Magnesium in PDB 4ep7: Functional Implications From the CID1 Poly(U) Polymerase Crystal Structure

The structure of Functional Implications From the CID1 Poly(U) Polymerase Crystal Structure, PDB code: 4ep7 was solved by P.Munoz-Tello, C.Gabus, S.Thore, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.19 / 2.28
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.490, 76.860, 81.860, 90.00, 91.17, 90.00
R / Rfree (%)	18.8 / 24.7

The binding sites of Magnesium atom in the Functional Implications From the CID1 Poly(U) Polymerase Crystal Structure (pdb code 4ep7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Functional Implications From the CID1 Poly(U) Polymerase Crystal Structure, PDB code: 4ep7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Functional Implications From the CID1 Poly(U) Polymerase Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Functional Implications From the CID1 Poly(U) Polymerase Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:11.9 occ:1.00 NH1 A:ARG277 3.0 53.2 1.0 O A:HOH675 3.2 28.1 1.0 NH2 A:ARG277 3.6 40.4 1.0 CZ A:ARG277 3.6 44.3 1.0 CG A:LYS282 4.1 36.7 1.0 CB A:LYS282 4.5 25.6 1.0 CB A:TYR281 4.7 25.6 1.0 NE A:ARG277 4.8 38.8 1.0 O A:HOH612 4.8 17.4 1.0 O A:ARG277 4.8 23.5 1.0 CB A:ARG277 4.9 26.4 1.0

Magnesium binding site 2 out of 7 in the Functional Implications From the CID1 Poly(U) Polymerase Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Functional Implications From the CID1 Poly(U) Polymerase Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:39.7 occ:1.00 O3G A:UTP501 2.2 38.8 1.0 O1A A:UTP501 2.4 25.0 1.0 O A:HOH725 2.5 35.9 1.0 O A:HOH685 2.8 44.4 1.0 O A:HOH713 2.9 46.1 1.0 O1B A:UTP501 3.0 35.0 1.0 OD2 A:ASP103 3.2 30.2 1.0 PG A:UTP501 3.3 34.8 1.0 O3B A:UTP501 3.3 30.3 1.0 PB A:UTP501 3.5 27.9 1.0 PA A:UTP501 3.6 26.7 1.0 OD1 A:ASP103 3.8 26.4 1.0 O3A A:UTP501 3.9 30.9 1.0 O A:HOH726 3.9 40.6 1.0 CG A:ASP103 3.9 27.8 1.0 C5' A:UTP501 4.1 19.6 1.0 O5' A:UTP501 4.3 21.4 1.0 O1G A:UTP501 4.3 28.7 1.0 O2G A:UTP501 4.3 34.1 1.0 O A:HOH630 4.4 30.4 1.0 O A:ASP101 4.4 36.2 1.0 O2A A:UTP501 4.8 22.2 1.0 OG A:SER90 4.9 30.3 1.0 O2B A:UTP501 5.0 35.3 1.0

Magnesium binding site 3 out of 7 in the Functional Implications From the CID1 Poly(U) Polymerase Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Functional Implications From the CID1 Poly(U) Polymerase Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:32.8 occ:1.00 O A:HOH616 3.0 19.6 1.0 O A:HOH700 3.6 30.9 1.0 NZ A:LYS199 3.6 35.7 1.0 O A:SER372 3.9 22.2 1.0 CA A:LEU373 3.9 26.4 1.0 CE A:LYS199 4.0 27.1 1.0 CD1 A:LEU373 4.1 21.5 1.0 N A:ALA357 4.2 22.9 1.0 CA A:ALA357 4.2 21.3 1.0 C A:ALA356 4.2 24.4 1.0 CB A:ALA356 4.3 19.8 1.0 O A:ALA356 4.3 24.1 1.0 C A:SER372 4.4 28.4 1.0 O A:LEU373 4.4 26.8 1.0 N A:LEU373 4.4 28.4 1.0 OE2 A:GLU353 4.5 27.0 1.0 CD2 A:LEU360 4.5 23.2 1.0 C A:LEU373 4.6 25.4 1.0 CB A:ALA357 4.7 18.8 1.0 CB A:LEU373 4.8 28.6 1.0 NE1 A:TRP195 4.9 14.8 1.0 CA A:ALA356 4.9 24.5 1.0 OG A:SER372 5.0 31.8 1.0

