Sodium in PDB 7pv5: Rbd Domain of D. Melanogaster Trna (Uracil-5-)-Methyltransferase Homolog A (TRMT2A)

The structure of Rbd Domain of D. Melanogaster Trna (Uracil-5-)-Methyltransferase Homolog A (TRMT2A), PDB code: 7pv5 was solved by M.Witzenberger, R.Janowski, D.Niessing, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.64 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	92.41, 41.89, 48.82, 90, 110.8, 90
R / Rfree (%)	14.1 / 19.9

The structure of Rbd Domain of D. Melanogaster Trna (Uracil-5-)-Methyltransferase Homolog A (TRMT2A) also contains other interesting chemical elements:

Chlorine	(Cl)	46 atoms
Gold	(Au)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Sodium atom in the Rbd Domain of D. Melanogaster Trna (Uracil-5-)-Methyltransferase Homolog A (TRMT2A) (pdb code 7pv5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 16 binding sites of Sodium where determined in the Rbd Domain of D. Melanogaster Trna (Uracil-5-)-Methyltransferase Homolog A (TRMT2A), PDB code: 7pv5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 16 in the Rbd Domain of D. Melanogaster Trna (Uracil-5-)-Methyltransferase Homolog A (TRMT2A)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Rbd Domain of D. Melanogaster Trna (Uracil-5-)-Methyltransferase Homolog A (TRMT2A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na220 b:43.9 occ:1.00 CE1 A:HIS130 3.3 15.2 1.0 OE1 A:GLU64 3.8 18.0 1.0 CB A:ALA132 4.0 20.5 1.0 ND1 A:HIS130 4.0 16.0 1.0 CA A:ALA132 4.1 16.8 1.0 O A:VAL131 4.3 16.4 1.0 NE2 A:HIS130 4.4 16.1 1.0 CE1 A:PHE101 4.4 16.3 1.0 O4 A:SO4201 4.7 28.7 1.0 CZ A:PHE101 4.9 17.2 1.0 O A:HOH366 4.9 31.0 0.5 N A:LYS133 4.9 30.9 1.0 CD A:GLU64 4.9 15.2 1.0 CB A:GLU64 5.0 14.3 1.0

Sodium binding site 2 out of 16 in the Rbd Domain of D. Melanogaster Trna (Uracil-5-)-Methyltransferase Homolog A (TRMT2A)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Rbd Domain of D. Melanogaster Trna (Uracil-5-)-Methyltransferase Homolog A (TRMT2A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na221 b:34.1 occ:1.00 CL A:CL207 2.7 58.1 1.0 O A:HOH333 2.8 18.8 1.0 NZ A:LYS123 3.0 22.1 1.0 CE A:LYS123 3.5 16.6 1.0 O A:HOH357 4.0 38.9 1.0 O A:HOH304 4.1 56.8 1.0 CD A:LYS78 4.1 38.3 1.0 CB A:GLU75 4.2 23.5 1.0 NZ A:LYS78 4.2 52.7 1.0 CG A:GLU75 4.3 31.6 1.0 CA A:GLU75 4.3 16.6 1.0 OE2 A:GLU75 4.5 32.5 1.0 O A:GLU75 4.7 13.4 1.0 CL A:CL203 4.7 41.6 1.0 CD A:GLU75 4.7 25.6 1.0 CE A:LYS78 4.8 49.4 1.0

Sodium binding site 3 out of 16 in the Rbd Domain of D. Melanogaster Trna (Uracil-5-)-Methyltransferase Homolog A (TRMT2A)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Rbd Domain of D. Melanogaster Trna (Uracil-5-)-Methyltransferase Homolog A (TRMT2A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na222 b:30.7 occ:1.00 O A:HOH370 2.9 30.8 0.5 O A:HOH370 3.2 31.1 0.5

Sodium binding site 4 out of 16 in the Rbd Domain of D. Melanogaster Trna (Uracil-5-)-Methyltransferase Homolog A (TRMT2A)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Rbd Domain of D. Melanogaster Trna (Uracil-5-)-Methyltransferase Homolog A (TRMT2A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na223 b:50.7 occ:1.00 CL A:CL213 2.3 59.4 1.0 CB A:PRO94 4.0 18.6 1.0 O A:HOH344 4.2 47.2 1.0 CA A:PRO94 4.3 15.9 1.0 CL A:CL212 4.5 20.0 1.0 O A:PRO94 4.6 20.3 1.0 O A:HOH368 4.9 44.4 1.0 C A:PRO94 5.0 13.7 1.0

