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Bromine in PDB 5eai: Crystal Structure of Nad(P)H Dehydrogenase, Quinone 1 Complexed with A Chemotherapeutic Naphthoquinone E6A

Enzymatic activity of Crystal Structure of Nad(P)H Dehydrogenase, Quinone 1 Complexed with A Chemotherapeutic Naphthoquinone E6A

All present enzymatic activity of Crystal Structure of Nad(P)H Dehydrogenase, Quinone 1 Complexed with A Chemotherapeutic Naphthoquinone E6A:
1.6.5.2;

Protein crystallography data

The structure of Crystal Structure of Nad(P)H Dehydrogenase, Quinone 1 Complexed with A Chemotherapeutic Naphthoquinone E6A, PDB code: 5eai was solved by L.S.Pidugu, J.E.Mbimba, M.Ahmad, E.Pozharski, E.A.Sausville, A.Emadi, E.A.Toth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 95.67 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 95.600, 210.770, 228.080, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 22

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Nad(P)H Dehydrogenase, Quinone 1 Complexed with A Chemotherapeutic Naphthoquinone E6A (pdb code 5eai). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 5 binding sites of Bromine where determined in the Crystal Structure of Nad(P)H Dehydrogenase, Quinone 1 Complexed with A Chemotherapeutic Naphthoquinone E6A, PDB code: 5eai:
Jump to Bromine binding site number: 1; 2; 3; 4; 5;

Bromine binding site 1 out of 5 in 5eai

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Bromine binding site 1 out of 5 in the Crystal Structure of Nad(P)H Dehydrogenase, Quinone 1 Complexed with A Chemotherapeutic Naphthoquinone E6A


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Nad(P)H Dehydrogenase, Quinone 1 Complexed with A Chemotherapeutic Naphthoquinone E6A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br302

b:0.6
occ:1.00
 BR B:E6A302 0.0 0.6 1.0
C5 B:E6A302 2.0 0.4 1.0
C27 B:E6A302 2.9 98.8 1.0
C4 B:E6A302 2.9 0.0 1.0
O20 B:E6A302 3.0 0.7 1.0
C6 B:E6A302 3.1 0.2 1.0
O41 B:E6A302 3.2 98.9 1.0
C22 B:E6A302 3.5 0.4 1.0
C A:GLY149 3.5 65.2 1.0
CA A:GLY149 3.7 62.7 1.0
O A:GLY149 3.7 65.5 1.0
N A:GLY150 3.9 60.6 1.0
C26 B:E6A302 4.2 97.7 1.0
C1 B:E6A302 4.3 0.3 1.0
C23 B:E6A302 4.4 0.5 1.0
C18 B:E6A302 4.4 99.7 1.0
CA A:GLY150 4.5 61.0 1.0
N A:GLY149 4.8 61.4 1.0
O38 B:E6A302 4.8 98.2 1.0
N1 A:FAD601 4.9 68.1 1.0
C13 B:E6A302 5.0 96.9 1.0
O40 B:E6A302 5.0 0.4 1.0

Bromine binding site 2 out of 5 in 5eai

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Bromine binding site 2 out of 5 in the Crystal Structure of Nad(P)H Dehydrogenase, Quinone 1 Complexed with A Chemotherapeutic Naphthoquinone E6A


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Nad(P)H Dehydrogenase, Quinone 1 Complexed with A Chemotherapeutic Naphthoquinone E6A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Br602

