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Zinc in PDB 1d9f: Crystal Structure of the Complex of Dna Polymerase I Klenow Fragment with Dna Tetramer Carrying 2'-O-(3-Aminopropyl)- Rna Modification 5'-D(Tt)-Ap(U)-D(T)-3'

Enzymatic activity of Crystal Structure of the Complex of Dna Polymerase I Klenow Fragment with Dna Tetramer Carrying 2'-O-(3-Aminopropyl)- Rna Modification 5'-D(Tt)-Ap(U)-D(T)-3'

All present enzymatic activity of Crystal Structure of the Complex of Dna Polymerase I Klenow Fragment with Dna Tetramer Carrying 2'-O-(3-Aminopropyl)- Rna Modification 5'-D(Tt)-Ap(U)-D(T)-3':
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of the Complex of Dna Polymerase I Klenow Fragment with Dna Tetramer Carrying 2'-O-(3-Aminopropyl)- Rna Modification 5'-D(Tt)-Ap(U)-D(T)-3', PDB code: 1d9f was solved by M.Teplova, S.T.Wallace, V.Tereshko, G.Minasov, A.M.Simons, P.D.Cook, M.Manoharan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.00
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 102.650, 102.650, 86.300, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 24.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Complex of Dna Polymerase I Klenow Fragment with Dna Tetramer Carrying 2'-O-(3-Aminopropyl)- Rna Modification 5'-D(Tt)-Ap(U)-D(T)-3' (pdb code 1d9f). 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 Crystal Structure of the Complex of Dna Polymerase I Klenow Fragment with Dna Tetramer Carrying 2'-O-(3-Aminopropyl)- Rna Modification 5'-D(Tt)-Ap(U)-D(T)-3', PDB code: 1d9f:

Zinc binding site 1 out of 1 in 1d9f

Go back to Zinc Binding Sites List in 1d9f
Zinc binding site 1 out of 1 in the Crystal Structure of the Complex of Dna Polymerase I Klenow Fragment with Dna Tetramer Carrying 2'-O-(3-Aminopropyl)- Rna Modification 5'-D(Tt)-Ap(U)-D(T)-3'


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 Complex of Dna Polymerase I Klenow Fragment with Dna Tetramer Carrying 2'-O-(3-Aminopropyl)- Rna Modification 5'-D(Tt)-Ap(U)-D(T)-3' within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:31.0
occ:0.50
OE2 A:GLU357 2.0 27.9 1.0
OP1 B:DT1004 2.5 52.0 0.5
OD2 A:ASP501 2.6 37.2 1.0
CD A:GLU357 2.7 24.9 1.0
OE1 A:GLU357 2.7 26.2 1.0
OD2 A:ASP355 2.9 35.5 1.0
CE2 A:TYR497 3.4 18.6 1.0
P B:DT1004 3.8 44.8 0.5
CG A:ASP501 3.8 37.1 1.0
CG A:ASP355 3.8 33.8 1.0
OP1 B:DT1004 3.9 44.6 0.5
OD1 A:ASP355 4.0 39.8 1.0
O3' B:U311003 4.0 47.3 0.5
O A:THR356 4.0 21.3 1.0
O2' B:U311003 4.1 48.8 0.5
CD2 A:TYR497 4.1 18.4 1.0
CG A:GLU357 4.2 25.1 1.0
CZ A:TYR497 4.2 20.5 1.0
OH A:TYR497 4.2 26.9 1.0
C1' B:U311003 4.4 48.2 0.5
C2' B:U311003 4.5 48.9 0.5
O5' B:DT1004 4.6 44.6 0.5
CB A:ASP501 4.6 33.5 1.0
CA' B:U311003 4.6 47.7 0.5
O5' B:DT1004 4.6 44.5 0.5
OD1 A:ASP501 4.7 38.0 1.0
N1 B:U311003 4.8 48.8 0.5
C3' B:U311003 4.9 47.6 0.5
O3' B:DT1004 4.9 44.6 0.5
O3' B:DT1004 4.9 44.6 0.5
P B:DT1004 4.9 44.6 0.5
OP2 B:DT1004 4.9 47.9 0.5
C A:THR356 5.0 21.0 1.0

Reference:

M.Teplova, S.T.Wallace, V.Tereshko, G.Minasov, A.M.Symons, P.D.Cook, M.Manoharan, M.Egli. Structural Origins of the Exonuclease Resistance of A Zwitterionic Rna. Proc.Natl.Acad.Sci.Usa V. 96 14240 1999.
ISSN: ISSN 0027-8424
PubMed: 10588690
DOI: 10.1073/PNAS.96.25.14240
Page generated: Mon Jan 25 16:08:19 2021

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