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Chlorine in PDB 3sm4: Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with A 5'-Phosphorylated 14-Mer/12-Mer Duplex and Magnesium

Enzymatic activity of Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with A 5'-Phosphorylated 14-Mer/12-Mer Duplex and Magnesium

All present enzymatic activity of Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with A 5'-Phosphorylated 14-Mer/12-Mer Duplex and Magnesium:
3.1.11.3;

Protein crystallography data

The structure of Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with A 5'-Phosphorylated 14-Mer/12-Mer Duplex and Magnesium, PDB code: 3sm4 was solved by C.E.Bell, J.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.89 / 1.88
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 78.391, 78.391, 247.534, 90.00, 90.00, 120.00
R / Rfree (%) 16 / 18.6

Other elements in 3sm4:

The structure of Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with A 5'-Phosphorylated 14-Mer/12-Mer Duplex and Magnesium also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with A 5'-Phosphorylated 14-Mer/12-Mer Duplex and Magnesium (pdb code 3sm4). 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 K131A Mutant of Lambda Exonuclease in Complex with A 5'-Phosphorylated 14-Mer/12-Mer Duplex and Magnesium, PDB code: 3sm4:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 3sm4

Go back to Chlorine Binding Sites List in 3sm4
Chlorine binding site 1 out of 2 in the Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with A 5'-Phosphorylated 14-Mer/12-Mer Duplex and Magnesium


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 K131A Mutant of Lambda Exonuclease in Complex with A 5'-Phosphorylated 14-Mer/12-Mer Duplex and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl228

b:25.5
occ:1.00
CL A:CL229 2.8 22.0 1.0
O A:HOH299 2.9 25.1 1.0
N A:ALA34 3.4 21.4 1.0
O A:HOH269 3.4 32.2 1.0
CB A:ALA34 3.5 23.2 1.0
N A:SER35 3.7 22.3 1.0
N A:SER117 3.7 21.1 1.0
CA A:ALA34 3.9 22.0 1.0
OG A:SER35 4.0 24.3 1.0
CB A:THR33 4.0 20.7 1.0
CA A:CYS116 4.1 20.8 1.0
O A:HOH394 4.1 29.4 1.0
C A:ALA34 4.3 22.1 1.0
C A:THR33 4.3 20.6 1.0
O A:HOH326 4.3 33.5 1.0
C A:CYS116 4.4 21.2 1.0
CB A:SER117 4.4 21.8 1.0
CB A:SER35 4.5 23.7 1.0
CA A:THR33 4.6 20.3 1.0
CA A:SER117 4.6 21.6 1.0
O A:ALA115 4.6 20.3 1.0
CB A:CYS116 4.7 20.9 1.0
CA A:SER35 4.7 22.9 1.0
OG A:SER117 4.7 22.1 1.0
OG1 A:THR33 4.8 20.4 1.0
NE2 A:GLN157 4.8 25.4 1.0
CG2 A:THR33 4.9 21.0 1.0
O A:HOH347 5.0 16.7 1.0
O A:SER117 5.0 21.3 1.0

Chlorine binding site 2 out of 2 in 3sm4

Go back to Chlorine Binding Sites List in 3sm4
Chlorine binding site 2 out of 2 in the Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with A 5'-Phosphorylated 14-Mer/12-Mer Duplex and Magnesium


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 K131A Mutant of Lambda Exonuclease in Complex with A 5'-Phosphorylated 14-Mer/12-Mer Duplex and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl229

b:22.0
occ:1.00
CL A:CL228 2.8 25.5 1.0
O A:HOH394 3.0 29.4 1.0
OG A:SER117 3.2 22.1 1.0
N A:SER117 3.4 21.1 1.0
CG2 A:THR33 3.5 21.0 1.0
C A:CYS116 3.5 21.2 1.0
CA A:CYS116 3.5 20.8 1.0
CB A:THR33 3.6 20.7 1.0
CB A:SER117 3.8 21.8 1.0
O A:ALA115 3.8 20.3 1.0
N A:CYS116 4.0 20.9 1.0
C A:ALA115 4.0 20.4 1.0
O A:CYS116 4.2 21.6 1.0
CA A:SER117 4.2 21.6 1.0
CA A:THR33 4.3 20.3 1.0
CD1 A:ILE105 4.4 21.9 1.0
CG A:ARG28 4.4 25.8 1.0
N A:ALA34 4.5 21.4 1.0
CB A:ALA115 4.6 20.7 1.0
CG1 A:ILE105 4.6 22.4 1.0
NE A:ARG28 4.7 28.7 1.0
OG1 A:THR33 4.8 20.4 1.0
CB A:CYS116 4.9 20.9 1.0
CA A:ALA115 4.9 20.5 1.0
C A:THR33 4.9 20.6 1.0

Reference:

J.Zhang, K.A.Mccabe, C.E.Bell. Crystal Structures of {Lambda} Exonuclease in Complex with Dna Suggest An Electrostatic Ratchet Mechanism For Processivity. Proc.Natl.Acad.Sci.Usa V. 108 11872 2011.
ISSN: ISSN 0027-8424
PubMed: 21730170
DOI: 10.1073/PNAS.1103467108
Page generated: Fri Jul 11 10:22:06 2025

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