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Arsenic in PDB 5zvb: APOBEC3F Chimeric Catalytic Domain in Complex with Dna(DT9)

Protein crystallography data

The structure of APOBEC3F Chimeric Catalytic Domain in Complex with Dna(DT9), PDB code: 5zvb was solved by C.Cheng, T.L.Zhang, C.X.Wang, W.X.Lan, J.P.Ding, C.Y.Cao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.01 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.990, 92.702, 93.674, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 22

Other elements in 5zvb:

The structure of APOBEC3F Chimeric Catalytic Domain in Complex with Dna(DT9) also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Arsenic Binding Sites:

The binding sites of Arsenic atom in the APOBEC3F Chimeric Catalytic Domain in Complex with Dna(DT9) (pdb code 5zvb). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 2 binding sites of Arsenic where determined in the APOBEC3F Chimeric Catalytic Domain in Complex with Dna(DT9), PDB code: 5zvb:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in 5zvb

Go back to Arsenic Binding Sites List in 5zvb
Arsenic binding site 1 out of 2 in the APOBEC3F Chimeric Catalytic Domain in Complex with Dna(DT9)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of APOBEC3F Chimeric Catalytic Domain in Complex with Dna(DT9) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As402

b:0.0
occ:0.80
AS A:CAC402 0.0 0.0 0.8
O2 A:CAC402 1.7 63.2 0.8
O1 A:CAC402 1.7 47.8 0.8
C2 A:CAC402 2.0 79.3 0.8
C1 A:CAC402 2.0 68.0 0.8
OE2 A:GLU251 3.5 43.7 1.0
ZN A:ZN401 3.6 40.4 1.0
ND1 A:HIS249 3.6 39.2 1.0
OG1 A:THR-2 3.6 37.5 1.0
OE1 A:GLU251 3.7 37.9 1.0
CG A:HIS249 4.0 41.0 1.0
CD A:GLU251 4.1 37.4 1.0
CE1 A:HIS249 4.1 44.7 1.0
N A:CYS280 4.3 35.3 1.0
O A:HOH536 4.3 56.4 1.0
CB A:HIS249 4.4 35.3 1.0
CB A:THR-2 4.5 33.1 1.0
O A:SER278 4.6 28.4 1.0
NE2 A:HIS249 4.6 48.1 1.0
CD2 A:HIS249 4.6 45.1 1.0
OD1 A:ASN240 4.7 39.1 1.0
CB A:CYS280 4.7 37.0 1.0
CG2 A:THR-2 4.7 33.4 1.0
CA A:PRO279 4.8 32.4 1.0
SG A:CYS280 4.9 38.0 1.0
C A:PRO279 5.0 35.7 1.0

Arsenic binding site 2 out of 2 in 5zvb

Go back to Arsenic Binding Sites List in 5zvb
Arsenic binding site 2 out of 2 in the APOBEC3F Chimeric Catalytic Domain in Complex with Dna(DT9)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of APOBEC3F Chimeric Catalytic Domain in Complex with Dna(DT9) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As402

b:55.2
occ:0.80
AS B:CAC402 0.0 55.2 0.8
O1 B:CAC402 1.7 54.0 0.8
O2 B:CAC402 1.7 48.8 0.8
C1 B:CAC402 2.0 48.9 0.8
C2 B:CAC402 2.0 43.7 0.8
OE2 B:GLU251 3.2 54.3 1.0
ZN B:ZN401 3.3 50.8 1.0
OG1 B:THR-2 3.9 44.3 1.0
OE1 B:GLU251 3.9 50.7 1.0
N B:CYS280 3.9 45.0 1.0
ND1 B:HIS249 3.9 56.9 1.0
CD B:GLU251 4.0 48.8 1.0
O4 C:DT9 4.2 59.5 1.0
CG B:HIS249 4.3 54.5 1.0
CB B:CYS280 4.4 54.2 1.0
SG B:CYS280 4.4 47.2 1.0
O B:SER278 4.4 39.2 1.0
CE1 B:HIS249 4.4 60.5 1.0
CA B:PRO279 4.5 40.0 1.0
CB B:HIS249 4.5 49.7 1.0
CE2 B:TYR307 4.5 47.2 1.0
CB B:THR-2 4.6 41.5 1.0
CD2 B:TYR307 4.6 44.0 1.0
C B:PRO279 4.6 45.1 1.0
CG2 B:THR-2 4.6 42.9 1.0
CA B:CYS280 4.8 51.5 1.0
SG B:CYS283 4.9 50.1 1.0
CD2 B:HIS249 5.0 55.7 1.0

Reference:

C.Cheng, T.Zhang, C.Wang, W.Lan, J.Ding, C.Cao. Crystal Structure of Cytidine Deaminase Human APOBEC3F Chimeric Catalytic Domain in Complex with Dna Chin.J.Chem. V. 36 1241 2018.
ISSN: ISSN 1001-604X
DOI: 10.1002/CJOC.201800508
Page generated: Wed Jul 10 13:13:06 2024

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