Sodium in PDB 4d1q: Hermes Transposase Bound to Its Terminal Inverted Repeat

The structure of Hermes Transposase Bound to Its Terminal Inverted Repeat, PDB code: 4d1q was solved by A.B.Hickman, H.Ewis, X.Li, J.Knapp, T.Laver, A.L.Doss, G.Tolun, A.Steven, A.Grishaev, A.Bax, P.Atkinson, N.L.Craig, F.Dyda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.0 / 3.40
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	265.150, 265.150, 157.640, 90.00, 90.00, 120.00
R / Rfree (%)	21.18 / 25.43

The binding sites of Sodium atom in the Hermes Transposase Bound to Its Terminal Inverted Repeat (pdb code 4d1q). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Hermes Transposase Bound to Its Terminal Inverted Repeat, PDB code: 4d1q:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Hermes Transposase Bound to Its Terminal Inverted Repeat


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hermes Transposase Bound to Its Terminal Inverted Repeat within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1610 b:44.1 occ:1.00 O A:LEU141 2.4 98.4 1.0 OP2 F:DG6 2.6 96.7 1.0 O A:GLU139 2.7 88.3 1.0 O A:GLU138 3.1 82.4 1.0 C A:LEU141 3.4 93.6 1.0 C A:GLU139 3.5 90.3 1.0 O5' F:DG6 3.6 0.7 1.0 P F:DG6 3.6 0.7 1.0 CA A:GLU139 3.9 91.3 1.0 C5' F:DG6 4.0 99.5 1.0 CA A:PRO142 4.0 86.3 1.0 NZ B:LYS91 4.0 0.1 1.0 N A:PRO142 4.1 88.3 1.0 C A:GLU138 4.1 89.1 1.0 C A:PRO142 4.2 86.7 1.0 N A:LEU141 4.3 95.2 1.0 CA A:LEU141 4.4 90.6 1.0 N A:SER143 4.4 87.3 1.0 C A:LEU140 4.5 95.0 1.0 N A:GLU139 4.5 88.6 1.0 OP1 F:DG6 4.5 0.8 1.0 N A:LEU140 4.6 89.8 1.0 O A:PRO142 4.7 89.8 1.0 CE B:LYS91 4.7 0.9 1.0 O A:LEU140 4.8 94.1 1.0 O3' F:DT5 4.9 96.0 1.0

Sodium binding site 2 out of 4 in the Hermes Transposase Bound to Its Terminal Inverted Repeat


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hermes Transposase Bound to Its Terminal Inverted Repeat within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1610 b:57.3 occ:1.00 OP2 D:DG6 2.4 0.8 1.0 O B:LEU141 2.5 95.4 1.0 O B:GLU139 2.6 94.0 1.0 O B:GLU138 2.8 90.6 1.0 C B:GLU139 3.4 96.1 1.0 C B:LEU141 3.4 91.2 1.0 P D:DG6 3.7 0.9 1.0 CA B:GLU139 3.9 98.7 1.0 C B:GLU138 3.9 91.1 1.0 O5' D:DG6 3.9 0.6 1.0 CA B:PRO142 4.0 83.2 1.0 N B:PRO142 4.1 86.0 1.0 NZ A:LYS91 4.1 93.8 1.0 CE A:LYS91 4.2 0.3 1.0 N B:LEU141 4.3 91.8 1.0 C B:LEU140 4.3 92.6 1.0 N B:GLU139 4.4 95.2 1.0 N B:LEU140 4.4 92.7 1.0 C B:PRO142 4.4 83.5 1.0 C5' D:DG6 4.4 0.2 1.0 CA B:LEU141 4.5 89.9 1.0 O B:LEU140 4.5 91.2 1.0 OP1 D:DG6 4.5 0.6 1.0 N B:SER143 4.5 87.4 1.0 O3' D:DT5 4.8 93.9 1.0 CA B:LEU140 4.9 92.0 1.0

Sodium binding site 3 out of 4 in the Hermes Transposase Bound to Its Terminal Inverted Repeat


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Hermes Transposase Bound to Its Terminal Inverted Repeat within 5.0Å range: probe atom residue distance (Å) B Occ G:Na1610 b:77.5 occ:1.00 OP2 L:DG6 2.6 0.4 1.0 O G:LEU141 2.6 0.5 1.0 O G:GLU138 2.7 0.5 1.0 O5' L:DG6 3.7 0.2 1.0 C G:GLU139 3.7 0.1 1.0 P L:DG6 3.7 0.0 1.0 C G:LEU141 3.7 0.8 1.0 C5' L:DG6 3.8 0.4 1.0 C G:GLU138 3.8 0.6 1.0 O G:GLU139 3.8 0.5 1.0 CA G:GLU139 3.9 0.4 1.0 O G:LEU140 3.9 1.0 1.0 NZ H:LYS91 4.0 87.1 1.0 CE H:LYS91 4.1 0.8 1.0 C G:LEU140 4.2 0.3 1.0 N G:LEU140 4.2 0.1 1.0 N G:GLU139 4.3 0.8 1.0 CA G:PRO142 4.3 0.1 1.0 N G:PRO142 4.5 0.4 1.0 OE1 G:GLU139 4.5 0.6 1.0 N G:LEU141 4.5 0.7 1.0 O3' L:DT5 4.7 0.9 1.0 CA G:LEU140 4.8 0.1 1.0 CA G:LEU141 4.8 0.4 1.0 OP1 L:DG6 4.8 0.9 1.0 C G:PRO142 4.9 0.9 1.0

Sodium binding site 4 out of 4 in the Hermes Transposase Bound to Its Terminal Inverted Repeat


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Hermes Transposase Bound to Its Terminal Inverted Repeat within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1610 b:59.0 occ:1.00 OP2 J:DG6 2.6 0.5 1.0 O H:GLU138 2.6 0.6 1.0 O H:GLU139 2.9 1.0 1.0 O H:LEU141 2.9 0.0 1.0 C H:GLU139 3.4 0.3 1.0 CA H:GLU139 3.6 0.4 1.0 O5' J:DG6 3.7 0.1 1.0 C H:GLU138 3.7 1.0 1.0 P J:DG6 3.7 0.4 1.0 C5' J:DG6 3.9 0.7 1.0 C H:LEU141 4.0 1.0 1.0 N H:GLU139 4.1 0.2 1.0 NZ G:LYS91 4.2 0.3 1.0 N H:LEU140 4.5 0.7 1.0 CA H:PRO142 4.6 0.5 1.0 OP1 J:DG6 4.7 0.5 1.0 C H:LEU140 4.7 0.7 1.0 N H:LEU141 4.8 0.9 1.0 N H:PRO142 4.8 0.5 1.0 O H:LEU140 4.8 0.2 1.0 C H:PRO142 4.9 0.1 1.0 O3' J:DT5 4.9 1.0 1.0 CE G:LYS91 5.0 0.2 1.0 N H:SER143 5.0 0.5 1.0

A.B.Hickman, H.E.Ewis, X.Li, J.A.Knapp, T.Laver, A.Doss, G.Tolun, A.C.Steven, A.Grishaev, A.Bax, P.W.Atkinson, N.L.Craig, F.Dyda. Structural Basis of Hat Transposon End Recognition By Hermes, An Octameric Dna Transposase From Musca Domestica. Cell(Cambridge,Mass.) V. 158 353 2014.
ISSN: ISSN 0092-8674
PubMed: 25036632
DOI: 10.1016/J.CELL.2014.05.037