Magnesium in PDB 4bpw: Crystal Structure of Human Primase Bound to Utp

The structure of Crystal Structure of Human Primase Bound to Utp, PDB code: 4bpw was solved by M.L.Kilkenny, R.L.Perera, L.Pellegrini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.784 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	116.394, 69.438, 127.087, 90.00, 104.90, 90.00
R / Rfree (%)	21.52 / 25.34

The structure of Crystal Structure of Human Primase Bound to Utp also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Human Primase Bound to Utp (pdb code 4bpw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human Primase Bound to Utp, PDB code: 4bpw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Human Primase Bound to Utp


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 Human Primase Bound to Utp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1412 b:42.2 occ:1.00 OD2 A:ASP306 2.7 59.5 1.0 OD2 A:ASP109 2.9 55.7 1.0 OD2 A:ASP111 3.1 78.0 1.0 H5'2 A:UTP1414 3.2 64.2 0.7 HB2 A:ASP306 3.3 63.4 1.0 HG22 A:VAL309 3.4 43.9 1.0 O2A A:UTP1414 3.4 69.8 0.7 H5'1 A:UTP1414 3.6 64.2 0.7 CG A:ASP306 3.6 74.8 1.0 HB3 A:ASP306 3.7 63.4 1.0 HG21 A:VAL309 3.7 43.9 1.0 CB A:ASP306 3.7 52.8 1.0 C5' A:UTP1414 3.8 53.5 0.7 CG2 A:VAL309 3.9 36.6 1.0 HB3 A:ASP109 4.0 26.8 1.0 CG A:ASP109 4.0 43.7 1.0 O5' A:UTP1414 4.1 43.9 0.7 HG23 A:VAL309 4.1 43.9 1.0 CG A:ASP111 4.1 67.5 1.0 PA A:UTP1414 4.2 69.7 0.7 OD1 A:ASP111 4.4 74.1 1.0 CB A:ASP109 4.5 22.3 1.0 O1A A:UTP1414 4.6 56.4 0.7 OD1 A:ASP306 4.8 63.9 1.0 OD1 A:ASP109 5.0 38.7 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Human Primase Bound to Utp


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 Human Primase Bound to Utp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1413 b:39.5 occ:1.00 O2B A:UTP1414 1.8 48.4 0.7 OD1 A:ASP111 2.4 74.1 1.0 O2G A:UTP1414 2.4 49.7 0.7 OD1 A:ASP109 2.8 38.7 1.0 PB A:UTP1414 2.8 37.4 0.7 HE2 A:HIS166 3.1 60.6 1.0 O3B A:UTP1414 3.2 40.6 0.7 PG A:UTP1414 3.2 41.0 0.7 O3A A:UTP1414 3.2 46.4 0.7 O2A A:UTP1414 3.2 69.8 0.7 OD2 A:ASP109 3.5 55.7 1.0 CG A:ASP109 3.5 43.7 1.0 CG A:ASP111 3.6 67.5 1.0 O1G A:UTP1414 3.6 36.5 0.7 PA A:UTP1414 3.6 69.7 0.7 HB2 A:SER160 3.8 47.6 1.0 O5' A:UTP1414 3.8 43.9 0.7 NE2 A:HIS166 3.9 50.5 1.0 OG A:SER160 3.9 52.5 1.0 HB3 A:SER160 4.1 47.6 1.0 HA A:ASP111 4.1 40.8 1.0 CB A:SER160 4.1 39.6 1.0 O1B A:UTP1414 4.2 30.2 0.7 HB2 A:ARG163 4.2 52.6 1.0 HG A:SER160 4.3 63.0 1.0 HD2 A:HIS166 4.3 59.2 1.0 O A:ILE110 4.4 35.3 1.0 OD2 A:ASP111 4.4 78.0 1.0 NH2 A:ARG163 4.4 49.8 1.0 HA3 A:GLY164 4.4 53.4 1.0 HH21 A:ARG163 4.5 59.8 1.0 HH22 A:ARG163 4.5 59.8 1.0 CD2 A:HIS166 4.5 49.4 1.0 CB A:ASP111 4.5 43.2 1.0 HB3 A:ASP111 4.6 51.9 1.0 O3G A:UTP1414 4.6 37.0 0.7 CZ A:ARG163 4.6 52.6 1.0 CA A:ASP111 4.7 34.0 1.0 C A:ILE110 4.8 35.9 1.0 H A:ILE110 4.8 21.0 1.0 N A:GLY164 4.9 44.3 1.0 H A:GLY164 4.9 53.2 1.0 HB3 A:ARG163 5.0 52.6 1.0 NE A:ARG163 5.0 46.2 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Human Primase Bound to Utp


