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Nickel in PDB 4rbm: Porphyromonas Gingivalis Gingipain K (Kgp) Catalytic and Immunoglobulin Superfamily-Like Domains

Enzymatic activity of Porphyromonas Gingivalis Gingipain K (Kgp) Catalytic and Immunoglobulin Superfamily-Like Domains

All present enzymatic activity of Porphyromonas Gingivalis Gingipain K (Kgp) Catalytic and Immunoglobulin Superfamily-Like Domains:
3.4.22.47;

Protein crystallography data

The structure of Porphyromonas Gingivalis Gingipain K (Kgp) Catalytic and Immunoglobulin Superfamily-Like Domains, PDB code: 4rbm was solved by I.De Diego, F.Veillard, M.N.Sztukowska, T.Guevara, B.Potempa, A.Pomowski, J.A.Huntington, J.Potempa, F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.41 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.640, 58.810, 135.500, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 17.2

Other elements in 4rbm:

The structure of Porphyromonas Gingivalis Gingipain K (Kgp) Catalytic and Immunoglobulin Superfamily-Like Domains also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Sodium (Na) 3 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Porphyromonas Gingivalis Gingipain K (Kgp) Catalytic and Immunoglobulin Superfamily-Like Domains (pdb code 4rbm). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Porphyromonas Gingivalis Gingipain K (Kgp) Catalytic and Immunoglobulin Superfamily-Like Domains, PDB code: 4rbm:

Nickel binding site 1 out of 1 in 4rbm

Go back to Nickel Binding Sites List in 4rbm
Nickel binding site 1 out of 1 in the Porphyromonas Gingivalis Gingipain K (Kgp) Catalytic and Immunoglobulin Superfamily-Like Domains


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Porphyromonas Gingivalis Gingipain K (Kgp) Catalytic and Immunoglobulin Superfamily-Like Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni705

b:12.4
occ:1.00
 NE2 A:HIS707 2.0 24.4 1.0
OE2 A:GLU379 2.0 17.1 1.0
OXT A:ACT708 2.1 24.3 1.0
CD A:GLU379 2.7 18.9 1.0
OE1 A:GLU379 2.7 16.0 1.0
CE1 A:HIS707 3.0 24.3 1.0
CD2 A:HIS707 3.0 24.5 1.0
C A:ACT708 3.1 27.3 1.0
O A:ACT708 3.6 36.7 1.0
ND1 A:HIS707 4.1 24.8 1.0
CG A:HIS707 4.1 23.6 1.0
CG A:GLU379 4.1 16.2 1.0
CH3 A:ACT708 4.4 23.2 1.0
CE A:MET599 4.5 13.8 1.0
CB A:SER376 4.7 11.7 1.0
CG2 A:THR415 4.8 12.4 1.0
CB A:GLU379 5.0 9.6 1.0

Reference:

I.De Diego, F.Veillard, M.Sztukowska, T.Guevara, B.Potempa, A.Pomowski, J.A.Huntington, J.Potempa, F.X.Gomis-Ruth. Structure and Mechanism of Cysteine Peptidase Kgp, A Major Virulence Factor of Porphyromonas Gingivalis in Periodontitis. J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25266723
DOI: 10.1074/JBC.M114.602052
Page generated: Wed Dec 16 01:34:46 2020

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