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Zinc in PDB 3pa0: Crystal Structure of Chiral Gamma-Pna with Complementary Dna Strand: Insight Into the Stability and Specificity of Recognition An Conformational Preorganization

Protein crystallography data

The structure of Crystal Structure of Chiral Gamma-Pna with Complementary Dna Strand: Insight Into the Stability and Specificity of Recognition An Conformational Preorganization, PDB code: 3pa0 was solved by J.I.Yeh, B.Shivachev, S.Du, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.190, 52.570, 61.150, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 24.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Chiral Gamma-Pna with Complementary Dna Strand: Insight Into the Stability and Specificity of Recognition An Conformational Preorganization (pdb code 3pa0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Chiral Gamma-Pna with Complementary Dna Strand: Insight Into the Stability and Specificity of Recognition An Conformational Preorganization, PDB code: 3pa0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3pa0

Go back to Zinc Binding Sites List in 3pa0
Zinc binding site 1 out of 2 in the Crystal Structure of Chiral Gamma-Pna with Complementary Dna Strand: Insight Into the Stability and Specificity of Recognition An Conformational Preorganization


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 Chiral Gamma-Pna with Complementary Dna Strand: Insight Into the Stability and Specificity of Recognition An Conformational Preorganization within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn12

b:23.0
occ:0.43
OP1 B:DT6 1.9 21.4 1.0
O C:HOH14 2.1 21.9 1.0
O B:HOH12 2.1 24.0 1.0
O B:HOH14 2.2 23.0 1.0
O C:HOH15 2.2 23.1 1.0
N7 C:40G4 2.4 17.6 1.0
C8 C:40G4 3.2 21.7 1.0
P B:DT6 3.4 23.0 1.0
C5 C:40G4 3.5 19.1 1.0
O6 C:40G4 3.8 20.8 1.0
O C:HOH1067 4.1 39.2 1.0
C6 C:40G4 4.1 20.3 1.0
O5' B:DT6 4.1 22.1 1.0
N7 C:40A5 4.1 21.6 1.0
OP2 B:DT6 4.2 20.9 1.0
N7 C:40A3 4.2 23.9 1.0
C5' B:DT6 4.3 19.8 1.0
O3' B:DG5 4.3 21.1 1.0
O B:HOH1047 4.4 27.1 1.0
N9 C:40G4 4.4 19.6 1.0
O B:HOH1147 4.4 47.4 1.0
C4 C:40G4 4.6 19.5 1.0
N6 C:40A5 4.6 19.6 1.0
C5 C:40A5 4.7 22.6 1.0
C8 C:40A3 4.8 24.2 1.0
OP2 B:DG7 4.8 26.5 1.0
C8 C:40A5 4.9 23.8 1.0
C6 C:40A5 5.0 25.5 1.0

Zinc binding site 2 out of 2 in 3pa0

Go back to Zinc Binding Sites List in 3pa0
Zinc binding site 2 out of 2 in the Crystal Structure of Chiral Gamma-Pna with Complementary Dna Strand: Insight Into the Stability and Specificity of Recognition An Conformational Preorganization


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Chiral Gamma-Pna with Complementary Dna Strand: Insight Into the Stability and Specificity of Recognition An Conformational Preorganization within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn12

b:25.0
occ:0.40
OP1 A:DG5 2.0 23.6 1.0
O D:HOH17 2.1 24.6 1.0
O D:HOH16 2.1 30.4 1.0
O D:HOH18 2.2 25.9 1.0
O A:HOH12 2.2 28.0 1.0
N7 D:40G4 2.3 23.1 1.0
C8 D:40G4 3.1 25.2 1.0
P A:DG5 3.2 24.8 1.0
C5 D:40G4 3.5 21.0 1.0
O D:HOH1100 3.7 55.6 1.0
OP2 A:DG5 3.8 27.1 1.0
O6 D:40G4 3.9 24.0 1.0
O5' A:DG5 4.0 23.0 1.0
N7 D:40A5 4.0 20.1 1.0
C6 D:40G4 4.1 24.5 1.0
O A:HOH1091 4.1 38.9 1.0
N7 D:40A3 4.2 24.7 1.0
O D:HOH1122 4.2 30.7 1.0
C5' A:DG5 4.3 24.0 1.0
N9 D:40G4 4.3 26.3 1.0
O3' A:DT4 4.5 26.3 1.0
C4 D:40G4 4.5 26.2 1.0
C5 D:40A5 4.6 21.9 1.0
N6 D:40A5 4.6 21.6 1.0
C8 D:40A5 4.7 20.9 1.0
C8 D:40A3 4.8 27.4 1.0
C6 D:40A5 4.8 23.8 1.0
O A:HOH1145 4.9 45.6 1.0

Reference:

J.I.Yeh, B.Shivachev, S.Rapireddy, M.J.Crawford, R.R.Gil, S.Du, M.Madrid, D.H.Ly. Crystal Structure of Chiral Gammapna with Complementary Dna Strand: Insights Into the Stability and Specificity of Recognition and Conformational Preorganization. J.Am.Chem.Soc. V. 132 10717 2010.
ISSN: ISSN 0002-7863
PubMed: 20681704
DOI: 10.1021/JA907225D
Page generated: Sat Sep 26 12:21:24 2020
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