Zinc in PDB 6bwy: Dna Substrate Selection By APOBEC3G

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

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 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 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 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 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

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