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Zinc in PDB 3wus: Crystal Structure of the Vif-Binding Domain of Human APOBEC3F

Protein crystallography data

The structure of Crystal Structure of the Vif-Binding Domain of Human APOBEC3F, PDB code: 3wus was solved by M.Nakashima, T.Kawamura, 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) 50.00 / 2.54
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.294, 117.294, 78.960, 90.00, 90.00, 120.00
R / Rfree (%) 20 / 25.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Vif-Binding Domain of Human APOBEC3F (pdb code 3wus). 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 Vif-Binding Domain of Human APOBEC3F, PDB code: 3wus:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3wus

Go back to Zinc Binding Sites List in 3wus
Zinc binding site 1 out of 2 in the Crystal Structure of the Vif-Binding Domain of Human APOBEC3F


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 Vif-Binding Domain of Human APOBEC3F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:70.6
occ:1.00
ND1 A:HIS249 2.0 75.6 1.0
SG A:CYS283 2.2 69.5 1.0
O A:HOH501 2.2 49.1 1.0
SG A:CYS280 2.5 72.2 1.0
CG A:HIS249 2.9 78.0 1.0
CE1 A:HIS249 3.0 78.5 1.0
CB A:CYS283 3.1 60.6 1.0
CB A:HIS249 3.3 69.2 1.0
CB A:CYS280 3.4 68.1 1.0
OE2 A:GLU251 3.9 64.9 1.0
NE2 A:HIS249 4.0 77.9 1.0
CD2 A:HIS249 4.0 76.5 1.0
N A:CYS280 4.1 69.0 1.0
N A:CYS283 4.1 64.4 1.0
CA A:CYS283 4.2 60.5 1.0
CA A:CYS280 4.3 69.8 1.0
CD A:GLU251 4.6 59.2 1.0
O A:CYS280 4.8 67.2 1.0
CA A:HIS249 4.8 70.3 1.0
NE A:ARG252 4.8 0.1 1.0
C A:CYS280 4.8 67.3 1.0
OE1 A:GLU251 4.8 60.0 1.0

Zinc binding site 2 out of 2 in 3wus

Go back to Zinc Binding Sites List in 3wus
Zinc binding site 2 out of 2 in the Crystal Structure of the Vif-Binding Domain of Human APOBEC3F


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 Vif-Binding Domain of Human APOBEC3F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:61.8
occ:1.00
O B:HOH501 2.0 39.8 1.0
SG B:CYS280 2.2 53.4 1.0
SG B:CYS283 2.3 57.3 1.0
ND1 B:HIS249 2.4 82.7 1.0
CG B:HIS249 3.0 75.4 1.0
CE1 B:HIS249 3.1 82.1 1.0
CB B:CYS283 3.1 46.8 1.0
CB B:HIS249 3.4 66.8 1.0
CB B:CYS280 3.5 45.7 1.0
CD2 B:HIS249 3.8 75.5 1.0
NE2 B:HIS249 3.9 78.6 1.0
N B:CYS280 3.9 46.4 1.0
OE2 B:GLU251 4.0 61.1 1.0
N B:CYS283 4.1 47.6 1.0
CA B:CYS283 4.2 45.9 1.0
CA B:CYS280 4.3 51.8 1.0
CD B:GLU251 4.5 57.9 1.0
OE1 B:GLU251 4.6 62.5 1.0
O B:CYS280 4.8 52.9 1.0
C B:CYS280 4.9 55.7 1.0
CA B:HIS249 4.9 61.6 1.0

Reference:

M.Nakashima, H.Ode, T.Kawamura, S.Kitamura, Y.Naganawa, H.Awazu, S.Tsuzuki, K.Matsuoka, M.Nemoto, A.Hachiya, W.Sugiura, Y.Yokomaku, N.Watanabe, Y.Iwatani. Structural Insights Into Hiv-1 Vif-APOBEC3F Interaction. J.Virol. V. 90 1034 2015.
ISSN: ISSN 0022-538X
PubMed: 26537685
DOI: 10.1128/JVI.02369-15
Page generated: Wed Dec 16 04:58:05 2020

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