Magnesium in PDB 6vzw: TTLL6 Bound to the Initiation Analog

The structure of TTLL6 Bound to the Initiation Analog, PDB code: 6vzw was solved by K.K.Mahalingan, E.K.Keenen, M.Strickland, Y.Li, Y.Liu, H.L.Ball, T.E.Tanner, N.Tjandra, A.Roll-Mecak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.92 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.254, 110.585, 173.579, 90.00, 90.14, 90.00
R / Rfree (%)	21.7 / 24.4

The binding sites of Magnesium atom in the TTLL6 Bound to the Initiation Analog (pdb code 6vzw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the TTLL6 Bound to the Initiation Analog, PDB code: 6vzw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the TTLL6 Bound to the Initiation Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of TTLL6 Bound to the Initiation Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg605 b:52.4 occ:1.00 O14 A:2TI601 2.0 43.9 1.0 O2A A:ADP604 2.0 50.5 1.0 OD2 A:ASP346 2.3 72.9 1.0 O3B A:ADP604 2.3 58.1 1.0 OE1 A:GLU359 2.6 59.0 1.0 ND2 A:ASN264 3.2 53.7 1.0 P13 A:2TI601 3.3 55.5 1.0 PA A:ADP604 3.3 63.8 1.0 PB A:ADP604 3.5 55.1 1.0 CG A:ASP346 3.6 73.3 1.0 O15 A:2TI601 3.7 51.2 1.0 CD A:GLU359 3.7 62.2 1.0 C5' A:ADP604 3.8 56.5 1.0 NH2 A:ARG241 3.8 81.2 1.0 O3A A:ADP604 3.8 66.0 1.0 O16 A:2TI601 3.8 54.0 1.0 NH1 A:ARG241 3.9 72.0 1.0 O1B A:ADP604 3.9 56.0 1.0 O5' A:ADP604 4.0 57.9 1.0 O3' A:ADP604 4.2 59.8 1.0 CZ A:ARG241 4.2 76.2 1.0 CG A:ASN264 4.3 56.2 1.0 CG A:GLU359 4.3 61.1 1.0 OD1 A:ASP346 4.4 72.8 1.0 C3' A:ADP604 4.4 56.0 1.0 NH2 A:ARG219 4.4 64.7 1.0 CB A:ASP346 4.5 70.1 1.0 O12 A:2TI601 4.5 56.7 1.0 MG A:MG606 4.6 43.2 1.0 O1A A:ADP604 4.6 57.9 1.0 C4' A:ADP604 4.6 57.6 1.0 OD1 A:ASN264 4.7 60.5 1.0 OE2 A:GLU359 4.7 70.4 1.0 ND2 A:ASN361 4.8 49.4 1.0 O2B A:ADP604 4.8 58.9 1.0 OD2 A:ASP217 4.9 94.3 1.0

Magnesium binding site 2 out of 8 in the TTLL6 Bound to the Initiation Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of TTLL6 Bound to the Initiation Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg606 b:43.2 occ:1.00 OE2 A:GLU359 2.2 70.4 1.0 O1B A:ADP604 2.2 56.0 1.0 O15 A:2TI601 2.4 51.2 1.0 OD1 A:ASN361 2.4 50.1 1.0 OE1 A:GLU359 2.5 59.0 1.0 CD A:GLU359 2.7 62.2 1.0 PB A:ADP604 3.4 55.1 1.0 CG A:ASN361 3.5 53.3 1.0 N05 A:2TI601 3.6 0.9 1.0 C07 A:2TI601 3.7 0.5 1.0 P13 A:2TI601 3.7 55.5 1.0 NZ A:LYS125 3.7 48.5 1.0 CA A:CYS179 3.7 54.5 1.0 O A:GLY178 3.7 66.2 1.0 CB A:CYS179 3.8 54.8 1.0 O3B A:ADP604 3.8 58.1 1.0 O14 A:2TI601 4.0 43.9 1.0 ND2 A:ASN361 4.0 49.4 1.0 CG A:GLU359 4.2 61.1 1.0 C06 A:2TI601 4.2 0.3 1.0 O2B A:ADP604 4.3 58.9 1.0 C08 A:2TI601 4.5 82.0 1.0 O12 A:2TI601 4.5 56.7 1.0 C A:GLY178 4.5 58.6 1.0 CE A:LYS125 4.6 47.9 1.0 MG A:MG605 4.6 52.4 1.0 N A:CYS179 4.6 54.8 1.0 O16 A:2TI601 4.6 54.0 1.0 O3A A:ADP604 4.6 66.0 1.0 N A:GLN180 4.6 51.7 1.0 O2A A:ADP604 4.7 50.5 1.0 C A:CYS179 4.7 53.0 1.0 CB A:ASN361 4.7 57.8 1.0 C03 A:2TI601 4.7 99.2 1.0 CB A:GLU359 4.9 57.7 1.0 C02 A:2TI601 4.9 87.5 1.0

