Iron in PDB 5v1s: Crystal Structure of Streptococcus Suis Suib Bound to S- Adenosylmethionine

The structure of Crystal Structure of Streptococcus Suis Suib Bound to S- Adenosylmethionine, PDB code: 5v1s was solved by K.M.Davis, J.P.Bacik, N.Ando, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.47 / 2.49
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	114.787, 85.473, 109.864, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 27

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Streptococcus Suis Suib Bound to S- Adenosylmethionine (pdb code 5v1s). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Crystal Structure of Streptococcus Suis Suib Bound to S- Adenosylmethionine, PDB code: 5v1s:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in the Crystal Structure of Streptococcus Suis Suib Bound to S- Adenosylmethionine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Streptococcus Suis Suib Bound to S- Adenosylmethionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:54.1 occ:1.00 FE1 A:SF4601 0.0 54.1 1.0 S4 A:SF4601 2.2 51.6 1.0 SG A:CYS121 2.3 58.5 1.0 S3 A:SF4601 2.3 55.4 1.0 S2 A:SF4601 2.3 54.3 1.0 FE4 A:SF4601 2.6 57.6 1.0 FE2 A:SF4601 2.8 54.8 1.0 FE3 A:SF4601 2.8 57.6 1.0 CB A:CYS121 3.3 58.0 1.0 S1 A:SF4601 3.8 55.7 1.0 N A:CYS121 4.0 51.3 1.0 CB A:CYS124 4.3 54.2 1.0 CA A:CYS121 4.3 56.6 1.0 OXT A:SAM604 4.3 53.6 1.0 CB A:LEU119 4.4 54.3 1.0 SG A:CYS124 4.5 58.4 1.0 SG A:CYS117 4.7 59.7 1.0 CD1 A:LEU119 4.7 53.6 1.0 CZ A:PHE123 4.8 57.7 1.0 CE A:MET223 4.8 48.5 1.0 CE1 A:PHE123 5.0 57.3 1.0

Iron binding site 2 out of 24 in the Crystal Structure of Streptococcus Suis Suib Bound to S- Adenosylmethionine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Streptococcus Suis Suib Bound to S- Adenosylmethionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:54.8 occ:1.00 FE2 A:SF4601 0.0 54.8 1.0 S3 A:SF4601 2.2 55.4 1.0 SG A:CYS117 2.2 59.7 1.0 S1 A:SF4601 2.3 55.7 1.0 S4 A:SF4601 2.3 51.6 1.0 FE3 A:SF4601 2.7 57.6 1.0 FE1 A:SF4601 2.8 54.1 1.0 FE4 A:SF4601 2.8 57.6 1.0 CB A:CYS117 3.2 55.3 1.0 N A:SAM604 3.9 62.0 1.0 S2 A:SF4601 3.9 54.3 1.0 CB A:LEU119 4.3 54.3 1.0 O A:LEU119 4.3 62.4 1.0 C A:LEU119 4.5 58.4 1.0 N A:LEU119 4.6 60.4 1.0 CA A:CYS117 4.6 60.6 1.0 CA A:LEU119 4.7 56.7 1.0 OXT A:SAM604 4.7 53.6 1.0 ND2 A:ASN187 4.8 50.9 1.0 SG A:CYS121 4.8 58.5 1.0 SG A:CYS124 4.9 58.4 1.0 N A:GLU161 5.0 62.8 1.0

Iron binding site 3 out of 24 in the Crystal Structure of Streptococcus Suis Suib Bound to S- Adenosylmethionine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Streptococcus Suis Suib Bound to S- Adenosylmethionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:57.6 occ:1.00 FE3 A:SF4601 0.0 57.6 1.0 OXT A:SAM604 2.2 53.6 1.0 S4 A:SF4601 2.3 51.6 1.0 S2 A:SF4601 2.4 54.3 1.0 S1 A:SF4601 2.4 55.7 1.0 N A:SAM604 2.5 62.0 1.0 FE2 A:SF4601 2.7 54.8 1.0 FE1 A:SF4601 2.8 54.1 1.0 FE4 A:SF4601 2.8 57.6 1.0 C A:SAM604 3.1 61.2 1.0 CA A:SAM604 3.2 60.4 1.0 CG A:SAM604 3.3 61.8 1.0 CB A:SAM604 3.8 65.1 1.0 S3 A:SF4601 3.9 55.4 1.0 O A:SAM604 4.2 63.0 1.0 SD A:SAM604 4.4 81.3 1.0 SG A:CYS117 4.4 59.7 1.0 O A:GLY160 4.8 59.8 1.0 SG A:CYS124 4.9 58.4 1.0 C3' A:SAM604 4.9 64.7 1.0 SG A:CYS121 5.0 58.5 1.0

Iron binding site 4 out of 24 in the Crystal Structure of Streptococcus Suis Suib Bound to S- Adenosylmethionine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Streptococcus Suis Suib Bound to S- Adenosylmethionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:57.6 occ:1.00 FE4 A:SF4601 0.0 57.6 1.0 S2 A:SF4601 2.2 54.3 1.0 S1 A:SF4601 2.2 55.7 1.0 SG A:CYS124 2.2 58.4 1.0 S3 A:SF4601 2.3 55.4 1.0 FE1 A:SF4601 2.6 54.1 1.0 FE2 A:SF4601 2.8 54.8 1.0 FE3 A:SF4601 2.8 57.6 1.0 CB A:CYS124 2.9 54.2 1.0 S4 A:SF4601 3.9 51.6 1.0 CA A:CYS124 4.4 61.6 1.0 CG A:SAM604 4.6 61.8 1.0 SG A:CYS121 4.6 58.5 1.0 CB A:CYS121 4.8 58.0 1.0 N A:SAM604 4.8 62.0 1.0 CB A:ALA127 4.8 74.3 1.0 O A:LEU126 4.9 81.1 1.0 C A:LEU126 4.9 78.1 1.0 OXT A:SAM604 4.9 53.6 1.0 SG A:CYS117 4.9 59.7 1.0

Iron binding site 5 out of 24 in the Crystal Structure of Streptococcus Suis Suib Bound to S- Adenosylmethionine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Streptococcus Suis Suib Bound to S- Adenosylmethionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:54.0 occ:1.00 FE1 A:SF4602 0.0 54.0 1.0 S4 A:SF4602 2.2 56.1 1.0 SG A:CYS321 2.3 52.6 1.0 S3 A:SF4602 2.3 55.5 1.0 S2 A:SF4602 2.3 59.7 1.0 FE2 A:SF4602 2.6 54.4 1.0 FE4 A:SF4602 2.7 54.8 1.0 FE3 A:SF4602 2.8 56.7 1.0 CB A:CYS321 3.4 51.0 1.0 S1 A:SF4602 3.9 52.3 1.0 SG A:CYS365 4.6 58.1 1.0 CA A:CYS321 4.8 57.6 1.0 SG A:CYS419 4.8 59.5 1.0 SG A:CYS347 4.9 52.7 1.0

Iron binding site 6 out of 24 in the Crystal Structure of Streptococcus Suis Suib Bound to S- Adenosylmethionine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Streptococcus Suis Suib Bound to S- Adenosylmethionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:54.4 occ:1.00 FE2 A:SF4602 0.0 54.4 1.0 S3 A:SF4602 2.2 55.5 1.0 S1 A:SF4602 2.3 52.3 1.0 SG A:CYS365 2.3 58.1 1.0 S4 A:SF4602 2.4 56.1 1.0 FE1 A:SF4602 2.6 54.0 1.0 FE3 A:SF4602 2.7 56.7 1.0 FE4 A:SF4602 2.7 54.8 1.0 CB A:CYS365 3.1 56.6 1.0 S2 A:SF4602 3.8 59.7 1.0 NZ A:LYS353 4.2 49.7 1.0 CB A:ALA349 4.2 57.4 1.0 CB A:ALA367 4.3 52.2 1.0 CA A:CYS365 4.6 55.5 1.0 SG A:CYS321 4.7 52.6 1.0 SG A:CYS347 4.8 52.7 1.0 SG A:CYS419 4.9 59.5 1.0 CE A:LYS353 4.9 60.0 1.0

Iron binding site 7 out of 24 in the Crystal Structure of Streptococcus Suis Suib Bound to S- Adenosylmethionine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Streptococcus Suis Suib Bound to S- Adenosylmethionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:56.7 occ:1.00 FE3 A:SF4602 0.0 56.7 1.0 S1 A:SF4602 2.3 52.3 1.0 SG A:CYS347 2.3 52.7 1.0 S2 A:SF4602 2.3 59.7 1.0 S4 A:SF4602 2.3 56.1 1.0 FE2 A:SF4602 2.7 54.4 1.0 FE4 A:SF4602 2.8 54.8 1.0 FE1 A:SF4602 2.8 54.0 1.0 CB A:CYS347 3.4 49.3 1.0 CB A:ALA349 3.7 57.4 1.0 CA A:CYS347 3.9 54.2 1.0 S3 A:SF4602 4.0 55.5 1.0 N A:ALA349 4.2 53.4 1.0 C A:CYS347 4.4 51.0 1.0 N A:ARG348 4.5 56.3 1.0 CD1 A:ILE396 4.5 55.5 1.0 CA A:ALA349 4.6 52.0 1.0 SG A:CYS321 4.7 52.6 1.0 SG A:CYS365 4.9 58.1 1.0 SG A:CYS419 5.0 59.5 1.0 CB A:CYS365 5.0 56.6 1.0

