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Nickel in PDB 8cwr: Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group R3

Enzymatic activity of Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group R3

All present enzymatic activity of Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group R3:
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 R3, PDB code: 8cwr 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) 34.87 / 1.50
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 120.809, 120.809, 31.758, 90, 90, 120
R / Rfree (%) 18.3 / 21.2

Other elements in 8cwr:

The structure of Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group R3 also contains other interesting chemical elements:

Iron (Fe) 4 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 R3 (pdb code 8cwr). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group R3, PDB code: 8cwr:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 8cwr

Go back to Nickel Binding Sites List in 8cwr
Nickel binding site 1 out of 3 in the Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group R3


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 R3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni603

b:27.9
occ:1.00
 ND1 B:HIS441 2.0 23.1 1.0
N B:HIS440 2.0 30.1 1.0
N B:HIS441 2.0 21.8 1.0
N B:ALA439 2.0 27.1 1.0
C B:HIS440 2.8 24.2 1.0
C B:ALA439 2.8 39.8 1.0
CA B:ALA439 2.8 39.0 1.0
CE1 B:HIS441 2.9 30.3 1.0
CA B:HIS440 2.9 30.7 1.0
O B:HOH754 3.0 38.1 1.0
CG B:HIS441 3.0 24.5 1.0
CA B:HIS441 3.1 22.5 1.0
CB B:HIS441 3.3 23.7 1.0
CD2 B:HIS440 3.8 25.5 1.0
N B:HIS442 3.9 21.8 1.0
CB B:ALA439 3.9 47.8 1.0
O B:HIS440 4.0 29.4 1.0
O B:ALA439 4.0 38.8 1.0
C B:HIS441 4.0 28.1 1.0
O B:HOH718 4.0 53.2 1.0
NE2 B:HIS441 4.0 29.6 1.0
CB B:HIS440 4.0 34.6 1.0
CG B:HIS440 4.1 29.1 1.0
CD2 B:HIS441 4.1 25.0 1.0
O B:HOH738 4.6 38.3 1.0
NE2 B:HIS440 4.8 25.9 1.0

Nickel binding site 2 out of 3 in 8cwr

Go back to Nickel Binding Sites List in 8cwr
Nickel binding site 2 out of 3 in the Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group R3


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 R3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni604

b:23.6
occ:1.00
 NE2 B:HIS440 2.0 25.9 1.0
O1 B:TRS602 2.1 27.6 1.0
O2 B:TRS602 2.2 29.2 1.0
C3 B:TRS602 2.3 23.0 1.0
O3 B:TRS602 2.4 51.4 1.0
C B:TRS602 2.7 35.5 1.0
C1 B:TRS602 2.8 30.5 1.0
CE1 B:HIS440 2.9 36.8 1.0
C2 B:TRS602 2.9 39.1 1.0
CD2 B:HIS440 3.1 25.5 1.0
ND1 B:HIS440 4.0 39.1 1.0
OE2 B:GLU537 4.0 28.1 1.0
CG B:HIS440 4.2 29.1 1.0
OE1 B:GLU537 4.2 27.3 1.0
N B:TRS602 4.2 54.0 1.0
CD B:GLU537 4.5 28.1 1.0

Nickel binding site 3 out of 3 in 8cwr

Go back to Nickel Binding Sites List in 8cwr
Nickel binding site 3 out of 3 in the Complex Structure of WHIB3 and the SIGMAAR4-Rnap Beta Flap Tip Chimera in Space Group R3


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 R3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni605

b:18.1
occ:0.33
 NE2 B:HIS445 2.1 17.4 1.0
NE2 B:HIS443 2.2 18.2 1.0
CE1 B:HIS445 3.0 19.2 1.0
CD2 B:HIS445 3.1 17.3 1.0
CD2 B:HIS443 3.1 19.4 1.0
CE1 B:HIS443 3.2 18.9 1.0
ND1 B:HIS445 4.2 21.3 1.0
CG B:HIS445 4.2 19.7 1.0
CG B:HIS443 4.3 16.5 1.0
ND1 B:HIS443 4.3 19.8 1.0

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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