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Bromine in PDB 5o0b: Crystal Structure of Phosphopantetheine Adenylyltransferase From Mycobacterium Abcessus in Complex with 3-Bromo-1H-Indazole-5- Carboxylic Acid (Fragment 2)

Enzymatic activity of Crystal Structure of Phosphopantetheine Adenylyltransferase From Mycobacterium Abcessus in Complex with 3-Bromo-1H-Indazole-5- Carboxylic Acid (Fragment 2)

All present enzymatic activity of Crystal Structure of Phosphopantetheine Adenylyltransferase From Mycobacterium Abcessus in Complex with 3-Bromo-1H-Indazole-5- Carboxylic Acid (Fragment 2):
2.7.7.3;

Protein crystallography data

The structure of Crystal Structure of Phosphopantetheine Adenylyltransferase From Mycobacterium Abcessus in Complex with 3-Bromo-1H-Indazole-5- Carboxylic Acid (Fragment 2), PDB code: 5o0b was solved by S.E.Thomas, S.Y.Kim, V.Mendes, M.Blaszczyk, T.L.Blundell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.72 / 1.74
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 76.069, 125.171, 119.435, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 22.9

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Phosphopantetheine Adenylyltransferase From Mycobacterium Abcessus in Complex with 3-Bromo-1H-Indazole-5- Carboxylic Acid (Fragment 2) (pdb code 5o0b). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 6 binding sites of Bromine where determined in the Crystal Structure of Phosphopantetheine Adenylyltransferase From Mycobacterium Abcessus in Complex with 3-Bromo-1H-Indazole-5- Carboxylic Acid (Fragment 2), PDB code: 5o0b:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6;

Bromine binding site 1 out of 6 in 5o0b

Go back to Bromine Binding Sites List in 5o0b
Bromine binding site 1 out of 6 in the Crystal Structure of Phosphopantetheine Adenylyltransferase From Mycobacterium Abcessus in Complex with 3-Bromo-1H-Indazole-5- Carboxylic Acid (Fragment 2)


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 Phosphopantetheine Adenylyltransferase From Mycobacterium Abcessus in Complex with 3-Bromo-1H-Indazole-5- Carboxylic Acid (Fragment 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br201

b:74.8
occ:1.00
 BR A:9FE201 0.0 74.8 1.0
C07 A:9FE201 1.9 53.7 1.0
N09 A:9FE201 2.9 49.0 1.0
O A:HOH376 2.9 38.8 1.0
C06 A:9FE201 3.0 54.6 1.0
SG A:CYS6 3.4 22.9 0.4
C05 A:9FE201 3.6 35.1 1.0
CD2 A:HIS17 3.9 26.5 1.0
CG1 A:VAL20 3.9 16.9 1.0
N10 A:9FE201 4.0 52.5 1.0
CB A:VAL20 4.0 17.3 1.0
C11 A:9FE201 4.1 48.1 1.0
CE1 A:PHE10 4.1 16.6 1.0
CG2 A:VAL20 4.2 19.0 1.0
N A:GLY88 4.2 14.7 1.0
CZ A:PHE10 4.4 14.3 1.0
CA A:HIS17 4.4 14.1 1.0
CE1 A:PHE21 4.5 13.4 1.0
BR A:9FE202 4.5 92.8 1.0
CG A:HIS17 4.5 16.7 1.0
O A:PRO7 4.6 17.2 1.0
CB A:HIS17 4.6 12.7 1.0
O A:HIS17 4.7 15.8 1.0
CA A:LYS87 4.9 19.7 1.0
NE2 A:HIS17 4.9 21.2 1.0

Bromine binding site 2 out of 6 in 5o0b

Go back to Bromine Binding Sites List in 5o0b
Bromine binding site 2 out of 6 in the Crystal Structure of Phosphopantetheine Adenylyltransferase From Mycobacterium Abcessus in Complex with 3-Bromo-1H-Indazole-5- Carboxylic Acid (Fragment 2)


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 Phosphopantetheine Adenylyltransferase From Mycobacterium Abcessus in Complex with 3-Bromo-1H-Indazole-5- Carboxylic Acid (Fragment 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br202

