Nickel in PDB 6kh5: Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes

Enzymatic activity of Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes

All present enzymatic activity of Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes:
1.16.3.1;

Protein crystallography data

The structure of Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes, PDB code: 6kh5 was solved by C.Gu, H.Chen, Y.Wang, T.Zhang, H.Wang, G.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	39.51 / 2.29
*Space group*	P 4 3 2
*Cell size a, b, c (Å), α, β, γ (°)*	118.533, 118.533, 118.533, 90.00, 90.00, 90.00
*R / R_free (%)*	15.9 / 20.3

Other elements in 6kh5:

The structure of Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes also contains other interesting chemical elements:

Iron

(Fe)

1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes (pdb code 6kh5). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes, PDB code: 6kh5:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 6kh5

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Nickel Binding Sites List in 6kh5

Nickel binding site 1 out of 3 in the Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes

Mono view

Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ni202 b:79.0 occ:1.00	ND1	A:HIS160	2.6	70.9	0.9
	CE1	A:HIS160	3.3	51.1	0.9
	CG	A:HIS160	3.8	74.1	0.9
	CB	A:HIS160	4.3	65.1	0.9
	CG2	A:THR93	4.4	32.1	1.0
	CA	A:HIS160	4.5	56.3	0.9
	NE2	A:HIS160	4.5	66.7	0.9
	CD2	A:HIS160	4.8	69.9	0.9
	OG1	A:THR93	5.0	39.5	1.0

Nickel binding site 2 out of 3 in 6kh5

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Nickel Binding Sites List in 6kh5

Nickel binding site 2 out of 3 in the Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes

Mono view

Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ni203 b:0.3 occ:1.00	OE2	A:GLU139	2.6	91.2	1.0
	OG	A:SER143	2.6	39.2	0.6
	OG	A:SER143	3.2	29.4	0.5
	CB	A:SER143	3.4	24.2	0.5
	CB	A:SER143	3.4	24.2	0.6
	OE2	A:GLU106	3.5	68.5	1.0
	CD	A:GLU139	3.7	65.9	1.0
	O	A:HOH317	3.8	44.0	1.0
	OE1	A:GLU139	4.1	75.4	1.0
	CD	A:GLU106	4.5	55.1	1.0
	OE2	A:GLU60	4.5	60.0	1.0
	OE2	A:GLU59	4.6	80.1	1.0
	CA	A:SER143	4.7	24.6	0.6
	CA	A:SER143	4.7	24.4	0.5
	OE1	A:GLU106	4.9	65.0	1.0
	CG	A:GLU139	4.9	56.8	1.0

Nickel binding site 3 out of 3 in 6kh5

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Nickel Binding Sites List in 6kh5

Nickel binding site 3 out of 3 in the Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes

Mono view

Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ni204 b:0.4 occ:1.00	O	A:HIS161	2.3	78.5	1.0
	O	A:HOH349	2.6	60.1	1.0
	O	A:HOH350	2.8	55.4	1.0
	ND1	A:HIS161	3.0	73.7	1.0
	C	A:HIS161	3.2	48.8	1.0
	CB	A:HIS161	3.3	48.4	1.0
	CG	A:HIS161	3.5	75.0	1.0
	CA	A:HIS161	3.7	53.4	1.0
	CE1	A:HIS161	4.2	65.7	1.0
	N	A:HIS161	4.2	41.4	1.0
	N	A:GLY162	4.2	35.0	1.0
	CA	A:GLY162	4.6	27.0	1.0
	C	A:HIS160	4.7	49.9	0.9
	O	A:HIS160	4.8	74.6	0.9
	CD2	A:HIS161	4.8	73.6	1.0

Reference:

C.Gu, H.Chen, Y.Wang, T.Zhang, H.Wang, G.Zhao. Structural Insight Into Binary Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes. Chemistry 2019.
ISSN: ISSN 0947-6539
PubMed: 31820500
DOI: 10.1002/CHEM.201905315

Page generated: Thu Oct 10 08:37:08 2024

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