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Zinc in PDB 4tma: Crystal Structure of Gyrase Bound to Its Inhibitor Yacg

Enzymatic activity of Crystal Structure of Gyrase Bound to Its Inhibitor Yacg

All present enzymatic activity of Crystal Structure of Gyrase Bound to Its Inhibitor Yacg:
5.99.1.3;

Protein crystallography data

The structure of Crystal Structure of Gyrase Bound to Its Inhibitor Yacg, PDB code: 4tma was solved by S.M.Vos, A.Y.Lyubimov, D.M.Hershey, A.J.Schoeffler, J.M.Berger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.32 / 3.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 107.210, 114.460, 462.120, 90.00, 90.00, 90.00
R / Rfree (%) 24.3 / 28.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Gyrase Bound to Its Inhibitor Yacg (pdb code 4tma). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Gyrase Bound to Its Inhibitor Yacg, PDB code: 4tma:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4tma

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Zinc binding site 1 out of 6 in the Crystal Structure of Gyrase Bound to Its Inhibitor Yacg


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Gyrase Bound to Its Inhibitor Yacg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:0.0
occ:1.00
 CB B:VAL501 3.1 0.2 1.0
OD1 B:ASP502 3.2 0.4 1.0
OD1 B:ASP500 3.2 0.9 1.0
N B:ASP502 3.3 1.0 1.0
CG B:ASP502 3.5 0.2 1.0
CG2 B:VAL501 3.8 0.5 1.0
OD2 B:ASP502 3.8 0.9 1.0
N B:VAL501 3.8 0.7 1.0
CA B:VAL501 3.8 0.0 1.0
C B:VAL501 3.9 0.8 1.0
CG1 B:VAL501 4.0 0.8 1.0
NH1 A:ARG32 4.2 0.3 1.0
CG B:ASP500 4.2 0.2 1.0
CB B:ASP502 4.3 0.1 1.0
CA B:ASP502 4.3 0.8 1.0
NH2 A:ARG32 4.3 0.2 1.0
CZ A:ARG32 4.7 0.0 1.0
CB B:ASP500 5.0 0.8 1.0
OD2 B:ASP500 5.0 0.5 1.0
O B:VAL501 5.0 0.0 1.0
C B:ASP500 5.0 0.7 1.0

Zinc binding site 2 out of 6 in 4tma

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Zinc binding site 2 out of 6 in the Crystal Structure of Gyrase Bound to Its Inhibitor Yacg


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Gyrase Bound to Its Inhibitor Yacg within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn601

b:0.0
occ:1.00
 O E:GLN327 2.2 91.2 1.0
O E:TYR321 2.3 85.6 1.0
O E:THR324 2.4 89.2 1.0
O E:SER322 2.9 83.7 1.0
C E:GLN327 3.3 85.2 1.0
C E:TYR321 3.4 82.2 1.0
C E:SER322 3.5 82.9 1.0
C E:THR324 3.5 84.4 1.0
CA E:SER322 3.7 82.8 1.0
CA E:GLN327 4.0 80.5 1.0
N E:THR324 4.0 81.9 1.0
CB E:GLN327 4.0 83.0 1.0
N E:GLN327 4.0 71.5 1.0
N E:SER322 4.1 81.1 1.0
CA E:THR324 4.4 79.4 1.0
N E:VAL328 4.4 78.7 1.0
N E:GLN325 4.5 82.5 1.0
N E:GLN323 4.5 83.3 1.0
CG E:GLN327 4.6 84.9 1.0
CA E:GLN325 4.6 82.2 1.0
CA E:TYR321 4.6 79.0 1.0
C E:GLN323 4.7 83.8 1.0
CA E:VAL328 4.7 69.5 1.0
O E:LEU320 4.8 87.1 1.0

Zinc binding site 3 out of 6 in 4tma

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Zinc binding site 3 out of 6 in the Crystal Structure of Gyrase Bound to Its Inhibitor Yacg


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Gyrase Bound to Its Inhibitor Yacg within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn101

b:95.6
occ:1.00
 SG I:CYS12 2.3 0.2 1.0
SG I:CYS32 2.3 98.1 1.0
SG I:CYS9 2.4 0.4 1.0
SG I:CYS28 2.5 0.3 1.0
CB I:CYS32 3.2 90.6 1.0
CB I:CYS12 3.2 0.3 1.0
CB I:CYS9 3.5 0.3 1.0
CB I:CYS28 3.7 0.0 1.0
N I:CYS12 3.8 0.8 1.0
N I:CYS28 4.0 95.4 1.0
CA I:CYS12 4.1 0.7 1.0
CA I:CYS28 4.4 99.0 1.0
N I:SER29 4.5 0.6 1.0
CB I:THR11 4.5 99.2 1.0
CA I:CYS32 4.6 89.9 1.0
N I:GLY13 4.8 0.8 1.0
C I:THR11 4.8 99.1 1.0
C I:CYS12 4.8 0.8 1.0
C I:CYS28 4.8 0.9 1.0
CA I:CYS9 4.9 0.3 1.0
C I:PHE27 4.9 95.0 1.0
CG2 I:THR11 5.0 99.2 1.0

