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Zinc in PDB 6bbo: Crystal Structure of Human APOBEC3H/Rna Complex

Protein crystallography data

The structure of Crystal Structure of Human APOBEC3H/Rna Complex, PDB code: 6bbo was solved by N.M.Shaban, K.Shi, S.Banerjee, R.S.Harris, H.Aihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.25 / 3.43
Space group P 31 1 2
Cell size a, b, c (Å), α, β, γ (°) 101.293, 101.293, 211.217, 90.00, 90.00, 120.00
R / Rfree (%) 36.4 / 39.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human APOBEC3H/Rna Complex (pdb code 6bbo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Human APOBEC3H/Rna Complex, PDB code: 6bbo:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6bbo

Go back to Zinc Binding Sites List in 6bbo
Zinc binding site 1 out of 2 in the Crystal Structure of Human APOBEC3H/Rna Complex


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 Human APOBEC3H/Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:96.8
occ:1.00
ND1 A:HIS54 2.0 98.3 1.0
SG A:CYS88 2.3 0.4 1.0
SG A:CYS85 2.3 78.6 1.0
O1 A:GOL202 2.4 65.4 1.0
CE1 A:HIS54 2.9 0.6 1.0
CG A:HIS54 3.1 95.1 1.0
CB A:CYS88 3.2 85.8 1.0
CB A:CYS85 3.4 0.9 1.0
C1 A:GOL202 3.4 82.9 1.0
CB A:HIS54 3.6 95.2 1.0
N A:CYS85 3.7 68.0 1.0
CA A:CYS85 4.1 79.5 1.0
NE2 A:HIS54 4.1 0.4 1.0
N A:CYS88 4.1 1.0 1.0
CD2 A:HIS54 4.2 0.4 1.0
CA A:CYS88 4.3 85.6 1.0
C2 A:GOL202 4.3 92.8 1.0
O2 A:GOL202 4.5 0.3 1.0
C A:CYS85 4.6 77.5 1.0
OG A:SER87 4.6 0.6 1.0
C A:PRO84 4.9 86.2 1.0
O A:CYS85 4.9 93.2 1.0

Zinc binding site 2 out of 2 in 6bbo

Go back to Zinc Binding Sites List in 6bbo
Zinc binding site 2 out of 2 in the Crystal Structure of Human APOBEC3H/Rna Complex


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 Human APOBEC3H/Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn201

b:0.4
occ:1.00
ND1 E:HIS54 2.0 79.8 1.0
SG E:CYS88 2.3 98.3 1.0
SG E:CYS85 2.3 0.3 1.0
O1 E:GOL202 2.3 45.4 1.0
CE1 E:HIS54 2.9 0.9 1.0
CG E:HIS54 3.1 66.9 1.0
CB E:CYS88 3.2 94.6 1.0
CB E:CYS85 3.4 0.5 1.0
C1 E:GOL202 3.4 84.6 1.0
CB E:HIS54 3.6 85.9 1.0
N E:CYS85 3.7 51.2 1.0
CA E:CYS85 4.0 69.3 1.0
NE2 E:HIS54 4.1 0.3 1.0
N E:CYS88 4.1 99.2 1.0
CD2 E:HIS54 4.2 88.2 1.0
CA E:CYS88 4.2 96.5 1.0
C2 E:GOL202 4.3 0.6 1.0
O2 E:GOL202 4.5 0.7 1.0
C E:CYS85 4.6 50.4 1.0
OG E:SER87 4.6 0.0 1.0
C E:PRO84 4.8 76.5 1.0
O E:CYS85 4.8 57.9 1.0

Reference:

N.M.Shaban, K.Shi, K.V.Lauer, M.A.Carpenter, C.M.Richards, D.Salamango, J.Wang, M.W.Lopresti, S.Banerjee, R.Levin-Klein, W.L.Brown, H.Aihara, R.S.Harris. The Antiviral and Cancer Genomic Dna Deaminase APOBEC3H Is Regulated By An Rna-Mediated Dimerization Mechanism. Mol. Cell V. 69 75 2018.
ISSN: ISSN 1097-4164
PubMed: 29290613
DOI: 10.1016/J.MOLCEL.2017.12.010
Page generated: Wed Dec 16 11:31:46 2020

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