Magnesium in PDB 4qpz: Crystal Structure of the Formolase FLS_V2 in Space Group P 21

The structure of Crystal Structure of the Formolase FLS_V2 in Space Group P 21, PDB code: 4qpz was solved by B.W.Shen, J.B.Siegel, B.L.Stoddard, D.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	166.33 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	99.878, 136.564, 167.062, 90.00, 95.36, 90.00
R / Rfree (%)	20.8 / 25.7

The binding sites of Magnesium atom in the Crystal Structure of the Formolase FLS_V2 in Space Group P 21 (pdb code 4qpz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of the Formolase FLS_V2 in Space Group P 21, PDB code: 4qpz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Crystal Structure of the Formolase FLS_V2 in Space Group P 21


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Formolase FLS_V2 in Space Group P 21 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:56.5 occ:1.00 OD1 A:ASN475 2.1 68.3 1.0 O1A A:TPP602 2.4 57.6 1.0 O3B A:TPP602 2.5 58.0 1.0 OD1 A:ASP448 2.5 64.3 1.0 O1B A:TPP602 2.7 58.7 1.0 O A:SER477 3.0 64.3 1.0 PB A:TPP602 3.0 58.2 1.0 CG A:ASN475 3.1 69.5 1.0 CG A:ASP448 3.2 66.3 1.0 O A:MET473 3.3 65.4 1.0 O3A A:TPP602 3.5 58.0 1.0 N A:ASP448 3.5 60.5 1.0 PA A:TPP602 3.5 57.7 1.0 ND2 A:ASN475 3.7 68.3 1.0 N A:ASN475 3.7 71.9 1.0 OD2 A:ASP448 3.8 70.1 1.0 CA A:GLY447 4.1 54.8 1.0 CB A:ASP448 4.2 64.9 1.0 C A:SER477 4.2 63.1 1.0 C A:GLY447 4.3 56.6 1.0 CB A:ASN475 4.3 72.4 1.0 CA A:ASP448 4.4 61.9 1.0 CA A:ASN475 4.4 72.8 1.0 C A:MET473 4.5 65.5 1.0 O2B A:TPP602 4.5 56.4 1.0 O7 A:TPP602 4.5 65.3 1.0 N A:GLY479 4.5 58.1 1.0 CG2 A:THR396 4.5 65.6 1.0 N A:GLY449 4.5 59.6 1.0 CA A:ASN474 4.6 70.2 1.0 C A:ASN474 4.6 72.9 1.0 O2A A:TPP602 4.6 55.5 1.0 N A:SER477 4.7 66.5 1.0 C A:ASN475 4.8 72.8 1.0 N A:GLN476 4.9 72.3 1.0 C A:ASP448 5.0 61.0 1.0 N A:ASN474 5.0 68.2 1.0

Magnesium binding site 2 out of 8 in the Crystal Structure of the Formolase FLS_V2 in Space Group P 21


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Formolase FLS_V2 in Space Group P 21 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:68.4 occ:1.00 OD1 B:ASP448 2.0 76.7 1.0 O3B B:TPP602 2.0 79.8 1.0 OD1 B:ASN475 2.1 78.2 1.0 O1A B:TPP602 2.3 81.9 1.0 O1B B:TPP602 2.6 80.5 1.0 PB B:TPP602 2.7 79.9 1.0 O B:SER477 2.8 75.1 1.0 CG B:ASN475 3.1 79.5 1.0 CG B:ASP448 3.2 75.9 1.0 O3A B:TPP602 3.3 77.9 1.0 PA B:TPP602 3.3 80.0 1.0 ND2 B:ASN475 3.5 79.7 1.0 O B:MET473 3.6 69.6 1.0 N B:ASP448 3.6 68.8 1.0 OD2 B:ASP448 4.0 77.8 1.0 N B:ASN475 4.0 77.8 1.0 C B:SER477 4.1 75.8 1.0 O2B B:TPP602 4.1 78.4 1.0 O7 B:TPP602 4.1 88.0 1.0 N B:GLY479 4.2 75.4 1.0 CA B:GLY447 4.2 64.1 1.0 CB B:ASP448 4.3 73.6 1.0 C B:GLY447 4.4 65.1 1.0 CB B:ASN475 4.4 82.0 1.0 CA B:ASP448 4.4 70.1 1.0 N B:GLY449 4.5 68.5 1.0 O2A B:TPP602 4.5 77.4 1.0 CA B:ASN475 4.6 81.6 1.0 CG2 B:THR396 4.7 79.7 1.0 CA B:GLY479 4.7 76.5 1.0 C B:MET473 4.7 70.6 1.0 N B:SER477 4.8 77.7 1.0 C B:ASN474 4.9 77.9 1.0 CA B:ASN474 5.0 75.4 1.0 C B:ASN475 5.0 82.8 1.0 CA B:SER477 5.0 78.3 1.0 N B:TRP478 5.0 74.4 1.0

