Manganese in PDB 6qfd: The Complex Structure of Hsrosr-S4 (VNG0258/Rosr-S4)

The structure of The Complex Structure of Hsrosr-S4 (VNG0258/Rosr-S4), PDB code: 6qfd was solved by B.Shaanan, N.Kutnowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.59 / 2.13
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.805, 83.995, 88.876, 81.53, 86.18, 74.48
R / Rfree (%)	21 / 23.2

The binding sites of Manganese atom in the The Complex Structure of Hsrosr-S4 (VNG0258/Rosr-S4) (pdb code 6qfd). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the The Complex Structure of Hsrosr-S4 (VNG0258/Rosr-S4), PDB code: 6qfd:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in the The Complex Structure of Hsrosr-S4 (VNG0258/Rosr-S4)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Complex Structure of Hsrosr-S4 (VNG0258/Rosr-S4) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn207 b:99.4 occ:1.00 H A:HIS50 2.5 59.7 1.0 HE3 A:LYS37 2.6 69.6 1.0 HB3 A:HIS50 2.9 57.0 1.0 ND1 A:HIS50 3.1 51.8 1.0 N A:HIS50 3.3 48.6 1.0 HA A:ASN49 3.4 59.6 1.0 CE A:LYS37 3.5 56.9 1.0 CB A:HIS50 3.7 46.4 1.0 CG A:HIS50 3.8 49.0 1.0 HE2 A:LYS37 3.8 69.6 1.0 O E:HOH201 4.0 26.8 1.0 HZ3 A:LYS37 4.0 72.4 1.0 O A:VAL48 4.0 49.0 1.0 CA A:HIS50 4.1 47.6 1.0 NZ A:LYS37 4.2 59.2 1.0 CE1 A:HIS50 4.2 54.8 1.0 HD2 A:LYS37 4.2 66.5 1.0 HZ1 A:LYS37 4.2 72.4 1.0 CA A:ASN49 4.3 48.6 1.0 C A:ASN49 4.3 48.3 1.0 HE1 A:HIS50 4.4 67.1 1.0 CD A:LYS37 4.5 54.3 1.0 HB2 A:HIS50 4.5 57.0 1.0 HA A:HIS50 4.7 58.5 1.0 H A:GLY51 4.7 67.2 1.0 O4 E:SO4101 4.8 0.3 1.0 HD3 A:LYS37 4.8 66.5 1.0 OD1 A:ASN49 4.9 56.3 1.0 C A:VAL48 4.9 47.0 1.0

Manganese binding site 2 out of 8 in the The Complex Structure of Hsrosr-S4 (VNG0258/Rosr-S4)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Complex Structure of Hsrosr-S4 (VNG0258/Rosr-S4) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn208 b:0.8 occ:1.00 HB3 A:GLU41 2.4 68.4 1.0 OD2 D:ASP115 2.9 58.0 1.0 HB2 A:GLU41 3.1 68.4 1.0 CB A:GLU41 3.1 55.9 1.0 HG22 D:THR111 3.1 48.6 1.0 CD A:GLU41 3.5 70.5 1.0 HG21 D:THR111 3.5 48.6 1.0 O A:HOH306 3.6 27.9 1.0 OE1 A:GLU41 3.6 73.0 1.0 CG2 D:THR111 3.7 39.4 1.0 HG23 D:THR111 3.7 48.6 1.0 CG A:GLU41 3.8 63.0 1.0 OE2 A:GLU41 3.8 73.7 1.0 OE2 A:GLU47 3.9 76.0 1.0 CG D:ASP115 4.0 56.6 1.0 HG2 A:GLU41 4.1 76.9 1.0 O A:HOH332 4.1 50.9 1.0 CA A:GLU41 4.3 47.9 1.0 C A:GLU41 4.4 45.2 1.0 OD1 D:ASP115 4.4 60.7 1.0 O A:GLU41 4.5 45.2 1.0 HA A:GLU47 4.5 73.7 1.0 HA A:ARG38 4.5 48.1 1.0 HG3 A:GLU41 4.6 76.9 1.0 HA A:GLU41 4.7 58.8 1.0 CD A:GLU47 4.9 79.1 1.0 N A:GLU42 4.9 43.7 1.0 O A:GLU46 4.9 43.3 1.0 HG2 A:ARG38 4.9 61.5 1.0 O A:ARG38 5.0 40.6 1.0

