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Magnesium in PDB 3ngo: Crystal Structure of the Human CNOT6L Nuclease Domain in Complex with Poly(A) Dna

Protein crystallography data

The structure of Crystal Structure of the Human CNOT6L Nuclease Domain in Complex with Poly(A) Dna, PDB code: 3ngo was solved by H.Wang, M.Morita, W.Yang, M.Bartlam, T.Yamamoto, Z.Rao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.20
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 77.373, 77.373, 167.177, 90.00, 90.00, 120.00
R / Rfree (%) 21.5 / 26.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Human CNOT6L Nuclease Domain in Complex with Poly(A) Dna (pdb code 3ngo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Human CNOT6L Nuclease Domain in Complex with Poly(A) Dna, PDB code: 3ngo:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3ngo

Go back to Magnesium Binding Sites List in 3ngo
Magnesium binding site 1 out of 2 in the Crystal Structure of the Human CNOT6L Nuclease Domain in Complex with Poly(A) Dna


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 Human CNOT6L Nuclease Domain in Complex with Poly(A) Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg556

b:39.5
occ:1.00
OP1 B:DA659 2.6 50.9 1.0
OD2 A:ASP410 2.6 30.3 1.0
ND2 A:ASN412 2.9 25.6 1.0
NE2 A:HIS529 3.2 33.7 1.0
P B:DA659 3.2 48.9 1.0
O5' B:DA659 3.3 51.3 1.0
CE1 A:HIS529 3.3 30.1 1.0
CG A:ASP410 3.4 30.8 1.0
O A:HOH587 3.4 42.3 1.0
OD1 A:ASP410 3.4 28.8 1.0
CD1 A:ILE488 3.5 27.5 1.0
OP2 B:DA659 3.5 46.0 1.0
C5' B:DA659 3.6 52.0 1.0
CG A:ASN412 3.7 30.6 1.0
OD1 A:ASN412 3.9 35.2 1.0
ND2 A:ASN195 4.0 30.1 1.0
NE2 A:HIS360 4.0 28.7 1.0
MG A:MG557 4.1 50.5 1.0
CD2 A:HIS529 4.5 28.6 1.0
ND1 A:HIS529 4.6 30.4 1.0
O3' B:DA658 4.7 57.1 1.0
CG1 A:ILE488 4.8 29.3 1.0
OE2 A:GLU240 4.8 33.4 1.0
CB A:ASP410 4.8 29.6 1.0
CD2 A:HIS360 4.9 27.0 1.0
CE1 A:HIS360 4.9 30.0 1.0
ND2 A:ASN479 4.9 31.6 1.0
C4' B:DA659 5.0 55.4 1.0

Magnesium binding site 2 out of 2 in 3ngo

Go back to Magnesium Binding Sites List in 3ngo
Magnesium binding site 2 out of 2 in the Crystal Structure of the Human CNOT6L Nuclease Domain in Complex with Poly(A) Dna


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 Human CNOT6L Nuclease Domain in Complex with Poly(A) Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg557

b:50.5
occ:1.00
O A:HOH560 2.0 31.9 1.0
OP1 B:DA659 2.1 50.9 1.0
O A:HOH624 2.2 32.0 1.0
OE2 A:GLU240 2.2 33.4 1.0
O A:HOH587 2.6 42.3 1.0
CD A:GLU240 3.2 32.6 1.0
P B:DA659 3.3 48.9 1.0
OE1 A:GLU240 3.4 34.2 1.0
C3' B:DA658 3.4 62.9 1.0
O3' B:DA658 3.7 57.1 1.0
C2' B:DA658 3.8 62.9 1.0
ND2 A:ASN195 3.9 30.1 1.0
MG A:MG556 4.1 39.5 1.0
CE1 A:HIS529 4.2 30.1 1.0
OP2 B:DA659 4.3 46.0 1.0
CD1 A:LEU197 4.3 24.5 1.0
OD2 A:ASP528 4.3 36.6 1.0
OD1 A:ASN195 4.3 28.2 1.0
O5' B:DA659 4.4 51.3 1.0
C5' B:DA659 4.5 52.0 1.0
CG A:ASN195 4.5 28.0 1.0
CG A:GLU240 4.5 29.8 1.0
OD1 A:ASP528 4.6 34.3 1.0
OH A:TYR207 4.7 28.8 1.0
C4' B:DA658 4.8 65.0 1.0
CE1 A:HIS360 4.9 30.0 1.0
ND1 A:HIS529 4.9 30.4 1.0
CG A:ASP528 4.9 32.9 1.0

Reference:

H.Wang, M.Morita, X.Yang, T.Suzuki, W.Yang, J.Wang, K.Ito, Q.Wang, C.Zhao, M.Bartlam, T.Yamamoto, Z.Rao. Crystal Structure of the Human CNOT6L Nuclease Domain Reveals Strict Poly(A) Substrate Specificity. Embo J. 2010.
ISSN: ESSN 1460-2075
PubMed: 20628353
DOI: 10.1038/EMBOJ.2010.152
Page generated: Mon Dec 14 08:28:26 2020

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