Cobalt in PDB 5laa: X-Ray Structure of the Methyltransferase Subunit A From Methanothermus Fervidus in Complex with Cobalamin

All present enzymatic activity of X-Ray Structure of the Methyltransferase Subunit A From Methanothermus Fervidus in Complex with Cobalamin:
2.1.1.86;

The structure of X-Ray Structure of the Methyltransferase Subunit A From Methanothermus Fervidus in Complex with Cobalamin, PDB code: 5laa was solved by T.Wagner, U.Ermler, S.Shima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	131.35 / 3.00
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	100.604, 100.604, 262.706, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 25.4

The binding sites of Cobalt atom in the X-Ray Structure of the Methyltransferase Subunit A From Methanothermus Fervidus in Complex with Cobalamin (pdb code 5laa). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the X-Ray Structure of the Methyltransferase Subunit A From Methanothermus Fervidus in Complex with Cobalamin, PDB code: 5laa:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the X-Ray Structure of the Methyltransferase Subunit A From Methanothermus Fervidus in Complex with Cobalamin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of X-Ray Structure of the Methyltransferase Subunit A From Methanothermus Fervidus in Complex with Cobalamin within 5.0Å range: probe atom residue distance (Å) B Occ A:Co201 b:65.0 occ:1.00 CO A:B12201 0.0 65.0 1.0 N24 A:B12201 1.8 64.8 1.0 N23 A:B12201 1.8 67.8 1.0 N22 A:B12201 1.8 64.0 1.0 N21 A:B12201 1.9 60.4 1.0 C19 A:B12201 2.7 63.3 1.0 NE2 A:HIS84 2.8 90.8 1.0 C1 A:B12201 2.8 61.6 1.0 C6 A:B12201 2.9 61.4 1.0 C11 A:B12201 2.9 69.8 1.0 C4 A:B12201 2.9 59.4 1.0 C14 A:B12201 2.9 72.3 1.0 C9 A:B12201 2.9 67.8 1.0 NE2 B:HIS35 2.9 0.8 1.0 C16 A:B12201 3.0 66.1 1.0 C5 A:B12201 3.3 57.7 1.0 CD2 B:HIS35 3.3 99.7 1.0 C20 A:B12201 3.3 62.9 1.0 C10 A:B12201 3.3 68.3 1.0 C15 A:B12201 3.4 70.7 1.0 CE1 A:HIS84 3.7 90.2 1.0 CD2 A:HIS84 3.7 88.8 1.0 C2 A:B12201 4.0 61.9 1.0 C18 A:B12201 4.0 63.9 1.0 C3 A:B12201 4.1 61.5 1.0 CE1 B:HIS35 4.1 0.4 1.0 C17 A:B12201 4.2 63.0 1.0 C7 A:B12201 4.2 65.4 1.0 C8 A:B12201 4.2 69.7 1.0 C12 A:B12201 4.2 75.6 1.0 C13 A:B12201 4.2 79.1 1.0 C26 A:B12201 4.4 65.5 1.0 CG B:HIS35 4.6 97.7 1.0 C35 A:B12201 4.8 56.6 1.0 C46 A:B12201 4.8 79.7 1.0 ND1 A:HIS84 4.8 88.1 1.0 C53 A:B12201 4.8 72.2 1.0 CG A:HIS84 4.9 86.2 1.0 ND1 B:HIS35 5.0 0.9 1.0 C37 A:B12201 5.0 65.9 1.0 C55 A:B12201 5.0 60.9 1.0