Manganese binding site 3 out of 8 in the The Complex Structure of Hsrosr-S4 (VNG0258/Rosr-S4)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Complex Structure of Hsrosr-S4 (VNG0258/Rosr-S4) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn205 b:0.2 occ:1.01 HB3 B:ASP90 2.3 47.5 1.0 HE B:ARG13 2.5 37.7 1.0 HH21 B:ARG13 2.6 38.6 1.0 CB B:ASP90 3.1 38.5 1.0 HG2 B:ARG9 3.1 56.7 1.0 O B:ASP90 3.1 38.5 1.0 C B:ASP90 3.2 34.7 1.0 NE B:ARG13 3.2 30.7 1.0 HB2 B:ASP90 3.3 47.5 1.0 HA B:ASP91 3.3 49.1 1.0 NH2 B:ARG13 3.3 31.1 1.0 O A:HOH301 3.4 36.7 1.0 HD21 C:ASN82 3.5 87.9 1.0 HG3 B:ARG9 3.5 56.7 1.0 N B:ASP91 3.5 35.7 1.0 HG2 B:ARG13 3.5 44.4 1.0 CA B:ASP90 3.7 33.3 1.0 CZ B:ARG13 3.7 30.5 1.0 CG B:ARG9 3.8 46.1 1.0 HB2 B:TRP94 3.9 51.8 0.5 CA B:ASP91 3.9 39.8 1.0 H B:ASP91 3.9 44.2 1.0 HD22 C:ASN82 4.0 87.9 1.0 HB3 B:TRP94 4.0 51.9 0.5 HH22 B:ARG13 4.0 38.6 1.0 ND2 C:ASN82 4.0 72.2 1.0 HE1 A:TYR43 4.1 43.0 1.0 HA B:ASP90 4.1 41.3 1.0 HA B:ARG9 4.1 61.0 1.0 CG B:ARG13 4.2 35.9 1.0 HB2 B:TRP94 4.2 51.9 0.5 HD3 B:ARG9 4.2 56.7 1.0 HG3 B:ARG13 4.2 44.4 1.0 CG B:ASP90 4.3 43.0 1.0 CD B:ARG13 4.3 34.4 1.0 HB2 B:ASP91 4.5 57.3 1.0 HH A:TYR43 4.5 43.6 1.0 HB3 B:TRP94 4.5 51.8 0.5 HH11 B:ARG9 4.5 58.4 1.0 CB B:TRP94 4.6 42.1 0.5 CD B:ARG9 4.6 46.2 1.0 CB B:TRP94 4.7 42.1 0.5 OD2 B:ASP90 4.7 46.1 1.0 HD3 B:ARG13 4.7 42.6 1.0 CE1 A:TYR43 4.7 34.8 1.0 CB B:ASP91 4.8 46.6 1.0 H B:TRP94 4.8 48.9 0.5 H B:TRP94 4.9 48.8 0.5 OH A:TYR43 4.9 35.3 1.0 CB B:ARG9 4.9 50.6 1.0 CA B:ARG9 4.9 49.7 1.0 N B:ASP90 5.0 34.2 1.0

