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Chlorine in PDB 4df8: Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Aminopentinyl-7- Deaza-2-Datp

Enzymatic activity of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Aminopentinyl-7- Deaza-2-Datp

All present enzymatic activity of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Aminopentinyl-7- Deaza-2-Datp:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Aminopentinyl-7- Deaza-2-Datp, PDB code: 4df8 was solved by K.Bergen, A.Steck, S.Struett, A.Baccaro, W.Welte, K.Diederichs, A.Marx, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.03 / 2.00
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 108.609, 108.609, 90.516, 90.00, 90.00, 120.00
R / Rfree (%) 19.5 / 23.4

Other elements in 4df8:

The structure of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Aminopentinyl-7- Deaza-2-Datp also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Aminopentinyl-7- Deaza-2-Datp (pdb code 4df8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Aminopentinyl-7- Deaza-2-Datp, PDB code: 4df8:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4df8

Go back to Chlorine Binding Sites List in 4df8
Chlorine binding site 1 out of 2 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Aminopentinyl-7- Deaza-2-Datp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Aminopentinyl-7- Deaza-2-Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl906

b:61.2
occ:1.00
NH1 A:ARG313 3.6 29.0 1.0
NH2 A:ARG313 3.9 39.0 1.0
CE3 A:TRP318 3.9 26.9 1.0
CZ3 A:TRP318 4.0 34.1 1.0
CD2 A:TRP318 4.0 25.5 1.0
CZ A:ARG313 4.2 33.9 1.0
CH2 A:TRP318 4.2 33.0 1.0
CE2 A:TRP318 4.3 31.3 1.0
CZ2 A:TRP318 4.4 26.9 1.0
CD2 A:LEU552 4.5 31.6 1.0
CG A:TRP318 4.7 27.2 1.0
NE1 A:TRP318 5.0 36.3 1.0

Chlorine binding site 2 out of 2 in 4df8

Go back to Chlorine Binding Sites List in 4df8
Chlorine binding site 2 out of 2 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Aminopentinyl-7- Deaza-2-Datp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Aminopentinyl-7- Deaza-2-Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl910

b:49.9
occ:1.00
NZ A:LYS663 3.2 27.2 1.0
N47 A:0L4901 3.4 33.3 1.0
NH2 A:ARG660 3.4 32.1 1.0
CG A:ARG660 3.5 46.4 1.0
CE A:LYS663 3.6 34.6 1.0
CB A:ARG660 3.6 48.8 1.0
CD A:ARG660 4.0 46.0 1.0
C46 A:0L4901 4.0 37.3 1.0
CA A:ARG660 4.1 40.3 1.0
O A:HOH1117 4.4 34.9 1.0
O A:HOH1049 4.4 27.8 1.0
CZ A:ARG660 4.5 36.6 1.0
CD A:LYS663 4.5 44.3 1.0
O A:HOH1019 4.6 24.0 1.0
C45 A:0L4901 4.6 30.7 1.0
NE A:ARG660 4.7 42.1 1.0
OP2 B:DOC112 4.7 24.0 1.0
N A:ARG660 4.8 40.7 1.0
O1A A:0L4901 4.8 22.6 1.0

Reference:

K.Bergen, A.L.Steck, S.Strutt, A.Baccaro, W.Welte, K.Diederichs, A.Marx. Structures of Klentaq Dna Polymerase Caught While Incorporating C5-Modified Pyrimidine and C7-Modified 7-Deazapurine Nucleoside Triphosphates. J.Am.Chem.Soc. V. 134 11840 2012.
ISSN: ISSN 0002-7863
PubMed: 22475415
DOI: 10.1021/JA3017889
Page generated: Sat Dec 12 10:31:53 2020

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