Magnesium binding site 3 out of 8 in the TTLL6 Bound to the Initiation Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of TTLL6 Bound to the Initiation Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg611 b:27.7 occ:1.00 O15 B:2TI601 1.9 28.4 1.0 O B:HOH712 2.0 27.6 1.0 ND2 B:ASN361 2.1 34.2 1.0 OE2 B:GLU359 2.1 31.8 1.0 OE1 B:GLU359 2.3 33.8 1.0 O2B B:ADP610 2.4 17.6 1.0 CD B:GLU359 2.5 32.0 1.0 CG B:ASN361 3.0 36.0 1.0 P13 B:2TI601 3.1 35.9 1.0 OD1 B:ASN361 3.2 43.3 1.0 O14 B:2TI601 3.5 38.2 1.0 PB B:ADP610 3.5 30.8 1.0 O1B B:ADP610 3.5 18.3 1.0 MG B:MG612 3.6 33.1 1.0 O12 B:2TI601 3.8 53.9 1.0 CG B:GLU359 3.9 40.3 1.0 NZ B:LYS125 4.0 29.6 1.0 CA B:CYS179 4.1 26.9 1.0 CB B:CYS179 4.2 27.6 1.0 C08 B:2TI601 4.2 20.9 1.0 O16 B:2TI601 4.2 28.5 1.0 O B:HOH713 4.4 33.2 1.0 N05 B:2TI601 4.4 50.9 1.0 CB B:ASN361 4.4 31.3 1.0 O1A B:ADP610 4.4 38.2 1.0 O3B B:ADP610 4.5 31.8 1.0 O B:GLY178 4.5 41.5 1.0 C07 B:2TI601 4.5 56.9 1.0 N B:GLN180 4.6 29.4 1.0 O3A B:ADP610 4.6 34.2 1.0 C03 B:2TI601 4.7 41.7 1.0 C02 B:2TI601 4.8 39.6 1.0 CE B:LYS125 4.8 30.2 1.0 C09 B:2TI601 4.8 21.6 1.0 OD2 B:ASP346 4.8 54.5 1.0 C B:CYS179 4.9 31.2 1.0 CB B:GLU359 4.9 40.1 1.0

Magnesium binding site 4 out of 8 in the TTLL6 Bound to the Initiation Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of TTLL6 Bound to the Initiation Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg612 b:33.1 occ:1.00 O14 B:2TI601 1.9 38.2 1.0 O1A B:ADP610 1.9 38.2 1.0 OE2 B:GLU359 2.0 31.8 1.0 OD2 B:ASP346 2.1 54.5 1.0 O B:HOH739 2.1 33.0 1.0 O1B B:ADP610 2.3 18.3 1.0 CD B:GLU359 3.1 32.0 1.0 P13 B:2TI601 3.1 35.9 1.0 O15 B:2TI601 3.3 28.4 1.0 PA B:ADP610 3.3 29.5 1.0 PB B:ADP610 3.3 30.8 1.0 CG B:ASP346 3.3 50.7 1.0 MG B:MG611 3.6 27.7 1.0 O2B B:ADP610 3.6 17.6 1.0 ND2 B:ASN264 3.6 36.2 1.0 CG B:GLU359 3.7 40.3 1.0 O3A B:ADP610 3.7 34.2 1.0 O16 B:2TI601 3.9 28.5 1.0 C5' B:ADP610 4.0 12.1 1.0 NH2 B:ARG241 4.0 53.0 1.0 OD1 B:ASP346 4.1 51.2 1.0 NH2 B:ARG219 4.1 38.9 1.0 O5' B:ADP610 4.1 20.7 1.0 OE1 B:GLU359 4.2 33.8 1.0 OD1 B:ASN361 4.3 43.3 1.0 O12 B:2TI601 4.3 53.9 1.0 CB B:ASP346 4.3 33.2 1.0 NH1 B:ARG241 4.4 44.8 1.0 O2A B:ADP610 4.5 28.3 1.0 O3' B:ADP610 4.6 42.5 1.0 O3B B:ADP610 4.7 31.8 1.0 CZ B:ARG241 4.7 56.9 1.0 C3' B:ADP610 4.8 38.5 1.0 CG B:ASN264 4.8 35.0 1.0 ND2 B:ASN361 4.9 34.2 1.0 C4' B:ADP610 5.0 29.0 1.0 CB B:GLU359 5.0 40.1 1.0