Zinc binding site 4 out of 6 in 4tma

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Zinc binding site 4 out of 6 in the Crystal Structure of Gyrase Bound to Its Inhibitor Yacg


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Gyrase Bound to Its Inhibitor Yacg within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:0.2
occ:1.00
 SG J:CYS12 2.0 95.2 1.0
SG J:CYS28 2.1 0.1 1.0
SG J:CYS32 2.2 80.9 1.0
SG J:CYS9 2.3 0.2 1.0
CB J:CYS32 3.1 88.0 1.0
CB J:CYS9 3.2 0.7 1.0
CB J:CYS28 3.3 91.7 1.0
CB J:CYS12 3.5 1.0 1.0
N J:CYS28 3.5 91.4 1.0
CA J:CYS28 3.9 90.9 1.0
N J:CYS12 4.0 0.8 1.0
N J:SER29 4.2 89.2 1.0
CA J:CYS12 4.3 0.8 1.0
C J:CYS28 4.6 91.3 1.0
CA J:CYS32 4.6 86.1 1.0
C J:PHE27 4.7 96.1 1.0
CA J:CYS9 4.7 0.5 1.0
CB J:THR11 4.8 98.5 1.0
CB J:LYS14 4.8 0.1 1.0
CA J:PHE27 4.9 99.5 1.0
C J:CYS12 5.0 0.1 1.0
C J:THR11 5.0 0.2 1.0

Zinc binding site 5 out of 6 in 4tma

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Zinc binding site 5 out of 6 in the Crystal Structure of Gyrase Bound to Its Inhibitor Yacg


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Gyrase Bound to Its Inhibitor Yacg within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn101

b:0.4
occ:1.00
 SG K:CYS12 2.3 0.4 1.0
SG K:CYS28 2.5 0.5 1.0
SG K:CYS9 2.5 0.2 1.0
SG K:CYS32 3.0 0.7 1.0
CB K:CYS32 3.6 0.2 1.0
CB K:CYS9 3.6 0.5 1.0
CB K:CYS28 3.7 0.2 1.0
CB K:CYS12 3.8 0.5 1.0
N K:CYS28 3.9 0.4 1.0
N K:SER29 4.2 0.1 1.0
N K:CYS12 4.3 0.0 1.0
CA K:CYS28 4.3 0.3 1.0
CD K:LYS14 4.4 0.5 1.0
CB K:LYS14 4.4 0.3 1.0
CA K:CYS12 4.6 0.0 1.0
CB K:THR11 4.7 1.0 1.0
CG K:LYS14 4.7 0.6 1.0
C K:CYS28 4.8 0.8 1.0
O K:SER29 4.9 0.7 1.0
N K:LYS14 5.0 0.3 1.0
C K:PHE27 5.0 0.8 1.0

Zinc binding site 6 out of 6 in 4tma

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Zinc binding site 6 out of 6 in the Crystal Structure of Gyrase Bound to Its Inhibitor Yacg


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Gyrase Bound to Its Inhibitor Yacg within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.2
occ:1.00
 SG L:CYS28 2.3 0.6 1.0
SG L:CYS12 2.4 0.0 1.0
SG L:CYS9 2.7 0.6 1.0
SG L:CYS32 2.8 0.5 1.0
CB L:CYS32 3.5 0.6 1.0
CB L:CYS9 3.5 0.3 1.0
CB L:CYS28 3.5 0.8 1.0
N L:CYS28 3.7 0.3 1.0
CB L:CYS12 3.7 0.3 1.0
N L:CYS12 4.0 0.1 1.0
CA L:CYS28 4.1 0.3 1.0
N L:SER29 4.3 0.4 1.0
CB L:THR11 4.4 0.1 1.0
CA L:CYS12 4.5 0.9 1.0
C L:CYS28 4.6 0.8 1.0
C L:PHE27 4.7 0.9 1.0
CA L:PHE27 4.9 0.5 1.0
CA L:CYS32 5.0 0.1 1.0
CB L:LYS14 5.0 0.0 1.0
CA L:CYS9 5.0 0.6 1.0
C L:THR11 5.0 0.0 1.0

Reference:

S.M.Vos, A.Y.Lyubimov, D.M.Hershey, A.J.Schoeffler, S.Sengupta, V.Nagaraja, J.M.Berger. Direct Control of Type Iia Topoisomerase Activity By A Chromosomally Encoded Regulatory Protein. Genes Dev. V. 28 1485 2014.
ISSN: ISSN 0890-9369
PubMed: 24990966
DOI: 10.1101/GAD.241984.114
Page generated: Sun Oct 27 08:23:12 2024

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