Magnesium in PDB 5zct: The Crystal Structure of the Poly-Alpha-L-Glutamate Peptides Synthetase Rimk at 2.05 Angstrom Resolution.

The structure of The Crystal Structure of the Poly-Alpha-L-Glutamate Peptides Synthetase Rimk at 2.05 Angstrom Resolution., PDB code: 5zct was solved by Y.Arimura, T.Kono, K.Kino, H.Kurumizaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.21 / 2.05
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	212.618, 121.628, 119.741, 90.00, 118.74, 90.00
R / Rfree (%)	19.6 / 24

The binding sites of Magnesium atom in the The Crystal Structure of the Poly-Alpha-L-Glutamate Peptides Synthetase Rimk at 2.05 Angstrom Resolution. (pdb code 5zct). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the The Crystal Structure of the Poly-Alpha-L-Glutamate Peptides Synthetase Rimk at 2.05 Angstrom Resolution., PDB code: 5zct:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the The Crystal Structure of the Poly-Alpha-L-Glutamate Peptides Synthetase Rimk at 2.05 Angstrom Resolution.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of the Poly-Alpha-L-Glutamate Peptides Synthetase Rimk at 2.05 Angstrom Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:35.4 occ:1.00 O A:HOH586 2.0 38.1 1.0 O A:HOH508 2.1 34.1 1.0 O1G A:ANP401 2.1 36.8 1.0 O A:HOH520 2.1 35.7 1.0 O1B A:ANP401 2.1 35.7 1.0 O1A A:ANP401 2.2 33.1 1.0 PG A:ANP401 3.3 42.4 1.0 PB A:ANP401 3.4 37.0 1.0 PA A:ANP401 3.4 30.2 1.0 O3A A:ANP401 3.7 34.3 1.0 N3B A:ANP401 3.8 30.7 1.0 O2G A:ANP401 3.9 42.3 1.0 O A:HOH569 4.1 42.7 1.0 O3' A:ANP401 4.1 36.6 1.0 OD2 A:ASP248 4.1 40.1 1.0 O A:HOH640 4.2 36.8 1.0 ND2 A:ASN213 4.2 37.2 1.0 O2 A:SO4404 4.4 45.9 1.0 NH2 A:ARG189 4.4 37.7 1.0 O5' A:ANP401 4.4 32.6 1.0 O2A A:ANP401 4.4 27.3 1.0 OE1 A:GLU260 4.5 47.0 1.0 O3G A:ANP401 4.5 43.7 1.0 C5' A:ANP401 4.5 32.8 1.0 O2B A:ANP401 4.7 46.9 1.0 CD A:GLU260 4.7 43.8 1.0 CG A:GLU260 4.7 34.9 1.0 NH2 A:ARG203 4.8 46.6 1.0 C3' A:ANP401 4.8 34.6 1.0 CE A:MET259 4.8 37.2 1.0 CB A:GLU260 4.9 34.5 1.0

Magnesium binding site 2 out of 8 in the The Crystal Structure of the Poly-Alpha-L-Glutamate Peptides Synthetase Rimk at 2.05 Angstrom Resolution.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of the Poly-Alpha-L-Glutamate Peptides Synthetase Rimk at 2.05 Angstrom Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:73.2 occ:1.00 O1G B:ANP401 1.9 83.0 1.0 OE2 B:GLU260 2.4 67.3 1.0 O2A B:ANP401 2.6 68.5 1.0 O1B B:ANP401 2.7 70.1 1.0 OE1 B:GLU260 3.1 65.8 1.0 CD B:GLU260 3.1 62.7 1.0 NH1 B:ARG189 3.2 77.3 1.0 PG B:ANP401 3.4 82.0 1.0 OD2 B:ASP248 3.7 73.9 1.0 O3G B:ANP401 3.7 85.3 1.0 PB B:ANP401 4.0 78.5 1.0 PA B:ANP401 4.0 60.2 1.0 OD1 B:ASN213 4.2 95.1 1.0 ND2 B:ASN213 4.3 90.7 1.0 O2G B:ANP401 4.4 90.5 1.0 NH1 B:ARG203 4.4 81.1 1.0 N3B B:ANP401 4.4 71.7 1.0 CZ B:ARG189 4.4 82.5 1.0 C5' B:ANP401 4.5 67.3 1.0 CG B:GLU260 4.5 57.5 1.0 O3A B:ANP401 4.5 68.5 1.0 O3' B:ANP401 4.5 75.9 1.0 CG B:ASN213 4.6 92.8 1.0 O5' B:ANP401 4.7 67.1 1.0 CG B:ASP248 4.9 66.2 1.0 CB B:GLU260 5.0 60.5 1.0

