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Sodium in PDB 6y8o: Mycobacterium Smegmatis Gyrb 22KDA Atpase Sub-Domain in Complex with Novobiocin

Enzymatic activity of Mycobacterium Smegmatis Gyrb 22KDA Atpase Sub-Domain in Complex with Novobiocin

All present enzymatic activity of Mycobacterium Smegmatis Gyrb 22KDA Atpase Sub-Domain in Complex with Novobiocin:
5.6.2.2;

Protein crystallography data

The structure of Mycobacterium Smegmatis Gyrb 22KDA Atpase Sub-Domain in Complex with Novobiocin, PDB code: 6y8o was solved by S.R.Henderson, C.E.M.Stevenson, B.Malone, Y.Zholnerovych, L.A.Mitchenall, M.Pichowicz, D.H.Mcgarry, I.R.Cooper, C.Charrier, A.Salisbury, D.M.Lawson, A.Maxwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 78.48 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 156.962, 56.112, 50.678, 90.00, 90.66, 90.00
R / Rfree (%) 13.4 / 18.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Mycobacterium Smegmatis Gyrb 22KDA Atpase Sub-Domain in Complex with Novobiocin (pdb code 6y8o). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Mycobacterium Smegmatis Gyrb 22KDA Atpase Sub-Domain in Complex with Novobiocin, PDB code: 6y8o:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6y8o

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Sodium binding site 1 out of 5 in the Mycobacterium Smegmatis Gyrb 22KDA Atpase Sub-Domain in Complex with Novobiocin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mycobacterium Smegmatis Gyrb 22KDA Atpase Sub-Domain in Complex with Novobiocin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na309

b:37.2
occ:1.00
 O A:HOH478 2.1 62.4 1.0
OG1 A:THR167 2.1 20.1 1.0
O A:ASP80 2.3 17.2 1.0
O A:GLY81 2.4 17.7 1.0
O A:THR167 2.7 17.3 1.0
C A:ASP80 3.0 16.9 1.0
C A:THR167 3.3 15.4 1.0
C A:GLY81 3.3 16.3 1.0
CB A:THR167 3.3 17.1 1.0
CA A:THR167 3.7 16.1 1.0
N A:GLY81 3.7 15.9 1.0
O A:HOH496 3.7 40.3 1.0
CA A:GLY81 3.8 16.2 1.0
O A:HOH491 3.8 44.7 1.0
CA A:ASP80 4.0 16.8 1.0
N A:THR167 4.0 17.0 1.0
O A:HOH505 4.0 46.6 1.0
O A:PHE61 4.1 27.0 1.0
N A:GLY168 4.2 14.9 1.0
CB A:ASP80 4.3 18.4 1.0
N A:ARG82 4.3 15.2 1.0
O A:HOH414 4.5 32.3 1.0
CG2 A:THR167 4.5 20.5 1.0
CA A:GLY168 4.7 16.4 1.0
CA A:ARG82 4.7 17.0 1.0
CG A:ASP80 4.9 20.4 1.0

Sodium binding site 2 out of 5 in 6y8o

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Sodium binding site 2 out of 5 in the Mycobacterium Smegmatis Gyrb 22KDA Atpase Sub-Domain in Complex with Novobiocin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Mycobacterium Smegmatis Gyrb 22KDA Atpase Sub-Domain in Complex with Novobiocin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na310

b:25.4
occ:1.00
 O A:HOH429 2.1 47.9 1.0
OE1 A:GLU136 2.3 28.7 1.0
OE1 B:GLU136 2.6 24.7 1.0
CD A:GLU136 2.9 24.6 1.0
OE2 A:GLU136 3.0 22.5 1.0
CD B:GLU136 3.2 20.5 1.0
OE2 B:GLU136 3.4 20.9 1.0
CG A:GLU136 4.1 19.6 1.0
O A:HOH485 4.4 16.4 0.5
CG B:GLU136 4.4 17.4 1.0
O B:HOH524 4.5 14.5 0.5
CB A:GLU136 4.6 17.8 1.0
NH2 A:ARG134 4.8 23.7 1.0
CB B:GLU136 4.8 15.5 1.0

