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Copper in PDB 1h1m: Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Kaempferol

Enzymatic activity of Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Kaempferol

All present enzymatic activity of Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Kaempferol:
1.13.11.24;

Protein crystallography data

The structure of Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Kaempferol, PDB code: 1h1m was solved by R.A.Steiner, B.W.Dijkstra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.39 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 109.272, 55.377, 123.929, 90.00, 98.33, 90.00
R / Rfree (%) 15.4 / 20.4

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Kaempferol (pdb code 1h1m). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Kaempferol, PDB code: 1h1m:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 1h1m

Go back to Copper Binding Sites List in 1h1m
Copper binding site 1 out of 4 in the Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Kaempferol


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Kaempferol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1361

b:9.4
occ:1.00
O27 A:KMP1360 2.0 20.1 1.0
NE2 A:HIS112 2.1 10.2 1.0
OE1 A:GLU73 2.1 23.2 1.0
NE2 A:HIS66 2.1 7.2 1.0
NE2 A:HIS68 2.1 9.4 1.0
C10 A:KMP1360 2.9 19.4 1.0
CD A:GLU73 2.9 22.4 1.0
CD2 A:HIS66 3.0 4.3 1.0
CE1 A:HIS112 3.0 8.2 1.0
CE1 A:HIS68 3.0 8.3 1.0
CD2 A:HIS112 3.0 9.3 1.0
CD2 A:HIS68 3.1 9.9 1.0
CE1 A:HIS66 3.1 8.8 1.0
OE2 A:GLU73 3.3 23.9 1.0
O13 A:KMP1360 3.4 20.0 1.0
C9 A:KMP1360 3.5 17.8 1.0
C11 A:KMP1360 3.9 16.3 1.0
ND1 A:HIS112 4.1 7.7 1.0
ND1 A:HIS68 4.1 10.8 1.0
CG A:HIS66 4.1 6.1 1.0
CG A:HIS112 4.1 7.4 1.0
ND1 A:HIS66 4.2 8.2 1.0
CG A:HIS68 4.2 9.1 1.0
CG A:GLU73 4.2 14.6 1.0
C19 A:KMP1360 4.3 15.4 1.0
C14 A:KMP1360 4.6 15.1 1.0
C3 A:KMP1360 4.9 16.0 1.0
CB A:GLU73 4.9 7.8 1.0
CZ A:PHE75 5.0 10.4 1.0

Copper binding site 2 out of 4 in 1h1m

Go back to Copper Binding Sites List in 1h1m
Copper binding site 2 out of 4 in the Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Kaempferol


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Kaempferol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1359

b:10.4
occ:1.00
OE1 B:GLU73 1.9 29.0 1.0
NE2 B:HIS66 2.0 6.7 1.0
NE2 B:HIS112 2.1 7.3 1.0
NE2 B:HIS68 2.1 13.1 1.0
O27 B:KMP1358 2.2 21.4 1.0
CD2 B:HIS66 2.9 4.7 1.0
CE1 B:HIS68 2.9 10.8 1.0
CD B:GLU73 2.9 29.5 1.0
CE1 B:HIS112 3.0 6.3 1.0
C10 B:KMP1358 3.0 19.9 1.0
CD2 B:HIS112 3.1 7.0 1.0
CE1 B:HIS66 3.1 7.9 1.0
CD2 B:HIS68 3.2 10.9 1.0
O13 B:KMP1358 3.3 21.7 1.0
OE2 B:GLU73 3.3 30.9 1.0
C9 B:KMP1358 3.5 18.9 1.0
C11 B:KMP1358 4.0 17.2 1.0
CG B:HIS66 4.1 6.8 1.0
ND1 B:HIS68 4.1 8.8 1.0
ND1 B:HIS112 4.1 7.6 1.0
ND1 B:HIS66 4.1 7.2 1.0
CG B:HIS112 4.2 8.0 1.0
CG B:GLU73 4.3 19.8 1.0
CG B:HIS68 4.3 7.8 1.0
C19 B:KMP1358 4.3 16.9 1.0
C14 B:KMP1358 4.6 20.1 1.0
CZ B:PHE75 4.8 11.7 1.0
CB B:GLU73 4.8 12.6 1.0
C3 B:KMP1358 4.9 19.1 1.0

