Chlorine in PDB 6ex7: Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement

Enzymatic activity of Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement

All present enzymatic activity of Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement, PDB code: 6ex7 was solved by Y.Kim, J.E.Raczynska, I.G.Shabalin, M.Jaskolski, W.Minor, A.Wlodawer, C.Tesar, R.Jedrzejczak, J.Babnigg, J.Mire, J.Sacchettini, A.Joachimiak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	74.20 / 1.95
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	145.062, 39.220, 75.233, 90.00, 99.99, 90.00
*R / R_free (%)*	19.5 / 22.6

Other elements in 6ex7:

The structure of Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement also contains other interesting chemical elements:

Cadmium

(Cd)

6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement (pdb code 6ex7). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement, PDB code: 6ex7:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6ex7

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Chlorine Binding Sites List in 6ex7

Chlorine binding site 1 out of 3 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl304 b:44.0 occ:1.00	N	A:LYS242	2.9	42.4	1.0
	C	A:PHE240	3.1	32.2	1.0
	CA	A:PHE240	3.3	29.7	1.0
	N	A:ALA243	3.3	40.6	1.0
	N	A:PRO241	3.4	33.3	1.0
	O	A:PHE240	3.5	34.5	1.0
	CB	A:LYS242	3.5	51.8	1.0
	CA	A:LYS242	3.5	49.9	1.0
	CD	A:PRO241	3.6	35.2	1.0
	CB	A:PHE240	3.7	30.3	1.0
	C	A:LYS242	3.9	48.4	1.0
	C	A:PRO241	3.9	40.6	1.0
	O	A:HOH421	4.1	37.8	1.0
	CA	A:PRO241	4.2	37.7	1.0
	CG	A:PRO241	4.3	36.1	1.0
	CG	A:LYS242	4.3	50.4	1.0
	CA	A:ALA243	4.3	39.2	1.0
	CB	A:ALA243	4.3	35.4	1.0
	N	A:PHE240	4.6	27.2	1.0
	CD1	A:PHE240	4.7	27.9	1.0
	CG	A:PHE240	4.8	28.4	1.0
	O	A:ALA239	4.8	26.2	1.0
	CB	A:PRO241	4.9	38.3	1.0

Chlorine binding site 2 out of 3 in 6ex7

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Chlorine Binding Sites List in 6ex7

Chlorine binding site 2 out of 3 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Cl303 b:39.3 occ:1.00	N	B:LYS242	3.1	28.2	1.0
	O	B:HOH472	3.2	39.9	1.0
	C	B:PHE240	3.2	20.4	1.0
	CA	B:PHE240	3.3	19.4	1.0
	N	B:PRO241	3.5	23.2	1.0
	N	B:ALA243	3.5	26.4	1.0
	CB	B:LYS242	3.6	34.8	1.0
	O	B:PHE240	3.6	21.2	1.0
	CD	B:PRO241	3.7	24.8	1.0
	CA	B:LYS242	3.7	31.8	1.0
	CB	B:PHE240	3.8	18.4	1.0
	C	B:LYS242	4.0	35.4	1.0
	C	B:PRO241	4.1	28.6	1.0
	CA	B:PRO241	4.3	25.5	1.0
	CG	B:PRO241	4.4	27.2	1.0
	O	B:HOH434	4.4	32.8	1.0
	CG	B:LYS242	4.4	37.2	1.0
	CB	B:ALA243	4.4	22.1	1.0
	CA	B:ALA243	4.4	24.6	1.0
	O	B:HOH460	4.5	39.9	1.0
	CD1	B:PHE240	4.6	17.5	1.0
	N	B:PHE240	4.6	18.7	1.0
	CG	B:PHE240	4.7	17.0	1.0
	O	B:ALA239	4.8	17.1	1.0

Chlorine binding site 3 out of 3 in 6ex7

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Chlorine Binding Sites List in 6ex7

Chlorine binding site 3 out of 3 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Cl304 b:50.5 occ:1.00	N	B:LYS216	3.5	31.6	1.0
	CE	B:LYS216	3.8	55.8	1.0
	N	B:SER217	4.2	29.5	1.0
	OG	B:SER217	4.2	32.4	1.0
	CB	B:LYS216	4.2	38.0	1.0
	CA	B:ALA215	4.3	34.7	1.0
	CB	B:ALA215	4.3	33.1	1.0
	CA	B:LYS216	4.3	34.1	1.0
	C	B:ALA215	4.4	34.9	1.0
	NZ	B:LYS216	4.5	63.5	1.0
	C	B:LYS216	4.6	32.2	1.0
	O	B:SER217	4.8	26.4	1.0
	CG	B:LYS216	4.9	42.0	1.0
	CD	B:LYS216	4.9	49.4	0.6

Reference:

J.E.Raczynska, I.G.Shabalin, W.Minor, A.Wlodawer, M.Jaskolski. A Close Look Onto Structural Models and Primary Ligands of Metallo-Beta-Lactamases. Drug Resist. Updat. V. 40 1 2018.
ISSN: ESSN 1532-2084
PubMed: 30466711
DOI: 10.1016/J.DRUP.2018.08.001

Page generated: Sat Jul 27 22:42:10 2024

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