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Zinc in PDB 6x91: Crystal Structure of Mbp-Fused Human APOBEC1

Enzymatic activity of Crystal Structure of Mbp-Fused Human APOBEC1

All present enzymatic activity of Crystal Structure of Mbp-Fused Human APOBEC1:
3.5.4.36;

Protein crystallography data

The structure of Crystal Structure of Mbp-Fused Human APOBEC1, PDB code: 6x91 was solved by A.D.Wolfe, S.-X.Li, X.S.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.61 / 3.51
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 177.715, 179.209, 210.505, 90.00, 90.00, 90.00
R / Rfree (%) 27.6 / 29.8

Other elements in 6x91:

The structure of Crystal Structure of Mbp-Fused Human APOBEC1 also contains other interesting chemical elements:

Arsenic (As) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Mbp-Fused Human APOBEC1 (pdb code 6x91). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Mbp-Fused Human APOBEC1, PDB code: 6x91:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6x91

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Zinc binding site 1 out of 8 in the Crystal Structure of Mbp-Fused Human APOBEC1


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 Mbp-Fused Human APOBEC1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1301

b:0.4
occ:1.00
 O2 A:CAC1302 1.9 0.5 1.0
CG A:HIS1061 2.2 0.7 1.0
SG A:CYS1093 2.3 99.0 1.0
SG A:CYS1096 2.3 0.9 1.0
ND1 A:HIS1061 2.3 0.4 1.0
CD2 A:HIS1061 2.5 1.0 1.0
CE1 A:HIS1061 2.8 0.9 1.0
CB A:HIS1061 2.8 0.7 1.0
NE2 A:HIS1061 2.9 0.9 1.0
AS A:CAC1302 3.4 0.1 1.0
CB A:CYS1093 3.6 96.7 1.0
CB A:CYS1096 3.7 0.9 1.0
C2 A:CAC1302 4.1 0.3 1.0
C1 A:CAC1302 4.1 0.1 1.0
CA A:HIS1061 4.2 0.9 1.0
N A:CYS1093 4.3 97.9 1.0
N A:CYS1096 4.5 0.4 1.0
CA A:CYS1093 4.6 96.4 1.0
CA A:CYS1096 4.6 0.8 1.0
O1 A:CAC1302 4.7 0.8 1.0
N A:HIS1061 5.0 0.5 1.0

Zinc binding site 2 out of 8 in 6x91

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Zinc binding site 2 out of 8 in the Crystal Structure of Mbp-Fused Human APOBEC1


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 Mbp-Fused Human APOBEC1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:0.4
occ:1.00
 O2 B:CAC1302 2.1 0.7 1.0
CG B:HIS1061 2.1 0.8 1.0
CD2 B:HIS1061 2.3 1.0 1.0
SG B:CYS1096 2.3 0.1 1.0
ND1 B:HIS1061 2.3 0.8 1.0
SG B:CYS1093 2.3 0.3 1.0
NE2 B:HIS1061 2.6 0.7 1.0
CE1 B:HIS1061 2.6 0.6 1.0
CB B:HIS1061 2.9 0.5 1.0
CB B:CYS1096 3.6 0.9 1.0
CB B:CYS1093 3.7 0.7 1.0
AS B:CAC1302 3.8 0.9 1.0
N B:CYS1096 4.2 0.2 1.0
N B:CYS1093 4.4 0.4 1.0
CA B:HIS1061 4.4 0.5 1.0
C1 B:CAC1302 4.4 91.4 1.0
CA B:CYS1096 4.4 0.2 1.0
CA B:CYS1093 4.6 0.5 1.0
O1 B:CAC1302 4.7 0.6 1.0
N B:HIS1061 5.0 0.1 1.0
C2 B:CAC1302 5.0 0.2 1.0

Zinc binding site 3 out of 8 in 6x91

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Zinc binding site 3 out of 8 in the Crystal Structure of Mbp-Fused Human APOBEC1


