Atomistry » Zinc » PDB 6y79-6yh8 » 6y8l
Atomistry »
  Zinc »
    PDB 6y79-6yh8 »
      6y8l »

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

Go back to Zinc Binding Sites List in 6y8l
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

Go back to Zinc Binding Sites List in 6y8l
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

Go back to Zinc Binding Sites List in 6y8l
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

Go back to Zinc Binding Sites List in 6y8l
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

Go back to Zinc Binding Sites List in 6y8l
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

Go back to Zinc Binding Sites List in 6y8l
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: Tue Oct 29 11:26:38 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy