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Cobalt in PDB 2q6q: Crystal Structure of SPC42P, A Critical Component of Spindle Pole Body in Budding Yeast

Protein crystallography data

The structure of Crystal Structure of SPC42P, A Critical Component of Spindle Pole Body in Budding Yeast, PDB code: 2q6q was solved by V.N.Malashkevich, J.R.Newman, P.S.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.36 / 1.97
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.860, 57.790, 57.170, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 29.7

Other elements in 2q6q:

The structure of Crystal Structure of SPC42P, A Critical Component of Spindle Pole Body in Budding Yeast also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of SPC42P, A Critical Component of Spindle Pole Body in Budding Yeast (pdb code 2q6q). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Crystal Structure of SPC42P, A Critical Component of Spindle Pole Body in Budding Yeast, PDB code: 2q6q:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in 2q6q

Go back to Cobalt Binding Sites List in 2q6q
Cobalt binding site 1 out of 3 in the Crystal Structure of SPC42P, A Critical Component of Spindle Pole Body in Budding Yeast


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of SPC42P, A Critical Component of Spindle Pole Body in Budding Yeast within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1

b:43.6
occ:1.00
OE1 A:GLU98 2.2 32.4 1.0
OD1 A:ASP102 2.2 24.6 1.0
O A:HOH190 2.3 33.1 1.0
CO A:CO2 2.8 45.4 1.0
CG A:ASP102 3.1 43.9 1.0
OD2 A:ASP102 3.2 23.1 1.0
CD A:GLU98 3.3 28.4 1.0
CG A:GLU98 3.7 33.0 1.0
O A:GLU98 4.0 27.5 1.0
OE2 A:GLU98 4.3 38.2 1.0
NZ A:LYS105 4.4 29.5 1.0
CB A:ASP102 4.4 23.5 1.0
N A:ASP102 4.7 28.0 1.0
C A:GLU98 4.7 26.2 1.0
CA A:ASP102 4.8 26.0 1.0
CB A:GLU98 5.0 24.1 1.0

Cobalt binding site 2 out of 3 in 2q6q

Go back to Cobalt Binding Sites List in 2q6q
Cobalt binding site 2 out of 3 in the Crystal Structure of SPC42P, A Critical Component of Spindle Pole Body in Budding Yeast


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of SPC42P, A Critical Component of Spindle Pole Body in Budding Yeast within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co2

b:45.4
occ:1.00
OE1 A:GLU98 2.0 32.4 1.0
OD2 A:ASP102 2.1 23.1 1.0
CO A:CO1 2.8 43.6 1.0
CG A:ASP102 3.0 43.9 1.0
CD A:GLU98 3.0 28.4 1.0
OD1 A:ASP102 3.3 24.6 1.0
OE2 A:GLU98 3.4 38.2 1.0
CB A:ASP102 4.3 23.5 1.0
CG A:GLU98 4.4 33.0 1.0
O A:GLU98 4.6 27.5 1.0
O A:HOH190 4.8 33.1 1.0

Cobalt binding site 3 out of 3 in 2q6q

Go back to Cobalt Binding Sites List in 2q6q
Cobalt binding site 3 out of 3 in the Crystal Structure of SPC42P, A Critical Component of Spindle Pole Body in Budding Yeast


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of SPC42P, A Critical Component of Spindle Pole Body in Budding Yeast within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co3

b:21.5
occ:1.00
O B:HOH204 1.9 23.1 1.0
OD1 B:ASP109 2.1 16.9 1.0
O B:HOH169 2.3 34.6 1.0
O B:HOH201 2.6 30.4 1.0
CG B:ASP109 3.1 45.0 1.0
OD2 B:ASP109 3.3 25.8 1.0
O B:LYS105 3.9 25.5 1.0
OE2 B:GLU108 4.0 41.6 1.0
CB B:ASP109 4.4 21.9 1.0
C B:LYS105 4.6 23.7 1.0
CA B:ASP109 4.7 21.5 1.0
N B:ASP109 4.7 20.0 1.0
CB B:LYS105 4.7 23.7 1.0
CA B:LYS105 4.8 22.1 1.0

Reference:

N.Zizlsperger, V.N.Malashkevich, S.Pillay, A.E.Keating. Analysis of Coiled-Coil Interactions Between Core Proteins of the Spindle Pole Body. Biochemistry V. 47 11858 2008.
ISSN: ISSN 0006-2960
PubMed: 18850724
DOI: 10.1021/BI801378Z
Page generated: Sun Dec 13 10:38:47 2020

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