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Zinc in PDB 1d9d: Crystall Structure of the Complex of Dna Polymerase I Klenow Fragment with Short Dna Fragment Carrying 2'-0- Aminopropyl-Rna Modifications 5'-D(Tcg)-Ap(Auc)-3'

Enzymatic activity of Crystall Structure of the Complex of Dna Polymerase I Klenow Fragment with Short Dna Fragment Carrying 2'-0- Aminopropyl-Rna Modifications 5'-D(Tcg)-Ap(Auc)-3'

All present enzymatic activity of Crystall Structure of the Complex of Dna Polymerase I Klenow Fragment with Short Dna Fragment Carrying 2'-0- Aminopropyl-Rna Modifications 5'-D(Tcg)-Ap(Auc)-3':
2.7.7.7;

Protein crystallography data

The structure of Crystall Structure of the Complex of Dna Polymerase I Klenow Fragment with Short Dna Fragment Carrying 2'-0- Aminopropyl-Rna Modifications 5'-D(Tcg)-Ap(Auc)-3', PDB code: 1d9d 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 / 2.18
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 102.550, 102.550, 86.280, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 23.8

Other elements in 1d9d:

The structure of Crystall Structure of the Complex of Dna Polymerase I Klenow Fragment with Short Dna Fragment Carrying 2'-0- Aminopropyl-Rna Modifications 5'-D(Tcg)-Ap(Auc)-3' also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystall Structure of the Complex of Dna Polymerase I Klenow Fragment with Short Dna Fragment Carrying 2'-0- Aminopropyl-Rna Modifications 5'-D(Tcg)-Ap(Auc)-3' (pdb code 1d9d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystall Structure of the Complex of Dna Polymerase I Klenow Fragment with Short Dna Fragment Carrying 2'-0- Aminopropyl-Rna Modifications 5'-D(Tcg)-Ap(Auc)-3', PDB code: 1d9d:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1d9d

Go back to Zinc Binding Sites List in 1d9d
Zinc binding site 1 out of 4 in the Crystall Structure of the Complex of Dna Polymerase I Klenow Fragment with Short Dna Fragment Carrying 2'-0- Aminopropyl-Rna Modifications 5'-D(Tcg)-Ap(Auc)-3'


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystall Structure of the Complex of Dna Polymerase I Klenow Fragment with Short Dna Fragment Carrying 2'-0- Aminopropyl-Rna Modifications 5'-D(Tcg)-Ap(Auc)-3' within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:24.2
occ:1.00
 O2P B:C311006 1.8 40.7 0.5
OE2 A:GLU357 2.1 17.7 1.0
OD2 A:ASP355 2.2 22.3 1.0
OD2 A:ASP501 2.3 14.3 1.0
CD A:GLU357 3.0 13.3 1.0
P B:C311006 3.0 37.6 0.5
CG A:ASP355 3.1 20.7 1.0
CG A:ASP501 3.2 16.6 1.0
OE1 A:GLU357 3.3 16.5 1.0
O5' B:C311006 3.3 37.3 0.5
OD1 A:ASP355 3.3 19.9 1.0
CB A:ASP501 3.5 15.8 1.0
O2' B:U311005 3.7 41.6 0.5
O A:THR356 3.8 16.5 1.0
CA' B:U311005 4.0 40.5 0.5
O1P B:C311006 4.0 34.9 0.5
CE2 A:TYR497 4.0 17.8 1.0
O A:HOH1143 4.2 33.2 1.0
O3' B:U311005 4.2 40.1 0.5
CG A:GLU357 4.2 12.3 1.0
OD1 A:ASP501 4.4 16.6 1.0
CB A:ASP355 4.4 17.5 1.0
C1' B:U311005 4.4 41.0 0.5
C2' B:U311005 4.5 41.7 0.5
CD2 A:TYR497 4.6 17.5 1.0
CA A:ALA498 4.6 16.8 1.0
O B:HOH364 4.6 40.0 1.0
C A:THR356 4.7 16.6 1.0
C5' B:C311006 4.8 34.2 0.5
CZ A:TYR497 4.9 20.5 1.0
O A:ALA498 4.9 15.9 1.0
N1 B:U311005 4.9 41.6 0.5
CB' B:U311005 5.0 39.2 0.5
OH A:TYR497 5.0 19.8 1.0
C3' B:U311005 5.0 40.4 0.5
CB A:ALA498 5.0 16.3 1.0

