Manganese in PDB 5ekd: Human Mitochondrial Tryptophanyl-Trna Synthetase Bound By Indolmycin and Mn*Atp.

All present enzymatic activity of Human Mitochondrial Tryptophanyl-Trna Synthetase Bound By Indolmycin and Mn*Atp.:
6.1.1.2;

The structure of Human Mitochondrial Tryptophanyl-Trna Synthetase Bound By Indolmycin and Mn*Atp., PDB code: 5ekd was solved by T.L.Williams, C.W.Carter Jr., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.06 / 1.82
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	58.289, 78.087, 153.996, 90.00, 96.55, 90.00
R / Rfree (%)	17 / 20.7

The binding sites of Manganese atom in the Human Mitochondrial Tryptophanyl-Trna Synthetase Bound By Indolmycin and Mn*Atp. (pdb code 5ekd). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Human Mitochondrial Tryptophanyl-Trna Synthetase Bound By Indolmycin and Mn*Atp., PDB code: 5ekd:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Human Mitochondrial Tryptophanyl-Trna Synthetase Bound By Indolmycin and Mn*Atp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Human Mitochondrial Tryptophanyl-Trna Synthetase Bound By Indolmycin and Mn*Atp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:16.8 occ:1.00 O3G A:ATP402 2.1 23.2 1.0 O2B A:ATP402 2.1 17.3 1.0 O A:HOH529 2.2 17.0 1.0 O A:HOH691 2.2 19.1 1.0 O2A A:ATP402 2.2 18.9 1.0 O A:HOH555 2.2 15.9 1.0 PB A:ATP402 3.2 19.7 1.0 PG A:ATP402 3.3 40.6 1.0 HE21 A:GLN42 3.3 26.7 1.0 PA A:ATP402 3.4 18.5 1.0 HZ2 A:LYS226 3.5 24.5 1.0 O3B A:ATP402 3.5 25.7 1.0 HE22 A:GLN42 3.6 26.7 1.0 O3A A:ATP402 3.6 17.0 1.0 NE2 A:GLN42 3.8 22.3 1.0 O5' A:ATP402 4.0 16.2 1.0 O1G A:ATP402 4.0 26.3 1.0 O06 A:5BX401 4.0 21.9 1.0 H8 A:ATP402 4.1 23.1 1.0 O A:HOH550 4.1 30.6 1.0 N04 A:5BX401 4.2 18.4 1.0 O A:HOH689 4.2 37.0 1.0 HE2 A:LYS226 4.2 23.5 1.0 OD2 A:ASP181 4.3 20.2 1.0 NZ A:LYS226 4.4 20.4 1.0 H2' A:ATP402 4.4 23.0 1.0 HE21 A:GLN182 4.4 24.2 1.0 O A:HOH740 4.4 35.5 1.0 C05 A:5BX401 4.5 20.2 1.0 O2G A:ATP402 4.5 30.6 1.0 O1B A:ATP402 4.5 21.5 1.0 HE3 A:LYS226 4.6 23.5 1.0 CE A:LYS226 4.7 19.6 1.0 O1A A:ATP402 4.7 15.3 1.0 O A:HOH563 4.8 34.3 1.0 HZ3 A:LYS226 4.8 24.5 1.0 HZ1 A:LYS226 4.9 24.5 1.0

Manganese binding site 2 out of 4 in the Human Mitochondrial Tryptophanyl-Trna Synthetase Bound By Indolmycin and Mn*Atp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Human Mitochondrial Tryptophanyl-Trna Synthetase Bound By Indolmycin and Mn*Atp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn404 b:25.4 occ:0.49 O A:HOH703 2.2 32.4 1.0 O A:HOH533 2.2 17.7 1.0 OE1 A:GLU312 2.2 25.7 1.0 CD A:GLU312 3.1 23.7 1.0 OE2 A:GLU312 3.4 24.1 1.0 O A:HOH537 4.0 26.9 1.0 O A:HOH602 4.4 37.0 1.0 O A:HOH705 4.5 35.5 1.0 HB3 A:GLU312 4.5 19.7 1.0 CG A:GLU312 4.5 22.8 1.0 HG22 A:THR283 4.6 31.7 1.0 HA A:ALA309 4.7 22.6 1.0 HG2 A:GLU312 4.9 27.4 1.0 HB2 A:GLU312 4.9 19.7 1.0 CB A:GLU312 4.9 16.4 1.0