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 Mbp-Fused Human APOBEC1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1301

b:0.5
occ:1.00
 O2 C:CAC1302 2.0 76.7 1.0
CG C:HIS1061 2.2 0.4 1.0
SG C:CYS1096 2.3 92.7 1.0
SG C:CYS1093 2.3 82.5 1.0
ND1 C:HIS1061 2.3 0.4 1.0
CD2 C:HIS1061 2.6 0.4 1.0
CE1 C:HIS1061 2.7 0.9 1.0
NE2 C:HIS1061 2.9 0.9 1.0
CB C:HIS1061 2.9 0.4 1.0
AS C:CAC1302 3.4 0.3 1.0
CB C:CYS1096 3.5 78.8 1.0
CB C:CYS1093 3.7 80.1 1.0
O1 C:CAC1302 3.8 0.2 1.0
N C:CYS1096 4.0 85.1 1.0
CA C:CYS1096 4.3 81.2 1.0
CA C:HIS1061 4.3 0.8 1.0
N C:CYS1093 4.3 77.7 1.0
C2 C:CAC1302 4.4 98.9 1.0
CA C:CYS1093 4.6 84.2 1.0
C1 C:CAC1302 5.0 0.6 1.0
CB C:GLU1095 5.0 98.5 1.0

Zinc binding site 4 out of 8 in 6x91

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Zinc binding site 4 out of 8 in the Crystal Structure of Mbp-Fused Human APOBEC1


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 Mbp-Fused Human APOBEC1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1301

b:0.3
occ:1.00
 O2 D:CAC1302 2.2 0.8 1.0
ND1 D:HIS1061 2.3 0.8 1.0
SG D:CYS1096 2.3 0.4 1.0
SG D:CYS1093 2.3 0.8 1.0
CG D:HIS1061 2.4 0.9 1.0
CE1 D:HIS1061 2.6 0.2 1.0
CD2 D:HIS1061 2.7 0.5 1.0
NE2 D:HIS1061 2.8 0.4 1.0
CB D:HIS1061 3.1 0.1 1.0
CB D:CYS1096 3.6 0.4 1.0
AS D:CAC1302 3.8 0.8 1.0
CB D:CYS1093 3.8 0.4 1.0
O1 D:CAC1302 4.1 0.0 1.0
N D:CYS1096 4.2 0.2 1.0
N D:CYS1093 4.4 0.6 1.0
CA D:CYS1096 4.4 0.6 1.0
CA D:HIS1061 4.5 0.8 1.0
CA D:CYS1093 4.6 0.1 1.0
C2 D:CAC1302 4.9 0.9 1.0

Zinc binding site 5 out of 8 in 6x91

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Zinc binding site 5 out of 8 in the Crystal Structure of Mbp-Fused Human APOBEC1


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 Mbp-Fused Human APOBEC1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1301

b:0.8
occ:1.00
 O2 E:CAC1302 2.1 0.2 1.0
CG E:HIS1061 2.2 0.8 1.0
SG E:CYS1096 2.3 0.5 1.0
SG E:CYS1093 2.3 0.0 1.0
ND1 E:HIS1061 2.3 0.1 1.0
CD2 E:HIS1061 2.3 0.6 1.0
CE1 E:HIS1061 2.5 0.6 1.0
NE2 E:HIS1061 2.5 0.4 1.0
CB E:HIS1061 3.1 0.4 1.0
CB E:CYS1096 3.7 0.0 1.0
AS E:CAC1302 3.7 0.9 1.0
CB E:CYS1093 3.9 0.8 1.0
O1 E:CAC1302 4.1 0.6 1.0
N E:CYS1096 4.2 0.7 1.0
CA E:CYS1096 4.4 1.0 1.0
CA E:HIS1061 4.5 0.3 1.0
N E:CYS1093 4.6 0.6 1.0
C1 E:CAC1302 4.8 0.1 1.0
CA E:CYS1093 4.8 0.8 1.0

Zinc binding site 6 out of 8 in 6x91

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Zinc binding site 6 out of 8 in the Crystal Structure of Mbp-Fused Human APOBEC1


