Atomistry » Nickel » PDB 8cjb-8ka3 » 8drd
Atomistry »
  Nickel »
    PDB 8cjb-8ka3 »
      8drd »

Nickel in PDB 8drd: Ni(II)-Bound B2 Dimer (H60/H100/H104)

Protein crystallography data

The structure of Ni(II)-Bound B2 Dimer (H60/H100/H104), PDB code: 8drd was solved by T.S.Choi, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.70 / 1.89
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.09, 55.43, 101.97, 90, 90, 90
R / Rfree (%) 18.9 / 21.6

Other elements in 8drd:

The structure of Ni(II)-Bound B2 Dimer (H60/H100/H104) also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Ni(II)-Bound B2 Dimer (H60/H100/H104) (pdb code 8drd). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Ni(II)-Bound B2 Dimer (H60/H100/H104), PDB code: 8drd:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 8drd

Go back to Nickel Binding Sites List in 8drd
Nickel binding site 1 out of 2 in the Ni(II)-Bound B2 Dimer (H60/H100/H104)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Ni(II)-Bound B2 Dimer (H60/H100/H104) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni202

b:11.7
occ:1.00
NE2 A:HIS60 2.1 10.5 1.0
NE2 A:HIS104 2.1 11.3 1.0
O B:HOH319 2.1 12.4 1.0
O A:HOH334 2.1 13.0 1.0
NE2 B:HIS100 2.1 11.2 1.0
NE2 B:HIS104 2.1 11.4 1.0
CE1 A:HIS104 3.0 15.4 1.0
CE1 A:HIS60 3.0 10.3 1.0
CE1 B:HIS104 3.1 11.7 1.0
CD2 A:HIS60 3.1 13.7 1.0
CE1 B:HIS100 3.1 11.0 1.0
CD2 B:HIS100 3.1 10.8 1.0
CD2 A:HIS104 3.2 12.1 1.0
CD2 B:HIS104 3.2 14.3 1.0
ND1 A:HIS60 4.2 11.2 1.0
ND1 A:HIS104 4.2 11.8 1.0
ND1 B:HIS104 4.2 10.1 1.0
CG A:HIS60 4.2 11.2 1.0
ND1 B:HIS100 4.2 12.3 1.0
CG A:HIS104 4.3 12.5 1.0
O A:HOH349 4.3 7.6 1.0
CG B:HIS100 4.3 13.2 1.0
CG B:HIS104 4.3 11.4 1.0
O A:HOH342 4.5 14.8 1.0
O A:HIS100 4.5 12.5 1.0
OE1 B:GLN103 4.7 21.6 1.0
CB A:HIS100 4.8 12.7 1.0
O2 B:MPD201 4.9 22.9 1.0
C A:HIS100 5.0 11.1 1.0

Nickel binding site 2 out of 2 in 8drd

Go back to Nickel Binding Sites List in 8drd
Nickel binding site 2 out of 2 in the Ni(II)-Bound B2 Dimer (H60/H100/H104)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Ni(II)-Bound B2 Dimer (H60/H100/H104) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni203

b:38.7
occ:1.00
OD2 B:ASP2 2.1 20.4 1.0
CG B:ASP2 3.1 21.9 1.0
OD1 B:ASP2 3.4 20.7 1.0
OD1 B:ASP5 4.1 21.3 1.0
OE1 B:GLU4 4.2 35.9 1.0
OD2 B:ASP5 4.3 25.7 1.0
CG B:ASP5 4.4 24.9 1.0
CB B:ASP2 4.4 15.8 1.0
CD B:GLU4 4.7 35.5 1.0
O B:HOH303 4.7 17.2 1.0
CB B:GLU4 4.7 22.7 1.0
O B:HOH318 4.9 22.5 1.0

Reference:

T.S.Choi, F.A.Tezcan. Design of A Flexible, Zn-Selective Protein Scaffold That Displays Anti-Irving-Williams Behavior. J.Am.Chem.Soc. V. 144 18090 2022.
ISSN: ESSN 1520-5126
PubMed: 36154053
DOI: 10.1021/JACS.2C08050
Page generated: Thu Oct 10 09:40:21 2024

Last articles

Zn in 1GUP
Zn in 1GUQ
Zn in 1GTQ
Zn in 1GS8
Zn in 1GS7
Zn in 1GKR
Zn in 1GLU
Zn in 1GR0
Zn in 1GPC
Zn in 1GO8
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy