Zinc in PDB 6bwy: Dna Substrate Selection By APOBEC3G

Protein crystallography data

The structure of Dna Substrate Selection By APOBEC3G, PDB code: 6bwy was solved by S.J.Ziegler, O.Buzovetsky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.19 / 2.90
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 79.072, 79.072, 266.411, 90.00, 90.00, 90.00
R / Rfree (%) 23.4 / 28.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Dna Substrate Selection By APOBEC3G (pdb code 6bwy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Dna Substrate Selection By APOBEC3G, PDB code: 6bwy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6bwy

Go back to Zinc Binding Sites List in 6bwy
Zinc binding site 1 out of 4 in the Dna Substrate Selection By APOBEC3G


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dna Substrate Selection By APOBEC3G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:0.6
occ:1.00
ND1 A:HIS257 2.1 75.8 1.0
CE1 A:HIS257 2.5 77.8 1.0
SG A:CYS291 2.6 81.2 1.0
SG A:CYS288 2.6 79.1 1.0
CB A:CYS288 3.2 71.1 1.0
OE2 A:GLU259 3.3 77.4 1.0
N A:CYS288 3.4 82.6 1.0
CG A:HIS257 3.4 77.1 1.0
CB A:CYS291 3.6 85.0 1.0
CD A:GLU259 3.7 76.2 1.0
OE1 A:GLU259 3.7 74.5 1.0
NE2 A:HIS257 3.8 80.0 1.0
CA A:CYS288 3.9 79.4 1.0
CB A:HIS257 4.2 77.8 1.0
CD2 A:HIS257 4.2 76.0 1.0
O A:HOH511 4.3 73.5 1.0
C A:PRO287 4.5 76.6 1.0
N A:CYS291 4.5 86.3 1.0
CA A:PRO287 4.6 74.1 1.0
CA A:CYS291 4.7 84.4 1.0
CG A:GLU259 4.7 75.7 1.0
C A:CYS288 4.7 87.5 1.0
O A:CYS288 4.9 99.4 1.0

Zinc binding site 2 out of 4 in 6bwy

Go back to Zinc Binding Sites List in 6bwy
Zinc binding site 2 out of 4 in the Dna Substrate Selection By APOBEC3G


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dna Substrate Selection By APOBEC3G within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:73.0
occ:1.00
SG B:CYS291 1.9 52.4 1.0
ND1 B:HIS257 2.3 67.0 1.0
SG B:CYS288 2.9 65.5 1.0
CE1 B:HIS257 3.1 61.7 1.0
CG B:HIS257 3.2 65.2 1.0
CB B:CYS291 3.3 65.1 1.0
OE2 B:GLU259 3.3 62.2 1.0
N B:CYS288 3.5 62.6 1.0
CB B:HIS257 3.5 70.1 1.0
CB B:CYS288 3.6 73.0 1.0
CD B:GLU259 3.8 57.6 1.0
OE1 B:GLU259 3.9 66.2 1.0
CA B:CYS288 4.0 72.2 1.0
NE2 B:HIS257 4.0 63.5 1.0
CD2 B:HIS257 4.1 63.1 1.0
N B:CYS291 4.2 60.4 1.0
CA B:CYS291 4.3 65.0 1.0
C B:PRO287 4.6 55.8 1.0
O B:HOH511 4.6 65.1 1.0
CG B:GLU259 4.7 50.6 1.0
C B:CYS288 4.8 73.4 1.0
CA B:PRO287 4.9 56.4 1.0
O B:CYS288 4.9 70.0 1.0
CB B:GLU259 5.0 55.1 1.0

Zinc binding site 3 out of 4 in 6bwy

Go back to Zinc Binding Sites List in 6bwy
Zinc binding site 3 out of 4 in the Dna Substrate Selection By APOBEC3G


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Dna Substrate Selection By APOBEC3G within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:0.8
occ:1.00
SG E:CYS291 1.9 89.1 1.0
ND1 E:HIS257 1.9 0.2 1.0
CE1 E:HIS257 2.2 0.9 1.0
SG E:CYS288 2.3 74.2 1.0
CG E:HIS257 2.8 98.8 1.0
CB E:CYS291 3.0 96.5 1.0
NE2 E:HIS257 3.0 0.1 1.0
CB E:CYS288 3.3 80.1 1.0
CD2 E:HIS257 3.3 95.6 1.0
N E:CYS288 3.6 77.5 1.0
OE1 E:GLU259 3.6 94.5 1.0
CB E:HIS257 3.7 0.1 1.0
N E:CYS291 3.7 95.2 1.0
CA E:CYS291 3.9 96.0 1.0
CA E:CYS288 4.0 79.3 1.0
CD E:GLU259 4.0 87.2 1.0
OE2 E:GLU259 4.3 85.3 1.0
C E:CYS288 4.5 85.2 1.0
O E:CYS288 4.6 91.1 1.0
C E:PRO287 4.6 78.7 1.0
C E:SER290 4.8 94.1 1.0
CA E:PRO287 4.8 79.3 1.0
CG E:GLU259 4.8 84.3 1.0
N E:SER290 5.0 97.3 1.0
CB E:GLU259 5.0 81.5 1.0
CB E:SER290 5.0 89.2 1.0

Zinc binding site 4 out of 4 in 6bwy

Go back to Zinc Binding Sites List in 6bwy
Zinc binding site 4 out of 4 in the Dna Substrate Selection By APOBEC3G


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Dna Substrate Selection By APOBEC3G within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn401

b:0.8
occ:1.00
ND1 G:HIS257 1.8 89.6 1.0
CE1 G:HIS257 2.1 85.3 1.0
SG G:CYS291 2.3 55.8 1.0
SG G:CYS288 2.3 62.0 1.0
CG G:HIS257 2.9 93.7 1.0
NE2 G:HIS257 3.2 74.2 1.0
CB G:CYS288 3.3 50.7 1.0
CB G:CYS291 3.4 66.6 1.0
CD2 G:HIS257 3.6 81.1 1.0
N G:CYS288 3.7 57.6 1.0
OE2 G:GLU259 3.7 69.9 1.0
CB G:HIS257 3.8 0.8 1.0
CA G:CYS288 4.0 56.6 1.0
N G:CYS291 4.1 62.0 1.0
CD G:GLU259 4.2 67.6 1.0
CA G:CYS291 4.4 64.5 1.0
OE1 G:GLU259 4.5 70.5 1.0
C G:CYS288 4.7 56.9 1.0
C G:PRO287 4.7 52.0 1.0
O G:CYS288 4.8 60.1 1.0

Reference:

S.J.Ziegler, C.Liu, M.Landau, O.Buzovetsky, B.A.Desimmie, Q.Zhao, T.Sasaki, R.C.Burdick, V.K.Pathak, K.S.Anderson, Y.Xiong. Insights Into Dna Substrate Selection By APOBEC3G From Structural, Biochemical, and Functional Studies. Plos One V. 13 95048 2018.
ISSN: ESSN 1932-6203
PubMed: 29596531
DOI: 10.1371/JOURNAL.PONE.0195048
Page generated: Wed Dec 16 11:33:34 2020

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