Zinc binding site 2 out of 4 in 1d9d

Go back to Zinc Binding Sites List in 1d9d
Zinc binding site 2 out of 4 in the Crystall Structure of the Complex of Dna Polymerase I Klenow Fragment with Short Dna Fragment Carrying 2'-0- Aminopropyl-Rna Modifications 5'-D(Tcg)-Ap(Auc)-3'


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystall Structure of the Complex of Dna Polymerase I Klenow Fragment with Short Dna Fragment Carrying 2'-0- Aminopropyl-Rna Modifications 5'-D(Tcg)-Ap(Auc)-3' within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3

b:44.4
occ:1.00
 OE2 A:GLU905 2.3 36.8 1.0
NE2 A:HIS901 2.4 36.3 1.0
CD A:GLU905 2.9 39.2 1.0
OE1 A:GLU905 3.1 35.6 1.0
CD2 A:HIS901 3.2 36.4 1.0
CE1 A:HIS901 3.4 36.7 1.0
CG A:GLU905 4.0 37.9 1.0
CG A:HIS901 4.4 35.0 1.0
ND1 A:HIS901 4.5 39.1 1.0
O A:HOH1093 4.9 43.0 1.0

Zinc binding site 3 out of 4 in 1d9d

Go back to Zinc Binding Sites List in 1d9d
Zinc binding site 3 out of 4 in the Crystall Structure of the Complex of Dna Polymerase I Klenow Fragment with Short Dna Fragment Carrying 2'-0- Aminopropyl-Rna Modifications 5'-D(Tcg)-Ap(Auc)-3'


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystall Structure of the Complex of Dna Polymerase I Klenow Fragment with Short Dna Fragment Carrying 2'-0- Aminopropyl-Rna Modifications 5'-D(Tcg)-Ap(Auc)-3' within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn320

b:59.8
occ:0.50
 OD2 A:ASP882 2.4 23.1 1.0
O A:HOH1068 2.8 46.5 1.0
CG A:ASP882 3.2 23.2 1.0
O A:HOH1134 3.2 38.6 1.0
OD1 A:ASP882 3.3 23.4 1.0
NH2 A:ARG668 3.5 44.9 1.0
CG A:GLU710 3.9 34.5 1.0
CD A:GLU710 4.0 36.2 1.0
OE2 A:GLU710 4.1 40.0 1.0
O A:HOH1170 4.3 53.4 1.0
OE1 A:GLU710 4.4 43.0 1.0
CG2 A:ILE709 4.5 17.2 1.0
CZ A:ARG668 4.5 45.8 1.0
CB A:ASP882 4.6 22.8 1.0
CB A:GLU710 4.6 27.2 1.0
NH1 A:ARG668 5.0 47.6 1.0

Zinc binding site 4 out of 4 in 1d9d

Go back to Zinc Binding Sites List in 1d9d
Zinc binding site 4 out of 4 in the Crystall Structure of the Complex of Dna Polymerase I Klenow Fragment with Short Dna Fragment Carrying 2'-0- Aminopropyl-Rna Modifications 5'-D(Tcg)-Ap(Auc)-3'


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystall Structure of the Complex of Dna Polymerase I Klenow Fragment with Short Dna Fragment Carrying 2'-0- Aminopropyl-Rna Modifications 5'-D(Tcg)-Ap(Auc)-3' within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn322

b:42.4
occ:0.50
 O A:HOH1173 2.3 50.7 1.0
OE2 A:GLU883 2.7 38.1 1.0
CE1 A:HIS928 2.7 44.3 1.0
O A:HOH1137 3.3 29.7 1.0
NE2 A:HIS928 3.5 43.1 1.0
CD A:GLU883 3.7 35.7 1.0
ND1 A:HIS928 3.8 44.1 1.0
ND1 A:HIS881 4.1 38.8 1.0
CG A:GLU883 4.4 34.3 1.0
CB A:HIS881 4.5 31.8 1.0
OE1 A:GLU883 4.5 35.2 1.0
CD2 A:HIS928 4.7 43.5 1.0
CG A:HIS881 4.7 38.4 1.0
CB A:GLU883 4.8 29.2 1.0
O A:VAL880 4.8 26.7 1.0
CG A:HIS928 4.8 44.1 1.0
OD1 A:ASP705 4.9 40.7 1.0
CG1 A:VAL681 4.9 54.0 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: Tue Aug 19 19:40:47 2025

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