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Zinc in PDB 1noy: Dna Polymerase (E.C.2.7.7.7)/Dna Complex

Protein crystallography data

The structure of Dna Polymerase (E.C.2.7.7.7)/Dna Complex, PDB code: 1noy was solved by J.Wang, P.Yu, T.C.Lin, W.H.Konigsberg, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 114.701, 109.656, 70.268, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / n/a

Other elements in 1noy:

The structure of Dna Polymerase (E.C.2.7.7.7)/Dna Complex also contains other interesting chemical elements:

Manganese (Mn) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Dna Polymerase (E.C.2.7.7.7)/Dna Complex (pdb code 1noy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Dna Polymerase (E.C.2.7.7.7)/Dna Complex, PDB code: 1noy:

Zinc binding site 1 out of 1 in 1noy

Go back to Zinc Binding Sites List in 1noy
Zinc binding site 1 out of 1 in the Dna Polymerase (E.C.2.7.7.7)/Dna Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dna Polymerase (E.C.2.7.7.7)/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2000

b:20.0
occ:1.00
OE2 B:GLU114 2.5 59.4 1.0
OD2 B:ASP324 2.6 45.2 1.0
OP1 S:DT5 2.7 20.0 1.0
OD1 B:ASP112 3.1 52.7 1.0
CG B:ASP324 3.5 42.2 1.0
CD B:GLU114 3.7 58.1 1.0
CB B:ASP324 4.0 40.2 1.0
CG B:ASP112 4.1 50.1 1.0
P S:DT5 4.1 20.0 1.0
OE1 B:GLU114 4.2 59.9 1.0
CA B:ASN321 4.5 44.1 1.0
C5' S:DT5 4.5 20.0 1.0
OD1 B:ASP324 4.6 42.9 1.0
MN B:MN3000 4.6 20.0 1.0
OD1 B:ASN321 4.6 46.0 1.0
OD2 B:ASP112 4.6 51.1 1.0
O B:TYR320 4.8 45.2 1.0
NZ B:LYS299 4.8 60.7 1.0
O5' S:DT5 4.8 20.0 1.0
N B:ASN321 4.8 44.4 1.0
OP2 S:DT5 4.9 20.0 1.0
CG B:GLU114 4.9 55.2 1.0
C B:TYR320 4.9 45.2 1.0
O3' S:DT4 4.9 20.0 1.0

Reference:

J.Wang, P.Yu, T.C.Lin, W.H.Konigsberg, T.A.Steitz. Crystal Structures of An NH2-Terminal Fragment of T4 Dna Polymerase and Its Complexes with Single-Stranded Dna and with Divalent Metal Ions. Biochemistry V. 35 8110 1996.
ISSN: ISSN 0006-2960
PubMed: 8679562
DOI: 10.1021/BI960178R
Page generated: Mon Jan 25 16:10:29 2021

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