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Magnesium in PDB 6ai6: Crystal Structure of SPCAS9-Ng

Protein crystallography data

The structure of Crystal Structure of SPCAS9-Ng, PDB code: 6ai6 was solved by H.Nishimasu, S.Hirano, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.17 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 177.377, 68.568, 187.968, 90.00, 111.51, 90.00
R / Rfree (%) 21.8 / 24.4

Other elements in 6ai6:

The structure of Crystal Structure of SPCAS9-Ng also contains other interesting chemical elements:

Potassium (K) 10 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of SPCAS9-Ng (pdb code 6ai6). 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 SPCAS9-Ng, PDB code: 6ai6:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6ai6

Go back to Magnesium Binding Sites List in 6ai6
Magnesium binding site 1 out of 3 in the Crystal Structure of SPCAS9-Ng


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 SPCAS9-Ng within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1409

b:52.8
occ:1.00
O A:HOH1515 2.1 53.8 1.0
O B:HOH220 2.3 62.9 1.0
O B:HOH208 2.3 42.4 1.0
N7 B:G19 3.8 48.0 1.0
NH2 A:ARG71 4.3 61.5 1.0
CE1 A:TYR72 4.5 43.6 1.0
OH A:TYR72 4.6 44.7 1.0
O6 B:G19 4.6 47.6 1.0
C8 B:G19 4.7 50.3 1.0
CZ A:TYR72 4.8 44.3 1.0
C5 B:G19 4.8 50.8 1.0
NH1 A:ARG75 4.8 36.6 1.0

Magnesium binding site 2 out of 3 in 6ai6

Go back to Magnesium Binding Sites List in 6ai6
Magnesium binding site 2 out of 3 in the Crystal Structure of SPCAS9-Ng


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 SPCAS9-Ng within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg102

b:67.4
occ:1.00
O B:HOH219 2.1 67.5 1.0
OP1 B:U50 2.3 61.1 1.0
O B:HOH204 2.3 71.1 1.0
P B:U50 3.7 53.5 1.0
OP1 B:A52 3.9 52.9 1.0
O6 B:G62 4.1 58.0 1.0
O6 B:G53 4.1 51.8 1.0
N7 B:G53 4.2 52.2 1.0
OP2 B:A52 4.4 48.5 1.0
OP2 B:U50 4.4 53.1 1.0
O5' B:U50 4.4 50.9 1.0
O B:HOH217 4.5 48.8 1.0
P B:A52 4.7 46.3 1.0
O3' B:A49 4.7 47.4 1.0
C5' B:U50 4.7 49.8 1.0
NZ A:LYS1123 4.7 60.8 1.0
OP1 B:A51 4.8 38.6 1.0
C6 B:G53 4.8 51.8 1.0
N1 B:G62 4.9 53.9 1.0
C5 B:G53 4.9 52.1 1.0
C6 B:G62 4.9 54.9 1.0

Magnesium binding site 3 out of 3 in 6ai6

Go back to Magnesium Binding Sites List in 6ai6
Magnesium binding site 3 out of 3 in the Crystal Structure of SPCAS9-Ng


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 SPCAS9-Ng within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg103

b:59.7
occ:1.00
OP2 B:G21 3.5 53.6 1.0
O4 B:U22 3.7 46.4 1.0
N7 B:G21 4.2 50.4 1.0
K B:K101 4.4 77.7 1.0
NH1 A:ARG403 4.6 42.7 1.0
C4 B:U22 4.7 47.7 1.0
O B:HOH205 4.8 35.8 1.0
C8 B:G21 4.8 51.9 1.0
P B:G21 5.0 55.6 1.0

Reference:

H.Nishimasu, X.Shi, S.Ishiguro, L.Gao, S.Hirano, S.Okazaki, T.Noda, O.O.Abudayyeh, J.S.Gootenberg, H.Mori, S.Oura, B.Holmes, M.Tanaka, M.Seki, H.Hirano, H.Aburatani, R.Ishitani, M.Ikawa, N.Yachie, F.Zhang, O.Nureki. Engineered Crispr-CAS9 Nuclease with Expanded Targeting Space Science V. 361 1259 2018.
ISSN: ESSN 1095-9203
PubMed: 30166441
DOI: 10.1126/SCIENCE.AAS9129
Page generated: Wed Aug 13 02:14:43 2025

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