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Arsenic in PDB 2gbm: Crystal Structure of the 35-36 8 Glycine Insertion Mutant of Ubiquitin

Protein crystallography data

The structure of Crystal Structure of the 35-36 8 Glycine Insertion Mutant of Ubiquitin, PDB code: 2gbm was solved by D.M.Ferraro, D.J.Ferraro, S.Ramaswamy, A.D.Robertson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.51 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.817, 49.786, 123.147, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 22.7

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Crystal Structure of the 35-36 8 Glycine Insertion Mutant of Ubiquitin (pdb code 2gbm). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 3 binding sites of Arsenic where determined in the Crystal Structure of the 35-36 8 Glycine Insertion Mutant of Ubiquitin, PDB code: 2gbm:
Jump to Arsenic binding site number: 1; 2; 3;

Arsenic binding site 1 out of 3 in 2gbm

Go back to Arsenic Binding Sites List in 2gbm
Arsenic binding site 1 out of 3 in the Crystal Structure of the 35-36 8 Glycine Insertion Mutant of Ubiquitin


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Crystal Structure of the 35-36 8 Glycine Insertion Mutant of Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As503

b:17.7
occ:1.00
OD2 B:ASP60 2.0 16.2 1.0
O B:HOH590 2.0 5.6 1.0
O B:HOH589 2.1 6.0 1.0
OD2 C:ASP47 2.1 10.3 1.0
OE1 B:GLU24 2.1 14.9 1.0
OD1 C:ASP47 2.4 15.2 1.0
CG C:ASP47 2.6 13.9 1.0
CG B:ASP60 3.0 16.0 1.0
CD B:GLU24 3.0 18.5 1.0
OE2 B:GLU24 3.3 21.2 1.0
CB B:ASP60 3.3 15.3 1.0
OD1 B:ASP47 3.8 14.7 1.0
NZ B:LYS27 3.9 18.1 1.0
O C:HOH521 4.0 11.2 1.0
CB C:ASP47 4.1 15.7 1.0
O B:HOH506 4.1 6.4 1.0
OD1 B:ASP60 4.1 16.8 1.0
O B:HOH512 4.2 8.2 1.0
CG B:GLU24 4.4 16.8 1.0
O C:HOH588 4.6 6.2 1.0
CD B:LYS27 4.7 20.9 1.0
CA B:ASP60 4.8 16.0 1.0
O B:HOH505 4.8 6.3 1.0
CE B:LYS27 4.8 23.0 1.0
CG B:ASP47 4.9 15.1 1.0
CA B:ASP47 4.9 17.3 1.0
CB B:GLU24 4.9 16.2 1.0
CA C:ASP47 5.0 16.9 1.0

Arsenic binding site 2 out of 3 in 2gbm

Go back to Arsenic Binding Sites List in 2gbm
Arsenic binding site 2 out of 3 in the Crystal Structure of the 35-36 8 Glycine Insertion Mutant of Ubiquitin


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Crystal Structure of the 35-36 8 Glycine Insertion Mutant of Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As501

b:19.4
occ:1.00
OD2 C:ASP60 2.0 18.5 1.0
O C:HOH588 2.0 6.2 1.0
OE1 C:GLU24 2.1 15.6 1.0
OD2 B:ASP47 2.1 12.2 1.0
O C:HOH589 2.2 6.4 1.0
OD1 B:ASP47 2.4 14.7 1.0
CG B:ASP47 2.6 15.1 1.0
CD C:GLU24 3.0 17.5 1.0
CG C:ASP60 3.0 17.9 1.0
OE2 C:GLU24 3.2 20.0 1.0
CB C:ASP60 3.3 15.4 1.0
OD1 C:ASP47 3.8 15.2 1.0
NZ C:LYS27 4.0 23.2 1.0
O C:HOH503 4.0 6.4 1.0
CB B:ASP47 4.1 16.6 1.0
OD1 C:ASP60 4.1 18.9 1.0
O C:HOH510 4.2 8.4 1.0
O B:HOH530 4.3 12.8 1.0
CG C:GLU24 4.4 16.2 1.0
O B:HOH590 4.6 5.6 1.0
CD C:LYS27 4.8 22.4 1.0
CE C:LYS27 4.8 26.3 1.0
CB C:GLU24 4.8 17.1 1.0
CG C:ASP47 4.8 13.9 1.0
CA C:ASP60 4.8 16.1 1.0
CA C:ASP47 4.9 16.9 1.0
O C:HOH505 5.0 6.1 1.0
CA B:ASP47 5.0 17.3 1.0

Arsenic binding site 3 out of 3 in 2gbm

Go back to Arsenic Binding Sites List in 2gbm
Arsenic binding site 3 out of 3 in the Crystal Structure of the 35-36 8 Glycine Insertion Mutant of Ubiquitin


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Crystal Structure of the 35-36 8 Glycine Insertion Mutant of Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As502

b:21.9
occ:1.00
OD2 D:ASP60 2.0 21.5 1.0
OE1 D:GLU24 2.1 21.1 1.0
O D:HOH591 2.2 4.0 1.0
O D:HOH592 2.3 3.2 1.0
CD D:GLU24 2.9 20.5 1.0
CG D:ASP60 3.0 18.8 1.0
OE2 D:GLU24 3.2 24.9 1.0
CB D:ASP60 3.3 19.6 1.0
NZ D:LYS27 3.9 22.4 1.0
OD1 D:ASP60 4.1 22.6 1.0
CG D:GLU24 4.3 18.2 1.0
CD D:LYS27 4.5 21.5 1.0
CE D:LYS27 4.7 23.5 1.0
CB D:GLU24 4.7 17.3 1.0
CA D:ASP60 4.8 18.6 1.0
O D:HOH537 4.9 12.1 1.0

Reference:

D.M.Ferraro, D.J.Ferraro, S.Ramaswamy, A.D.Robertson. Structures of Ubiquitin Insertion Mutants Support Site-Specific Reflex Response to Insertions Hypothesis. J.Mol.Biol. V. 359 390 2006.
ISSN: ISSN 0022-2836
PubMed: 16647719
DOI: 10.1016/J.JMB.2006.03.047
Page generated: Tue Oct 27 16:48:47 2020

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