Iron in PDB 9ccb: X-Ray Crystal Structure of Methyl-Coenzyme M Reductase Glutamine Methylase (Mgma) From Methanothermobacter Marburgensis with Hydroxycobalamin

The structure of X-Ray Crystal Structure of Methyl-Coenzyme M Reductase Glutamine Methylase (Mgma) From Methanothermobacter Marburgensis with Hydroxycobalamin, PDB code: 9ccb was solved by C.T.Lloyd, S.J.Booker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.93 / 2.08
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.7, 72.143, 114.868, 90, 90, 90
R / Rfree (%)	19.8 / 25

The structure of X-Ray Crystal Structure of Methyl-Coenzyme M Reductase Glutamine Methylase (Mgma) From Methanothermobacter Marburgensis with Hydroxycobalamin also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Cobalt	(Co)	1 atom

The binding sites of Iron atom in the X-Ray Crystal Structure of Methyl-Coenzyme M Reductase Glutamine Methylase (Mgma) From Methanothermobacter Marburgensis with Hydroxycobalamin (pdb code 9ccb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the X-Ray Crystal Structure of Methyl-Coenzyme M Reductase Glutamine Methylase (Mgma) From Methanothermobacter Marburgensis with Hydroxycobalamin, PDB code: 9ccb:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the X-Ray Crystal Structure of Methyl-Coenzyme M Reductase Glutamine Methylase (Mgma) From Methanothermobacter Marburgensis with Hydroxycobalamin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Crystal Structure of Methyl-Coenzyme M Reductase Glutamine Methylase (Mgma) From Methanothermobacter Marburgensis with Hydroxycobalamin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:25.6 occ:1.00 FE1 A:SF4501 0.0 25.6 1.0 SG A:CYS169 2.3 26.8 1.0 S2 A:SF4501 2.3 24.6 1.0 S4 A:SF4501 2.3 27.7 1.0 S3 A:SF4501 2.3 26.5 1.0 FE3 A:SF4501 2.7 24.3 1.0 FE4 A:SF4501 2.7 25.0 1.0 FE2 A:SF4501 2.7 30.9 1.0 CB A:CYS169 3.3 23.6 1.0 S1 A:SF4501 3.9 26.6 1.0 N A:CYS169 4.3 26.8 1.0 NH1 A:ARG250 4.4 24.3 1.0 CB A:CYS172 4.4 20.4 1.0 CA A:CYS169 4.5 25.3 1.0 NZ A:LYS287 4.5 25.0 1.0 SG A:CYS172 4.7 21.9 1.0 SG A:CYS165 4.8 23.4 1.0 CA A:GLY167 4.9 28.3 1.0 O A:HOH691 5.0 26.3 1.0

Iron binding site 2 out of 4 in the X-Ray Crystal Structure of Methyl-Coenzyme M Reductase Glutamine Methylase (Mgma) From Methanothermobacter Marburgensis with Hydroxycobalamin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Crystal Structure of Methyl-Coenzyme M Reductase Glutamine Methylase (Mgma) From Methanothermobacter Marburgensis with Hydroxycobalamin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:30.9 occ:1.00 FE2 A:SF4501 0.0 30.9 1.0 S1 A:SF4501 2.3 26.6 1.0 S3 A:SF4501 2.3 26.5 1.0 S4 A:SF4501 2.3 27.7 1.0 FE4 A:SF4501 2.7 25.0 1.0 FE3 A:SF4501 2.7 24.3 1.0 FE1 A:SF4501 2.7 25.6 1.0 OD2 A:ASP248 2.8 52.4 1.0 CG A:ASP248 3.8 54.3 1.0 S2 A:SF4501 3.9 24.6 1.0 OD1 A:ASP248 4.2 50.8 1.0 N A:THR211 4.6 36.1 1.0 SG A:CYS165 4.7 23.4 1.0 CB A:THR211 4.7 35.0 1.0 SG A:CYS172 4.8 21.9 1.0 O A:HOH743 4.8 27.5 1.0 CA A:THR211 4.8 41.1 1.0 SG A:CYS169 4.9 26.8 1.0

Iron binding site 3 out of 4 in the X-Ray Crystal Structure of Methyl-Coenzyme M Reductase Glutamine Methylase (Mgma) From Methanothermobacter Marburgensis with Hydroxycobalamin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of X-Ray Crystal Structure of Methyl-Coenzyme M Reductase Glutamine Methylase (Mgma) From Methanothermobacter Marburgensis with Hydroxycobalamin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:24.3 occ:1.00 FE3 A:SF4501 0.0 24.3 1.0 SG A:CYS172 2.3 21.9 1.0 S4 A:SF4501 2.3 27.7 1.0 S2 A:SF4501 2.3 24.6 1.0 S1 A:SF4501 2.3 26.6 1.0 FE1 A:SF4501 2.7 25.6 1.0 FE4 A:SF4501 2.7 25.0 1.0 FE2 A:SF4501 2.7 30.9 1.0 CB A:CYS172 3.0 20.4 1.0 S3 A:SF4501 3.9 26.5 1.0 CB A:VAL174 4.3 19.7 1.0 CD A:PRO175 4.4 21.0 1.0 CA A:CYS172 4.5 19.9 1.0 CG2 A:VAL174 4.6 19.0 1.0 SG A:CYS169 4.6 26.8 1.0 CB A:CYS169 4.7 23.6 1.0 SG A:CYS165 4.8 23.4 1.0 CG A:PRO175 4.9 22.3 1.0

Iron binding site 4 out of 4 in the X-Ray Crystal Structure of Methyl-Coenzyme M Reductase Glutamine Methylase (Mgma) From Methanothermobacter Marburgensis with Hydroxycobalamin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of X-Ray Crystal Structure of Methyl-Coenzyme M Reductase Glutamine Methylase (Mgma) From Methanothermobacter Marburgensis with Hydroxycobalamin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:25.0 occ:1.00 FE4 A:SF4501 0.0 25.0 1.0 SG A:CYS165 2.3 23.4 1.0 S3 A:SF4501 2.3 26.5 1.0 S1 A:SF4501 2.3 26.6 1.0 S2 A:SF4501 2.3 24.6 1.0 FE2 A:SF4501 2.7 30.9 1.0 FE3 A:SF4501 2.7 24.3 1.0 FE1 A:SF4501 2.7 25.6 1.0 CB A:CYS165 3.4 21.7 1.0 S4 A:SF4501 3.9 27.7 1.0 CA A:GLY167 4.4 28.3 1.0 N A:GLY167 4.5 24.8 1.0 N A:THR211 4.7 36.1 1.0 CA A:CYS165 4.8 18.2 1.0 CG A:PRO175 4.8 22.3 1.0 SG A:CYS169 4.8 26.8 1.0 SG A:CYS172 4.9 21.9 1.0 CG2 A:THR211 4.9 36.3 1.0 CB A:THR211 5.0 35.0 1.0 CD A:PRO175 5.0 21.0 1.0

C.T.Lloyd, S.J.Booker. Genetic and Biochemical Characterization of A Radical Sam Enzyme Required For Post-Translational Glutamine Methylation of Methyl-Coenzyme M Reductase To Be Published.