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Nickel in PDB 2gw4: Crystal Structure of Stony Coral Fluorescent Protein Kaede, Red Form

Protein crystallography data

The structure of Crystal Structure of Stony Coral Fluorescent Protein Kaede, Red Form, PDB code: 2gw4 was solved by I.Hayashi, H.Mizuno, A.Miyawako, M.Ikura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 132.197, 81.169, 53.512, 90.00, 113.92, 90.00
R / Rfree (%) 19.8 / 21.3

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Stony Coral Fluorescent Protein Kaede, Red Form (pdb code 2gw4). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of Stony Coral Fluorescent Protein Kaede, Red Form, PDB code: 2gw4:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 2gw4

Go back to Nickel Binding Sites List in 2gw4
Nickel binding site 1 out of 4 in the Crystal Structure of Stony Coral Fluorescent Protein Kaede, Red Form


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 Stony Coral Fluorescent Protein Kaede, Red Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni438

b:19.7
occ:1.00
O A:HOH484 2.1 23.8 1.0
O A:HOH485 2.2 22.8 1.0
O B:HOH598 3.9 34.1 1.0
N A:PRO0 4.1 20.9 1.0
O B:HOH592 4.7 34.5 1.0
CA A:PRO0 4.8 20.8 1.0
CG A:MET1 4.8 22.8 1.0
C A:PRO0 4.9 20.4 1.0
CE A:MET1 5.0 22.7 1.0
O A:PRO0 5.0 20.9 1.0

Nickel binding site 2 out of 4 in 2gw4

Go back to Nickel Binding Sites List in 2gw4
Nickel binding site 2 out of 4 in the Crystal Structure of Stony Coral Fluorescent Protein Kaede, Red Form


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 Stony Coral Fluorescent Protein Kaede, Red Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni439

b:37.8
occ:1.00
NE2 B:HIS201 2.2 19.8 1.0
O B:HOH580 2.4 46.5 1.0
O B:HOH602 2.6 50.3 1.0
O B:HOH581 2.9 53.6 1.0
CD2 B:HIS201 3.2 18.5 1.0
CE1 B:HIS201 3.2 18.9 1.0
O B:HOH594 3.3 44.4 1.0
O B:HOH609 3.8 40.5 1.0
O B:HOH504 3.9 28.0 1.0
OH B:TYR205 4.3 21.3 1.0
ND1 B:HIS201 4.3 18.9 1.0
CG B:HIS201 4.3 18.3 1.0
O B:HOH585 4.5 26.1 1.0
O B:HOH540 4.5 33.7 1.0

Nickel binding site 3 out of 4 in 2gw4

Go back to Nickel Binding Sites List in 2gw4
Nickel binding site 3 out of 4 in the Crystal Structure of Stony Coral Fluorescent Protein Kaede, Red Form


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 Stony Coral Fluorescent Protein Kaede, Red Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni440

b:19.7
occ:1.00
O C:HOH486 2.1 19.3 1.0
O C:HOH479 4.1 32.4 1.0
N C:PRO0 4.1 20.1 1.0
O D:HOH595 4.7 39.2 1.0
CG C:MET1 4.8 24.2 1.0
CA C:PRO0 4.8 20.4 1.0
C C:PRO0 4.9 20.5 1.0

Nickel binding site 4 out of 4 in 2gw4

Go back to Nickel Binding Sites List in 2gw4
Nickel binding site 4 out of 4 in the Crystal Structure of Stony Coral Fluorescent Protein Kaede, Red Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Stony Coral Fluorescent Protein Kaede, Red Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni441

b:36.0
occ:1.00
NE2 D:HIS201 2.3 19.5 1.0
O D:HOH587 2.5 49.6 1.0
O D:HOH597 2.6 47.1 1.0
O D:HOH596 2.6 47.4 1.0
CD2 D:HIS201 3.2 18.5 1.0
CE1 D:HIS201 3.2 18.8 1.0
O D:HOH525 3.9 28.8 1.0
OH D:TYR205 4.2 21.7 1.0
ND1 D:HIS201 4.3 19.0 1.0
CG D:HIS201 4.3 17.7 1.0
O D:HOH522 4.5 38.6 1.0
O D:HOH543 4.6 26.8 1.0

Reference:

I.Hayashi, H.Mizuno, K.I.Tong, T.Furuta, F.Tanaka, M.Yoshimura, A.Miyawaki, M.Ikura. Crystallographic Evidence For Water-Assisted Photo-Induced Peptide Cleavage in the Stony Coral Fluorescent Protein Kaede. J.Mol.Biol. V. 372 918 2007.
ISSN: ISSN 0022-2836
PubMed: 17692334
DOI: 10.1016/J.JMB.2007.06.037
Page generated: Fri Sep 25 08:09:48 2020
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