b:0.5
occ:1.00
 BR E:E6A602 0.0 0.5 1.0
C5 E:E6A602 2.0 0.8 1.0
C4 E:E6A602 2.9 97.6 1.0
C27 E:E6A602 2.9 94.7 1.0
O20 E:E6A602 3.0 99.4 1.0
C6 E:E6A602 3.1 97.1 1.0
O41 E:E6A602 3.2 93.8 1.0
C22 E:E6A602 3.4 94.0 1.0
CE2 E:TYR128 3.5 68.2 1.0
C F:GLY149 3.6 66.5 1.0
CA F:GLY149 3.9 56.6 1.0
O F:GLY149 3.9 69.6 1.0
CE2 K:PHE232 4.0 85.8 1.0
N F:GLY150 4.0 62.0 1.0
CA K:GLN233 4.0 84.1 1.0
C1 E:E6A602 4.1 94.2 1.0
CD2 K:PHE232 4.1 82.6 1.0
C26 E:E6A602 4.2 93.3 1.0
CD2 E:TYR128 4.3 69.5 1.0
CB K:GLN233 4.3 87.8 1.0
C18 E:E6A602 4.3 86.0 1.0
OH E:TYR128 4.3 76.1 0.0
CZ E:TYR128 4.3 76.1 0.0
C23 E:E6A602 4.4 88.3 1.0
CA F:GLY150 4.6 61.4 1.0
N K:GLN233 4.7 82.4 1.0
O K:GLN233 4.8 88.7 1.0
O38 E:E6A602 4.8 95.8 1.0
C13 E:E6A602 4.8 87.4 1.0
O19 E:E6A602 4.8 96.4 1.0
O40 E:E6A602 4.9 86.5 1.0
N1 F:FAD301 4.9 56.2 1.0
C K:GLN233 4.9 87.2 1.0

Bromine binding site 3 out of 5 in 5eai

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Bromine binding site 3 out of 5 in the Crystal Structure of Nad(P)H Dehydrogenase, Quinone 1 Complexed with A Chemotherapeutic Naphthoquinone E6A


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of Nad(P)H Dehydrogenase, Quinone 1 Complexed with A Chemotherapeutic Naphthoquinone E6A within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Br302

b:0.2
occ:1.00
 BR H:E6A302 0.0 0.2 1.0
C5 H:E6A302 2.0 0.3 1.0
C4 H:E6A302 2.9 96.2 1.0
O20 H:E6A302 3.0 97.4 1.0
C6 H:E6A302 3.1 95.7 1.0
C27 H:E6A302 3.2 88.8 1.0
O41 H:E6A302 3.3 88.1 1.0
CA G:GLY149 3.5 58.5 1.0
C G:GLY149 3.6 64.3 1.0
C22 H:E6A302 3.6 92.5 1.0
N G:GLY150 3.9 59.8 1.0
O G:GLY149 3.9 65.1 1.0
CE1 I:PHE232 4.0 88.5 1.0
C1 H:E6A302 4.1 91.6 1.0
CA I:GLN233 4.1 76.8 1.0
OH H:TYR128 4.2 77.9 1.0
CD1 I:PHE232 4.2 86.8 1.0
C18 H:E6A302 4.3 87.4 1.0
CZ H:TYR128 4.3 83.1 1.0
CE1 H:TYR128 4.5 78.0 0.0
C26 H:E6A302 4.5 86.8 1.0
CB I:GLN233 4.6 79.5 1.0
N G:GLY149 4.6 57.5 1.0
O I:GLN233 4.7 79.6 1.0
C23 H:E6A302 4.7 92.5 1.0
CA G:GLY150 4.7 59.3 1.0
N1 G:FAD601 4.7 59.5 1.0
O19 H:E6A302 4.7 93.2 1.0
C13 H:E6A302 4.8 86.7 1.0
N I:GLN233 4.8 75.4 1.0
C I:GLN233 4.9 79.3 1.0
C1' G:FAD601 5.0 49.5 1.0
CE2 H:TYR128 5.0 78.5 1.0

Bromine binding site 4 out of 5 in 5eai

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Bromine binding site 4 out of 5 in the Crystal Structure of Nad(P)H Dehydrogenase, Quinone 1 Complexed with A Chemotherapeutic Naphthoquinone E6A