Sodium binding site 3 out of 5 in 6y8o

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Sodium binding site 3 out of 5 in the Mycobacterium Smegmatis Gyrb 22KDA Atpase Sub-Domain in Complex with Novobiocin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Mycobacterium Smegmatis Gyrb 22KDA Atpase Sub-Domain in Complex with Novobiocin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na308

b:21.2
occ:1.00
 OG1 B:THR167 2.2 19.7 1.0
O B:HOH573 2.3 39.8 1.0
O B:ASP80 2.4 16.6 1.0
O B:GLY81 2.4 18.0 1.0
O B:HOH570 2.5 28.5 1.0
O B:THR167 2.6 16.9 1.0
C B:ASP80 3.1 15.3 1.0
C B:GLY81 3.3 16.2 1.0
C B:THR167 3.3 15.1 1.0
CB B:THR167 3.3 17.2 1.0
O B:HOH488 3.4 39.4 1.0
CA B:THR167 3.7 16.6 1.0
N B:GLY81 3.8 14.5 1.0
CA B:GLY81 3.8 16.6 1.0
CA B:ASP80 4.0 16.4 1.0
N B:THR167 4.0 18.3 1.0
O B:HOH416 4.0 35.0 1.0
CB B:ASP80 4.2 19.2 1.0
N B:GLY168 4.2 14.8 1.0
O B:HOH497 4.3 41.5 1.0
N B:ARG82 4.3 16.9 1.0
O B:HOH557 4.4 32.1 1.0
O B:PHE61 4.5 27.1 1.0
CG2 B:THR167 4.6 18.8 1.0
CA B:ARG82 4.7 15.7 1.0
CA B:GLY168 4.7 15.8 1.0
CG B:ASP80 4.9 18.0 1.0
O B:HOH538 5.0 40.9 1.0

Sodium binding site 4 out of 5 in 6y8o

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Sodium binding site 4 out of 5 in the Mycobacterium Smegmatis Gyrb 22KDA Atpase Sub-Domain in Complex with Novobiocin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Mycobacterium Smegmatis Gyrb 22KDA Atpase Sub-Domain in Complex with Novobiocin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na309

b:30.2
occ:1.00
 O B:HOH593 1.9 47.5 1.0
O B:HOH444 2.0 49.8 1.0
OE1 B:GLU48 2.5 21.5 1.0
O B:HOH482 2.5 45.2 1.0
OE2 B:GLU48 2.6 22.4 1.0
CD B:GLU48 2.8 19.9 1.0
CG B:GLU48 4.4 17.8 1.0
OD1 B:ASN52 4.4 30.2 1.0
O B:HOH505 4.4 41.6 1.0
O B:HOH530 4.6 26.6 1.0
CA B:GLY124 4.7 20.0 1.0
O B:HOH518 4.8 32.0 1.0
O B:HOH571 4.8 45.1 1.0
O1 B:EDO304 4.9 39.6 1.0

Sodium binding site 5 out of 5 in 6y8o

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Sodium binding site 5 out of 5 in the Mycobacterium Smegmatis Gyrb 22KDA Atpase Sub-Domain in Complex with Novobiocin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Mycobacterium Smegmatis Gyrb 22KDA Atpase Sub-Domain in Complex with Novobiocin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na310

b:30.9
occ:1.00
 O B:HOH548 2.2 58.4 1.0
O2 B:EDO304 2.2 48.8 1.0
O B:HOH571 2.3 45.1 1.0
O B:HOH583 2.4 39.4 1.0
O B:TYR33 2.6 30.3 1.0
C1 B:EDO304 3.1 43.9 1.0
C2 B:EDO304 3.2 39.3 1.0
O B:HOH575 3.7 49.7 1.0
C B:TYR33 3.8 23.5 1.0
O1 B:EDO304 4.4 39.6 1.0
CA B:ILE34 4.5 21.8 1.0
N B:ILE34 4.6 21.5 1.0
O B:HOH433 4.7 37.5 1.0
O B:HOH501 4.7 35.2 1.0
O B:HOH482 4.7 45.2 1.0
CA B:TYR33 4.8 20.6 1.0

Reference:

S.R.Henderson, C.E.M.Stevenson, B.Malone, Y.Zholnerovych, L.A.Mitchenall, M.Pichowicz, D.H.Mcgarry, I.R.Cooper, C.Charrier, A.M.Salisbury, D.M.Lawson, A.Maxwell. Structural and Mechanistic Analysis of Atpase Inhibitors Targeting Mycobacterial Dna Gyrase. J.Antimicrob.Chemother. V. 75 2835 2020.
ISSN: ESSN 1460-2091
PubMed: 32728686
DOI: 10.1093/JAC/DKAA286
Page generated: Tue Oct 8 14:59:16 2024

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