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Zinc in PDB 1a4l: Ada Structure Complexed with Deoxycoformycin at pH 7.0

Enzymatic activity of Ada Structure Complexed with Deoxycoformycin at pH 7.0

All present enzymatic activity of Ada Structure Complexed with Deoxycoformycin at pH 7.0:
3.5.4.4;

Protein crystallography data

The structure of Ada Structure Complexed with Deoxycoformycin at pH 7.0, PDB code: 1a4l was solved by Z.Wang, F.A.Quiocho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 88.929, 93.355, 101.953, 90.00, 102.94, 90.00
R / Rfree (%) 18.5 / 27.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Ada Structure Complexed with Deoxycoformycin at pH 7.0 (pdb code 1a4l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Ada Structure Complexed with Deoxycoformycin at pH 7.0, PDB code: 1a4l:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1a4l

Go back to Zinc Binding Sites List in 1a4l
Zinc binding site 1 out of 4 in the Ada Structure Complexed with Deoxycoformycin at pH 7.0


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ada Structure Complexed with Deoxycoformycin at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:25.2
occ:1.00
O8 A:DCF353 1.8 12.6 1.0
OD1 A:ASP295 2.4 19.3 1.0
NE2 A:HIS17 2.5 2.0 1.0
NE2 A:HIS15 2.6 9.9 1.0
NE2 A:HIS214 2.7 2.0 1.0
CD2 A:HIS17 3.0 2.3 1.0
CD2 A:HIS15 3.2 5.0 1.0
C8 A:DCF353 3.2 5.8 1.0
CG A:ASP295 3.4 12.7 1.0
C9 A:DCF353 3.5 6.4 1.0
CE1 A:HIS214 3.6 2.0 1.0
CE1 A:HIS15 3.6 7.8 1.0
OD2 A:ASP295 3.7 11.9 1.0
CE1 A:HIS17 3.7 10.4 1.0
CD2 A:HIS214 3.7 2.0 1.0
N1 A:DCF353 3.9 12.4 1.0
C10 A:DCF353 4.1 5.8 1.0
C7 A:DCF353 4.3 11.5 1.0
NE2 A:HIS238 4.3 4.0 1.0
CG A:HIS15 4.3 14.1 1.0
CG A:HIS17 4.3 7.5 1.0
CD A:ARG101 4.4 3.7 1.0
N6 A:DCF353 4.4 2.0 1.0
ND1 A:HIS15 4.5 11.9 1.0
N4 A:DCF353 4.5 8.7 1.0
C2 A:DCF353 4.5 6.8 1.0
ND1 A:HIS17 4.6 11.2 1.0
N3 A:DCF353 4.7 6.2 1.0
OD1 A:ASP296 4.7 2.0 1.0
ND1 A:HIS214 4.7 2.1 1.0
C5 A:DCF353 4.7 2.0 1.0
CB A:ASP295 4.7 3.3 1.0
NH1 A:ARG101 4.8 5.2 1.0
CG A:HIS214 4.8 2.0 1.0
CA A:ASP295 5.0 5.5 1.0

Zinc binding site 2 out of 4 in 1a4l

Go back to Zinc Binding Sites List in 1a4l
Zinc binding site 2 out of 4 in the Ada Structure Complexed with Deoxycoformycin at pH 7.0


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ada Structure Complexed with Deoxycoformycin at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn900

b:20.7
occ:1.00
O8 B:DCF853 1.8 10.6 1.0
OD1 B:ASP795 2.4 5.7 1.0
NE2 B:HIS714 2.7 2.0 1.0
NE2 B:HIS517 2.7 2.0 1.0
NE2 B:HIS515 2.8 5.7 1.0
CD2 B:HIS517 3.0 5.5 1.0
C8 B:DCF853 3.1 6.9 1.0
CG B:ASP795 3.3 7.5 1.0
CD2 B:HIS714 3.4 2.0 1.0
C9 B:DCF853 3.4 5.5 1.0
CD2 B:HIS515 3.4 12.1 1.0
OD2 B:ASP795 3.6 2.1 1.0
N1 B:DCF853 3.7 8.0 1.0
CE1 B:HIS714 3.7 2.0 1.0
CE1 B:HIS515 3.7 8.0 1.0
CE1 B:HIS517 4.0 9.7 1.0
NE2 B:HIS738 4.1 6.7 1.0
C7 B:DCF853 4.2 9.1 1.0
C10 B:DCF853 4.2 4.7 1.0
N6 B:DCF853 4.3 7.4 1.0
CG B:HIS517 4.4 11.3 1.0
C2 B:DCF853 4.5 2.0 1.0
CG B:HIS515 4.5 12.3 1.0
CD B:ARG601 4.5 2.0 1.0
CG B:HIS714 4.6 2.0 1.0
ND1 B:HIS515 4.6 17.7 1.0
N4 B:DCF853 4.7 2.8 1.0
ND1 B:HIS714 4.7 4.3 1.0
C5 B:DCF853 4.7 2.0 1.0
OD1 B:ASP796 4.7 2.0 1.0
CB B:ASP795 4.7 5.3 1.0
NH1 B:ARG601 4.8 4.0 1.0
ND1 B:HIS517 4.8 12.4 1.0
N3 B:DCF853 4.8 2.0 1.0
CD2 B:HIS738 4.9 4.8 1.0

