Magnesium in PDB 6vzs: Engineered TTLL6 Mutant Bound to Gamma-Elongation Analog

The structure of Engineered TTLL6 Mutant Bound to Gamma-Elongation Analog, PDB code: 6vzs was solved by K.K.Mahalingan, E.K.Keenen, M.Strickland, Y.Li, Y.Liu, H.L.Ball, M.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)	45.84 / 2.66
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.738, 108.648, 170.888, 90.00, 90.02, 90.00
R / Rfree (%)	21.9 / 25.6

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

Magnesium binding site 1 out of 8 in the Engineered TTLL6 Mutant Bound to Gamma-Elongation Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Engineered TTLL6 Mutant Bound to Gamma-Elongation Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg613 b:24.8 occ:1.00 O1A A:ADP601 1.9 47.7 1.0 O26 A:S3A602 1.9 44.1 1.0 OD2 A:ASP346 2.0 59.3 1.0 O A:HOH724 2.1 29.2 1.0 OE2 A:GLU359 2.1 48.9 1.0 O1B A:ADP601 2.6 32.4 1.0 CD A:GLU359 3.1 36.0 1.0 P24 A:S3A602 3.2 27.1 1.0 CG A:ASP346 3.2 45.9 1.0 PA A:ADP601 3.3 50.8 1.0 O2B A:ADP601 3.3 21.7 1.0 PB A:ADP601 3.4 33.2 1.0 MG A:MG614 3.5 30.1 1.0 CG A:GLU359 3.5 36.4 1.0 O27 A:S3A602 3.6 19.0 1.0 O3A A:ADP601 3.7 50.0 1.0 ND2 A:ASN264 3.8 38.2 1.0 O25 A:S3A602 3.9 34.0 1.0 OD1 A:ASP346 4.0 58.1 1.0 O5' A:ADP601 4.1 24.4 1.0 OE1 A:GLU359 4.1 36.9 1.0 NH1 A:ARG241 4.2 42.4 1.0 ND2 A:ASN361 4.2 34.7 1.0 CB A:ASP346 4.2 41.2 1.0 C5' A:ADP601 4.2 16.7 1.0 NH2 A:ARG241 4.3 51.6 1.0 NH2 A:ARG219 4.3 33.0 1.0 O12 A:S3A602 4.4 52.9 1.0 O2A A:ADP601 4.4 43.1 1.0 OD1 A:ASN361 4.6 43.2 1.0 CZ A:ARG241 4.7 49.5 1.0 O3' A:ADP601 4.8 47.8 1.0 O3B A:ADP601 4.8 51.0 1.0 C3' A:ADP601 4.8 29.6 1.0 CG A:ASN361 4.9 33.7 1.0 CB A:GLU359 4.9 38.0 1.0 CG A:ASN264 4.9 29.4 1.0

Magnesium binding site 2 out of 8 in the Engineered TTLL6 Mutant Bound to Gamma-Elongation Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Engineered TTLL6 Mutant Bound to Gamma-Elongation Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg614 b:30.1 occ:1.00 OE2 A:GLU359 2.0 48.9 1.0 O27 A:S3A602 2.1 19.0 1.0 O A:HOH740 2.1 32.8 1.0 OD1 A:ASN361 2.1 43.2 1.0 O2B A:ADP601 2.3 21.7 1.0 OE1 A:GLU359 2.5 36.9 1.0 CD A:GLU359 2.6 36.0 1.0 P24 A:S3A602 3.1 27.1 1.0 CG A:ASN361 3.1 33.7 1.0 O26 A:S3A602 3.2 44.1 1.0 PB A:ADP601 3.5 33.2 1.0 MG A:MG613 3.5 24.8 1.0 ND2 A:ASN361 3.5 34.7 1.0 O1B A:ADP601 3.8 32.4 1.0 O A:HOH702 3.8 49.0 1.0 O12 A:S3A602 3.9 52.9 1.0 C9 A:S3A602 4.0 32.4 1.0 CA A:ALA179 4.0 30.5 1.0 CG A:GLU359 4.1 36.4 1.0 NZ A:LYS125 4.1 31.3 1.0 CB A:ALA179 4.2 32.0 1.0 O1A A:ADP601 4.3 47.7 1.0 O25 A:S3A602 4.3 34.0 1.0 O A:GLY178 4.4 40.5 1.0 O3B A:ADP601 4.4 51.0 1.0 N A:ARG180 4.4 28.4 1.0 CB A:ASN361 4.5 35.0 1.0 O3A A:ADP601 4.6 50.0 1.0 C6 A:S3A602 4.7 60.0 1.0 C1 A:S3A602 4.7 45.2 1.0 OD2 A:ASP346 4.7 59.3 1.0 CE A:LYS125 4.8 30.7 1.0 C A:ALA179 4.8 29.1 1.0 C10 A:S3A602 4.8 20.8 1.0 O7 A:S3A602 4.9 67.6 1.0 O8 A:S3A602 4.9 63.7 1.0 CB A:GLU359 5.0 38.0 1.0