Magnesium binding site 5 out of 8 in the TTLL6 Bound to the Initiation Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of TTLL6 Bound to the Initiation Analog within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg606 b:48.4 occ:1.00 O1B C:ADP605 2.0 59.6 1.0 OD1 C:ASN361 2.2 50.7 1.0 O15 C:2TI601 2.3 50.4 1.0 OE2 C:GLU359 2.3 62.2 1.0 OE1 C:GLU359 2.6 53.1 1.0 CD C:GLU359 2.7 54.0 1.0 C06 C:2TI601 3.1 89.1 1.0 N05 C:2TI601 3.2 88.9 1.0 PB C:ADP605 3.3 57.9 1.0 CG C:ASN361 3.4 53.5 1.0 P13 C:2TI601 3.6 55.9 1.0 O C:GLY178 3.7 71.6 1.0 CA C:CYS179 3.7 55.3 1.0 O3B C:ADP605 3.7 52.3 1.0 CB C:CYS179 3.7 57.3 1.0 ND2 C:ASN361 4.0 58.4 1.0 O14 C:2TI601 4.1 46.9 1.0 NZ C:LYS125 4.1 55.1 1.0 O3A C:ADP605 4.1 50.4 1.0 CG C:GLU359 4.2 50.7 1.0 C03 C:2TI601 4.3 81.5 1.0 O12 C:2TI601 4.4 57.0 1.0 O2B C:ADP605 4.5 44.7 1.0 C C:GLY178 4.5 62.5 1.0 O16 C:2TI601 4.5 56.9 1.0 CE C:LYS125 4.5 59.8 1.0 C07 C:2TI601 4.6 85.1 1.0 N C:CYS179 4.6 55.2 1.0 CB C:ASN361 4.6 56.3 1.0 N C:GLN180 4.7 56.7 1.0 MG C:MG607 4.7 49.0 1.0 C C:CYS179 4.7 54.2 1.0 C08 C:2TI601 4.8 77.0 1.0 C09 C:2TI601 4.9 68.2 1.0 O2A C:ADP605 4.9 44.7 1.0

Magnesium binding site 6 out of 8 in the TTLL6 Bound to the Initiation Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of TTLL6 Bound to the Initiation Analog within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg607 b:49.0 occ:1.00 O14 C:2TI601 2.0 46.9 1.0 O3B C:ADP605 2.1 52.3 1.0 O2A C:ADP605 2.1 44.7 1.0 OD2 C:ASP346 2.2 82.2 1.0 OE1 C:GLU359 2.7 53.1 1.0 ND2 C:ASN264 3.1 67.0 1.0 PA C:ADP605 3.2 50.3 1.0 P13 C:2TI601 3.3 55.9 1.0 O5' C:ADP605 3.3 62.1 1.0 CG C:ASP346 3.4 76.9 1.0 PB C:ADP605 3.5 57.9 1.0 O15 C:2TI601 3.6 50.4 1.0 NH2 C:ARG241 3.6 79.6 1.0 O16 C:2TI601 3.7 56.9 1.0 O3A C:ADP605 3.7 50.4 1.0 NH1 C:ARG241 3.8 75.6 1.0 O3' C:ADP605 3.8 63.8 1.0 CD C:GLU359 3.8 54.0 1.0 CZ C:ARG241 4.1 76.2 1.0 CG C:ASN264 4.2 67.1 1.0 OD1 C:ASP346 4.2 80.3 1.0 O1B C:ADP605 4.2 59.6 1.0 C3' C:ADP605 4.3 58.6 1.0 CG C:GLU359 4.3 50.7 1.0 CB C:ASP346 4.4 67.7 1.0 NH2 C:ARG219 4.4 59.6 1.0 OD1 C:ASN264 4.6 71.1 1.0 C5' C:ADP605 4.6 60.9 1.0 O1A C:ADP605 4.6 43.3 1.0 O2B C:ADP605 4.6 44.7 1.0 O12 C:2TI601 4.6 57.0 1.0 MG C:MG606 4.7 48.4 1.0 ND2 C:ASN361 4.8 58.4 1.0 OE2 C:GLU359 4.8 62.2 1.0 C4' C:ADP605 4.8 59.9 1.0 OD2 C:ASP217 4.9 81.8 1.0