Sodium binding site 5 out of 16 in the Rbd Domain of D. Melanogaster Trna (Uracil-5-)-Methyltransferase Homolog A (TRMT2A)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Rbd Domain of D. Melanogaster Trna (Uracil-5-)-Methyltransferase Homolog A (TRMT2A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na224 b:44.8 occ:1.00 OE1 A:GLU98 2.4 30.5 0.5 O A:HOH325 2.9 44.3 1.0 N A:ASN67 3.0 13.8 1.0 CG A:GLU98 3.2 21.1 0.5 CD A:GLU98 3.2 20.0 0.5 CA A:ASN67 3.5 15.1 1.0 CE A:LYS66 3.9 26.4 1.0 O A:GLU98 3.9 13.4 0.5 O A:GLU98 3.9 13.8 0.5 CL A:CL202 3.9 22.0 1.0 O A:HOH324 3.9 44.3 1.0 CB A:LYS66 4.1 18.0 1.0 C A:LYS66 4.1 12.8 1.0 CA A:LYS66 4.3 13.9 1.0 NZ A:LYS66 4.3 27.6 1.0 CB A:GLU98 4.4 16.6 0.5 OE2 A:GLU98 4.4 27.6 0.5 CB A:ASN67 4.4 14.1 1.0 CB A:GLU98 4.5 16.2 0.5 C A:GLU98 4.5 13.9 0.5 C A:GLU98 4.6 13.8 0.5 CA A:GLU98 4.6 14.2 0.5 C A:ASN67 4.7 14.1 1.0 CA A:GLU98 4.7 13.9 0.5 OD1 A:ASN67 4.7 18.9 1.0 CD A:LYS66 4.8 21.4 1.0 N A:MET68 4.8 13.3 1.0 NZ A:LYS128 4.9 43.0 1.0 CG A:GLU98 4.9 17.8 0.5 CG A:LYS66 5.0 22.2 1.0

Sodium binding site 6 out of 16 in the Rbd Domain of D. Melanogaster Trna (Uracil-5-)-Methyltransferase Homolog A (TRMT2A)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Rbd Domain of D. Melanogaster Trna (Uracil-5-)-Methyltransferase Homolog A (TRMT2A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na225 b:40.2 occ:1.00 CL A:CL216 2.5 39.2 1.0 O B:GLY119 2.9 16.9 1.0 N A:LYS121 3.1 17.9 1.0 CL B:CL214 3.6 61.4 1.0 CA A:TYR120 3.6 16.3 1.0 C B:GLY119 3.6 13.6 1.0 O A:GLY119 3.7 18.5 1.0 CA B:TYR120 3.8 16.2 1.0 C A:TYR120 3.8 15.0 1.0 CB A:LYS121 3.9 24.2 1.0 N B:TYR120 4.0 13.9 1.0 CA A:LYS121 4.0 16.9 1.0 CD1 A:TYR120 4.1 17.3 1.0 CG A:TYR120 4.3 14.0 1.0 O B:HOH334 4.3 32.3 1.0 N B:LYS121 4.3 16.1 1.0 O A:LYS121 4.4 18.0 1.0 C A:GLY119 4.5 16.7 1.0 CB A:TYR120 4.5 15.4 1.0 C B:TYR120 4.5 12.9 1.0 CE1 A:TYR120 4.6 19.2 1.0 N A:TYR120 4.6 16.1 1.0 CA B:GLY119 4.7 15.1 1.0 C A:LYS121 4.7 15.2 1.0 CB B:TYR120 4.8 16.1 1.0 CG B:LYS121 4.8 26.1 1.0 CD1 B:TYR120 4.8 15.2 1.0 CD2 A:TYR120 4.8 14.2 1.0

