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Nickel in PDB 8cwt: Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212

Enzymatic activity of Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212

All present enzymatic activity of Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212:
2.7.7.6;

Protein crystallography data

The structure of Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212, PDB code: 8cwt was solved by T.Wan, L.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.68 / 1.35
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 121.826, 121.826, 114.305, 90, 90, 90
R / Rfree (%) 15.2 / 17.4

Other elements in 8cwt:

The structure of Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212 also contains other interesting chemical elements:

Iron (Fe) 12 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212 (pdb code 8cwt). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 7 binding sites of Nickel where determined in the Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212, PDB code: 8cwt:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7;

Nickel binding site 1 out of 7 in 8cwt

Go back to Nickel Binding Sites List in 8cwt
Nickel binding site 1 out of 7 in the Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni601

b:14.8
occ:1.00
 NE2 F:HIS443 2.1 15.3 1.0
NE2 D:HIS445 2.1 14.7 1.0
NE2 B:HIS443 2.1 14.5 1.0
NE2 B:HIS445 2.1 15.1 1.0
NE2 F:HIS445 2.1 15.2 1.0
NE2 D:HIS443 2.1 14.7 1.0
CE1 B:HIS443 3.1 15.8 1.0
CE1 B:HIS445 3.1 15.9 1.0
CE1 F:HIS443 3.1 15.5 1.0
CE1 D:HIS445 3.1 15.6 1.0
CE1 D:HIS443 3.1 16.2 1.0
CE1 F:HIS445 3.1 15.9 1.0
CD2 D:HIS445 3.2 14.9 1.0
CD2 B:HIS443 3.2 14.6 1.0
CD2 F:HIS445 3.2 15.5 1.0
CD2 B:HIS445 3.2 14.9 1.0
CD2 F:HIS443 3.2 15.7 1.0
CD2 D:HIS443 3.2 15.1 1.0
ND1 B:HIS445 4.3 15.9 1.0
ND1 D:HIS445 4.3 15.8 1.0
ND1 B:HIS443 4.3 15.8 1.0
ND1 F:HIS445 4.3 16.4 1.0
ND1 F:HIS443 4.3 15.9 1.0
ND1 D:HIS443 4.3 16.4 1.0
CG D:HIS445 4.3 15.5 1.0
CG B:HIS445 4.3 15.1 1.0
CG F:HIS445 4.3 15.7 1.0
CG B:HIS443 4.3 14.8 1.0
CG F:HIS443 4.3 15.5 1.0
CG D:HIS443 4.3 14.8 1.0

Nickel binding site 2 out of 7 in 8cwt

Go back to Nickel Binding Sites List in 8cwt
Nickel binding site 2 out of 7 in the Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni602

b:18.8
occ:1.00
 NE2 F:HIS440 2.1 24.5 1.0
NE2 B:HIS444 2.1 18.6 1.0
NE2 B:HIS442 2.1 18.6 1.0
O2 F:TRS607 2.1 26.0 1.0
O3 F:TRS607 2.1 21.2 1.0
O1 F:TRS607 2.2 23.7 1.0
CE1 F:HIS440 3.0 27.2 1.0
C3 F:TRS607 3.0 29.1 1.0
CE1 B:HIS442 3.1 20.0 1.0
CE1 B:HIS444 3.1 20.6 1.0
C1 F:TRS607 3.1 30.2 1.0
CD2 B:HIS444 3.1 17.4 1.0
CD2 F:HIS440 3.1 25.3 1.0
CD2 B:HIS442 3.1 17.4 1.0
C F:TRS607 3.2 30.3 1.0
C2 F:TRS607 3.2 38.3 1.0
OE2 F:GLU537 4.0 19.7 1.0
ND1 F:HIS440 4.1 28.6 1.0
ND1 B:HIS442 4.2 19.7 1.0
ND1 B:HIS444 4.2 20.7 1.0
OE1 F:GLU537 4.2 20.2 1.0
CG B:HIS444 4.2 18.5 1.0
CG F:HIS440 4.3 25.2 1.0
CG B:HIS442 4.3 17.4 1.0
O F:HOH727 4.3 45.3 1.0
CD F:GLU537 4.5 19.2 1.0
OE1 B:GLN457 4.6 32.2 1.0
N F:TRS607 4.7 37.4 1.0