Magnesium binding site 3 out of 8 in the Engineered TTLL6 Mutant Bound to Gamma-Elongation Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Engineered TTLL6 Mutant Bound to Gamma-Elongation Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg607 b:56.4 occ:1.00 OE1 B:GLU359 2.0 90.1 1.0 O27 B:S3A602 2.4 64.6 1.0 ND2 B:ASN361 2.5 52.1 1.0 O1B B:ADP601 2.5 41.2 1.0 CD B:GLU359 3.0 67.8 1.0 O7 B:S3A602 3.1 87.5 1.0 CB B:ALA179 3.2 53.9 1.0 CA B:ALA179 3.3 53.8 1.0 O B:GLY178 3.4 62.7 1.0 OE2 B:GLU359 3.4 75.6 1.0 CG B:ASN361 3.8 56.7 1.0 P24 B:S3A602 3.8 53.5 1.0 NZ B:LYS125 3.9 53.5 1.0 C9 B:S3A602 3.9 70.5 1.0 PB B:ADP601 4.0 53.0 1.0 C6 B:S3A602 4.1 87.7 1.0 C B:GLY178 4.2 55.5 1.0 O26 B:S3A602 4.2 43.2 1.0 N B:ALA179 4.3 55.2 1.0 C1 B:S3A602 4.3 77.5 1.0 MG B:MG608 4.3 44.6 1.0 CG B:GLU359 4.4 66.7 1.0 N B:ARG180 4.4 60.5 1.0 OD1 B:ASN361 4.4 60.6 1.0 C B:ALA179 4.4 60.9 1.0 O2B B:ADP601 4.5 70.1 1.0 O12 B:S3A602 4.5 52.2 1.0 NZ D:LYS194 4.5 99.7 1.0 O B:HOH716 4.5 48.4 1.0 C10 B:S3A602 4.8 62.7 1.0 O3B B:ADP601 4.8 71.3 1.0 CB B:ASN361 4.9 63.6 1.0 CE B:LYS125 4.9 53.5 1.0 O25 B:S3A602 4.9 66.7 1.0 O3A B:ADP601 4.9 34.9 1.0

Magnesium binding site 4 out of 8 in the Engineered TTLL6 Mutant Bound to Gamma-Elongation Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Engineered TTLL6 Mutant Bound to Gamma-Elongation Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg608 b:44.6 occ:1.00 O26 B:S3A602 1.9 43.2 1.0 O2A B:ADP601 1.9 47.0 1.0 OE2 B:GLU359 2.1 75.6 1.0 O2B B:ADP601 2.2 70.1 1.0 OD2 B:ASP346 2.2 79.8 1.0 O B:HOH707 2.3 44.9 1.0 PB B:ADP601 3.1 53.0 1.0 P24 B:S3A602 3.2 53.5 1.0 PA B:ADP601 3.2 38.5 1.0 CD B:GLU359 3.2 67.8 1.0 O1B B:ADP601 3.2 41.2 1.0 CG B:ASP346 3.4 72.8 1.0 O3A B:ADP601 3.4 34.9 1.0 O27 B:S3A602 3.5 64.6 1.0 OE1 B:GLU359 3.9 90.1 1.0 O25 B:S3A602 3.9 66.7 1.0 OD1 B:ASN361 4.0 60.6 1.0 ND2 B:ASN264 4.1 57.1 1.0 O5' B:ADP601 4.1 48.6 1.0 OD1 B:ASP346 4.2 74.7 1.0 C5' B:ADP601 4.2 43.0 1.0 O12 B:S3A602 4.3 52.2 1.0 MG B:MG607 4.3 56.4 1.0 CB B:GLU359 4.3 52.0 1.0 O1A B:ADP601 4.3 45.9 1.0 CG B:GLU359 4.4 66.7 1.0 NH2 B:ARG219 4.4 50.6 1.0 CB B:ASP346 4.4 66.6 1.0 ND2 B:ASN361 4.4 52.1 1.0 NH2 B:ARG241 4.5 69.5 1.0 NH1 B:ARG241 4.5 70.3 1.0 O3B B:ADP601 4.5 71.3 1.0 CG B:ASN361 4.7 56.7 1.0 CZ B:ARG241 5.0 71.8 1.0

