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Nickel in PDB 7jgk: Crystal Structure of the Ni-Bound Human Heavy-Chain Variant 122H-Delta C-Star with 2,5-Furandihyrdoxamate Collected at 100K

Enzymatic activity of Crystal Structure of the Ni-Bound Human Heavy-Chain Variant 122H-Delta C-Star with 2,5-Furandihyrdoxamate Collected at 100K

All present enzymatic activity of Crystal Structure of the Ni-Bound Human Heavy-Chain Variant 122H-Delta C-Star with 2,5-Furandihyrdoxamate Collected at 100K:
1.16.3.1;

Protein crystallography data

The structure of Crystal Structure of the Ni-Bound Human Heavy-Chain Variant 122H-Delta C-Star with 2,5-Furandihyrdoxamate Collected at 100K, PDB code: 7jgk was solved by J.B.Bailey, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.77 / 2.68
Space group I 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 155.990, 155.990, 155.990, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 24.4

Other elements in 7jgk:

The structure of Crystal Structure of the Ni-Bound Human Heavy-Chain Variant 122H-Delta C-Star with 2,5-Furandihyrdoxamate Collected at 100K also contains other interesting chemical elements:

Sodium (Na) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of the Ni-Bound Human Heavy-Chain Variant 122H-Delta C-Star with 2,5-Furandihyrdoxamate Collected at 100K (pdb code 7jgk). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of the Ni-Bound Human Heavy-Chain Variant 122H-Delta C-Star with 2,5-Furandihyrdoxamate Collected at 100K, PDB code: 7jgk:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 7jgk

Go back to Nickel Binding Sites List in 7jgk
Nickel binding site 1 out of 3 in the Crystal Structure of the Ni-Bound Human Heavy-Chain Variant 122H-Delta C-Star with 2,5-Furandihyrdoxamate Collected at 100K


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of the Ni-Bound Human Heavy-Chain Variant 122H-Delta C-Star with 2,5-Furandihyrdoxamate Collected at 100K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni202

b:77.4
occ:0.33
O12 A:V9Y201 2.0 81.1 0.2
O11 A:V9Y201 2.0 77.4 0.2
NE2 A:HIS122 2.1 88.2 1.0
CE1 A:HIS122 2.2 80.8 1.0
C09 A:V9Y201 2.6 82.8 0.2
N10 A:V9Y201 2.7 82.5 0.2
CD2 A:HIS122 3.5 76.0 1.0
ND1 A:HIS122 3.5 92.2 1.0
C08 A:V9Y201 4.1 84.9 0.2
CG A:HIS122 4.1 69.6 1.0
C07 A:V9Y201 4.9 83.7 0.2

Nickel binding site 2 out of 3 in 7jgk

Go back to Nickel Binding Sites List in 7jgk
Nickel binding site 2 out of 3 in the Crystal Structure of the Ni-Bound Human Heavy-Chain Variant 122H-Delta C-Star with 2,5-Furandihyrdoxamate Collected at 100K


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the Ni-Bound Human Heavy-Chain Variant 122H-Delta C-Star with 2,5-Furandihyrdoxamate Collected at 100K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni203

b:93.6
occ:0.25
NE2 A:HIS173 2.1 69.2 1.0
O A:HOH317 2.5 43.7 0.2
CE1 A:HIS173 2.8 65.4 1.0
CD2 A:HIS173 3.3 61.9 1.0
ND1 A:HIS173 4.0 68.7 1.0
CG A:HIS173 4.3 64.6 1.0

Nickel binding site 3 out of 3 in 7jgk

Go back to Nickel Binding Sites List in 7jgk
Nickel binding site 3 out of 3 in the Crystal Structure of the Ni-Bound Human Heavy-Chain Variant 122H-Delta C-Star with 2,5-Furandihyrdoxamate Collected at 100K


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of the Ni-Bound Human Heavy-Chain Variant 122H-Delta C-Star with 2,5-Furandihyrdoxamate Collected at 100K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni204

b:75.7
occ:1.00
OE1 A:GLU27 2.1 82.8 1.0
OE2 A:GLU62 2.1 78.2 1.0
ND1 A:HIS65 2.3 88.6 1.0
CD A:GLU62 2.8 68.0 1.0
CD A:GLU27 2.8 80.9 1.0
OE1 A:GLU62 2.9 70.0 1.0
OE2 A:GLU27 2.9 85.2 1.0
CE1 A:HIS65 3.0 81.2 1.0
CG A:HIS65 3.5 82.1 1.0
OE1 A:GLN141 3.5 73.2 1.0
O A:HOH301 3.7 89.4 1.0
CB A:HIS65 4.0 64.8 1.0
NE2 A:HIS65 4.2 85.0 1.0
CG1 A:VAL110 4.2 56.1 1.0
CG A:GLU62 4.2 53.0 1.0
CG A:GLU27 4.3 53.2 1.0
CD2 A:HIS65 4.4 77.9 1.0
OE2 A:GLU107 4.5 89.2 1.0
CD A:GLN141 4.6 60.5 1.0
CB A:GLU62 4.7 52.5 1.0
CA A:GLU62 4.8 58.1 1.0
CB A:GLU27 4.9 52.9 1.0
OE1 A:GLU107 4.9 83.0 1.0

Reference:

J.B.Bailey, F.A.Tezcan. Tunable and Cooperative Thermomechanical Properties of Protein-Metal-Organic Frameworks. J.Am.Chem.Soc. V. 142 17265 2020.
ISSN: ESSN 1520-5126
PubMed: 32972136
DOI: 10.1021/JACS.0C07835
Page generated: Wed Dec 16 02:00:02 2020

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