Nickel binding site 3 out of 7 in 8cwt

Go back to Nickel Binding Sites List in 8cwt
Nickel binding site 3 out of 7 in the Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni603

b:25.2
occ:1.00
 N B:HIS440 1.8 25.1 1.0
ND1 B:HIS441 1.8 13.0 1.0
N B:ALA439 1.9 28.1 1.0
N B:HIS441 1.9 20.3 1.0
C B:HIS440 2.7 23.1 1.0
C B:ALA439 2.7 31.2 1.0
CE1 B:HIS441 2.7 23.3 1.0
CA B:HIS440 2.8 25.8 1.0
CA B:ALA439 2.8 33.4 1.0
CG B:HIS441 3.0 21.0 1.0
O B:HOH799 3.1 32.8 1.0
CA B:HIS441 3.1 18.7 1.0
CB B:HIS441 3.4 19.8 1.0
CD2 B:HIS440 3.6 26.3 1.0
CB B:ALA439 3.8 36.7 1.0
O B:ALA439 3.9 33.5 1.0
CB B:HIS440 3.9 27.8 1.0
O B:HIS440 3.9 26.9 1.0
CE1 D:HIS442 4.0 20.8 1.0
CG B:HIS440 4.0 28.6 1.0
NE2 B:HIS441 4.0 25.6 1.0
N B:HIS442 4.0 16.6 1.0
C B:HIS441 4.0 19.4 1.0
CD2 B:HIS441 4.1 22.5 1.0
O1 D:SO4603 4.1 37.8 0.5
ND1 D:HIS442 4.3 21.2 1.0
NE2 B:HIS440 4.7 24.4 1.0
NE2 D:HIS442 4.8 19.4 1.0
O B:HOH780 4.8 33.3 1.0
O2 D:SO4603 5.0 34.4 0.5

Nickel binding site 4 out of 7 in 8cwt

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Nickel binding site 4 out of 7 in the Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni601

b:25.3
occ:1.00
 ND1 D:HIS441 1.8 12.4 1.0
N D:HIS440 1.8 26.0 1.0
N D:HIS441 1.9 20.2 1.0
N D:ALA439 1.9 30.6 1.0
C D:HIS440 2.7 24.1 1.0
C D:ALA439 2.7 34.2 1.0
CE1 D:HIS441 2.8 24.6 1.0
CA D:HIS440 2.8 27.0 1.0
CA D:ALA439 2.8 35.7 1.0
CG D:HIS441 3.0 21.4 1.0
O D:HOH788 3.1 32.5 1.0
CA D:HIS441 3.1 19.5 1.0
CB D:HIS441 3.4 21.5 1.0
CD2 D:HIS440 3.6 24.8 1.0
CB D:ALA439 3.7 36.0 1.0
CB D:HIS440 3.9 26.7 1.0
O D:ALA439 3.9 35.9 1.0
O D:HIS440 3.9 24.9 1.0
CE1 F:HIS442 4.0 21.1 1.0
CG D:HIS440 4.0 26.7 1.0
N D:HIS442 4.0 17.0 1.0
NE2 D:HIS441 4.0 25.7 1.0
C D:HIS441 4.0 19.1 1.0
CD2 D:HIS441 4.1 21.2 1.0
O D:HOH701 4.1 48.8 1.0
O4 F:SO4603 4.2 37.4 0.5
ND1 F:HIS442 4.3 21.3 1.0
NE2 D:HIS440 4.7 23.8 1.0
NE2 F:HIS442 4.8 19.8 1.0
O D:HOH771 4.9 33.3 1.0

Nickel binding site 5 out of 7 in 8cwt

Go back to Nickel Binding Sites List in 8cwt
Nickel binding site 5 out of 7 in the Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni602

b:19.0
occ:1.00
 NE2 D:HIS444 2.1 19.1 1.0
NE2 B:HIS440 2.1 24.4 1.0
NE2 D:HIS442 2.1 19.4 1.0
O2 B:TRS610 2.1 20.1 1.0
O1 B:TRS610 2.1 21.6 1.0
O3 B:TRS610 2.1 24.6 1.0
CE1 B:HIS440 3.0 27.5 1.0
C2 B:TRS610 3.0 30.3 1.0
CE1 D:HIS442 3.0 20.8 1.0
CE1 D:HIS444 3.0 21.0 1.0
C1 B:TRS610 3.1 29.3 1.0
CD2 D:HIS444 3.1 17.8 1.0
CD2 D:HIS442 3.1 18.4 1.0
CD2 B:HIS440 3.1 26.3 1.0
C B:TRS610 3.2 33.4 1.0
C3 B:TRS610 3.3 36.4 1.0
OE2 B:GLU537 4.0 19.7 1.0
ND1 B:HIS440 4.1 29.4 1.0
ND1 D:HIS442 4.1 21.2 1.0
ND1 D:HIS444 4.2 20.2 1.0
OE1 B:GLU537 4.2 20.2 1.0
CG D:HIS444 4.2 18.8 1.0
CG D:HIS442 4.2 18.8 1.0
CG B:HIS440 4.3 28.6 1.0
O B:HOH749 4.4 49.7 1.0
CD B:GLU537 4.5 19.9 1.0
OE1 D:GLN457 4.7 33.9 1.0
N B:TRS610 4.7 35.8 1.0
O D:HOH726 5.0 51.5 1.0