Magnesium binding site 5 out of 8 in the Engineered TTLL6 Mutant Bound to Gamma-Elongation Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Engineered TTLL6 Mutant Bound to Gamma-Elongation Analog within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1221 b:48.3 occ:1.00 O27 C:S3A1203 1.9 46.6 1.0 O1A C:ADP1202 1.9 47.9 1.0 OD2 C:ASP346 2.0 69.5 1.0 OE1 C:GLU359 2.1 41.5 1.0 O C:HOH1304 2.4 23.9 1.0 O1B C:ADP1202 2.6 22.1 1.0 MG C:MG1222 3.0 32.4 1.0 CG C:ASP346 3.2 51.2 1.0 P24 C:S3A1203 3.3 23.2 1.0 PA C:ADP1202 3.3 23.0 1.0 CD C:GLU359 3.3 41.5 1.0 O2B C:ADP1202 3.4 18.3 1.0 PB C:ADP1202 3.4 35.8 1.0 O25 C:S3A1203 3.6 28.8 1.0 O3A C:ADP1202 3.8 40.8 1.0 OD1 C:ASP346 3.9 53.2 1.0 ND2 C:ASN361 3.9 32.0 1.0 OE2 C:GLU359 4.0 48.9 1.0 NH2 C:ARG219 4.1 27.4 1.0 ND2 C:ASN264 4.1 33.1 1.0 O26 C:S3A1203 4.1 30.0 1.0 O2A C:ADP1202 4.2 18.4 1.0 CB C:ASP346 4.2 40.4 1.0 O12 C:S3A1203 4.2 48.3 1.0 CB C:GLU359 4.3 33.0 1.0 OD1 C:ASN361 4.3 32.6 1.0 O5' C:ADP1202 4.3 9.8 1.0 CG C:GLU359 4.4 45.0 1.0 NH2 C:ARG241 4.4 50.0 1.0 NH1 C:ARG241 4.5 44.1 1.0 C5' C:ADP1202 4.5 16.4 1.0 CG C:ASN361 4.6 30.4 1.0 O3B C:ADP1202 4.8 36.7 1.0 CZ C:ARG241 5.0 49.0 1.0

Magnesium binding site 6 out of 8 in the Engineered TTLL6 Mutant Bound to Gamma-Elongation Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Engineered TTLL6 Mutant Bound to Gamma-Elongation Analog within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1222 b:32.4 occ:1.00 O25 C:S3A1203 2.0 28.8 1.0 OE2 C:GLU359 2.1 48.9 1.0 O C:HOH1301 2.1 25.5 1.0 OD1 C:ASN361 2.3 32.6 1.0 OE1 C:GLU359 2.3 41.5 1.0 O2B C:ADP1202 2.3 18.3 1.0 CD C:GLU359 2.5 41.5 1.0 O27 C:S3A1203 3.0 46.6 1.0 P24 C:S3A1203 3.0 23.2 1.0 MG C:MG1221 3.0 48.3 1.0 CG C:ASN361 3.3 30.4 1.0 PB C:ADP1202 3.3 35.8 1.0 O1B C:ADP1202 3.4 22.1 1.0 ND2 C:ASN361 3.6 32.0 1.0 O12 C:S3A1203 3.7 48.3 1.0 CG C:GLU359 4.0 45.0 1.0 C9 C:S3A1203 4.1 25.3 1.0 CA C:ALA179 4.1 30.1 1.0 O1A C:ADP1202 4.2 47.9 1.0 O26 C:S3A1203 4.2 30.0 1.0 CB C:ALA179 4.3 31.1 1.0 O3B C:ADP1202 4.4 36.7 1.0 N C:ARG180 4.4 27.6 1.0 O C:HOH1302 4.4 45.3 1.0 NZ C:LYS125 4.4 36.4 1.0 O3A C:ADP1202 4.5 40.8 1.0 O C:GLY178 4.6 49.7 1.0 OD2 C:ASP346 4.6 69.5 1.0 CB C:ASN361 4.6 34.7 1.0 O8 C:S3A1203 4.7 65.1 1.0 C C:ALA179 4.8 28.6 1.0 CE C:LYS125 4.8 31.4 1.0 C6 C:S3A1203 4.8 49.1 1.0 CB C:GLU359 4.9 33.0 1.0 PA C:ADP1202 4.9 23.0 1.0 C10 C:S3A1203 4.9 19.9 1.0 C1 C:S3A1203 4.9 40.7 1.0 P11 C:S3A1203 5.0 71.0 1.0

