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Nickel in PDB 1jvl: Azurin Dimer, Covalently Crosslinked Through Bis- Maleimidomethylether

Protein crystallography data

The structure of Azurin Dimer, Covalently Crosslinked Through Bis- Maleimidomethylether, PDB code: 1jvl was solved by I.M.C.Van Amsterdam, M.Ubbink, O.Einsle, A.Messerschmidt, A.Merli, D.Cavazzini, G.L.Rossi, G.W.Canters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.00
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 48.605, 48.605, 284.809, 90.00, 90.00, 120.00
R / Rfree (%) 19 / 22.7

Other elements in 1jvl:

The structure of Azurin Dimer, Covalently Crosslinked Through Bis- Maleimidomethylether also contains other interesting chemical elements:

Copper (Cu) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Azurin Dimer, Covalently Crosslinked Through Bis- Maleimidomethylether (pdb code 1jvl). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Azurin Dimer, Covalently Crosslinked Through Bis- Maleimidomethylether, PDB code: 1jvl:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1jvl

Go back to Nickel Binding Sites List in 1jvl
Nickel binding site 1 out of 2 in the Azurin Dimer, Covalently Crosslinked Through Bis- Maleimidomethylether


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Azurin Dimer, Covalently Crosslinked Through Bis- Maleimidomethylether within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni130

b:40.1
occ:1.00
O A:HOH553 2.1 36.7 1.0
O2 A:144503 2.1 39.3 1.0
O A:ALA1 2.1 42.6 1.0
N A:ALA1 2.2 43.8 1.0
C1 A:144503 2.3 36.3 1.0
C2 A:144503 2.6 40.5 1.0
C A:ALA1 2.9 44.7 1.0
N A:144503 3.0 43.9 1.0
CA A:ALA1 3.1 44.4 1.0
C4 A:144503 3.6 41.2 1.0
CB A:ALA1 3.9 45.1 1.0
OG A:SER25 4.2 40.8 1.0
N A:GLU2 4.2 45.1 1.0
C3 A:144503 4.3 39.4 1.0
SG A:CYS3 4.3 41.5 1.0
O A:HOH526 4.5 56.0 1.0
O4 A:144503 4.5 50.2 1.0
O A:HOH527 4.5 48.0 1.0
O A:HOH531 4.6 61.4 1.0
CA A:GLU2 4.9 45.6 1.0

Nickel binding site 2 out of 2 in 1jvl

Go back to Nickel Binding Sites List in 1jvl
Nickel binding site 2 out of 2 in the Azurin Dimer, Covalently Crosslinked Through Bis- Maleimidomethylether


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Azurin Dimer, Covalently Crosslinked Through Bis- Maleimidomethylether within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni130

b:41.1
occ:1.00
O B:HOH557 2.0 38.6 1.0
O2 B:144504 2.1 40.1 1.0
O B:ALA1 2.2 44.0 1.0
N B:ALA1 2.2 43.7 1.0
C1 B:144504 2.3 35.5 1.0
C2 B:144504 2.6 40.3 1.0
N B:144504 2.9 42.7 1.0
C B:ALA1 2.9 45.1 1.0
CA B:ALA1 3.1 44.6 1.0
C4 B:144504 3.6 39.8 1.0
CB B:ALA1 3.9 44.7 1.0
OG B:SER25 4.2 41.6 1.0
N B:GLU2 4.2 45.5 1.0
C3 B:144504 4.2 36.9 1.0
SG B:CYS3 4.3 40.1 1.0
O4 B:144504 4.5 48.7 1.0
O B:HOH530 4.6 46.3 1.0
O B:HOH534 4.6 58.9 1.0
O B:HOH529 4.7 57.7 1.0
CA B:GLU2 4.9 46.0 1.0

Reference:

I.M.C.Van Amsterdam, M.Ubbink, O.Einsle, A.Messerschmidt, A.Merli, D.Cavazzini, G.L.Rossi, G.W.Canters. Dramatic Modulation of Electron Transfer in Protein Complexes By Crosslinking Nat.Struct.Biol. V. 9 48 2002.
ISSN: ISSN 1072-8368
PubMed: 11740504
DOI: 10.1038/NSB736
Page generated: Thu Oct 29 06:14:41 2020
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