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Zinc in PDB 6y8l: Mycobacterium Thermoresistibile GYRB21 in Complex with Novobiocin

Enzymatic activity of Mycobacterium Thermoresistibile GYRB21 in Complex with Novobiocin

All present enzymatic activity of Mycobacterium Thermoresistibile GYRB21 in Complex with Novobiocin:
5.6.2.2;

Protein crystallography data

The structure of Mycobacterium Thermoresistibile GYRB21 in Complex with Novobiocin, PDB code: 6y8l 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) 81.86 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.962, 51.114, 83.205, 90.00, 100.32, 90.00
R / Rfree (%) 14 / 18.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Mycobacterium Thermoresistibile GYRB21 in Complex with Novobiocin (pdb code 6y8l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Mycobacterium Thermoresistibile GYRB21 in Complex with Novobiocin, PDB code: 6y8l:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 6y8l

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Zinc binding site 1 out of 7 in the Mycobacterium Thermoresistibile GYRB21 in Complex with Novobiocin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mycobacterium Thermoresistibile GYRB21 in Complex with Novobiocin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:16.7
occ:1.00
 OD2 A:ASP55 1.9 17.2 1.0
OD2 A:ASP51 2.0 17.9 1.0
NE2 B:HIS44 2.0 17.5 1.0
O A:HOH697 2.0 17.4 1.0
CG A:ASP55 2.7 17.2 1.0
CG A:ASP51 2.8 17.0 1.0
OD1 A:ASP55 2.8 16.5 1.0
CE1 B:HIS44 3.0 17.7 1.0
OD1 A:ASP51 3.0 19.6 1.0
CD2 B:HIS44 3.0 17.0 1.0
O A:HOH696 3.9 20.9 1.0
O A:ASP51 4.0 15.7 1.0
C B:ILE34 4.0 19.5 1.0
O B:ILE34 4.0 19.3 1.0
O A:HOH623 4.1 24.4 1.0
ND1 B:HIS44 4.1 16.7 1.0
CB A:ASP55 4.1 16.0 1.0
CG B:HIS44 4.1 16.9 1.0
ND2 A:ASN52 4.2 15.7 1.0
CB A:ASP51 4.2 16.3 1.0
C A:ASP51 4.3 16.3 1.0
N B:GLY35 4.3 20.8 1.0
CA B:ILE34 4.4 21.3 1.0
O A:HOH721 4.5 44.4 1.0
CA B:GLY35 4.5 20.2 1.0
N A:ASN52 4.6 15.6 1.0
CA A:ASN52 4.6 14.7 1.0
CA A:ASP51 4.8 16.3 1.0
NH2 B:ARG40 4.9 19.7 1.0
O B:HOH459 5.0 21.4 1.0

Zinc binding site 2 out of 7 in 6y8l

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Zinc binding site 2 out of 7 in the Mycobacterium Thermoresistibile GYRB21 in Complex with Novobiocin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mycobacterium Thermoresistibile GYRB21 in Complex with Novobiocin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:31.8
occ:0.50
 O A:HOH736 1.7 36.5 0.5
NE2 A:HIS61 2.0 36.1 0.5
O A:HOH707 2.2 44.8 0.5
O A:HOH731 2.3 51.6 0.5
CE1 A:HIS61 2.3 40.2 0.5
NE2 A:HIS61 2.4 40.4 0.5
O A:HOH602 2.8 40.5 0.5
CE1 A:HIS61 2.9 34.5 0.5
CD2 A:HIS61 3.1 34.0 0.5
ND1 A:HIS61 3.5 35.3 0.5
CD2 A:HIS61 3.7 35.9 0.5
O A:HOH731 3.8 37.3 0.5
ND1 A:HIS61 4.0 35.1 0.5
CG A:HIS61 4.1 27.6 0.5
CG A:HIS61 4.2 29.1 0.5
O A:HOH700 4.2 42.3 1.0
O A:HOH727 4.5 34.6 0.5
O A:ALA59 4.8 26.0 1.0
ZN A:ZN504 4.8 32.6 0.5
O A:HOH713 4.8 38.3 1.0

Zinc binding site 3 out of 7 in 6y8l

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Zinc binding site 3 out of 7 in the Mycobacterium Thermoresistibile GYRB21 in Complex with Novobiocin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mycobacterium Thermoresistibile GYRB21 in Complex with Novobiocin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:32.6
occ:0.50
 O A:HOH730 1.5 26.0 0.5
O A:HOH727 2.1 34.6 0.5
ND1 A:HIS61 2.4 35.3 0.5
O A:HOH731 2.6 37.3 0.5
CD2 A:HIS61 2.9 34.0 0.5
O A:HOH737 2.9 44.3 1.0
CE1 A:HIS61 3.1 40.2 0.5
O A:HOH607 3.2 58.7 1.0
CG A:HIS61 3.6 29.1 0.5
CG A:HIS61 3.7 27.6 0.5
O A:HOH731 3.7 51.6 0.5
NE2 A:HIS61 3.8 36.1 0.5
O A:HOH749 3.9 48.5 1.0
CB A:HIS61 4.0 26.4 0.5
CB A:HIS61 4.0 25.9 0.5
O A:GLY60 4.3 23.8 1.0
NE2 A:HIS61 4.4 40.4 0.5
CD2 A:HIS61 4.6 35.9 0.5
ZN A:ZN503 4.8 31.8 0.5
ND1 A:HIS61 4.8 35.1 0.5
C A:GLY60 4.9 23.0 1.0
CE1 A:HIS61 4.9 34.5 0.5
O A:HOH707 5.0 44.8 0.5

