9 23.9 1.0

Zinc binding site 5 out of 8 in 5k8p

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Zinc binding site 5 out of 8 in the ZN2+/Tetrahedral Intermediate-Bound R289A 5-Nitroanthranilate Aminohydrolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of ZN2+/Tetrahedral Intermediate-Bound R289A 5-Nitroanthranilate Aminohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn501

b:33.4
occ:0.71
 OD1 E:ASN124 2.0 35.0 1.0
NE2 E:HIS86 2.1 23.7 1.0
O E:HOH603 2.1 48.2 1.0
OE2 E:GLU196 2.1 31.2 1.0
OE1 E:GLU196 2.2 36.6 1.0
CD E:GLU196 2.5 32.2 1.0
O14 E:6R8502 2.5 39.0 1.0
CE1 E:HIS86 3.0 21.9 1.0
CD2 E:HIS86 3.0 20.8 1.0
O12 E:6R8502 3.1 54.6 1.0
CG E:ASN124 3.2 35.0 1.0
ND2 E:ASN124 3.7 32.4 1.0
C10 E:6R8502 3.7 47.9 1.0
OE1 E:GLU158 3.7 28.5 1.0
C01 E:6R8502 3.8 42.0 1.0
NH1 E:ARG373 4.0 41.5 1.0
O E:HOH622 4.0 26.6 1.0
CG E:GLU196 4.0 28.8 1.0
C06 E:6R8502 4.1 42.1 1.0
CB E:CYS125 4.1 24.1 1.0
ND1 E:HIS86 4.1 23.8 1.0
CD E:GLU158 4.2 26.5 1.0
CG E:HIS86 4.2 20.7 1.0
N13 E:6R8502 4.2 41.1 1.0
OE2 E:GLU158 4.3 28.9 1.0
CB E:ASN124 4.4 29.1 1.0
SG E:CYS125 4.5 29.8 1.0
O11 E:6R8502 4.5 57.2 1.0
O E:HOH733 4.8 24.8 1.0
CA E:ASN124 4.8 25.6 1.0
CB E:GLU196 4.8 27.3 1.0
C02 E:6R8502 5.0 36.0 1.0

Zinc binding site 6 out of 8 in 5k8p

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Zinc binding site 6 out of 8 in the ZN2+/Tetrahedral Intermediate-Bound R289A 5-Nitroanthranilate Aminohydrolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of ZN2+/Tetrahedral Intermediate-Bound R289A 5-Nitroanthranilate Aminohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn501

b:39.1
occ:0.75
 OD1 F:ASN124 2.1 37.7 1.0
NE2 F:HIS86 2.1 25.1 1.0
OE1 F:GLU196 2.1 33.4 1.0
OE2 F:GLU196 2.1 41.7 1.0
CD F:GLU196 2.4 29.3 1.0
CE1 F:HIS86 3.0 22.8 1.0
CD2 F:HIS86 3.1 22.4 1.0
CG F:ASN124 3.1 34.4 1.0
ND2 F:ASN124 3.6 36.0 1.0
OE1 F:GLU158 3.9 26.4 1.0
O F:HOH629 4.0 30.6 1.0
CG F:GLU196 4.0 26.4 1.0
CB F:CYS125 4.1 28.0 1.0
ND1 F:HIS86 4.2 24.5 1.0
NH1 F:ARG373 4.2 28.2 1.0
CG F:HIS86 4.2 23.1 1.0
CD F:GLU158 4.3 27.3 1.0
OE2 F:GLU158 4.3 29.4 1.0
SG F:CYS125 4.4 29.8 1.0
CB F:ASN124 4.4 31.8 1.0
CA F:ASN124 4.8 28.8 1.0
CB F:GLU196 4.8 26.1 1.0

