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Zinc in PDB 2nyt: The APOBEC2 Crystal Structure and Functional Implications For Aid

Protein crystallography data

The structure of The APOBEC2 Crystal Structure and Functional Implications For Aid, PDB code: 2nyt was solved by C.Prochnow, R.Bransteitter, M.Klein, M.Goodman, X.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.841, 89.410, 245.770, 90.00, 90.00, 90.00
R / Rfree (%) 24.6 / 29.5

Zinc Binding Sites:

The binding sites of Zinc atom in the The APOBEC2 Crystal Structure and Functional Implications For Aid (pdb code 2nyt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The APOBEC2 Crystal Structure and Functional Implications For Aid, PDB code: 2nyt:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2nyt

Go back to Zinc Binding Sites List in 2nyt
Zinc binding site 1 out of 4 in the The APOBEC2 Crystal Structure and Functional Implications For Aid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The APOBEC2 Crystal Structure and Functional Implications For Aid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2000

b:25.5
occ:1.00
SG A:CYS131 2.1 33.9 1.0
ND1 A:HIS98 2.2 31.6 1.0
OE1 A:GLU60 2.3 37.8 1.0
SG A:CYS128 2.3 19.6 1.0
CB A:CYS131 3.0 30.6 1.0
CE1 A:HIS98 3.1 31.6 1.0
CD A:GLU60 3.2 36.9 1.0
CG A:HIS98 3.2 30.2 1.0
CB A:CYS128 3.4 19.7 1.0
OE2 A:GLU60 3.6 35.9 1.0
CB A:HIS98 3.6 29.1 1.0
OE1 A:GLU100 3.8 42.3 1.0
N A:CYS128 3.8 19.2 1.0
N A:CYS131 4.1 28.8 1.0
CA A:CYS131 4.1 29.6 1.0
CA A:CYS128 4.2 20.2 1.0
NE2 A:HIS98 4.2 30.9 1.0
NH2 A:ARG134 4.3 43.8 1.0
CD2 A:HIS98 4.3 30.5 1.0
CG A:GLU60 4.4 36.9 1.0
CB A:GLU60 4.4 35.2 1.0
CA A:GLU60 4.5 35.9 1.0
O A:GLU60 4.6 38.7 1.0
CD A:GLU100 4.6 41.5 1.0
C A:CYS128 4.9 21.5 1.0
O A:CYS128 4.9 21.2 1.0
C A:PRO127 4.9 19.1 1.0
C A:GLU60 5.0 37.6 1.0

Zinc binding site 2 out of 4 in 2nyt

Go back to Zinc Binding Sites List in 2nyt
Zinc binding site 2 out of 4 in the The APOBEC2 Crystal Structure and Functional Implications For Aid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The APOBEC2 Crystal Structure and Functional Implications For Aid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2001

b:31.2
occ:1.00
SG B:CYS131 2.2 32.8 1.0
ND1 B:HIS98 2.2 32.5 1.0
SG B:CYS128 2.5 24.2 1.0
CB B:CYS131 3.1 30.1 1.0
CE1 B:HIS98 3.1 32.5 1.0
CG B:HIS98 3.1 33.2 1.0
CB B:HIS98 3.5 30.9 1.0
CB B:CYS128 3.5 23.0 1.0
N B:CYS128 3.6 20.9 1.0
OE1 B:GLU100 3.8 30.4 1.0
NE2 B:HIS98 4.2 32.9 1.0
CA B:CYS128 4.2 22.9 1.0
CD2 B:HIS98 4.2 33.0 1.0
CA B:CYS131 4.3 29.9 1.0
N B:CYS131 4.3 28.8 1.0
CD B:GLU100 4.4 32.6 1.0
OE2 B:GLU100 4.6 34.0 1.0
C B:PRO127 4.7 19.1 1.0
CA B:PRO127 4.8 18.7 1.0
C B:CYS128 4.9 23.7 1.0
OE2 B:GLU101 5.0 42.5 1.0

Zinc binding site 3 out of 4 in 2nyt

Go back to Zinc Binding Sites List in 2nyt
Zinc binding site 3 out of 4 in the The APOBEC2 Crystal Structure and Functional Implications For Aid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The APOBEC2 Crystal Structure and Functional Implications For Aid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2002

b:28.6
occ:1.00
OE1 C:GLU60 2.1 35.7 1.0
SG C:CYS128 2.2 18.2 1.0
SG C:CYS131 2.3 34.2 1.0
ND1 C:HIS98 2.4 32.8 1.0
CB C:CYS131 3.0 31.3 1.0
CD C:GLU60 3.0 37.1 1.0
CB C:CYS128 3.2 18.9 1.0
CE1 C:HIS98 3.3 31.6 1.0
CG C:HIS98 3.5 32.3 1.0
OE2 C:GLU60 3.5 38.8 1.0
N C:CYS128 3.6 19.8 1.0
CB C:HIS98 3.8 33.4 1.0
OE1 C:GLU100 3.9 41.1 1.0
CA C:CYS128 4.0 19.5 1.0
N C:CYS131 4.1 28.7 1.0
CA C:CYS131 4.1 31.3 1.0
CG C:GLU60 4.2 37.2 1.0
CB C:GLU60 4.2 36.2 1.0
NE2 C:HIS98 4.4 33.1 1.0
CA C:GLU60 4.5 36.8 1.0
O C:GLU60 4.5 39.7 1.0
NH2 C:ARG134 4.5 43.3 1.0
CD2 C:HIS98 4.5 32.7 1.0
CD C:GLU100 4.6 40.2 1.0
C C:CYS128 4.7 21.0 1.0
O C:CYS128 4.7 19.6 1.0
C C:PRO127 4.7 19.1 1.0
C C:GLU60 4.9 39.0 1.0
CA C:PRO127 4.9 17.3 1.0

Zinc binding site 4 out of 4 in 2nyt

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Zinc binding site 4 out of 4 in the The APOBEC2 Crystal Structure and Functional Implications For Aid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The APOBEC2 Crystal Structure and Functional Implications For Aid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2003

b:52.2
occ:1.00
ND1 D:HIS98 2.3 35.5 1.0
SG D:CYS131 2.4 33.1 1.0
SG D:CYS128 2.5 30.7 1.0
CE1 D:HIS98 3.1 35.0 1.0
CB D:CYS131 3.2 32.0 1.0
CB D:CYS128 3.3 26.2 1.0
CG D:HIS98 3.3 34.6 1.0
N D:CYS128 3.5 24.4 1.0
O D:HOH1067 3.5 50.8 1.0
CB D:HIS98 3.7 32.2 1.0
OE1 D:GLU100 4.0 31.5 1.0
CA D:CYS128 4.0 26.2 1.0
NE2 D:HIS98 4.2 34.2 1.0
CD2 D:HIS98 4.3 35.4 1.0
N D:CYS131 4.3 30.7 1.0
CA D:CYS131 4.4 31.2 1.0
C D:PRO127 4.5 22.1 1.0
CD D:GLU100 4.5 33.3 1.0
CA D:PRO127 4.7 21.0 1.0
OE2 D:GLU100 4.7 34.3 1.0
C D:CYS128 4.8 27.5 1.0
O D:CYS128 4.9 29.4 1.0

Reference:

C.Prochnow, R.Bransteitter, M.G.Klein, M.F.Goodman, X.S.Chen. The Apobec-2 Crystal Structure and Functional Implications For the Deaminase Aid. Nature V. 445 447 2007.
ISSN: ISSN 0028-0836
PubMed: 17187054
DOI: 10.1038/NATURE05492
Page generated: Wed Dec 16 03:44:55 2020

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