Zinc binding site 4 out of 7 in 6y8l

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Zinc binding site 4 out of 7 in the Mycobacterium Thermoresistibile GYRB21 in Complex with Novobiocin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Mycobacterium Thermoresistibile GYRB21 in Complex with Novobiocin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn507

b:17.7
occ:1.00
 OD2 B:ASP55 1.9 18.3 1.0
OD2 B:ASP51 2.0 17.7 1.0
NE2 A:HIS44 2.0 17.1 1.0
O B:HOH472 2.0 19.6 1.0
CG B:ASP55 2.7 20.1 1.0
CG B:ASP51 2.8 17.8 1.0
OD1 B:ASP55 2.8 17.8 1.0
CD2 A:HIS44 3.0 16.9 1.0
CE1 A:HIS44 3.0 18.4 1.0
OD1 B:ASP51 3.0 19.9 1.0
O B:HOH486 4.0 23.4 1.0
O B:ASP51 4.0 17.9 1.0
C A:ILE34 4.1 18.6 1.0
O A:ILE34 4.1 18.9 1.0
ND1 A:HIS44 4.1 16.4 1.0
O B:HOH414 4.1 31.2 1.0
CB B:ASP55 4.1 18.6 1.0
CG A:HIS44 4.1 16.6 1.0
ND2 B:ASN52 4.1 18.9 1.0
CB B:ASP51 4.2 17.3 1.0
C B:ASP51 4.3 17.4 1.0
N A:GLY35 4.3 20.2 1.0
CA A:ILE34 4.5 18.7 1.0
CA A:GLY35 4.6 21.1 1.0
N B:ASN52 4.6 17.1 1.0
CA B:ASN52 4.6 16.8 1.0
O B:HOH518 4.7 37.5 1.0
O B:HOH507 4.7 41.9 1.0
CA B:ASP51 4.8 16.3 1.0
O A:TYR33 4.9 22.5 1.0

Zinc binding site 5 out of 7 in 6y8l

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Zinc binding site 5 out of 7 in the Mycobacterium Thermoresistibile GYRB21 in Complex with Novobiocin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Mycobacterium Thermoresistibile GYRB21 in Complex with Novobiocin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:31.2
occ:0.50
 ZN B:ZN302 0.0 31.2 0.5
ZN B:ZN302 2.0 39.4 0.5
O B:HOH497 2.1 40.8 1.0
NE2 B:HIS61 2.1 33.6 1.0
O B:HOH520 2.4 34.5 0.5
CD2 B:HIS61 3.1 31.9 1.0
CE1 B:HIS61 3.2 35.5 1.0
CG B:HIS61 4.2 31.1 1.0
ND1 B:HIS61 4.2 32.2 1.0

Zinc binding site 6 out of 7 in 6y8l

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Zinc binding site 6 out of 7 in the Mycobacterium Thermoresistibile GYRB21 in Complex with Novobiocin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Mycobacterium Thermoresistibile GYRB21 in Complex with Novobiocin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:39.4
occ:0.50
 ZN B:ZN302 0.0 39.4 0.5
O B:HOH497 1.8 40.8 1.0
ZN B:ZN302 2.0 31.2 0.5
O B:HOH520 2.3 34.5 0.5
NE2 B:HIS61 2.3 33.6 1.0
CE1 B:HIS61 3.1 35.5 1.0
O B:HOH530 3.2 49.6 1.0
CD2 B:HIS61 3.3 31.9 1.0
ND1 B:HIS61 4.2 32.2 1.0
CG B:HIS61 4.3 31.1 1.0
O B:ALA59 4.5 26.7 1.0

Zinc binding site 7 out of 7 in 6y8l

Go back to Zinc Binding Sites List in 6y8l
Zinc binding site 7 out of 7 in the Mycobacterium Thermoresistibile GYRB21 in Complex with Novobiocin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Mycobacterium Thermoresistibile GYRB21 in Complex with Novobiocin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:28.5
occ:0.50
 O B:HOH527 1.9 31.4 0.5
O B:HOH521 2.0 27.1 0.5
O A:HOH747 2.3 31.1 0.5
O B:HOH542 2.3 42.0 1.0
CE A:MET58 3.8 40.1 1.0
OE1 B:GLU39 3.8 42.2 1.0
O B:HOH409 4.1 36.5 0.5
CD B:GLU39 4.5 39.4 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: Thu Aug 21 21:23:51 2025

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