Magnesium binding site 3 out of 8 in the Crystal Structure of the Formolase FLS_V2 in Space Group P 21


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Formolase FLS_V2 in Space Group P 21 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:50.0 occ:1.00 OD1 C:ASP448 1.8 61.9 1.0 OD1 C:ASN475 2.1 70.1 1.0 O3B C:TPP602 2.5 63.1 1.0 O1A C:TPP602 2.5 65.1 1.0 O1B C:TPP602 2.6 62.4 1.0 PB C:TPP602 3.0 62.3 1.0 CG C:ASN475 3.0 71.4 1.0 CG C:ASP448 3.0 63.7 1.0 O C:SER477 3.1 67.8 1.0 O C:MET473 3.3 66.2 1.0 N C:ASP448 3.4 59.5 1.0 O3A C:TPP602 3.5 63.1 1.0 ND2 C:ASN475 3.6 71.4 1.0 PA C:TPP602 3.6 63.9 1.0 N C:ASN475 3.7 70.4 1.0 OD2 C:ASP448 3.8 66.0 1.0 CB C:ASP448 4.0 64.1 1.0 CA C:GLY447 4.1 55.8 1.0 CB C:ASN475 4.2 73.8 1.0 CA C:ASP448 4.3 61.4 1.0 C C:GLY447 4.3 57.4 1.0 C C:SER477 4.3 67.2 1.0 O2B C:TPP602 4.4 60.8 1.0 CA C:ASN475 4.4 74.9 1.0 C C:MET473 4.4 66.3 1.0 N C:GLY479 4.5 59.1 1.0 CG2 C:THR396 4.5 73.5 1.0 N C:GLY449 4.5 60.0 1.0 O7 C:TPP602 4.6 69.2 1.0 CA C:ASN474 4.6 67.9 1.0 C C:ASN474 4.7 69.8 1.0 O2A C:TPP602 4.7 62.4 1.0 N C:SER477 4.8 71.8 1.0 C C:ASN475 4.8 78.3 1.0 C C:ASP448 4.9 61.1 1.0 CA C:GLY479 4.9 59.9 1.0 N C:GLN476 5.0 80.1 1.0 N C:ASN474 5.0 67.9 1.0

Magnesium binding site 4 out of 8 in the Crystal Structure of the Formolase FLS_V2 in Space Group P 21


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Formolase FLS_V2 in Space Group P 21 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:75.7 occ:1.00 OD1 D:ASN475 1.9 82.7 1.0 OD1 D:ASP448 2.0 82.6 1.0 O3B D:TPP602 2.1 78.6 1.0 O1A D:TPP602 2.5 78.7 1.0 O1B D:TPP602 2.8 77.9 1.0 O D:SER477 2.8 77.7 1.0 PB D:TPP602 2.8 77.7 1.0 CG D:ASN475 2.9 86.4 1.0 CG D:ASP448 3.2 82.7 1.0 ND2 D:ASN475 3.4 87.0 1.0 O3A D:TPP602 3.4 76.5 1.0 PA D:TPP602 3.5 76.3 1.0 O D:MET473 3.6 77.7 1.0 N D:ASP448 3.7 77.5 1.0 N D:ASN475 3.9 84.5 1.0 OD2 D:ASP448 3.9 84.6 1.0 C D:SER477 4.0 79.0 1.0 N D:GLY479 4.0 80.2 1.0 CB D:ASN475 4.2 89.0 1.0 CB D:ASP448 4.2 81.5 1.0 O2B D:TPP602 4.2 77.1 1.0 O7 D:TPP602 4.3 82.1 1.0 CA D:ASN475 4.4 88.2 1.0 CA D:GLY479 4.5 81.2 1.0 CA D:ASP448 4.5 78.5 1.0 CA D:GLY447 4.5 73.0 1.0 N D:GLY449 4.6 76.5 1.0 C D:GLY447 4.6 74.3 1.0 N D:SER477 4.6 83.2 1.0 CG2 D:THR396 4.7 75.8 1.0 O2A D:TPP602 4.8 73.2 1.0 C D:MET473 4.8 78.9 1.0 C D:ASN475 4.8 88.9 1.0 CA D:SER477 4.9 82.3 1.0 C D:ASN474 4.9 84.1 1.0 N D:TRP478 5.0 77.8 1.0 CA D:ASN474 5.0 81.1 1.0 OG D:SER477 5.0 84.4 1.0