b:92.8
occ:1.00
 BR A:9FE202 0.0 92.8 1.0
C07 A:9FE202 1.9 69.6 1.0
N09 A:9FE202 2.9 60.9 1.0
C06 A:9FE202 3.0 60.3 1.0
O A:HOH329 3.2 39.6 1.0
O A:HOH360 3.6 38.7 1.0
C05 A:9FE202 3.6 37.3 1.0
N09 A:9FE201 3.8 49.0 1.0
O A:GLY16 3.9 18.4 1.0
CG2 A:VAL20 3.9 19.0 1.0
C A:GLY16 4.0 19.1 1.0
C07 A:9FE201 4.0 53.7 1.0
N10 A:9FE202 4.0 63.2 1.0
C11 A:9FE202 4.1 60.0 1.0
CD2 A:HIS17 4.1 26.5 1.0
N A:HIS17 4.2 15.6 1.0
N10 A:9FE201 4.3 52.5 1.0
CA A:GLY88 4.4 12.6 1.0
O A:HOH316 4.4 23.6 1.0
BR A:9FE201 4.5 74.8 1.0
CA A:HIS17 4.5 14.1 1.0
CA A:GLY16 4.5 19.3 1.0
C06 A:9FE201 4.6 54.6 1.0
C A:GLY88 4.7 19.8 1.0
O A:HOH358 4.7 30.4 1.0
C11 A:9FE201 4.8 48.1 1.0
O A:GLY88 4.8 21.9 1.0
NE2 A:HIS17 4.8 21.2 1.0
N A:GLY88 4.9 14.7 1.0
CG A:ARG90 4.9 30.5 1.0
C04 A:9FE202 5.0 43.4 1.0
CG A:HIS17 5.0 16.7 1.0

Bromine binding site 3 out of 6 in 5o0b

Go back to Bromine Binding Sites List in 5o0b
Bromine binding site 3 out of 6 in the Crystal Structure of Phosphopantetheine Adenylyltransferase From Mycobacterium Abcessus in Complex with 3-Bromo-1H-Indazole-5- Carboxylic Acid (Fragment 2)


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 Phosphopantetheine Adenylyltransferase From Mycobacterium Abcessus in Complex with 3-Bromo-1H-Indazole-5- Carboxylic Acid (Fragment 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br201

b:64.9
occ:1.00
 BR B:9FE201 0.0 64.9 1.0
C07 B:9FE201 1.9 45.6 1.0
N09 B:9FE201 2.9 40.6 1.0
C06 B:9FE201 3.0 39.1 1.0
SG B:CYS6 3.6 17.4 0.6
C05 B:9FE201 3.6 34.7 1.0
CD2 B:HIS17 3.9 23.5 1.0
CE1 B:PHE10 3.9 17.8 1.0
N10 B:9FE201 4.0 40.4 1.0
CG1 B:VAL20 4.0 19.4 1.0
C11 B:9FE201 4.1 47.8 1.0
CB B:VAL20 4.2 14.9 1.0
CZ B:PHE10 4.3 12.7 1.0
CG2 B:VAL20 4.3 17.5 1.0
N B:GLY88 4.3 13.3 1.0
BR B:9FE202 4.4 64.5 1.0
CA B:HIS17 4.4 14.9 1.0
CE1 B:PHE21 4.5 19.2 1.0
CG B:HIS17 4.5 19.6 1.0
CB B:HIS17 4.6 18.0 1.0
O B:PRO7 4.7 21.7 1.0
O B:HIS17 4.8 15.2 1.0
CA B:LYS87 4.9 18.9 1.0
NE2 B:HIS17 4.9 23.1 1.0
C07 B:9FE202 4.9 48.1 1.0
C04 B:9FE201 5.0 29.5 1.0

Bromine binding site 4 out of 6 in 5o0b

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Bromine binding site 4 out of 6 in the Crystal Structure of Phosphopantetheine Adenylyltransferase From Mycobacterium Abcessus in Complex with 3-Bromo-1H-Indazole-5- Carboxylic Acid (Fragment 2)


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 Phosphopantetheine Adenylyltransferase From Mycobacterium Abcessus in Complex with 3-Bromo-1H-Indazole-5- Carboxylic Acid (Fragment 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br202

b:64.5
occ:1.00
 BR B:9FE202 0.0 64.5 1.0
C07 B:9FE202 1.9 48.1 1.0
N09 B:9FE202 2.9 41.3 1.0
C06 B:9FE202 3.0 43.0 1.0
O B:HOH381 3.1 40.8 1.0
O B:HOH335 3.3 40.2 1.0
O B:GLY16 3.6 16.9 1.0
C05 B:9FE202 3.7 43.5 1.0
O B:HOH360 3.7 35.5 1.0
C B:GLY16 3.7 22.1 1.0
CG2 B:VAL20 3.9 17.5 1.0
N B:HIS17 4.0 14.0 1.0
CD2 B:HIS17 4.0 23.5 1.0
N10 B:9FE202 4.0 47.0 1.0
C11 B:9FE202 4.1 46.0 1.0
C07 B:9FE201 4.2 45.6 1.0
CA B:HIS17 4.2 14.9 1.0
N09 B:9FE201 4.3 40.6 1.0
CA B:GLY16 4.3 17.3 1.0
O B:HOH337 4.4 24.1 1.0
BR B:9FE201 4.4 64.9 1.0
CA B:GLY88 4.5 15.2 1.0
NE2 B:HIS17 4.8 23.1 1.0
CG B:HIS17 4.8 19.6 1.0
N10 B:9FE201 4.8 40.4 1.0
C06 B:9FE201 4.8 39.1 1.0
CD B:ARG90 4.9 43.1 1.0
CG B:ARG90 4.9 30.5 1.0
O B:HOH333 5.0 30.0 1.0
C B:GLY88 5.0 26.3 1.0
N B:GLY88 5.0 13.3 1.0
CB B:VAL20 5.0 14.9 1.0