Magnesium binding site 7 out of 8 in the TTLL6 Bound to the Initiation Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of TTLL6 Bound to the Initiation Analog within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg610 b:30.5 occ:1.00 O D:HOH710 1.9 24.6 1.0 O15 D:2TI601 1.9 21.4 1.0 OD1 D:ASN361 2.0 44.4 1.0 OE2 D:GLU359 2.1 35.9 1.0 OE1 D:GLU359 2.4 36.2 1.0 O3B D:ADP609 2.4 9.7 1.0 CD D:GLU359 2.5 35.9 1.0 CG D:ASN361 3.0 40.7 1.0 P13 D:2TI601 3.1 34.2 1.0 ND2 D:ASN361 3.3 36.4 1.0 O14 D:2TI601 3.4 33.0 1.0 PB D:ADP609 3.6 24.2 1.0 O1B D:ADP609 3.7 11.0 1.0 MG D:MG611 3.7 24.2 1.0 O12 D:2TI601 3.8 46.8 1.0 CG D:GLU359 4.0 35.6 1.0 NZ D:LYS125 4.0 28.6 1.0 CA D:CYS179 4.0 27.0 1.0 C08 D:2TI601 4.1 23.7 1.0 CB D:CYS179 4.1 36.8 1.0 O16 D:2TI601 4.2 25.0 1.0 O D:HOH704 4.2 35.0 1.0 N05 D:2TI601 4.3 48.7 1.0 O D:GLY178 4.4 37.6 1.0 CB D:ASN361 4.4 34.6 1.0 C07 D:2TI601 4.5 61.2 1.0 O1A D:ADP609 4.6 40.3 1.0 N D:GLN180 4.6 31.2 1.0 O3A D:ADP609 4.6 38.2 1.0 O2B D:ADP609 4.6 38.0 1.0 C03 D:2TI601 4.7 39.8 1.0 C02 D:2TI601 4.7 36.1 1.0 OD2 D:ASP346 4.8 63.0 1.0 CE D:LYS125 4.8 35.1 1.0 C09 D:2TI601 4.8 12.3 1.0 C D:CYS179 4.8 30.9 1.0 CB D:GLU359 5.0 36.0 1.0 P10 D:2TI601 5.0 26.7 1.0

Magnesium binding site 8 out of 8 in the TTLL6 Bound to the Initiation Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of TTLL6 Bound to the Initiation Analog within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg611 b:24.2 occ:1.00 O14 D:2TI601 1.9 33.0 1.0 O1A D:ADP609 1.9 40.3 1.0 OD2 D:ASP346 2.0 63.0 1.0 OE2 D:GLU359 2.1 35.9 1.0 O D:HOH728 2.2 25.0 1.0 O1B D:ADP609 2.4 11.0 1.0 CD D:GLU359 3.2 35.9 1.0 P13 D:2TI601 3.2 34.2 1.0 CG D:ASP346 3.3 51.4 1.0 PA D:ADP609 3.3 23.1 1.0 PB D:ADP609 3.4 24.2 1.0 O15 D:2TI601 3.4 21.4 1.0 ND2 D:ASN264 3.7 33.6 1.0 MG D:MG610 3.7 30.5 1.0 O3B D:ADP609 3.7 9.7 1.0 CG D:GLU359 3.7 35.6 1.0 O3A D:ADP609 3.8 38.2 1.0 C5' D:ADP609 3.9 15.1 1.0 O16 D:2TI601 3.9 25.0 1.0 NH2 D:ARG241 3.9 39.7 1.0 OD1 D:ASP346 4.0 53.9 1.0 O5' D:ADP609 4.1 16.6 1.0 NH2 D:ARG219 4.2 38.7 1.0 CB D:ASP346 4.2 34.8 1.0 OE1 D:GLU359 4.2 36.2 1.0 ND2 D:ASN361 4.3 36.4 1.0 NH1 D:ARG241 4.4 49.2 1.0 O12 D:2TI601 4.4 46.8 1.0 O2A D:ADP609 4.5 34.1 1.0 O3' D:ADP609 4.5 41.8 1.0 CZ D:ARG241 4.6 52.1 1.0 C3' D:ADP609 4.7 36.8 1.0 O2B D:ADP609 4.8 38.0 1.0 CG D:ASN264 4.8 33.9 1.0 C4' D:ADP609 4.9 27.0 1.0 OD1 D:ASN361 5.0 44.4 1.0 CB D:GLU359 5.0 36.0 1.0

K.K.Mahalingan, E.K.Keenen, M.Strickland, Y.Li, Y.Liu, H.L.Ball, T.E.Tanner, N.Tjandra, A.Roll-Mecak. TTLL6 Bound to the Initiation Analog To Be Published.