Magnesium binding site 3 out of 8 in the The Crystal Structure of the Poly-Alpha-L-Glutamate Peptides Synthetase Rimk at 2.05 Angstrom Resolution.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of the Poly-Alpha-L-Glutamate Peptides Synthetase Rimk at 2.05 Angstrom Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:41.2 occ:1.00 O1A C:ANP401 2.0 40.4 1.0 O C:HOH513 2.0 42.4 1.0 O C:HOH623 2.1 41.9 1.0 O C:HOH514 2.1 42.3 1.0 O2B C:ANP401 2.3 45.7 1.0 O3G C:ANP401 2.3 39.7 1.0 PA C:ANP401 3.3 40.1 1.0 PB C:ANP401 3.3 44.8 1.0 PG C:ANP401 3.5 45.5 1.0 O3A C:ANP401 3.7 43.7 1.0 O4 C:SO4403 3.9 50.9 1.0 O1G C:ANP401 3.9 47.6 1.0 ND2 C:ASN213 3.9 41.5 1.0 N3B C:ANP401 4.0 44.4 1.0 O3' C:ANP401 4.1 43.9 1.0 OD2 C:ASP248 4.1 39.9 1.0 O5' C:ANP401 4.2 41.5 1.0 C5' C:ANP401 4.2 41.4 1.0 NH2 C:ARG189 4.3 40.2 1.0 O C:HOH606 4.3 48.2 1.0 O C:HOH557 4.3 40.5 1.0 OE1 C:GLU260 4.4 46.3 1.0 O2A C:ANP401 4.5 42.0 1.0 CD C:GLU260 4.5 46.2 1.0 O1B C:ANP401 4.6 47.3 1.0 C3' C:ANP401 4.7 41.1 1.0 NH1 C:ARG203 4.7 44.2 1.0 O2G C:ANP401 4.8 51.3 1.0 OE2 C:GLU260 4.8 50.9 1.0 CG C:ASN213 4.8 48.0 1.0 O2 C:SO4403 4.8 53.8 1.0 S C:SO4403 4.9 59.9 1.0 C4' C:ANP401 5.0 38.3 1.0

Magnesium binding site 4 out of 8 in the The Crystal Structure of the Poly-Alpha-L-Glutamate Peptides Synthetase Rimk at 2.05 Angstrom Resolution.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structure of the Poly-Alpha-L-Glutamate Peptides Synthetase Rimk at 2.05 Angstrom Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:76.4 occ:1.00 O D:HOH506 2.0 66.4 1.0 O D:HOH523 2.2 63.3 1.0 O3G D:ANP401 2.2 68.1 1.0 OE2 D:GLU260 2.4 62.9 1.0 O2B D:ANP401 2.4 77.1 1.0 O2A D:ANP401 2.5 66.6 1.0 OE1 D:GLU260 2.7 63.8 1.0 CD D:GLU260 2.8 58.0 1.0 ND2 D:ASN213 3.5 76.5 1.0 PB D:ANP401 3.6 78.1 1.0 PA D:ANP401 3.7 60.5 1.0 PG D:ANP401 3.7 85.2 1.0 O3A D:ANP401 3.9 69.4 1.0 N3B D:ANP401 4.1 78.7 1.0 CG D:GLU260 4.2 50.4 1.0 OD2 D:ASP248 4.3 51.2 1.0 O D:HOH513 4.5 57.6 1.0 O2G D:ANP401 4.6 77.1 1.0 O1G D:ANP401 4.6 75.8 1.0 O1A D:ANP401 4.7 55.6 1.0 O5' D:ANP401 4.7 59.1 1.0 CB D:GLU260 4.8 46.0 1.0 CG D:ASN213 4.8 76.6 1.0 O1B D:ANP401 4.9 77.8 1.0 NH2 D:ARG189 5.0 55.0 1.0

