Magnesium in PDB 4oge: Crystal Structure of the Type II-C CAS9 Enzyme From Actinomyces Naeslundii

The structure of Crystal Structure of the Type II-C CAS9 Enzyme From Actinomyces Naeslundii, PDB code: 4oge was solved by F.Jiang, E.Ma, S.Lin, J.A.Doudna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.69 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.415, 133.025, 80.690, 90.00, 96.22, 90.00
R / Rfree (%)	18.6 / 22.6

The structure of Crystal Structure of the Type II-C CAS9 Enzyme From Actinomyces Naeslundii also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of the Type II-C CAS9 Enzyme From Actinomyces Naeslundii (pdb code 4oge). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Type II-C CAS9 Enzyme From Actinomyces Naeslundii, PDB code: 4oge:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the Type II-C CAS9 Enzyme From Actinomyces Naeslundii


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 Type II-C CAS9 Enzyme From Actinomyces Naeslundii within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1202 b:19.5 occ:1.00 O A:HOH1639 2.1 34.2 1.0 OD1 A:ASP581 2.1 27.8 1.0 O A:HOH1640 2.1 35.0 1.0 O A:HOH1638 2.1 37.1 1.0 O A:HOH1637 2.2 21.1 1.0 OD1 A:ASN606 2.3 24.8 1.0 CG A:ASP581 3.3 24.2 1.0 CG A:ASN606 3.3 26.5 1.0 ND2 A:ASN606 3.7 26.2 1.0 O A:HOH1633 3.9 59.1 1.0 CB A:ASP581 4.0 22.1 1.0 CA A:ASP581 4.1 22.1 1.0 OD2 A:ASP581 4.2 22.4 1.0 O A:SER610 4.3 26.8 1.0 O A:ASN606 4.4 29.3 1.0 O A:HOH1621 4.4 35.9 1.0 O A:LEU580 4.6 28.9 1.0 N A:HIS582 4.6 21.3 1.0 CB A:ASN606 4.6 23.9 1.0 O A:HOH1641 4.8 27.4 1.0 CA A:ASN606 4.8 27.8 1.0 O A:HOH1311 4.9 29.5 1.0 C A:ASP581 4.9 21.6 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Type II-C CAS9 Enzyme From Actinomyces Naeslundii


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 Type II-C CAS9 Enzyme From Actinomyces Naeslundii within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1203 b:53.2 occ:1.00 OE1 A:GLU505 2.0 69.3 1.0 O A:HOH1643 2.1 63.3 1.0 OD1 A:ASP17 2.2 38.1 1.0 CD A:GLU505 3.1 60.0 1.0 CG A:ASP17 3.3 29.1 1.0 OD2 A:ASP17 3.7 44.6 1.0 OE2 A:GLU505 3.8 61.2 1.0 OD2 A:ASP739 4.0 49.9 1.0 CG A:GLU505 4.1 47.1 1.0 OG1 A:THR706 4.3 34.3 1.0 O A:HOH1487 4.3 39.2 1.0 O A:GLY703 4.5 53.1 1.0 CB A:ASP17 4.6 24.9 1.0 CB A:GLU505 4.6 33.6 1.0 O A:VAL18 4.7 31.9 1.0 CB A:ASP739 4.7 32.0 1.0 CG A:ASP739 4.7 45.2 1.0 O A:HIS506 4.8 44.0 1.0 O A:HOH1584 4.8 51.9 1.0 CA A:GLY703 4.9 35.2 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Type II-C CAS9 Enzyme From Actinomyces Naeslundii


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 Type II-C CAS9 Enzyme From Actinomyces Naeslundii within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1204 b:14.9 occ:1.00 O A:HOH1635 2.1 50.6 1.0 O A:HOH1634 2.2 35.8 1.0 O A:HOH1636 2.3 22.9 1.0 O A:GLY590 2.4 26.8 1.0 O A:GLY588 2.4 25.1 1.0 O A:GLN586 2.5 27.6 1.0 C A:GLY590 3.5 30.0 1.0 C A:GLN586 3.6 22.2 1.0 C A:GLY588 3.6 31.5 1.0 N A:GLY590 3.8 32.2 1.0 C A:PRO589 4.1 33.3 1.0 CA A:GLY590 4.2 21.5 1.0 N A:GLN586 4.2 23.3 1.0 CB A:GLN586 4.2 25.5 1.0 CA A:GLN586 4.3 24.7 1.0 OE2 A:GLU763 4.3 46.3 1.0 OG A:SER591 4.4 29.5 1.0 N A:GLY588 4.4 30.4 1.0 C A:ALA587 4.4 29.3 1.0 CA A:PRO589 4.5 33.3 1.0 N A:PRO589 4.5 38.1 1.0 O A:HOH1387 4.5 40.2 1.0 CA A:GLY588 4.6 26.2 1.0 N A:SER591 4.6 25.1 1.0 O A:PRO589 4.6 29.8 1.0 O A:ALA587 4.7 25.2 1.0 N A:ALA587 4.7 21.9 1.0 CG A:GLN586 4.9 26.8 1.0 CA A:SER591 4.9 23.1 1.0 CA A:ALA587 4.9 24.5 1.0 O A:HOH1571 5.0 48.9 1.0

M.Jinek, F.Jiang, D.W.Taylor, S.H.Sternberg, E.Kaya, E.Ma, C.Anders, M.Hauer, K.Zhou, S.Lin, M.Kaplan, A.T.Iavarone, E.Charpentier, E.Nogales, J.A.Doudna. Structures of CAS9 Endonucleases Reveal Rna-Mediated Conformational Activation. Science V. 343 47997 2014.
ISSN: ISSN 0036-8075
PubMed: 24505130
DOI: 10.1126/SCIENCE.1247997