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

Go back to Zinc Binding Sites List in 6x91
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

Go back to Zinc Binding Sites List in 6x91
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

Go back to Zinc Binding Sites List in 6x91
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

Go back to Zinc Binding Sites List in 6x91
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

Go back to Zinc Binding Sites List in 6x91
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

Go back to Zinc Binding Sites List in 6x91
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

Go back to Zinc Binding Sites List in 6x91
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

Go back to Zinc Binding Sites List in 6x91
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: Wed Dec 16 13:09:07 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy