Cobalt in PDB 6kgh: Crystal Structure of Penicillin Binding Protein 3 (PBP3) From Mycobacterium Tuerculosis (Apo-Form)

The structure of Crystal Structure of Penicillin Binding Protein 3 (PBP3) From Mycobacterium Tuerculosis (Apo-Form), PDB code: 6kgh was solved by Z.K.Lu, A.L.Zhang, X.Liu, L.Guddat, H.T.Yang, Z.H.Rao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.04 / 2.11
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	97.710, 84.220, 90.500, 90.00, 111.60, 90.00
R / Rfree (%)	18.9 / 22.2

The structure of Crystal Structure of Penicillin Binding Protein 3 (PBP3) From Mycobacterium Tuerculosis (Apo-Form) also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Cobalt atom in the Crystal Structure of Penicillin Binding Protein 3 (PBP3) From Mycobacterium Tuerculosis (Apo-Form) (pdb code 6kgh). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Crystal Structure of Penicillin Binding Protein 3 (PBP3) From Mycobacterium Tuerculosis (Apo-Form), PDB code: 6kgh:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Crystal Structure of Penicillin Binding Protein 3 (PBP3) From Mycobacterium Tuerculosis (Apo-Form)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Penicillin Binding Protein 3 (PBP3) From Mycobacterium Tuerculosis (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co701 b:48.0 occ:0.85 O A:HOH938 2.1 50.9 1.0 NE2 A:HIS652 2.2 37.8 1.0 O A:HOH943 2.5 50.1 0.5 O A:HOH947 2.6 50.5 1.0 O A:HOH940 2.7 41.8 0.5 CD2 A:HIS652 3.1 36.6 1.0 CE1 A:HIS652 3.3 36.6 1.0 O A:HOH948 3.3 47.2 1.0 CG A:HIS652 4.3 35.6 1.0 ND1 A:HIS652 4.3 38.3 1.0 O A:HOH944 4.8 49.4 1.0

Cobalt binding site 2 out of 3 in the Crystal Structure of Penicillin Binding Protein 3 (PBP3) From Mycobacterium Tuerculosis (Apo-Form)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Penicillin Binding Protein 3 (PBP3) From Mycobacterium Tuerculosis (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co702 b:93.3 occ:1.00 NE2 A:HIS645 2.3 62.2 1.0 O A:HOH934 2.5 71.3 1.0 O A:HOH950 3.1 64.8 1.0 O A:HOH922 3.1 63.2 1.0 CE1 A:HIS645 3.1 53.6 1.0 CD2 A:HIS645 3.3 57.0 1.0 O A:HOH908 4.1 54.2 1.0 ND1 A:HIS645 4.3 50.4 1.0 CG A:HIS645 4.4 51.1 1.0 O A:HOH841 4.8 42.0 1.0

Cobalt binding site 3 out of 3 in the Crystal Structure of Penicillin Binding Protein 3 (PBP3) From Mycobacterium Tuerculosis (Apo-Form)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Penicillin Binding Protein 3 (PBP3) From Mycobacterium Tuerculosis (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co703 b:46.0 occ:1.00 O A:HOH842 1.6 35.6 1.0 NE2 A:HIS302 1.7 43.0 1.0 O A:HOH805 2.0 40.4 1.0 CE1 A:HIS302 2.5 43.0 1.0 CD2 A:HIS302 2.9 41.5 1.0 ND1 A:HIS302 3.7 41.0 1.0 CG A:HIS302 3.9 40.3 1.0

Z.Lu, H.Wang, A.Zhang, X.Liu, W.Zhou, C.Yang, L.Guddat, H.Yang, C.J.Schofield, Z.Rao. Structures Ofmycobacterium Tuberculosispenicillin-Binding Protein 3 in Complex with Fivebeta-Lactam Antibiotics Reveal Mechanism of Inactivation. Mol.Pharmacol. V. 97 287 2020.
ISSN: ESSN 1521-0111
PubMed: 32086254
DOI: 10.1124/MOL.119.118042