Zinc binding site 3 out of 4 in 1a4l

Go back to Zinc Binding Sites List in 1a4l
Zinc binding site 3 out of 4 in the Ada Structure Complexed with Deoxycoformycin at pH 7.0


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ada Structure Complexed with Deoxycoformycin at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1400

b:15.6
occ:1.00
O8 C:DCF1353 1.8 10.8 1.0
OD1 C:ASP1295 2.2 10.8 1.0
NE2 C:HIS1017 2.5 2.0 1.0
NE2 C:HIS1214 2.5 2.0 1.0
NE2 C:HIS1015 2.5 7.3 1.0
CD2 C:HIS1017 2.9 2.0 1.0
C8 C:DCF1353 3.1 2.7 1.0
CD2 C:HIS1015 3.2 10.1 1.0
CG C:ASP1295 3.2 16.7 1.0
C9 C:DCF1353 3.3 6.3 1.0
CD2 C:HIS1214 3.4 3.0 1.0
CE1 C:HIS1214 3.5 2.0 1.0
CE1 C:HIS1015 3.5 6.7 1.0
OD2 C:ASP1295 3.5 11.0 1.0
N1 C:DCF1353 3.5 8.8 1.0
CE1 C:HIS1017 3.6 7.8 1.0
C10 C:DCF1353 3.9 6.2 1.0
CG C:HIS1017 4.1 9.5 1.0
C7 C:DCF1353 4.2 6.0 1.0
NE2 C:HIS1238 4.2 4.8 1.0
C2 C:DCF1353 4.2 6.3 1.0
N4 C:DCF1353 4.4 8.1 1.0
CG C:HIS1015 4.4 13.8 1.0
ND1 C:HIS1017 4.4 9.5 1.0
N6 C:DCF1353 4.4 2.0 1.0
OD1 C:ASP1296 4.5 3.9 1.0
ND1 C:HIS1015 4.5 5.1 1.0
N3 C:DCF1353 4.5 2.0 1.0
CG C:HIS1214 4.5 3.2 1.0
ND1 C:HIS1214 4.5 8.7 1.0
CD C:ARG1101 4.6 2.0 1.0
CB C:ASP1295 4.6 11.4 1.0
C5 C:DCF1353 4.7 3.7 1.0
NH1 C:ARG1101 4.9 2.0 1.0
CA C:ASP1295 4.9 10.1 1.0

Zinc binding site 4 out of 4 in 1a4l

Go back to Zinc Binding Sites List in 1a4l
Zinc binding site 4 out of 4 in the Ada Structure Complexed with Deoxycoformycin at pH 7.0


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ada Structure Complexed with Deoxycoformycin at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1900

b:11.3
occ:1.00
O8 D:DCF1853 1.8 3.1 1.0
OD1 D:ASP1795 2.2 9.9 1.0
NE2 D:HIS1517 2.4 5.2 1.0
NE2 D:HIS1714 2.6 2.0 1.0
NE2 D:HIS1515 2.7 2.2 1.0
CD2 D:HIS1517 3.1 3.2 1.0
C8 D:DCF1853 3.2 6.7 1.0
CG D:ASP1795 3.2 8.1 1.0
CD2 D:HIS1714 3.2 2.0 1.0
CD2 D:HIS1515 3.3 5.1 1.0
CE1 D:HIS1517 3.4 10.1 1.0
C9 D:DCF1853 3.5 10.2 1.0
OD2 D:ASP1795 3.5 9.6 1.0
CE1 D:HIS1714 3.7 7.9 1.0
N1 D:DCF1853 3.7 12.4 1.0
CE1 D:HIS1515 3.7 2.0 1.0
C10 D:DCF1853 4.1 7.5 1.0
NE2 D:HIS1738 4.2 7.7 1.0
C7 D:DCF1853 4.2 7.0 1.0
N6 D:DCF1853 4.3 9.0 1.0
CG D:HIS1517 4.3 3.2 1.0
C2 D:DCF1853 4.4 7.6 1.0
ND1 D:HIS1517 4.4 7.9 1.0
CG D:HIS1515 4.4 11.5 1.0
CG D:HIS1714 4.5 6.8 1.0
ND1 D:HIS1515 4.6 12.2 1.0
OD1 D:ASP1796 4.6 13.6 1.0
CB D:ASP1795 4.6 2.0 1.0
N3 D:DCF1853 4.6 7.7 1.0
N4 D:DCF1853 4.6 8.0 1.0
ND1 D:HIS1714 4.6 10.1 1.0
C5 D:DCF1853 4.7 4.3 1.0
CD D:ARG1601 4.7 2.0 1.0
CD2 D:HIS1738 4.9 2.9 1.0
CA D:ASP1795 4.9 3.1 1.0

Reference:

Z.Wang, F.A.Quiocho. Complexes of Adenosine Deaminase with Two Potent Inhibitors: X-Ray Structures in Four Independent Molecules at pH of Maximum Activity. Biochemistry V. 37 8314 1998.
ISSN: ISSN 0006-2960
PubMed: 9622483
DOI: 10.1021/BI980324O
Page generated: Wed Dec 16 02:44:25 2020

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