Manganese binding site 4 out of 8 in the The Complex Structure of Hsrosr-S4 (VNG0258/Rosr-S4)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Complex Structure of Hsrosr-S4 (VNG0258/Rosr-S4) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn206 b:0.6 occ:0.71 H B:HIS50 2.4 86.3 1.0 ND1 B:HIS50 2.9 74.7 1.0 HZ2 B:LYS37 2.9 99.1 1.0 HA B:ASN49 3.0 89.2 1.0 N B:HIS50 3.2 70.8 1.0 HB3 B:HIS50 3.3 80.7 1.0 NZ B:LYS37 3.8 81.5 1.0 CG B:HIS50 3.8 69.0 1.0 CE1 B:HIS50 3.9 78.0 1.0 CA B:ASN49 3.9 73.3 1.0 CB B:HIS50 3.9 66.1 1.0 HE1 B:HIS50 4.0 92.5 1.0 HZ3 B:LYS37 4.0 99.1 1.0 HE2 B:LYS37 4.1 95.5 1.0 C B:ASN49 4.1 69.9 1.0 HD2 B:LYS37 4.1 88.5 1.0 O B:VAL48 4.1 67.5 1.0 OE2 B:GLU47 4.2 1.0 1.0 CA B:HIS50 4.2 65.7 1.0 OD1 B:ASN49 4.3 87.2 1.0 HZ1 B:LYS37 4.3 99.1 1.0 CE B:LYS37 4.4 78.5 1.0 H B:GLY51 4.5 83.6 1.0 HB3 B:ASN49 4.5 92.4 1.0 CB B:ASN49 4.7 75.9 1.0 CD B:LYS37 4.7 72.6 1.0 HA B:HIS50 4.8 80.2 1.0 HB2 B:HIS50 4.8 80.7 1.0 N B:ASN49 4.8 70.0 1.0 C B:VAL48 4.9 68.0 1.0 HG2 B:GLU47 4.9 0.7 1.0 CD2 B:HIS50 5.0 69.0 1.0 NE2 B:HIS50 5.0 74.5 1.0 CG B:ASN49 5.0 82.3 1.0

Manganese binding site 5 out of 8 in the The Complex Structure of Hsrosr-S4 (VNG0258/Rosr-S4)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of The Complex Structure of Hsrosr-S4 (VNG0258/Rosr-S4) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn207 b:20.4 occ:0.21 HG1 B:THR16 2.0 55.5 1.0 OD1 B:ASN56 2.5 55.3 1.0 OP1 F:DT17 2.6 68.0 1.0 HG3 B:GLN19 2.7 52.5 1.0 OG1 B:THR16 2.8 45.1 1.0 HB3 B:PHE18 2.9 52.6 1.0 HG21 B:THR16 3.0 49.2 1.0 HD21 B:ASN56 3.1 69.3 1.0 CG B:ASN56 3.2 54.6 1.0 HD2 B:PHE18 3.2 54.3 1.0 HG23 B:THR16 3.5 49.2 1.0 ND2 B:ASN56 3.5 56.6 1.0 P F:DT17 3.5 70.2 1.0 CG2 B:THR16 3.5 40.0 1.0 CG B:GLN19 3.6 42.7 1.0 CB B:THR16 3.7 40.6 1.0 H B:GLN19 3.7 50.3 1.0 OP2 F:DT17 3.8 71.9 1.0 HE21 B:GLN19 3.8 55.4 1.0 CB B:PHE18 3.9 42.7 1.0 H3' F:DG16 3.9 88.8 1.0 O3' F:DG16 3.9 70.2 1.0 CD B:GLN19 3.9 42.7 1.0 HG2 B:GLN19 3.9 52.5 1.0 HB B:THR16 4.0 50.0 1.0 NE2 B:GLN19 4.0 45.1 1.0 CD2 B:PHE18 4.0 44.2 1.0 HB2 B:PHE18 4.2 52.6 1.0 HD22 B:ASN56 4.3 69.3 1.0 N B:GLN19 4.3 40.8 1.0 HE B:ARG52 4.3 74.2 1.0 C3' F:DG16 4.4 72.9 1.0 HH21 B:ARG52 4.4 72.0 1.0 CG B:PHE18 4.4 43.3 1.0 HG22 B:THR16 4.5 49.2 1.0 HE22 B:GLN19 4.5 55.4 1.0 CB B:ASN56 4.6 52.2 1.0 HB3 B:ASN56 4.6 64.0 1.0 OE1 B:GLN19 4.6 41.8 1.0 H5'' F:DG16 4.6 88.7 1.0 H B:PHE18 4.6 57.4 1.0 CB B:GLN19 4.7 40.7 1.0 H B:THR16 4.7 48.7 1.0 HB2 B:GLN19 4.7 50.1 1.0 CA B:PHE18 4.9 45.3 1.0 H4' F:DG16 4.9 88.0 1.0 C B:PHE18 5.0 43.1 1.0 O5' F:DT17 5.0 74.3 1.0 CA B:THR16 5.0 39.8 1.0 CA B:GLN19 5.0 41.5 1.0