Magnesium binding site 5 out of 8 in the The Crystal Structure of the Poly-Alpha-L-Glutamate Peptides Synthetase Rimk at 2.05 Angstrom Resolution.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Crystal Structure of the Poly-Alpha-L-Glutamate Peptides Synthetase Rimk at 2.05 Angstrom Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg403 b:43.8 occ:1.00 O3G E:ANP402 1.9 46.0 1.0 O E:HOH564 2.0 39.6 1.0 O1A E:ANP402 2.0 37.2 1.0 O E:HOH502 2.1 45.7 1.0 O E:HOH559 2.2 45.8 1.0 O2B E:ANP402 2.2 42.0 1.0 PA E:ANP402 3.2 37.4 1.0 PG E:ANP402 3.3 52.9 1.0 PB E:ANP402 3.4 43.2 1.0 O3A E:ANP402 3.6 45.6 1.0 N3B E:ANP402 3.9 44.5 1.0 O1G E:ANP402 4.0 56.0 1.0 O5' E:ANP402 4.1 37.1 1.0 O3' E:ANP402 4.1 39.1 1.0 ND2 E:ASN213 4.1 46.8 1.0 C5' E:ANP402 4.2 34.7 1.0 O2A E:ANP402 4.2 39.9 1.0 OE1 E:GLU260 4.2 50.8 1.0 OD2 E:ASP248 4.3 37.8 1.0 O2G E:ANP402 4.4 48.4 1.0 C3' E:ANP402 4.6 35.5 1.0 O3 E:SO4401 4.6 64.1 1.0 O1B E:ANP402 4.7 50.3 1.0 NH2 E:ARG189 4.7 43.2 1.0 O2 E:SO4401 4.9 57.6 1.0 C4' E:ANP402 4.9 37.2 1.0

Magnesium binding site 6 out of 8 in the The Crystal Structure of the Poly-Alpha-L-Glutamate Peptides Synthetase Rimk at 2.05 Angstrom Resolution.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Crystal Structure of the Poly-Alpha-L-Glutamate Peptides Synthetase Rimk at 2.05 Angstrom Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:62.2 occ:1.00 OE2 F:GLU260 2.0 60.0 1.0 O2A F:ANP401 2.0 59.7 1.0 O2G F:ANP401 2.1 76.5 1.0 O2B F:ANP401 2.6 66.7 1.0 CD F:GLU260 3.2 56.6 1.0 PA F:ANP401 3.4 58.0 1.0 ND2 F:ASN213 3.5 78.9 1.0 PG F:ANP401 3.5 83.0 1.0 PB F:ANP401 3.7 66.8 1.0 OD2 F:ASP248 3.8 56.2 1.0 OE1 F:GLU260 3.8 57.1 1.0 O3A F:ANP401 4.0 56.1 1.0 C5' F:ANP401 4.1 58.2 1.0 N3B F:ANP401 4.1 62.1 1.0 O3G F:ANP401 4.1 71.2 1.0 O5' F:ANP401 4.2 62.2 1.0 CG F:GLU260 4.4 49.5 1.0 CG F:ASN213 4.4 79.1 1.0 O F:HOH593 4.5 52.0 1.0 CB F:GLU260 4.5 45.0 1.0 O1A F:ANP401 4.5 57.0 1.0 O3' F:ANP401 4.6 64.5 1.0 O1G F:ANP401 4.6 82.0 1.0 OD1 F:ASN213 4.6 77.5 1.0 C3' F:ANP401 4.9 55.9 1.0 O1B F:ANP401 4.9 66.6 1.0 CG F:ASP248 4.9 48.1 1.0

