Manganese in PDB 4lil: Crystal Structure of the Catalytic Subunit of Human Primase Bound to Utp and Mn

The structure of Crystal Structure of the Catalytic Subunit of Human Primase Bound to Utp and Mn, PDB code: 4lil was solved by S.Vaithiyalingam, B.F.Eichman, W.J.Chazin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.73 / 2.60
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.346, 79.346, 148.200, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 24.8

The structure of Crystal Structure of the Catalytic Subunit of Human Primase Bound to Utp and Mn also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

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

Manganese binding site 1 out of 2 in the Crystal Structure of the Catalytic Subunit of Human Primase Bound to Utp and Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Catalytic Subunit of Human Primase Bound to Utp and Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:71.8 occ:0.98 O1B A:UTP504 2.2 58.9 0.4 O2G A:UTP504 2.5 54.9 0.7 O1A A:UTP504 2.5 56.8 0.9 OD1 A:ASP109 2.6 32.2 1.0 NH1 A:ARG163 3.3 35.0 0.6 CG A:ASP109 3.4 32.5 1.0 PB A:UTP504 3.4 56.9 1.0 OD2 A:ASP109 3.4 33.5 1.0 NE2 A:HIS166 3.6 27.8 1.0 PG A:UTP504 3.6 54.0 0.7 PA A:UTP504 3.8 57.7 0.4 O3B A:UTP504 3.9 57.0 0.5 MN A:MN503 3.9 0.2 1.0 CB A:ASP111 4.0 34.8 1.0 O3A A:UTP504 4.0 55.6 0.5 CB A:SER160 4.2 29.8 1.0 CD2 A:HIS166 4.2 27.4 1.0 O1G A:UTP504 4.2 49.2 1.0 O A:ILE110 4.3 32.4 1.0 OG A:SER160 4.3 31.2 1.0 CG A:ASP111 4.5 35.5 1.0 CZ A:ARG163 4.5 37.1 0.8 CA A:ASP111 4.5 34.4 1.0 O2B A:UTP504 4.5 61.4 0.1 O2A A:UTP504 4.6 55.6 0.9 CE1 A:HIS166 4.7 27.7 1.0 C A:ILE110 4.8 33.5 1.0 O5' A:UTP504 4.8 56.6 1.0 OD1 A:ASP111 4.8 36.0 0.4 O3G A:UTP504 4.9 57.0 1.0 CB A:ASP109 4.9 32.5 1.0 N A:ASP111 4.9 34.2 1.0 CD A:ARG163 4.9 36.8 1.0 OD2 A:ASP111 5.0 36.4 0.3

Manganese binding site 2 out of 2 in the Crystal Structure of the Catalytic Subunit of Human Primase Bound to Utp and Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Catalytic Subunit of Human Primase Bound to Utp and Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:0.2 occ:1.00 OD2 A:ASP109 2.5 33.5 1.0 O A:HOH627 2.8 30.0 1.0 O1A A:UTP504 2.9 56.8 0.9 CG A:ASP109 3.1 32.5 1.0 O A:HOH628 3.5 30.0 1.0 OD1 A:ASP109 3.6 32.2 1.0 PA A:UTP504 3.9 57.7 0.4 MN A:MN502 3.9 71.8 1.0 O5' A:UTP504 3.9 56.6 1.0 CB A:ASP109 4.1 32.5 1.0 CB A:ASP111 4.2 34.8 1.0 O2A A:UTP504 4.3 55.6 0.9 OD2 A:ASP111 4.3 36.4 0.3 O A:ASP109 4.6 35.5 1.0 CG A:ASP111 4.7 35.5 1.0 NH1 A:ARG163 4.7 35.0 0.6 O1B A:UTP504 4.8 58.9 0.4

S.Vaithiyalingam, D.R.Arnett, A.Aggarwal, B.F.Eichman, E.Fanning, W.J.Chazin. Insights Into Eukaryotic Primer Synthesis From Structures of the P48 Subunit of Human Dna Primase. J.Mol.Biol. V. 426 558 2014.
ISSN: ISSN 0022-2836
PubMed: 24239947
DOI: 10.1016/J.JMB.2013.11.007