Magnesium binding site 5 out of 8 in the Crystal Structure of the Formolase FLS_V2 in Space Group P 21


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Formolase FLS_V2 in Space Group P 21 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg601 b:62.5 occ:1.00 OD1 E:ASP448 1.8 67.9 1.0 OD1 E:ASN475 2.0 79.6 1.0 O3B E:TPP602 2.4 69.1 1.0 O1A E:TPP602 2.5 71.6 1.0 O1B E:TPP602 2.7 68.5 1.0 O E:SER477 2.8 65.0 1.0 PB E:TPP602 2.9 69.2 1.0 CG E:ASN475 3.0 81.5 1.0 CG E:ASP448 3.1 66.7 1.0 N E:ASP448 3.5 63.0 1.0 O3A E:TPP602 3.5 69.0 1.0 PA E:TPP602 3.6 70.2 1.0 ND2 E:ASN475 3.6 83.7 1.0 O E:MET473 3.6 77.7 1.0 N E:ASN475 3.7 79.3 1.0 OD2 E:ASP448 3.8 66.6 1.0 C E:SER477 4.0 66.1 1.0 CB E:ASP448 4.1 65.5 1.0 CA E:GLY447 4.2 62.1 1.0 N E:GLY479 4.2 67.3 1.0 CB E:ASN475 4.3 83.0 1.0 CA E:ASP448 4.3 64.2 1.0 C E:GLY447 4.3 61.8 1.0 O2B E:TPP602 4.3 70.1 1.0 CA E:ASN475 4.4 82.0 1.0 N E:GLY449 4.4 64.2 1.0 O7 E:TPP602 4.5 75.8 1.0 CG2 E:THR396 4.5 69.1 1.0 N E:SER477 4.6 70.5 1.0 O2A E:TPP602 4.7 66.2 1.0 CA E:GLY479 4.7 70.6 1.0 C E:ASN474 4.8 81.0 1.0 C E:MET473 4.8 76.8 1.0 C E:ASN475 4.8 81.9 1.0 CA E:SER477 4.9 69.2 1.0 C E:ASP448 4.9 64.4 1.0 CA E:ASN474 4.9 77.7 1.0 N E:TRP478 4.9 64.2 1.0

Magnesium binding site 6 out of 8 in the Crystal Structure of the Formolase FLS_V2 in Space Group P 21


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Formolase FLS_V2 in Space Group P 21 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg601 b:45.5 occ:1.00 OD1 F:ASP448 1.9 53.0 1.0 OD1 F:ASN475 1.9 59.7 1.0 O3B F:TPP602 2.3 68.2 1.0 O1A F:TPP602 2.3 64.9 1.0 O F:SER477 2.8 57.8 1.0 O1B F:TPP602 2.9 67.7 1.0 CG F:ASN475 3.0 60.8 1.0 PB F:TPP602 3.0 65.3 1.0 CG F:ASP448 3.1 53.1 1.0 PA F:TPP602 3.5 64.1 1.0 O3A F:TPP602 3.5 63.9 1.0 ND2 F:ASN475 3.5 62.4 1.0 N F:ASP448 3.6 50.8 1.0 O F:MET473 3.6 54.9 1.0 N F:ASN475 3.8 57.9 1.0 OD2 F:ASP448 3.8 53.8 1.0 C F:SER477 4.1 59.1 1.0 CB F:ASP448 4.1 52.9 1.0 CB F:ASN475 4.2 60.9 1.0 N F:GLY479 4.3 63.5 1.0 O7 F:TPP602 4.3 70.7 1.0 CA F:ASP448 4.4 51.6 1.0 CA F:GLY447 4.4 49.1 1.0 CA F:ASN475 4.4 60.5 1.0 O2B F:TPP602 4.4 64.5 1.0 C F:GLY447 4.5 49.0 1.0 N F:GLY449 4.5 54.0 1.0 N F:SER477 4.6 60.8 1.0 O2A F:TPP602 4.6 61.3 1.0 CG2 F:THR396 4.7 64.6 1.0 C F:ASN475 4.7 61.3 1.0 C F:MET473 4.8 54.2 1.0 CA F:GLY479 4.9 66.7 1.0 C F:ASN474 4.9 58.0 1.0 CA F:SER477 4.9 61.4 1.0 N F:GLN476 4.9 61.5 1.0 C F:ASP448 4.9 52.2 1.0 CA F:ASN474 5.0 56.2 1.0

Magnesium binding site 7 out of 8 in the Crystal Structure of the Formolase FLS_V2 in Space Group P 21


