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Calcium 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
Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure Bacteriohage T5 D15 Flap Endonuclease (D155K) Pseudo-Enzyme-Product Complex with Dna and Metal Ions, PDB code: 5hp4:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5hp4

Go back to Calcium Binding Sites List in 5hp4
Calcium binding site 1 out of 2 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 Calcium with other atoms in the Ca 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:Ca101

b:37.0
occ:1.00
 O X:HOH223 2.4 52.3 1.0
O2 X:DC15 2.4 28.8 1.0
O X:HOH216 2.5 32.0 1.0
O X:HOH221 2.5 30.9 1.0
O X:HOH220 2.6 34.2 1.0
O X:HOH236 2.6 43.7 1.0
C2 X:DC15 3.5 39.5 1.0
N3 X:DC15 3.9 31.3 1.0
N7 X:DG16 4.5 31.9 1.0
O6 X:DG16 4.6 35.2 1.0
O X:HOH227 4.7 31.3 1.0
N1 X:DC15 4.7 29.7 1.0
C1' X:DC15 5.0 33.0 1.0

Calcium binding site 2 out of 2 in 5hp4

Go back to Calcium Binding Sites List in 5hp4
Calcium binding site 2 out of 2 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 Calcium with other atoms in the Ca binding site number 2 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
A:Ca301

b:30.6
occ:1.00
 O A:HOH430 2.3 32.1 1.0
O A:HOH413 2.3 23.7 1.0
O A:HOH405 2.4 30.6 1.0
O A:HOH522 2.4 38.5 1.0
OD1 A:ASP130 2.5 32.4 1.0
OE1 A:GLU128 2.6 34.3 1.0
OE2 A:GLU128 2.6 38.1 1.0
CD A:GLU128 3.0 70.7 1.0
CG A:ASP130 3.3 38.9 1.0
OD2 A:ASP130 3.3 35.4 1.0
OD2 A:ASP153 4.0 26.4 1.0
OD2 A:ASP68 4.4 55.6 1.0
CG A:GLU128 4.5 48.6 1.0
N A:ASP130 4.5 21.2 1.0
OD1 A:ASP68 4.5 36.1 1.0
OD2 A:ASP26 4.6 25.9 1.0
NZ A:LYS83 4.6 31.3 1.0
NE1 A:TRP156 4.6 27.2 1.0
CB A:ASP130 4.6 27.0 1.0
OD1 A:ASP26 4.7 23.4 1.0
CG A:ASP68 4.9 40.4 1.0
O A:HOH547 5.0 38.5 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: Sun Jul 14 20:07:59 2024

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