Nickel binding site 6 out of 7 in 8cwt

Go back to Nickel Binding Sites List in 8cwt
Nickel binding site 6 out of 7 in the Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni601

b:19.1
occ:1.00
 NE2 D:HIS440 2.0 23.8 1.0
NE2 F:HIS442 2.1 19.8 1.0
NE2 F:HIS444 2.1 19.3 1.0
O2 D:TRS609 2.1 21.0 1.0
O3 D:TRS609 2.1 21.7 1.0
O1 D:TRS609 2.1 38.7 1.0
C1 D:TRS609 2.3 25.5 1.0
C D:TRS609 2.9 30.3 1.0
CE1 D:HIS440 3.0 26.6 1.0
C3 D:TRS609 3.0 27.1 1.0
CE1 F:HIS442 3.0 21.1 1.0
CE1 F:HIS444 3.1 20.7 1.0
C2 D:TRS609 3.1 28.7 1.0
CD2 F:HIS444 3.1 17.5 1.0
CD2 F:HIS442 3.1 17.7 1.0
CD2 D:HIS440 3.1 24.8 1.0
OE2 D:GLU537 4.0 20.9 1.0
ND1 D:HIS440 4.1 29.6 1.0
ND1 F:HIS442 4.1 21.3 1.0
OE1 D:GLU537 4.2 20.7 1.0
ND1 F:HIS444 4.2 20.4 1.0
CG F:HIS442 4.2 18.3 1.0
CG D:HIS440 4.2 26.7 1.0
CG F:HIS444 4.2 18.6 1.0
N D:TRS609 4.4 34.4 1.0
CD D:GLU537 4.5 21.0 1.0
OE1 F:GLN457 4.6 34.8 1.0
O F:HOH722 4.9 47.9 1.0

Nickel binding site 7 out of 7 in 8cwt

Go back to Nickel Binding Sites List in 8cwt
Nickel binding site 7 out of 7 in the Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group P43212 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni602

b:24.6
occ:1.00
 ND1 F:HIS441 1.8 14.2 1.0
N F:HIS440 1.9 24.9 1.0
N F:ALA439 1.9 29.1 1.0
N F:HIS441 1.9 20.2 1.0
CE1 F:HIS441 2.7 24.7 1.0
C F:HIS440 2.7 23.1 1.0
C F:ALA439 2.7 29.8 1.0
CA F:HIS440 2.8 27.0 1.0
CA F:ALA439 2.8 31.4 1.0
O F:HOH778 3.0 34.8 1.0
CG F:HIS441 3.0 20.4 1.0
CA F:HIS441 3.1 19.5 1.0
CB F:HIS441 3.4 20.1 1.0
CD2 F:HIS440 3.6 25.3 1.0
CB F:ALA439 3.7 33.3 1.0
O F:ALA439 3.9 32.4 1.0
O F:HIS440 3.9 25.8 1.0
CE1 B:HIS442 3.9 20.0 1.0
CB F:HIS440 3.9 26.9 1.0
NE2 F:HIS441 3.9 26.4 1.0
N F:HIS442 4.0 17.3 1.0
CG F:HIS440 4.0 25.2 1.0
C F:HIS441 4.0 18.4 1.0
CD2 F:HIS441 4.1 21.4 1.0
O2 B:SO4605 4.1 36.4 0.6
ND1 B:HIS442 4.2 19.7 1.0
NE2 F:HIS440 4.8 24.5 1.0
NE2 B:HIS442 4.8 18.6 1.0
O F:HOH758 4.9 31.7 1.0
O4 B:SO4605 4.9 31.7 0.6

Reference:

T.Wan, M.Horova, V.Khetrapal, S.Li, C.Jones, A.Schacht, X.Sun, L.Zhang. Structural Basis of Dna Binding By the Whib-Like Transcription Factor WHIB3 in Mycobacterium Tuberculosis. J.Biol.Chem. 04777 2023.
ISSN: ESSN 1083-351X
PubMed: 37142222
DOI: 10.1016/J.JBC.2023.104777
Page generated: Thu Oct 10 09:39:10 2024

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