Cobalt binding site 2 out of 3 in the X-Ray Structure of the Methyltransferase Subunit A From Methanothermus Fervidus in Complex with Cobalamin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of X-Ray Structure of the Methyltransferase Subunit A From Methanothermus Fervidus in Complex with Cobalamin within 5.0Å range: probe atom residue distance (Å) B Occ B:Co201 b:80.7 occ:1.00 CO B:B12201 0.0 80.7 1.0 N23 B:B12201 1.8 86.8 1.0 N24 B:B12201 1.8 85.3 1.0 N22 B:B12201 1.8 80.0 1.0 N21 B:B12201 1.9 81.6 1.0 C19 B:B12201 2.8 80.7 1.0 NE2 B:HIS84 2.9 73.9 1.0 C9 B:B12201 2.9 81.9 1.0 C11 B:B12201 2.9 88.6 1.0 C1 B:B12201 2.9 77.5 1.0 C14 B:B12201 2.9 91.1 1.0 C16 B:B12201 2.9 86.0 1.0 C6 B:B12201 2.9 82.1 1.0 C4 B:B12201 3.0 79.7 1.0 NE2 C:HIS35 3.0 94.5 1.0 CD2 C:HIS35 3.1 92.9 1.0 C10 B:B12201 3.3 85.9 1.0 C15 B:B12201 3.3 89.0 1.0 C20 B:B12201 3.4 74.1 1.0 C5 B:B12201 3.4 83.4 1.0 CE1 B:HIS84 3.8 74.1 1.0 CD2 B:HIS84 3.8 73.2 1.0 C18 B:B12201 4.1 80.5 1.0 C2 B:B12201 4.1 75.8 1.0 C12 B:B12201 4.1 90.8 1.0 C13 B:B12201 4.2 95.2 1.0 C17 B:B12201 4.2 79.9 1.0 C7 B:B12201 4.2 81.0 1.0 C8 B:B12201 4.2 82.0 1.0 C3 B:B12201 4.2 75.8 1.0 CE1 C:HIS35 4.3 93.4 1.0 CG C:HIS35 4.4 90.0 1.0 C26 B:B12201 4.5 75.4 1.0 C46 B:B12201 4.6 90.5 1.0 C53 B:B12201 4.7 85.8 1.0 C37 B:B12201 4.8 83.0 1.0 C35 B:B12201 4.9 84.4 1.0 ND1 B:HIS84 4.9 73.0 1.0 ND1 C:HIS35 5.0 90.4 1.0 CG B:HIS84 5.0 72.1 1.0

Cobalt binding site 3 out of 3 in the X-Ray Structure of the Methyltransferase Subunit A From Methanothermus Fervidus in Complex with Cobalamin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of X-Ray Structure of the Methyltransferase Subunit A From Methanothermus Fervidus in Complex with Cobalamin within 5.0Å range: probe atom residue distance (Å) B Occ C:Co201 b:70.8 occ:1.00 CO C:B12201 0.0 70.8 1.0 N23 C:B12201 1.8 70.9 1.0 N22 C:B12201 1.8 68.8 1.0 N24 C:B12201 1.8 68.1 1.0 N21 C:B12201 1.9 68.9 1.0 C19 C:B12201 2.7 69.6 1.0 C1 C:B12201 2.8 68.4 1.0 C9 C:B12201 2.8 70.3 1.0 C11 C:B12201 2.9 70.0 1.0 C14 C:B12201 2.9 71.9 1.0 NE2 C:HIS84 2.9 85.6 1.0 C6 C:B12201 2.9 71.3 1.0 C16 C:B12201 3.0 66.0 1.0 C4 C:B12201 3.0 68.8 1.0 NE2 A:HIS35 3.0 0.9 1.0 C10 C:B12201 3.3 68.7 1.0 CD2 A:HIS35 3.3 0.2 1.0 C20 C:B12201 3.3 69.5 1.0 C5 C:B12201 3.3 68.9 1.0 C15 C:B12201 3.4 65.5 1.0 CD2 C:HIS84 3.8 83.4 1.0 CE1 C:HIS84 3.9 85.6 1.0 C2 C:B12201 4.0 66.6 1.0 C18 C:B12201 4.0 71.5 1.0 CE1 A:HIS35 4.1 0.8 1.0 C12 C:B12201 4.1 72.1 1.0 C3 C:B12201 4.2 69.0 1.0 C13 C:B12201 4.2 77.8 1.0 C8 C:B12201 4.2 74.3 1.0 C17 C:B12201 4.2 69.4 1.0 C7 C:B12201 4.2 74.6 1.0 C26 C:B12201 4.4 66.3 1.0 CG A:HIS35 4.5 0.8 1.0 C46 C:B12201 4.6 73.7 1.0 C35 C:B12201 4.8 67.8 1.0 ND1 A:HIS35 4.8 0.5 1.0 C53 C:B12201 4.9 64.7 1.0 C48 C:B12201 5.0 91.0 1.0 CG C:HIS84 5.0 80.7 1.0 ND1 C:HIS84 5.0 82.9 1.0

T.Wagner, U.Ermler, S.Shima. Mtra of the Sodium Ion Pumping Methyltransferase Binds Cobalamin in A Unique Mode. Sci Rep V. 6 28226 2016.
ISSN: ESSN 2045-2322
PubMed: 27324530
DOI: 10.1038/SREP28226