Sodium binding site 7 out of 16 in the Rbd Domain of D. Melanogaster Trna (Uracil-5-)-Methyltransferase Homolog A (TRMT2A)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Rbd Domain of D. Melanogaster Trna (Uracil-5-)-Methyltransferase Homolog A (TRMT2A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na226 b:43.8 occ:1.00 O A:HOH355 2.9 56.6 1.0 OD1 A:ASN82 3.1 35.2 0.6 O A:ARG81 3.1 14.6 0.5 NZ A:LYS85 3.1 35.4 0.8 CA A:ASN82 3.6 18.4 0.4 CA A:ASN82 3.6 17.2 0.6 O A:ARG81 3.7 17.0 0.5 CG A:ASN82 3.8 22.5 0.6 C A:ARG81 4.0 15.8 0.5 CB A:ASN82 4.1 20.0 0.4 CB A:ASN82 4.1 18.4 0.6 N A:ASN82 4.2 16.6 0.4 C A:ARG81 4.2 16.7 0.5 CD A:LYS85 4.2 27.3 1.0 N A:ASN82 4.2 15.7 0.6 CE A:LYS85 4.2 33.1 1.0 CG A:ASN82 4.3 22.5 0.4 O A:HOH312 4.4 31.9 1.0 O A:ASN82 4.4 20.9 0.4 O A:ASN82 4.5 22.7 0.6 OD1 A:ASN82 4.5 24.9 0.4 C A:ASN82 4.6 15.6 0.4 C A:ASN82 4.6 16.6 0.6 ND2 A:ASN82 4.8 29.7 0.4 ND2 A:ASN82 4.8 22.0 0.6

Sodium binding site 8 out of 16 in the Rbd Domain of D. Melanogaster Trna (Uracil-5-)-Methyltransferase Homolog A (TRMT2A)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Rbd Domain of D. Melanogaster Trna (Uracil-5-)-Methyltransferase Homolog A (TRMT2A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na225 b:41.9 occ:1.00 CL B:CL207 2.6 50.5 1.0 CL B:CL221 3.9 45.3 1.0 CA B:GLY124 4.0 15.7 1.0 N B:GLY124 4.2 14.6 1.0 O1 B:SO4201 4.6 31.5 1.0

Sodium binding site 9 out of 16 in the Rbd Domain of D. Melanogaster Trna (Uracil-5-)-Methyltransferase Homolog A (TRMT2A)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Rbd Domain of D. Melanogaster Trna (Uracil-5-)-Methyltransferase Homolog A (TRMT2A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na226 b:54.6 occ:1.00 O B:LYS121 2.8 22.4 1.0 CL B:CL212 2.9 42.9 1.0 CL B:CL220 3.0 39.9 1.0 O B:HOH346 3.7 36.2 1.0 CA B:TRP122 3.8 13.3 1.0 C B:LYS121 3.8 16.1 1.0 CD1 B:TRP122 3.9 14.0 1.0 CE2 B:TYR120 4.2 14.8 1.0 N B:TRP122 4.2 17.8 1.0 O A:HOH343 4.3 40.8 1.0 CB B:TRP122 4.3 13.4 1.0 O A:HOH369 4.3 32.1 0.5 CG B:TRP122 4.5 13.6 1.0 CL B:CL221 4.6 45.3 1.0 OH B:TYR120 4.7 25.0 1.0 N B:LYS123 4.7 13.9 1.0 CZ B:TYR120 4.8 17.1 1.0 C B:TRP122 4.8 14.3 1.0 NE1 B:TRP122 5.0 15.6 1.0

Sodium binding site 10 out of 16 in the Rbd Domain of D. Melanogaster Trna (Uracil-5-)-Methyltransferase Homolog A (TRMT2A)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Rbd Domain of D. Melanogaster Trna (Uracil-5-)-Methyltransferase Homolog A (TRMT2A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na227 b:47.3 occ:1.00 O B:HOH357 2.3 43.6 1.0 CL B:CL223 3.0 51.3 1.0 O B:HOH358 3.3 39.7 1.0 NA B:NA230 4.0 49.3 1.0 O B:HOH321 4.1 19.3 0.5 O B:HOH347 4.6 28.0 1.0

M.Witzenberger, R.Janowski, D.Niessing. Rbd Domain of D. Melanogaster Trna (Uracil-5-)-Methyltransferase Homolog A (TRMT2A) To Be Published.