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 Human Primase Bound to Utp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1410 b:90.3 occ:1.00 HB2 C:ASP306 2.5 0.3 1.0 OD2 C:ASP109 2.8 87.5 1.0 HB3 C:ASP306 3.1 0.3 1.0 OD2 C:ASP306 3.1 0.8 1.0 CB C:ASP306 3.2 96.9 1.0 CG C:ASP306 3.6 0.2 1.0 HG22 C:VAL309 3.6 91.7 1.0 HB2 C:ASP111 3.6 0.6 1.0 HB3 C:ASP109 3.6 0.5 1.0 H5'2 C:UTP1412 3.8 0.2 0.7 CG C:ASP109 3.9 87.7 1.0 O2A C:UTP1412 4.0 0.8 0.7 HG21 C:VAL309 4.0 91.7 1.0 CB C:ASP109 4.3 90.4 1.0 CG2 C:VAL309 4.3 76.4 1.0 H C:ASP306 4.3 0.1 1.0 OD2 C:ASP114 4.3 93.3 1.0 O C:ASP109 4.3 81.3 1.0 CA C:ASP306 4.5 96.8 1.0 CB C:ASP111 4.5 95.5 1.0 C5' C:UTP1412 4.6 0.8 0.7 H5'1 C:UTP1412 4.7 0.2 0.7 HB3 C:ASP111 4.8 0.6 1.0 N C:ASP306 4.8 91.8 1.0 HG23 C:VAL309 4.8 91.7 1.0 C C:ASP109 4.8 74.0 1.0 OD1 C:ASP306 4.8 0.9 1.0 H C:ASP111 4.9 71.1 1.0 OD2 C:ASP111 4.9 0.0 1.0 HA C:ASP306 4.9 0.1 1.0 HB2 C:ASP109 4.9 0.5 1.0 OD1 C:ASP109 4.9 90.5 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Human Primase Bound to Utp


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 Human Primase Bound to Utp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1411 b:95.3 occ:1.00 OD2 C:ASP111 2.5 0.0 1.0 O2B C:UTP1412 2.5 90.4 0.7 O2G C:UTP1412 2.7 0.9 0.7 OD1 C:ASP109 3.3 90.5 1.0 HE2 C:HIS166 3.4 0.4 1.0 CG C:ASP111 3.5 0.5 1.0 PB C:UTP1412 3.5 0.0 0.7 HA C:ASP111 3.5 90.6 1.0 OG C:SER160 3.5 89.8 1.0 PG C:UTP1412 3.6 0.3 0.7 HA3 C:GLY164 3.7 0.2 1.0 HB2 C:ARG163 3.7 0.1 1.0 O3A C:UTP1412 3.7 0.8 0.7 O1G C:UTP1412 3.7 92.6 0.7 HB2 C:SER160 3.8 0.8 1.0 O C:ILE110 3.8 68.3 1.0 O3B C:UTP1412 3.8 0.0 0.7 HB3 C:SER160 3.8 0.8 1.0 O2A C:UTP1412 3.9 0.8 0.7 HG C:SER160 3.9 0.7 1.0 CB C:SER160 4.0 93.1 1.0 OD2 C:ASP109 4.0 87.5 1.0 CG C:ASP109 4.0 87.7 1.0 N C:GLY164 4.1 83.3 1.0 HB2 C:ASP111 4.1 0.6 1.0 H C:GLY164 4.1 0.0 1.0 NE2 C:HIS166 4.1 90.3 1.0 CB C:ASP111 4.2 95.5 1.0 CA C:ASP111 4.2 75.5 1.0 HD2 C:HIS166 4.2 95.1 1.0 CA C:GLY164 4.2 84.3 1.0 OD1 C:ASP111 4.2 0.8 1.0 PA C:UTP1412 4.3 0.1 0.7 C C:ILE110 4.4 71.4 1.0 HB3 C:ARG163 4.4 0.1 1.0 H C:ARG163 4.4 97.6 1.0 C C:ARG163 4.4 75.0 1.0 CB C:ARG163 4.4 91.7 1.0 CD2 C:HIS166 4.6 79.3 1.0 N C:ASP111 4.6 59.2 1.0 C C:GLY164 4.6 80.2 1.0 H C:ILE110 4.6 99.6 1.0 O5' C:UTP1412 4.7 0.0 0.7 H C:VAL165 4.8 90.6 1.0 O C:ARG163 4.9 63.6 1.0 CA C:ARG163 4.9 74.0 1.0 O1B C:UTP1412 4.9 0.5 0.7 N C:VAL165 4.9 75.5 1.0 O3G C:UTP1412 4.9 88.8 0.7 HH21 C:ARG163 5.0 0.9 1.0

M.L.Kilkenny, M.A.Longo, R.L.Perera, L.Pellegrini. Structures of Human Primase Reveal Design of Nucleotide Elongation Site and Mode of Pol Alpha Tethering Proc.Natl.Acad.Sci.Usa V. 110 15961 2013.
ISSN: ISSN 0027-8424
PubMed: 24043831
DOI: 10.1073/PNAS.1311185110