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of Nad(P)H Dehydrogenase, Quinone 1 Complexed with A Chemotherapeutic Naphthoquinone E6A within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Br602

b:0.5
occ:1.00
 BR K:E6A602 0.0 0.5 1.0
C5 K:E6A602 2.0 0.9 1.0
C4 K:E6A602 2.9 95.7 1.0
O20 K:E6A602 3.0 95.9 1.0
C27 K:E6A602 3.0 97.9 1.0
C6 K:E6A602 3.1 98.9 1.0
O41 K:E6A602 3.3 99.7 1.0
C22 K:E6A602 3.6 96.7 1.0
C L:GLY149 3.6 64.5 1.0
CA L:GLY149 3.6 61.1 1.0
O L:GLY149 3.9 68.3 1.0
CE1 K:TYR128 3.9 91.0 1.0
N L:GLY150 3.9 57.0 1.0
CE1 E:PHE232 4.0 98.0 1.0
C1 K:E6A602 4.0 95.4 1.0
O E:GLN233 4.1 83.9 1.0
CA E:GLN233 4.2 84.0 1.0
CD1 E:PHE232 4.2 95.9 1.0
OH K:TYR128 4.2 97.2 1.0
C18 K:E6A602 4.3 88.8 1.0
C26 K:E6A602 4.3 96.4 1.0
CZ K:TYR128 4.3 97.8 1.0
C23 K:E6A602 4.5 94.6 1.0
O19 K:E6A602 4.6 94.6 1.0
CA L:GLY150 4.6 55.9 1.0
C E:GLN233 4.7 85.2 1.0
N L:GLY149 4.7 60.1 1.0
CD1 K:TYR128 4.7 90.7 1.0
C13 K:E6A602 4.8 90.8 1.0
O38 K:E6A602 4.8 98.6 1.0
N1 L:FAD301 4.8 64.3 1.0
N E:GLN233 4.9 83.5 1.0
O40 K:E6A602 5.0 95.8 1.0

Bromine binding site 5 out of 5 in 5eai

Go back to Bromine Binding Sites List in 5eai
Bromine binding site 5 out of 5 in the Crystal Structure of Nad(P)H Dehydrogenase, Quinone 1 Complexed with A Chemotherapeutic Naphthoquinone E6A


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of Nad(P)H Dehydrogenase, Quinone 1 Complexed with A Chemotherapeutic Naphthoquinone E6A within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Br602

b:0.1
occ:1.00
 BR M:E6A602 0.0 0.1 1.0
C5 M:E6A602 2.1 1.0 1.0
C4 M:E6A602 3.0 0.8 1.0
O20 M:E6A602 3.0 0.8 1.0
C6 M:E6A602 3.2 0.1 1.0
C27 M:E6A602 3.2 0.8 1.0
O41 M:E6A602 3.4 0.2 1.0
C N:GLY149 3.6 63.8 1.0
C22 M:E6A602 3.6 0.4 1.0
O N:GLY149 3.7 64.0 1.0
CA N:GLY149 3.8 60.1 1.0
N N:GLY150 3.9 60.0 1.0
C1 M:E6A602 4.3 0.4 1.0
C18 M:E6A602 4.4 0.5 1.0
CA N:GLY150 4.4 60.9 1.0
C23 M:E6A602 4.5 0.5 1.0
C26 M:E6A602 4.6 0.0 1.0
CE1 M:TYR128 4.9 83.7 0.0
C13 M:E6A602 5.0 0.3 1.0

Reference:

L.S.Pidugu, J.C.Mbimba, M.Ahmad, E.Pozharski, E.A.Sausville, A.Emadi, E.A.Toth. A Direct Interaction Between NQO1 and A Chemotherapeutic Dimeric Naphthoquinone. Bmc Struct.Biol. V. 16 1 2016.
ISSN: ESSN 1472-6807
PubMed: 26822308
DOI: 10.1186/S12900-016-0052-X
Page generated: Wed Jul 10 23:28:22 2024

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