Magnesium binding site 7 out of 8 in the The Crystal Structure of the Poly-Alpha-L-Glutamate Peptides Synthetase Rimk at 2.05 Angstrom Resolution.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Crystal Structure of the Poly-Alpha-L-Glutamate Peptides Synthetase Rimk at 2.05 Angstrom Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg402 b:36.9 occ:1.00 O2A G:ANP401 2.1 34.8 1.0 O1B G:ANP401 2.1 40.4 1.0 O G:HOH576 2.1 36.2 1.0 O1G G:ANP401 2.1 38.0 1.0 O G:HOH505 2.2 41.9 1.0 O G:HOH532 2.2 39.5 1.0 PB G:ANP401 3.1 36.4 1.0 PG G:ANP401 3.2 40.4 1.0 PA G:ANP401 3.3 37.5 1.0 O3A G:ANP401 3.5 38.2 1.0 O2G G:ANP401 3.6 47.1 1.0 N3B G:ANP401 3.7 42.5 1.0 O2 G:SO4403 4.0 50.1 1.0 O G:HOH582 4.1 41.1 1.0 ND2 G:ASN213 4.2 39.3 1.0 O1A G:ANP401 4.2 34.9 1.0 OD2 G:ASP248 4.3 34.8 1.0 O G:HOH516 4.3 47.7 1.0 O3' G:ANP401 4.3 41.1 1.0 O5' G:ANP401 4.3 36.6 1.0 OE1 G:GLU260 4.4 44.1 1.0 O2B G:ANP401 4.4 39.3 1.0 O3G G:ANP401 4.5 42.5 1.0 C5' G:ANP401 4.5 35.1 1.0 NH2 G:ARG189 4.5 36.2 1.0 CG G:GLU260 4.7 38.0 1.0 CD G:GLU260 4.8 40.8 1.0 CB G:GLU260 4.8 31.4 1.0 CE G:MET259 4.8 44.3 1.0 C3' G:ANP401 4.9 36.3 1.0

Magnesium binding site 8 out of 8 in the The Crystal Structure of the Poly-Alpha-L-Glutamate Peptides Synthetase Rimk at 2.05 Angstrom Resolution.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Crystal Structure of the Poly-Alpha-L-Glutamate Peptides Synthetase Rimk at 2.05 Angstrom Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg402 b:77.2 occ:1.00 O2G H:ANP401 2.2 79.4 1.0 O1A H:ANP401 2.5 75.6 1.0 OD2 H:ASP248 2.7 47.3 1.0 OE2 H:GLU260 2.9 72.1 1.0 NH2 H:ARG203 3.3 76.5 1.0 O3' H:ANP401 3.5 71.8 1.0 ND2 H:ASN213 3.5 94.5 1.0 PG H:ANP401 3.6 97.1 1.0 CD H:GLU260 3.6 64.6 1.0 O3G H:ANP401 3.9 94.4 1.0 CG H:ASP248 3.9 44.5 1.0 CE H:MET259 3.9 55.9 1.0 PA H:ANP401 3.9 72.7 1.0 O1B H:ANP401 4.0 75.5 1.0 OE1 H:GLU260 4.0 65.7 1.0 CZ H:ARG203 4.2 75.8 1.0 CG H:ASN213 4.2 92.7 1.0 C3' H:ANP401 4.2 65.3 1.0 NH1 H:ARG203 4.2 71.0 1.0 OD1 H:ASN213 4.3 87.0 1.0 NH2 H:ARG189 4.4 63.0 1.0 CB H:GLU260 4.5 47.4 1.0 CB H:ASP248 4.6 38.0 1.0 C5' H:ANP401 4.6 70.2 1.0 O1G H:ANP401 4.6 92.9 1.0 O2A H:ANP401 4.6 64.2 1.0 N3B H:ANP401 4.7 79.3 1.0 CG H:GLU260 4.7 51.9 1.0 PB H:ANP401 4.7 81.8 1.0 O5' H:ANP401 4.8 70.5 1.0 O3A H:ANP401 4.9 77.2 1.0 OD1 H:ASP248 4.9 37.2 1.0 C4' H:ANP401 5.0 69.6 1.0

Y.Arimura, T.Kono, K.Kino, H.Kurumizaka. Structural Polymorphism of the Escherichia Coli Poly-Alpha-L-Glutamate Synthetase Rimk Acta Crystallogr F Struct V. 74 385 2018BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 29969101
DOI: 10.1107/S2053230X18007689