Magnesium binding site 4 out of 7 in the Functional Implications From the CID1 Poly(U) Polymerase Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Functional Implications From the CID1 Poly(U) Polymerase Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:34.3 occ:1.00 O A:HOH701 2.7 41.9 1.0 ND2 A:ASN165 3.3 27.7 1.0 N1 A:UTP501 3.4 19.5 1.0 C2 A:UTP501 3.5 21.4 1.0 C1' A:UTP501 3.8 18.9 1.0 O2 A:UTP501 3.8 19.0 1.0 C6 A:UTP501 3.9 20.2 1.0 O A:HOH645 3.9 26.9 1.0 N3 A:UTP501 4.0 21.0 1.0 O4' A:UTP501 4.0 15.5 1.0 C5 A:UTP501 4.3 19.4 1.0 C4 A:UTP501 4.4 21.0 1.0 CG A:ASN165 4.4 27.8 1.0 CB A:ALA168 4.4 16.2 1.0 OD1 A:ASN165 4.6 24.6 1.0 CE1 A:PHE88 4.8 19.1 1.0 O A:HOH644 4.9 26.4 1.0 O A:HOH711 5.0 36.7 1.0

Magnesium binding site 5 out of 7 in the Functional Implications From the CID1 Poly(U) Polymerase Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Functional Implications From the CID1 Poly(U) Polymerase Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:14.1 occ:1.00 CD1 B:LEU74 3.0 27.5 1.0 O B:HOH642 3.9 27.2 1.0 CG B:LYS77 3.9 22.2 1.0 CA B:LEU74 4.1 22.9 1.0 N B:LEU74 4.3 22.0 1.0 CG B:ARG73 4.3 33.1 1.0 O B:ARG73 4.4 21.9 1.0 CG B:LEU74 4.4 31.5 1.0 C B:ARG73 4.4 22.1 1.0 CB B:LYS77 4.5 15.4 1.0 CB B:LEU74 4.8 21.2 1.0 CB B:ARG73 4.9 23.5 1.0 CD B:ARG73 4.9 35.0 1.0 NE B:ARG73 4.9 40.6 1.0

Magnesium binding site 6 out of 7 in the Functional Implications From the CID1 Poly(U) Polymerase Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Functional Implications From the CID1 Poly(U) Polymerase Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:39.7 occ:1.00 O3G B:UTP501 2.3 51.1 1.0 O1B B:UTP501 2.4 34.6 1.0 OD2 B:ASP103 2.4 30.6 1.0 O B:HOH715 2.7 49.3 1.0 OD2 B:ASP101 2.8 44.7 1.0 O1A B:UTP501 3.0 30.9 1.0 PG B:UTP501 3.4 42.9 1.0 PB B:UTP501 3.5 32.8 1.0 CG B:ASP103 3.5 30.8 1.0 O B:HOH701 3.8 32.1 1.0 O3B B:UTP501 3.8 30.0 1.0 O2G B:UTP501 3.9 43.8 1.0 OD1 B:ASP103 3.9 31.0 1.0 CG B:ASP101 4.0 49.9 1.0 PA B:UTP501 4.0 26.6 1.0 C5' B:UTP501 4.0 27.3 1.0 O B:ASP101 4.0 37.3 1.0 O3A B:UTP501 4.0 31.0 1.0 OG B:SER90 4.0 30.4 1.0 N B:SER90 4.4 23.8 1.0 O5' B:UTP501 4.4 31.6 1.0 OD1 B:ASP101 4.6 55.3 1.0 O2B B:UTP501 4.7 37.1 1.0 CB B:ASP103 4.7 29.8 1.0 O1G B:UTP501 4.8 39.0 1.0 C B:ASP101 4.8 34.6 1.0 CB B:SER90 4.9 25.7 1.0 CA B:GLY89 5.0 22.3 1.0

Magnesium binding site 7 out of 7 in the Functional Implications From the CID1 Poly(U) Polymerase Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Functional Implications From the CID1 Poly(U) Polymerase Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:24.9 occ:1.00 O B:HOH634 3.0 34.0 1.0 ND2 B:ASN165 3.2 21.6 1.0 N1 B:UTP501 3.5 18.6 1.0 O B:HOH628 3.6 23.9 1.0 C2 B:UTP501 3.6 22.0 1.0 C1' B:UTP501 3.7 20.5 1.0 O2 B:UTP501 3.9 22.6 1.0 O4' B:UTP501 4.0 22.2 1.0 C6 B:UTP501 4.0 19.8 1.0 N3 B:UTP501 4.2 19.5 1.0 CG B:ASN165 4.2 30.5 1.0 OD1 B:ASN165 4.4 27.8 1.0 CB B:ALA168 4.5 19.1 1.0 C5 B:UTP501 4.5 19.0 1.0 C4 B:UTP501 4.6 22.9 1.0 CE1 B:PHE88 4.9 21.6 1.0

P.Munoz-Tello, C.Gabus, S.Thore. Functional Implications From the CID1 Poly(U) Polymerase Crystal Structure. Structure V. 20 977 2012.
ISSN: ISSN 0969-2126
PubMed: 22608966
DOI: 10.1016/J.STR.2012.04.006