Manganese in PDB 6qv4: Crystal Structure of the SKI2 Rna-Helicase BRR2 From Chaetomium Thermophilum Bound to Atp-Gamma-S

The structure of Crystal Structure of the SKI2 Rna-Helicase BRR2 From Chaetomium Thermophilum Bound to Atp-Gamma-S, PDB code: 6qv4 was solved by E.Absmeier, K.F.Santos, M.C.Wahl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.53 / 2.80
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	124.818, 124.818, 127.087, 90.00, 90.00, 120.00
R / Rfree (%)	20.9 / 26

The binding sites of Manganese atom in the Crystal Structure of the SKI2 Rna-Helicase BRR2 From Chaetomium Thermophilum Bound to Atp-Gamma-S (pdb code 6qv4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of the SKI2 Rna-Helicase BRR2 From Chaetomium Thermophilum Bound to Atp-Gamma-S, PDB code: 6qv4:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of the SKI2 Rna-Helicase BRR2 From Chaetomium Thermophilum Bound to Atp-Gamma-S


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 SKI2 Rna-Helicase BRR2 From Chaetomium Thermophilum Bound to Atp-Gamma-S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2201 b:0.9 occ:1.00 OE2 A:GLU1663 2.1 94.8 1.0 NE2 A:HIS1667 2.4 74.2 1.0 CE1 A:HIS1667 2.9 76.7 1.0 CD A:GLU1663 3.2 85.2 1.0 CD2 A:HIS1667 3.6 75.2 1.0 OE1 A:GLU1663 3.7 86.0 1.0 ND1 A:HIS1667 4.1 69.3 1.0 OG A:SER1666 4.4 68.2 1.0 CG A:GLU1663 4.4 81.4 1.0 CG A:HIS1667 4.5 65.2 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of the SKI2 Rna-Helicase BRR2 From Chaetomium Thermophilum Bound to Atp-Gamma-S


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 SKI2 Rna-Helicase BRR2 From Chaetomium Thermophilum Bound to Atp-Gamma-S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2202 b:0.0 occ:1.00 S1G A:AGS2204 2.2 0.5 1.0 O2B A:AGS2204 2.3 0.5 1.0 OE2 A:GLU664 2.9 0.1 1.0 OD2 A:ASP663 3.0 76.2 1.0 OD1 A:ASP663 3.5 77.2 1.0 CG A:ASP663 3.6 78.3 1.0 PB A:AGS2204 3.7 0.6 1.0 PG A:AGS2204 3.8 0.9 1.0 OG1 A:THR558 4.1 80.3 1.0 CD A:GLU664 4.1 0.3 1.0 O A:HOH2316 4.2 71.4 1.0 O3A A:AGS2204 4.2 0.3 1.0 O3B A:AGS2204 4.2 0.6 1.0 O2G A:AGS2204 4.4 0.1 1.0 OH A:TYR588 4.7 80.0 1.0 CD2 A:LEU595 4.7 86.6 1.0 NZ A:LYS557 4.8 77.1 1.0 NE2 A:GLN901 4.8 92.6 1.0 O1B A:AGS2204 4.8 0.7 1.0 CG A:GLU664 4.9 92.5 1.0 OE1 A:GLN901 4.9 97.5 1.0 NE2 A:GLN599 5.0 99.8 1.0 OE1 A:GLU664 5.0 0.9 1.0 O1A A:AGS2204 5.0 0.4 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of the SKI2 Rna-Helicase BRR2 From Chaetomium Thermophilum Bound to Atp-Gamma-S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the SKI2 Rna-Helicase BRR2 From Chaetomium Thermophilum Bound to Atp-Gamma-S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2203 b:0.2 occ:1.00 S1G A:AGS2206 1.9 0.1 1.0 O1B A:AGS2206 2.0 0.3 1.0 PG A:AGS2206 2.2 1.0 1.0 O3B A:AGS2206 2.4 0.1 1.0 PB A:AGS2206 2.5 82.2 1.0 O2G A:AGS2206 2.5 0.8 1.0 O3A A:AGS2206 3.0 85.2 1.0 OG1 A:THR1408 3.3 59.7 1.0 O3G A:AGS2206 3.7 0.0 1.0 O2B A:AGS2206 3.9 61.0 1.0 OD2 A:ASP1506 4.0 50.5 1.0 OD1 A:ASP1506 4.0 48.8 1.0 N A:THR1408 4.1 53.7 1.0 PA A:AGS2206 4.2 74.4 1.0 CB A:LYS1407 4.2 49.0 1.0 O2A A:AGS2206 4.3 69.7 1.0 CE A:LYS1407 4.4 58.4 1.0 CG A:ASP1506 4.5 49.8 1.0 NZ A:LYS1407 4.5 76.5 1.0 CB A:THR1408 4.6 58.2 1.0 O1A A:AGS2206 4.6 78.0 1.0 C A:LYS1407 4.6 59.3 1.0 CA A:THR1408 4.7 56.5 1.0 CA A:LYS1407 4.8 53.6 1.0 OD1 A:ASP1507 4.8 70.0 1.0 N A:LYS1407 4.9 55.0 1.0

E.Absmeier, K.F.Santos, M.C.Wahl. Molecular Mechanism Underlying Inhibition of Intrinsic Atpase Activity in A SKI2-Like Rna Helicase. Structure 2019.
ISSN: ISSN 0969-2126
PubMed: 31859026
DOI: 10.1016/J.STR.2019.11.014