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 Mbp-Fused Human APOBEC1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1301

b:0.7
occ:1.00
 O2 F:CAC1302 2.0 99.5 1.0
CG F:HIS1061 2.1 0.1 1.0
CD2 F:HIS1061 2.3 0.5 1.0
SG F:CYS1096 2.3 98.6 1.0
ND1 F:HIS1061 2.3 0.3 1.0
SG F:CYS1093 2.3 0.5 1.0
NE2 F:HIS1061 2.6 0.2 1.0
CE1 F:HIS1061 2.6 0.0 1.0
CB F:HIS1061 2.9 0.7 1.0
CB F:CYS1096 3.6 98.1 1.0
CB F:CYS1093 3.7 0.6 1.0
AS F:CAC1302 3.8 0.9 1.0
N F:CYS1096 4.3 0.0 1.0
N F:CYS1093 4.3 0.2 1.0
CA F:HIS1061 4.4 0.7 1.0
CA F:CYS1096 4.4 0.5 1.0
C1 F:CAC1302 4.5 94.0 1.0
CA F:CYS1093 4.6 0.2 1.0
O1 F:CAC1302 4.7 0.2 1.0
C2 F:CAC1302 4.8 0.8 1.0
N F:HIS1061 4.9 0.2 1.0

Zinc binding site 7 out of 8 in 6x91

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Zinc binding site 7 out of 8 in the Crystal Structure of Mbp-Fused Human APOBEC1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Mbp-Fused Human APOBEC1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn1301

b:0.2
occ:1.00
 O2 G:CAC1302 2.1 78.2 1.0
SG G:CYS1096 2.3 0.5 1.0
SG G:CYS1093 2.3 89.7 1.0
ND1 G:HIS1061 2.3 0.4 1.0
CG G:HIS1061 2.3 0.4 1.0
CE1 G:HIS1061 2.8 0.3 1.0
CD2 G:HIS1061 2.9 0.8 1.0
CB G:HIS1061 3.0 0.3 1.0
NE2 G:HIS1061 3.1 0.7 1.0
CB G:CYS1096 3.4 94.4 1.0
AS G:CAC1302 3.8 0.0 1.0
CB G:CYS1093 3.8 83.1 1.0
N G:CYS1096 3.9 83.0 1.0
CA G:CYS1096 4.1 90.0 1.0
CA G:HIS1061 4.4 0.9 1.0
N G:CYS1093 4.4 82.2 1.0
C2 G:CAC1302 4.5 92.1 1.0
CA G:CYS1093 4.6 87.5 1.0
C1 G:CAC1302 4.7 0.9 1.0
O1 G:CAC1302 4.8 0.1 1.0
CB G:GLU1095 4.8 0.2 1.0
C G:GLU1095 4.9 99.3 1.0

Zinc binding site 8 out of 8 in 6x91

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Zinc binding site 8 out of 8 in the Crystal Structure of Mbp-Fused Human APOBEC1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Mbp-Fused Human APOBEC1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn1301

b:0.7
occ:1.00
 O2 H:CAC1302 1.9 0.3 1.0
ND1 H:HIS1061 2.3 0.4 1.0
SG H:CYS1093 2.3 0.8 1.0
SG H:CYS1096 2.3 0.4 1.0
CE1 H:HIS1061 3.0 0.2 1.0
CG H:HIS1061 3.2 0.5 1.0
CB H:CYS1096 3.5 0.6 1.0
AS H:CAC1302 3.6 0.0 1.0
CB H:CYS1093 3.6 0.1 1.0
CB H:HIS1061 3.6 0.9 1.0
NE2 H:HIS1061 4.0 0.4 1.0
CD2 H:HIS1061 4.1 0.2 1.0
N H:CYS1093 4.2 0.9 1.0
O1 H:CAC1302 4.3 0.4 1.0
N H:CYS1096 4.4 0.8 1.0
C1 H:CAC1302 4.4 0.0 1.0
CA H:CYS1093 4.5 0.7 1.0
CA H:CYS1096 4.5 0.2 1.0
C2 H:CAC1302 4.9 0.7 1.0

Reference:

A.D.Wolfe, S.Li, C.Goedderz, X.S.Chen. The Structure of APOBEC1 and Insights Into Its Rna and Dna Substrate Selectivity. Nar Cancer V. 2 AA027 2020.
ISSN: ISSN 2632-8674
PubMed: 33094286
DOI: 10.1093/NARCAN/ZCAA027
Page generated: Tue Oct 29 10:39:23 2024

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