Manganese binding site 3 out of 4 in the Human Mitochondrial Tryptophanyl-Trna Synthetase Bound By Indolmycin and Mn*Atp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Human Mitochondrial Tryptophanyl-Trna Synthetase Bound By Indolmycin and Mn*Atp. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn403 b:18.3 occ:1.00 O1G B:ATP402 2.0 21.2 1.0 O1B B:ATP402 2.1 18.9 1.0 O2A B:ATP402 2.2 21.0 1.0 O B:HOH522 2.2 14.8 1.0 O B:HOH678 2.2 23.9 1.0 O B:HOH618 2.2 14.7 1.0 PB B:ATP402 3.2 25.6 1.0 PG B:ATP402 3.3 31.0 1.0 PA B:ATP402 3.4 22.3 1.0 HZ1 B:LYS226 3.5 27.8 1.0 O3B B:ATP402 3.5 27.8 1.0 HE21 B:GLN42 3.7 27.5 1.0 O3A B:ATP402 3.7 20.8 1.0 HE22 B:GLN42 3.9 27.5 1.0 O5' B:ATP402 4.0 19.4 1.0 O06 B:5BX401 4.0 19.3 1.0 O3G B:ATP402 4.0 28.0 1.0 H8 B:ATP402 4.1 24.5 1.0 O B:HOH595 4.1 42.3 1.0 O B:HOH630 4.1 31.2 1.0 NE2 B:GLN42 4.1 22.9 1.0 HE2 B:LYS226 4.2 30.8 1.0 N04 B:5BX401 4.3 17.3 1.0 O B:HOH509 4.3 23.5 1.0 HE21 B:GLN141 4.3 33.1 1.0 H2' B:ATP402 4.3 18.7 1.0 OD2 B:ASP181 4.3 21.8 1.0 HE22 B:GLN182 4.4 21.0 1.0 NZ B:LYS226 4.4 23.1 1.0 O2G B:ATP402 4.5 34.0 1.0 C05 B:5BX401 4.5 15.1 1.0 O2B B:ATP402 4.6 28.9 1.0 CE B:LYS226 4.7 25.7 1.0 O1A B:ATP402 4.7 20.1 1.0 HE3 B:LYS226 4.8 30.8 1.0 HZ2 B:LYS226 4.9 27.8 1.0 HZ1 B:LYS145 4.9 50.0 1.0 HE22 B:GLN141 4.9 33.1 1.0 HZ3 B:LYS226 4.9 27.8 1.0 NE2 B:GLN141 4.9 27.6 1.0 C8 B:ATP402 5.0 20.4 1.0

Manganese binding site 4 out of 4 in the Human Mitochondrial Tryptophanyl-Trna Synthetase Bound By Indolmycin and Mn*Atp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Human Mitochondrial Tryptophanyl-Trna Synthetase Bound By Indolmycin and Mn*Atp. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn404 b:30.5 occ:0.40 O B:HOH511 2.0 37.8 1.0 OE1 B:GLU312 2.1 31.7 1.0 O B:HOH705 2.2 33.9 1.0 CD B:GLU312 3.0 30.6 1.0 OE2 B:GLU312 3.2 30.2 1.0 O B:HOH575 4.1 28.8 1.0 O B:HOH725 4.3 41.8 1.0 CG B:GLU312 4.4 29.7 1.0 HB3 B:GLU312 4.5 28.1 1.0 HG2 B:GLU312 4.7 35.7 1.0 HA B:ALA309 4.9 30.6 1.0 HB2 B:GLU312 4.9 28.1 1.0 CB B:GLU312 4.9 23.4 1.0

T.L.Williams, C.W.Carter Jr.. Binding of MG2+Atp Enhances Inhibition of Human Mitochondrial Tryptophanyl-Trna Synthetase By Indolmycin To Be Published.