Iron binding site 8 out of 24 in the Crystal Structure of Streptococcus Suis Suib Bound to S- Adenosylmethionine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Streptococcus Suis Suib Bound to S- Adenosylmethionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:54.8 occ:1.00 FE4 A:SF4602 0.0 54.8 1.0 S2 A:SF4602 2.2 59.7 1.0 S1 A:SF4602 2.3 52.3 1.0 S3 A:SF4602 2.4 55.5 1.0 SG A:CYS419 2.4 59.5 1.0 FE2 A:SF4602 2.7 54.4 1.0 FE1 A:SF4602 2.7 54.0 1.0 FE3 A:SF4602 2.8 56.7 1.0 CB A:CYS419 3.2 57.9 1.0 CA A:CYS419 3.9 54.9 1.0 S4 A:SF4602 3.9 56.1 1.0 C A:CYS419 4.4 53.2 1.0 N A:TYR420 4.5 56.1 1.0 CG2 A:VAL421 4.6 59.5 1.0 SG A:CYS347 4.7 52.7 1.0 SG A:CYS365 4.8 58.1 1.0 N A:VAL421 4.8 59.6 1.0 CB A:ALA367 4.8 52.2 1.0 SG A:CYS321 4.9 52.6 1.0 CB A:VAL421 4.9 61.1 1.0

Iron binding site 9 out of 24 in the Crystal Structure of Streptococcus Suis Suib Bound to S- Adenosylmethionine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Streptococcus Suis Suib Bound to S- Adenosylmethionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:64.0 occ:1.00 FE1 A:SF4603 0.0 64.0 1.0 S2 A:SF4603 2.2 76.1 1.0 S4 A:SF4603 2.3 62.3 1.0 SG A:CYS437 2.4 78.4 1.0 S3 A:SF4603 2.4 56.2 1.0 FE2 A:SF4603 2.7 62.0 1.0 FE4 A:SF4603 2.7 65.3 1.0 FE3 A:SF4603 2.8 71.6 1.0 CB A:CYS437 3.3 72.9 1.0 S1 A:SF4603 3.8 64.5 1.0 CD A:ARG433 4.5 71.7 1.0 CG2 A:THR325 4.5 64.1 1.0 SG A:CYS415 4.6 65.5 1.0 NH1 A:ARG433 4.7 83.8 1.0 SG A:CYS409 4.7 75.3 1.0 CA A:CYS437 4.8 75.9 1.0 SG A:CYS406 4.9 71.3 1.0 CD2 A:LEU439 4.9 80.0 1.0

Iron binding site 10 out of 24 in the Crystal Structure of Streptococcus Suis Suib Bound to S- Adenosylmethionine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Streptococcus Suis Suib Bound to S- Adenosylmethionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:62.0 occ:1.00 FE2 A:SF4603 0.0 62.0 1.0 SG A:CYS415 2.2 65.5 1.0 S3 A:SF4603 2.3 56.2 1.0 S4 A:SF4603 2.3 62.3 1.0 S1 A:SF4603 2.3 64.5 1.0 FE1 A:SF4603 2.7 64.0 1.0 FE3 A:SF4603 2.8 71.6 1.0 FE4 A:SF4603 2.8 65.3 1.0 CB A:CYS415 3.0 61.3 1.0 S2 A:SF4603 3.9 76.1 1.0 N A:GLY417 4.0 61.8 1.0 CA A:GLY417 4.3 69.2 1.0 N A:GLY418 4.3 60.4 1.0 CA A:CYS415 4.3 57.8 1.0 C A:CYS415 4.5 58.4 1.0 SG A:CYS406 4.6 71.3 1.0 C A:GLY417 4.6 66.2 1.0 N A:GLU416 4.6 58.0 1.0 CE1 A:PHE324 4.8 57.5 1.0 SG A:CYS437 4.8 78.4 1.0

K.M.Davis, K.R.Schramma, W.A.Hansen, J.P.Bacik, S.D.Khare, M.R.Seyedsayamdost, N.Ando. Structures of the Peptide-Modifying Radical Sam Enzyme Suib Elucidate the Basis of Substrate Recognition. Proc. Natl. Acad. Sci. V. 114 10420 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28893989
DOI: 10.1073/PNAS.1703663114