Bromine binding site 5 out of 6 in 5o0b

Go back to Bromine Binding Sites List in 5o0b
Bromine binding site 5 out of 6 in the Crystal Structure of Phosphopantetheine Adenylyltransferase From Mycobacterium Abcessus in Complex with 3-Bromo-1H-Indazole-5- Carboxylic Acid (Fragment 2)


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 Phosphopantetheine Adenylyltransferase From Mycobacterium Abcessus in Complex with 3-Bromo-1H-Indazole-5- Carboxylic Acid (Fragment 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br201

b:82.0
occ:1.00
 BR C:9FE201 0.0 82.0 1.0
C07 C:9FE201 1.9 55.3 1.0
N09 C:9FE201 2.9 63.9 1.0
O C:HOH355 3.0 41.0 1.0
C06 C:9FE201 3.0 51.9 1.0
C05 C:9FE201 3.7 42.7 1.0
CD2 C:HIS17 3.8 28.2 1.0
SG C:CYS6 3.8 21.4 0.3
N C:GLY88 3.9 18.6 1.0
N10 C:9FE201 4.0 63.2 1.0
CG1 C:VAL20 4.1 18.7 1.0
C11 C:9FE201 4.1 57.3 1.0
CB C:VAL20 4.1 21.1 1.0
BR C:9FE202 4.2 95.4 1.0
CG2 C:VAL20 4.2 25.5 1.0
CE1 C:PHE10 4.3 25.6 1.0
CA C:HIS17 4.6 20.8 1.0
CG C:HIS17 4.6 20.3 1.0
CZ C:PHE10 4.6 20.0 1.0
CA C:GLY88 4.7 19.1 1.0
O C:PRO7 4.7 25.1 1.0
CA C:LYS87 4.8 21.4 1.0
CB C:HIS17 4.8 18.9 1.0
NE2 C:HIS17 4.8 26.9 1.0
C07 C:9FE202 4.8 63.8 1.0
C C:LYS87 4.8 19.4 1.0
CE1 C:PHE21 4.8 21.5 1.0
O C:HIS17 5.0 18.3 1.0

Bromine binding site 6 out of 6 in 5o0b

Go back to Bromine Binding Sites List in 5o0b
Bromine binding site 6 out of 6 in the Crystal Structure of Phosphopantetheine Adenylyltransferase From Mycobacterium Abcessus in Complex with 3-Bromo-1H-Indazole-5- Carboxylic Acid (Fragment 2)


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Crystal Structure of Phosphopantetheine Adenylyltransferase From Mycobacterium Abcessus in Complex with 3-Bromo-1H-Indazole-5- Carboxylic Acid (Fragment 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br202

b:95.4
occ:1.00
 BR C:9FE202 0.0 95.4 1.0
C07 C:9FE202 1.9 63.8 1.0
N09 C:9FE202 2.9 57.7 1.0
C06 C:9FE202 3.0 54.9 1.0
C05 C:9FE202 3.7 54.9 1.0
O C:GLY16 3.7 21.6 1.0
C C:GLY16 3.8 19.1 1.0
CG2 C:VAL20 4.0 25.5 1.0
N10 C:9FE202 4.0 57.0 1.0
CD2 C:HIS17 4.1 28.2 1.0
C11 C:9FE202 4.1 60.8 1.0
N C:HIS17 4.2 19.1 1.0
BR C:9FE201 4.2 82.0 1.0
C07 C:9FE201 4.2 55.3 1.0
N09 C:9FE201 4.3 63.9 1.0
CA C:HIS17 4.4 20.8 1.0
CA C:GLY16 4.4 16.6 1.0
O C:HOH320 4.5 25.7 1.0
CA C:GLY88 4.5 19.1 1.0
CG2 C:THR118 4.6 28.9 0.4
NE2 C:HIS17 4.7 26.9 1.0
C C:GLY88 4.8 23.1 1.0
CG C:HIS17 4.8 20.3 1.0
C06 C:9FE201 4.9 51.9 1.0
CD C:ARG90 5.0 42.8 1.0
O C:GLY88 5.0 24.5 1.0
N10 C:9FE201 5.0 63.2 1.0

Reference:

S.E.Thomas, V.Mendes, S.Y.Kim, S.Malhotra, B.Ochoa-Montano, M.Blaszczyk, T.L.Blundell. Structural Biology and the Design of New Therapeutics: From Hiv and Cancer to Mycobacterial Infections: A Paper Dedicated to John Kendrew. J. Mol. Biol. V. 429 2677 2017.
ISSN: ESSN 1089-8638
PubMed: 28648615
DOI: 10.1016/J.JMB.2017.06.014
Page generated: Thu Jul 11 00:32:23 2024

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