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Formolase FLS_V2 in Space Group P 21 within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg601 b:36.6 occ:1.00 OD1 G:ASP448 1.8 50.4 1.0 OD1 G:ASN475 2.2 59.8 1.0 O1A G:TPP602 2.3 55.4 1.0 O3B G:TPP602 2.6 57.8 1.0 O1B G:TPP602 2.8 58.0 1.0 CG G:ASP448 3.1 49.7 1.0 PB G:TPP602 3.1 57.0 1.0 O G:SER477 3.1 52.0 1.0 CG G:ASN475 3.2 60.9 1.0 O G:MET473 3.2 53.3 1.0 N G:ASP448 3.3 45.3 1.0 O3A G:TPP602 3.4 57.3 1.0 PA G:TPP602 3.4 57.4 1.0 N G:ASN475 3.7 55.9 1.0 ND2 G:ASN475 3.7 62.4 1.0 OD2 G:ASP448 3.9 51.2 1.0 CA G:GLY447 3.9 45.5 1.0 C G:GLY447 4.1 43.5 1.0 CB G:ASP448 4.1 47.3 1.0 CA G:ASP448 4.2 45.3 1.0 CB G:ASN475 4.3 62.0 1.0 C G:SER477 4.4 52.3 1.0 C G:MET473 4.4 52.6 1.0 N G:GLY449 4.4 44.2 1.0 CA G:ASN475 4.4 60.2 1.0 O7 G:TPP602 4.5 62.8 1.0 O2A G:TPP602 4.5 55.3 1.0 CG2 G:THR396 4.6 65.7 1.0 O2B G:TPP602 4.6 56.5 1.0 C G:ASN474 4.6 55.4 1.0 CA G:ASN474 4.6 52.5 1.0 N G:GLY479 4.7 50.9 1.0 N G:SER477 4.8 54.4 1.0 C G:ASP448 4.9 44.6 1.0 C G:ASN475 4.9 60.3 1.0 N G:GLN476 4.9 58.2 1.0

Magnesium binding site 8 out of 8 in the Crystal Structure of the Formolase FLS_V2 in Space Group P 21


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Formolase FLS_V2 in Space Group P 21 within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg601 b:43.9 occ:1.00 OD1 H:ASP448 1.8 44.8 1.0 OD1 H:ASN475 2.1 54.7 1.0 O1A H:TPP602 2.2 56.6 1.0 O3B H:TPP602 2.2 57.1 1.0 O H:SER477 2.7 48.8 1.0 O1B H:TPP602 2.8 57.2 1.0 PB H:TPP602 2.9 55.3 1.0 CG H:ASP448 3.1 44.5 1.0 CG H:ASN475 3.1 56.9 1.0 PA H:TPP602 3.3 54.8 1.0 O3A H:TPP602 3.4 54.7 1.0 N H:ASP448 3.6 41.0 1.0 ND2 H:ASN475 3.6 57.8 1.0 O H:MET473 3.7 56.4 1.0 OD2 H:ASP448 3.8 45.7 1.0 C H:SER477 3.9 50.2 1.0 N H:ASN475 4.1 56.1 1.0 N H:GLY479 4.1 53.6 1.0 O7 H:TPP602 4.1 59.7 1.0 CB H:ASP448 4.2 42.7 1.0 CA H:GLY447 4.3 39.7 1.0 O2B H:TPP602 4.3 56.4 1.0 C H:GLY447 4.4 39.6 1.0 CA H:ASP448 4.4 40.9 1.0 N H:GLY449 4.4 42.6 1.0 CB H:ASN475 4.4 59.0 1.0 O2A H:TPP602 4.5 52.3 1.0 N H:SER477 4.5 53.7 1.0 CA H:GLY479 4.6 55.6 1.0 CA H:ASN475 4.6 59.5 1.0 CA H:SER477 4.8 52.9 1.0 CG2 H:THR396 4.8 52.2 1.0 N H:TRP478 4.8 49.1 1.0 C H:MET473 4.9 53.3 1.0 C H:ASP448 4.9 41.4 1.0 C H:ASN475 4.9 60.5 1.0 CA H:TRP478 4.9 49.1 1.0 C H:TRP478 5.0 52.3 1.0

J.B.Siegel, A.L Smith, S.Poust, A.Wargacki, A.Bar-Even, C.Louw, B.W.Shen, C.B.Eiben, H.Tran, E.Noor, J.Gallaher, J.Bale, Y.Yoshikuni, M.H.Gelb, J.D.Keasling, B.L.Stoddard, M.E.Lidstrom, D.Baker. Computational Protein Design Enables A Novel One-Carbon Assimilation Pathway-Carbon Assimilation Pathway. To Be Published.