Manganese binding site 6 out of 8 in the The Complex Structure of Hsrosr-S4 (VNG0258/Rosr-S4)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of The Complex Structure of Hsrosr-S4 (VNG0258/Rosr-S4) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn206 b:0.5 occ:1.00 H C:HIS50 2.5 64.4 1.0 HE3 C:LYS37 2.5 91.1 1.0 HA C:ASN49 3.0 67.7 1.0 HB3 C:HIS50 3.2 60.1 1.0 ND1 C:HIS50 3.2 56.5 1.0 N C:HIS50 3.3 52.6 1.0 OE2 C:GLU47 3.4 91.4 1.0 CE C:LYS37 3.4 74.8 1.0 HE2 C:LYS37 3.5 91.1 1.0 CB C:HIS50 3.8 49.0 1.0 O H:HOH201 3.8 48.3 1.0 CA C:ASN49 3.9 55.3 1.0 CG C:HIS50 4.0 52.3 1.0 O C:VAL48 4.0 52.5 1.0 C C:ASN49 4.1 53.3 1.0 HZ2 C:LYS37 4.1 97.3 1.0 HD2 C:LYS37 4.1 80.2 1.0 CA C:HIS50 4.2 48.5 1.0 NZ C:LYS37 4.3 80.0 1.0 CE1 C:HIS50 4.3 59.5 1.0 CD C:LYS37 4.4 65.7 1.0 CD C:GLU47 4.4 90.2 1.0 HE1 C:HIS50 4.5 71.0 1.0 HZ3 C:LYS37 4.5 97.3 1.0 OD1 C:ASN49 4.6 68.2 1.0 HB3 C:ASN49 4.7 72.4 1.0 HA C:HIS50 4.7 59.6 1.0 HB2 C:HIS50 4.7 60.1 1.0 H C:GLY51 4.8 63.4 1.0 C C:VAL48 4.8 52.0 1.0 N C:ASN49 4.8 53.4 1.0 CB C:ASN49 4.8 59.2 1.0 HG2 C:GLU47 4.8 0.9 1.0 HD3 C:LYS37 4.9 80.2 1.0

