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Sodium in PDB 5hp4: Crystal Structure Bacteriohage T5 D15 Flap Endonuclease (D155K) Pseudo-Enzyme-Product Complex with Dna and Metal Ions

Enzymatic activity of Crystal Structure Bacteriohage T5 D15 Flap Endonuclease (D155K) Pseudo-Enzyme-Product Complex with Dna and Metal Ions

All present enzymatic activity of Crystal Structure Bacteriohage T5 D15 Flap Endonuclease (D155K) Pseudo-Enzyme-Product Complex with Dna and Metal Ions:
3.1.11.3;

Protein crystallography data

The structure of Crystal Structure Bacteriohage T5 D15 Flap Endonuclease (D155K) Pseudo-Enzyme-Product Complex with Dna and Metal Ions, PDB code: 5hp4 was solved by F.A.Almalki, J.Zhang, S.E.Sedelnikova, J.B.Rafferty, J.R.Sayers, P.A.Artymiuk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.81 / 1.86
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 67.510, 67.510, 187.810, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 18.8

Other elements in 5hp4:

The structure of Crystal Structure Bacteriohage T5 D15 Flap Endonuclease (D155K) Pseudo-Enzyme-Product Complex with Dna and Metal Ions also contains other interesting chemical elements:

Potassium (K) 1 atom
Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure Bacteriohage T5 D15 Flap Endonuclease (D155K) Pseudo-Enzyme-Product Complex with Dna and Metal Ions (pdb code 5hp4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure Bacteriohage T5 D15 Flap Endonuclease (D155K) Pseudo-Enzyme-Product Complex with Dna and Metal Ions, PDB code: 5hp4:

Sodium binding site 1 out of 1 in 5hp4

Go back to Sodium Binding Sites List in 5hp4
Sodium binding site 1 out of 1 in the Crystal Structure Bacteriohage T5 D15 Flap Endonuclease (D155K) Pseudo-Enzyme-Product Complex with Dna and Metal Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure Bacteriohage T5 D15 Flap Endonuclease (D155K) Pseudo-Enzyme-Product Complex with Dna and Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Na102

b:41.7
occ:1.00
 O2 X:DT7 2.2 42.6 1.0
C2 X:DT7 3.4 44.6 1.0
O4' X:DA8 3.4 0.8 1.0
N3 X:DA8 3.5 62.1 1.0
C2 X:DA8 4.0 54.4 1.0
C4 X:DA8 4.0 44.4 1.0
N3 X:DT7 4.1 36.0 1.0
C1' X:DA8 4.3 95.4 1.0
N9 X:DA8 4.4 0.6 1.0
N1 X:DT7 4.4 44.5 1.0
C4' X:DA8 4.5 66.9 1.0
C1' X:DT7 4.5 52.9 1.0
N1 X:DA8 4.9 41.1 1.0
C5 X:DA8 4.9 54.6 1.0

Reference:

F.A.Almalki, C.S.Flemming, J.Zhang, M.Feng, S.E.Sedelnikova, T.Ceska, J.B.Rafferty, J.R.Sayers, P.J.Artymiuk. Direct Observation of Dna Threading in Flap Endonuclease Complexes. Nat.Struct.Mol.Biol. V. 23 640 2016.
ISSN: ESSN 1545-9985
PubMed: 27273516
DOI: 10.1038/NSMB.3241
Page generated: Mon Oct 7 21:27:56 2024

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