Copper binding site 3 out of 4 in 1h1m

Go back to Copper Binding Sites List in 1h1m
Copper binding site 3 out of 4 in the Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Kaempferol


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Kaempferol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu1359

b:11.2
occ:1.00
NE2 C:HIS66 1.9 8.3 1.0
OE1 C:GLU73 2.0 31.9 1.0
NE2 C:HIS112 2.1 5.2 1.0
NE2 C:HIS68 2.1 9.5 1.0
O27 C:KMP1358 2.1 18.0 1.0
CE1 C:HIS66 2.9 6.1 1.0
CE1 C:HIS112 2.9 5.5 1.0
CD2 C:HIS66 2.9 5.4 1.0
C10 C:KMP1358 3.0 18.9 1.0
CE1 C:HIS68 3.0 12.0 1.0
CD C:GLU73 3.0 28.7 1.0
CD2 C:HIS112 3.1 5.3 1.0
CD2 C:HIS68 3.2 8.4 1.0
O13 C:KMP1358 3.3 23.3 1.0
OE2 C:GLU73 3.4 33.7 1.0
C9 C:KMP1358 3.4 20.1 1.0
C11 C:KMP1358 3.9 18.2 1.0
ND1 C:HIS66 4.0 5.3 1.0
CG C:HIS66 4.1 5.1 1.0
ND1 C:HIS112 4.1 5.8 1.0
ND1 C:HIS68 4.1 8.2 1.0
CG C:HIS112 4.2 6.8 1.0
CG C:HIS68 4.2 7.4 1.0
CG C:GLU73 4.3 21.5 1.0
C19 C:KMP1358 4.4 19.6 1.0
C14 C:KMP1358 4.6 20.4 1.0
C3 C:KMP1358 4.8 17.7 1.0
CZ C:PHE75 4.9 14.2 1.0
CB C:GLU73 4.9 12.6 1.0

Copper binding site 4 out of 4 in 1h1m

Go back to Copper Binding Sites List in 1h1m
Copper binding site 4 out of 4 in the Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Kaempferol


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Kaempferol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu1357

b:11.1
occ:1.00
NE2 D:HIS66 2.0 10.0 1.0
O27 D:KMP1356 2.1 17.0 1.0
NE2 D:HIS112 2.1 10.3 1.0
OE1 D:GLU73 2.2 23.0 1.0
NE2 D:HIS68 2.2 14.2 1.0
CE1 D:HIS66 3.0 8.8 1.0
C10 D:KMP1356 3.0 16.0 1.0
CD2 D:HIS66 3.0 7.9 1.0
CE1 D:HIS112 3.0 7.3 1.0
CD D:GLU73 3.1 21.6 1.0
CD2 D:HIS112 3.1 7.9 1.0
CE1 D:HIS68 3.2 10.4 1.0
CD2 D:HIS68 3.2 13.2 1.0
OE2 D:GLU73 3.4 22.9 1.0
O13 D:KMP1356 3.4 17.6 1.0
C9 D:KMP1356 3.5 18.7 1.0
C11 D:KMP1356 4.0 17.0 1.0
ND1 D:HIS66 4.1 10.1 1.0
CG D:HIS66 4.1 6.6 1.0
ND1 D:HIS112 4.2 7.3 1.0
CG D:HIS112 4.2 7.9 1.0
ND1 D:HIS68 4.3 9.2 1.0
CG D:HIS68 4.3 10.7 1.0
C19 D:KMP1356 4.3 19.6 1.0
CG D:GLU73 4.4 13.5 1.0
C14 D:KMP1356 4.6 18.5 1.0
C3 D:KMP1356 4.9 15.4 1.0
CB D:GLU73 4.9 10.2 1.0
CZ D:PHE75 4.9 9.3 1.0

Reference:

R.A.Steiner, K.H.Kalk, B.W.Dijkstra. Anaerobic Enzyme.Substrate Structures Provide Insight Into the Reaction Mechanism of the Copper- Dependent Quercetin 2,3-Dioxygenase. Proc.Natl.Acad.Sci.Usa V. 99 16625 2002.
ISSN: ISSN 0027-8424
PubMed: 12486225
DOI: 10.1073/PNAS.262506299
Page generated: Sun Dec 13 10:59:09 2020

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