Manganese binding site 7 out of 8 in the The Complex Structure of Hsrosr-S4 (VNG0258/Rosr-S4)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of The Complex Structure of Hsrosr-S4 (VNG0258/Rosr-S4) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn207 b:68.7 occ:1.00 H C:GLU83 2.7 43.1 1.0 HB C:THR81 2.8 37.9 1.0 HB3 C:ASN82 3.0 86.3 1.0 H C:ASN82 3.2 40.9 1.0 HB3 B:GLU93 3.2 36.8 1.0 HB2 C:GLU83 3.2 47.9 1.0 HB2 C:ASN82 3.3 86.3 1.0 N C:GLU83 3.4 38.4 1.0 CB C:ASN82 3.5 70.8 1.0 O B:HOH304 3.6 29.3 1.0 N C:ASN82 3.6 38.4 1.0 CB C:THR81 3.7 36.9 1.0 OE2 B:GLU93 3.7 41.7 1.0 O A:HOH305 3.7 42.1 1.0 HG1 C:THR81 3.8 38.0 1.0 HG2 B:GLU93 3.8 40.3 1.0 CD B:GLU93 3.9 38.8 1.0 CA C:ASN82 3.9 39.1 1.0 CB C:GLU83 4.0 40.3 1.0 OG1 C:THR81 4.0 35.4 1.0 HG23 A:ILE112 4.0 32.5 1.0 CB B:GLU93 4.0 29.6 1.0 HB3 C:GLU83 4.1 47.9 1.0 C C:ASN82 4.1 37.8 1.0 CG B:GLU93 4.1 32.5 1.0 CA C:GLU83 4.3 37.9 1.0 HG21 C:THR81 4.4 38.2 1.0 C C:THR81 4.4 35.0 1.0 OD1 A:ASP116 4.4 31.8 1.0 OE1 B:GLU93 4.5 41.1 1.0 CG2 C:THR81 4.6 37.2 1.0 CA C:THR81 4.6 35.0 1.0 HG12 A:ILE112 4.6 31.2 1.0 HB2 B:GLU93 4.6 36.8 1.0 O C:GLY64 4.6 29.8 1.0 HA C:GLU83 4.7 41.4 1.0 HA C:THR81 4.7 35.5 1.0 HG22 C:THR81 4.8 38.2 1.0 OE1 C:GLU83 4.8 54.0 1.0 O B:GLU93 4.8 30.0 1.0 HB3 B:SER97 4.9 42.2 1.0 HA B:GLU93 4.9 37.6 1.0 HA C:ASN82 4.9 40.5 1.0 CG2 A:ILE112 4.9 26.0 1.0 CG C:ASN82 4.9 72.3 1.0 HA A:ILE112 5.0 31.4 1.0 CA B:GLU93 5.0 30.2 1.0 HG21 A:ILE112 5.0 32.5 1.0

Manganese binding site 8 out of 8 in the The Complex Structure of Hsrosr-S4 (VNG0258/Rosr-S4)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of The Complex Structure of Hsrosr-S4 (VNG0258/Rosr-S4) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn206 b:77.7 occ:0.57 H D:HIS50 2.5 78.7 1.0 HZ3 D:LYS37 2.6 94.0 1.0 ND1 D:HIS50 2.9 72.1 1.0 HB3 D:HIS50 3.0 80.6 1.0 HA D:ASN49 3.2 79.9 1.0 N D:HIS50 3.3 64.5 1.0 NZ D:LYS37 3.4 77.3 1.0 HZ2 D:LYS37 3.7 94.0 1.0 CG D:HIS50 3.7 69.5 1.0 CB D:HIS50 3.7 66.1 1.0 HD2 D:LYS37 3.8 84.1 1.0 HZ1 D:LYS37 3.8 94.0 1.0 CE1 D:HIS50 3.9 76.1 1.0 O D:VAL48 4.1 72.0 1.0 CA D:ASN49 4.1 65.5 1.0 HE1 D:HIS50 4.1 92.6 1.0 OE1 D:GLU47 4.1 97.6 1.0 CA D:HIS50 4.1 63.9 1.0 C D:ASN49 4.1 64.0 1.0 CE D:LYS37 4.4 73.4 1.0 HE2 D:LYS37 4.5 89.4 1.0 CD D:LYS37 4.5 69.0 1.0 HB2 D:HIS50 4.6 80.6 1.0 HA D:HIS50 4.6 78.0 1.0 H D:GLY51 4.7 83.5 1.0 HG3 D:GLU47 4.8 0.1 1.0 HD3 D:LYS37 4.9 84.1 1.0 OD1 D:ASN49 4.9 71.2 1.0 HB3 D:ASN49 4.9 82.1 1.0 C D:VAL48 4.9 68.4 1.0 CD2 D:HIS50 4.9 72.4 1.0 N D:ASN49 5.0 65.2 1.0 NE2 D:HIS50 5.0 73.5 1.0

N.Kutnowski, F.Shmulevich, G.Davidov, A.Shahar, D.Bar-Zvi, J.Eichler, R.Zarivach, B.Shaanan. Specificity of Protein-Dna Interactions in Hypersaline Environment: Structural Studies on Complexes of Halobacterium Salinarum Oxidative Stress-Dependent Protein Hsrosr. Nucleic Acids Res. V. 47 8860 2019.
ISSN: ESSN 1362-4962
PubMed: 31310308
DOI: 10.1093/NAR/GKZ604