Magnesium binding site 7 out of 8 in the Engineered TTLL6 Mutant Bound to Gamma-Elongation Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Engineered TTLL6 Mutant Bound to Gamma-Elongation Analog within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg604 b:48.3 occ:1.00 O25 D:S3A602 1.9 40.2 1.0 O2A D:ADP601 2.0 52.5 1.0 OD2 D:ASP346 2.1 86.1 1.0 O2B D:ADP601 2.5 63.5 1.0 OE2 D:GLU359 3.2 51.2 1.0 P24 D:S3A602 3.3 50.8 1.0 CG D:ASP346 3.3 69.2 1.0 PA D:ADP601 3.4 50.4 1.0 ND2 D:ASN264 3.5 53.6 1.0 PB D:ADP601 3.6 56.4 1.0 O27 D:S3A602 3.6 59.5 1.0 NH2 D:ARG241 3.8 81.7 1.0 NH1 D:ARG241 3.9 72.5 1.0 O3A D:ADP601 3.9 49.7 1.0 O1B D:ADP601 4.0 58.5 1.0 O26 D:S3A602 4.0 57.4 1.0 C5' D:ADP601 4.0 45.3 1.0 MG D:MG605 4.1 47.0 1.0 OD1 D:ASP346 4.1 76.1 1.0 O5' D:ADP601 4.1 54.0 1.0 CZ D:ARG241 4.3 76.7 1.0 CB D:ASP346 4.4 60.6 1.0 CD D:GLU359 4.4 60.1 1.0 NH2 D:ARG219 4.4 49.2 1.0 O12 D:S3A602 4.4 49.9 1.0 O3' D:ADP601 4.4 60.2 1.0 CG D:ASN264 4.5 54.2 1.0 C3' D:ADP601 4.6 55.2 1.0 O1A D:ADP601 4.6 43.9 1.0 ND2 D:ASN361 4.6 49.7 1.0 OD1 D:ASN264 4.8 54.4 1.0 OD2 D:ASP217 4.8 97.0 1.0 C4' D:ADP601 4.9 53.4 1.0 O3B D:ADP601 4.9 70.8 1.0

Magnesium binding site 8 out of 8 in the Engineered TTLL6 Mutant Bound to Gamma-Elongation Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Engineered TTLL6 Mutant Bound to Gamma-Elongation Analog within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg605 b:47.0 occ:1.00 OE1 D:GLU359 2.1 77.1 1.0 O26 D:S3A602 2.1 57.4 1.0 OD1 D:ASN361 2.3 60.7 1.0 O1B D:ADP601 2.4 58.5 1.0 OE2 D:GLU359 2.5 51.2 1.0 CD D:GLU359 2.6 60.1 1.0 O25 D:S3A602 3.0 40.2 1.0 P24 D:S3A602 3.1 50.8 1.0 PB D:ADP601 3.4 56.4 1.0 CG D:ASN361 3.4 50.4 1.0 O2B D:ADP601 3.4 63.5 1.0 O7 D:S3A602 3.8 76.7 1.0 ND2 D:ASN361 3.8 49.7 1.0 CA D:ALA179 3.8 57.1 1.0 CB D:ALA179 3.9 58.3 1.0 O12 D:S3A602 3.9 49.9 1.0 C9 D:S3A602 4.0 61.8 1.0 CG D:GLU359 4.1 66.3 1.0 MG D:MG604 4.1 48.3 1.0 O D:GLY178 4.2 71.5 1.0 O3B D:ADP601 4.2 70.8 1.0 N D:ARG180 4.3 60.5 1.0 O27 D:S3A602 4.3 59.5 1.0 NZ D:LYS125 4.4 55.3 1.0 O2A D:ADP601 4.5 52.5 1.0 C D:ALA179 4.6 57.0 1.0 C6 D:S3A602 4.6 77.8 1.0 O3A D:ADP601 4.6 49.7 1.0 CB D:ASN361 4.7 55.0 1.0 C1 D:S3A602 4.7 72.2 1.0 C10 D:S3A602 4.8 59.6 1.0 N D:ALA179 4.8 66.4 1.0 CE D:LYS125 4.9 57.0 1.0 C D:GLY178 4.9 69.3 1.0 OD2 D:ASP346 4.9 86.1 1.0

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