Zinc binding site 7 out of 8 in 5k8p

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Zinc binding site 7 out of 8 in the ZN2+/Tetrahedral Intermediate-Bound R289A 5-Nitroanthranilate Aminohydrolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of ZN2+/Tetrahedral Intermediate-Bound R289A 5-Nitroanthranilate Aminohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn501

b:67.4
occ:1.00
 OE1 G:GLU196 2.0 50.9 1.0
OD1 G:ASN124 2.1 55.6 1.0
OE2 G:GLU196 2.1 44.1 1.0
NE2 G:HIS86 2.2 31.0 1.0
O11 G:6R8502 2.3 62.2 1.0
O14 G:6R8502 2.4 48.4 1.0
CD G:GLU196 2.4 37.8 1.0
CD2 G:HIS86 3.1 28.5 1.0
CE1 G:HIS86 3.2 30.6 1.0
CG G:ASN124 3.3 47.3 1.0
C10 G:6R8502 3.3 58.6 1.0
C01 G:6R8502 3.5 50.1 1.0
C06 G:6R8502 3.8 53.2 1.0
ND2 G:ASN124 3.9 46.1 1.0
N13 G:6R8502 3.9 50.5 1.0
OE1 G:GLU158 3.9 32.4 1.0
CG G:GLU196 3.9 33.1 1.0
O G:HOH642 3.9 32.4 1.0
NH1 G:ARG373 4.0 43.2 1.0
CB G:CYS125 4.1 33.6 1.0
ND1 G:HIS86 4.3 28.5 1.0
CG G:HIS86 4.3 26.4 1.0
O12 G:6R8502 4.3 60.0 1.0
SG G:CYS125 4.3 34.0 1.0
CD G:GLU158 4.3 32.0 1.0
OE2 G:GLU158 4.5 34.5 1.0
CB G:ASN124 4.5 41.6 1.0
CB G:GLU196 4.7 30.7 1.0
CA G:ASN124 4.8 39.1 1.0
C02 G:6R8502 4.8 44.5 1.0
O G:HOH707 4.8 26.8 1.0
C05 G:6R8502 4.8 55.1 1.0

Zinc binding site 8 out of 8 in 5k8p

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Zinc binding site 8 out of 8 in the ZN2+/Tetrahedral Intermediate-Bound R289A 5-Nitroanthranilate Aminohydrolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of ZN2+/Tetrahedral Intermediate-Bound R289A 5-Nitroanthranilate Aminohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn501

b:34.1
occ:0.70
 O14 H:6R8502 2.0 39.6 1.0
OD1 H:ASN124 2.1 34.0 1.0
OE2 H:GLU196 2.1 33.7 1.0
OE1 H:GLU196 2.1 33.2 1.0
NE2 H:HIS86 2.2 25.9 1.0
CD H:GLU196 2.4 27.9 1.0
CD2 H:HIS86 3.1 22.4 1.0
CE1 H:HIS86 3.1 23.2 1.0
CG H:ASN124 3.2 34.6 1.0
O11 H:6R8502 3.2 45.7 1.0
C10 H:6R8502 3.2 44.7 1.0
C01 H:6R8502 3.3 38.5 1.0
C06 H:6R8502 3.6 38.0 1.0
O12 H:6R8502 3.7 54.4 1.0
N13 H:6R8502 3.8 41.6 1.0
ND2 H:ASN124 3.8 34.6 1.0
OE1 H:GLU158 3.8 26.5 1.0
NH1 H:ARG373 3.9 40.4 1.0
O H:HOH617 3.9 30.1 1.0
CG H:GLU196 4.0 30.5 1.0
CD H:GLU158 4.1 27.4 1.0
OE2 H:GLU158 4.1 29.9 1.0
ND1 H:HIS86 4.2 23.4 1.0
CB H:CYS125 4.2 25.6 1.0
CG H:HIS86 4.3 20.4 1.0
C02 H:6R8502 4.4 37.8 1.0
CB H:ASN124 4.5 30.2 1.0
SG H:CYS125 4.6 29.4 1.0
O H:HOH702 4.7 28.1 1.0
C05 H:6R8502 4.7 41.5 1.0
CB H:GLU196 4.8 28.6 1.0
CA H:ASN124 4.8 30.4 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 27 20:12:24 2024

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