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Zinc in PDB 5z98: Crystal Structure of the Primate APOBEC3H Dimer Mediated By Rna Duplex

Protein crystallography data

The structure of Crystal Structure of the Primate APOBEC3H Dimer Mediated By Rna Duplex, PDB code: 5z98 was solved by T.Matsuoka, T.Nagae, H.Ode, N.Watanabe, Y.Iwatani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.49 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 38.341, 86.970, 77.363, 90.00, 102.63, 90.00
R / Rfree (%) 25.1 / 32

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Primate APOBEC3H Dimer Mediated By Rna Duplex (pdb code 5z98). 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 the Primate APOBEC3H Dimer Mediated By Rna Duplex, PDB code: 5z98:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5z98

Go back to Zinc Binding Sites List in 5z98
Zinc binding site 1 out of 2 in the Crystal Structure of the Primate APOBEC3H Dimer Mediated By Rna Duplex


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 the Primate APOBEC3H Dimer Mediated By Rna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn300

b:44.0
occ:1.00
SG A:CYS85 2.0 52.3 1.0
ND1 A:HIS54 2.1 41.3 1.0
O A:HOH409 2.1 42.6 1.0
SG A:CYS88 2.3 46.1 1.0
CB A:CYS85 2.4 41.9 1.0
CE1 A:HIS54 3.0 49.6 1.0
CG A:HIS54 3.2 44.3 1.0
CB A:CYS88 3.3 42.5 1.0
CA A:CYS85 3.5 43.5 1.0
N A:CYS85 3.6 45.6 1.0
CB A:HIS54 3.6 45.3 1.0
OE2 A:GLU56 3.8 39.8 1.0
N A:CYS88 4.1 40.5 1.0
NE2 A:HIS54 4.1 51.5 1.0
CD2 A:HIS54 4.2 47.2 1.0
OE1 A:GLU56 4.3 40.9 1.0
CA A:CYS88 4.3 40.0 1.0
CD A:GLU56 4.4 41.1 1.0
O A:HOH440 4.4 34.2 1.0
O A:HOH431 4.4 45.9 1.0
O A:HOH433 4.4 43.9 1.0
C A:CYS85 4.7 44.8 1.0
O A:HOH412 4.7 39.3 1.0
C A:PRO84 4.8 41.5 1.0
O A:HOH434 4.9 47.6 1.0

Zinc binding site 2 out of 2 in 5z98

Go back to Zinc Binding Sites List in 5z98
Zinc binding site 2 out of 2 in the Crystal Structure of the Primate APOBEC3H Dimer Mediated By Rna Duplex


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 the Primate APOBEC3H Dimer Mediated By Rna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn300

b:55.0
occ:1.00
SG B:CYS85 2.2 47.6 1.0
ND1 B:HIS54 2.3 46.9 1.0
SG B:CYS88 2.5 57.0 1.0
CB B:CYS85 2.7 45.5 1.0
CE1 B:HIS54 3.0 59.4 1.0
CB B:CYS88 3.1 49.4 1.0
CG B:HIS54 3.5 60.0 1.0
N B:CYS85 3.8 49.2 1.0
OE1 B:GLU56 3.8 58.6 1.0
CA B:CYS85 3.8 49.7 1.0
OE2 B:GLU56 3.8 54.1 1.0
CB B:HIS54 4.0 58.5 1.0
N B:CYS88 4.1 42.9 1.0
CD B:GLU56 4.1 56.5 1.0
CA B:CYS88 4.2 45.9 1.0
NE2 B:HIS54 4.2 62.2 1.0
CD2 B:HIS54 4.5 56.8 1.0
C B:PRO84 5.0 44.5 1.0
C B:CYS85 5.0 43.8 1.0

Reference:

T.Matsuoka, T.Nagae, H.Ode, H.Awazu, T.Kurosawa, A.Hamano, K.Matsuoka, A.Hachiya, M.Imahashi, Y.Yokomaku, N.Watanabe, Y.Iwatani. Structural Basis of Chimpanzee APOBEC3H Dimerization Stabilized By Double-Stranded Rna. Nucleic Acids Res. V. 46 10368 2018.
ISSN: ESSN 1362-4962
PubMed: 30060196
DOI: 10.1093/NAR/GKY676
Page generated: Wed Dec 16 11:25:41 2020

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