Atomistry » Cobalt » PDB 4j2m-4ngl » 4jka
Atomistry »
  Cobalt »
    PDB 4j2m-4ngl »
      4jka »

Cobalt in PDB 4jka: Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion

Protein crystallography data

The structure of Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion, PDB code: 4jka was solved by M.J.Schellenberg, T.Wu, D.B.Ritchie, K.A.Atta, A.M.Macmillan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.13 / 1.32
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.249, 78.223, 94.373, 90.00, 90.00, 90.00
R / Rfree (%) 14.2 / 16.6

Other elements in 4jka:

The structure of Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion (pdb code 4jka). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion, PDB code: 4jka:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in 4jka

Go back to Cobalt Binding Sites List in 4jka
Cobalt binding site 1 out of 8 in the Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co2001

b:20.4
occ:0.50
CO A:CO2001 0.0 20.4 0.5
O A:HOH2380 1.8 31.0 1.0
O A:HOH2274 1.9 35.8 1.0
OE2 A:GLU1873 2.2 21.8 1.0
O A:HOH2122 2.3 24.1 1.0
OE1 A:GLU1873 2.3 24.1 1.0
CO A:CO2001 2.4 44.1 0.5
CD A:GLU1873 2.6 20.7 1.0
O A:HOH2421 3.9 53.7 1.0
O A:HOH2241 4.0 27.6 1.0
CG A:GLU1873 4.0 17.8 1.0
O A:GLU1873 4.2 17.1 1.0
CD2 A:LEU1877 4.3 28.7 1.0
O A:HOH2397 4.3 33.5 0.5
O A:HOH2297 4.3 27.4 1.0
CA A:GLU1873 4.8 14.8 1.0
CB A:GLU1873 4.8 16.4 1.0
C A:GLU1873 4.9 14.9 1.0
O A:HOH2143 5.0 30.4 1.0

Cobalt binding site 2 out of 8 in 4jka

Go back to Cobalt Binding Sites List in 4jka
Cobalt binding site 2 out of 8 in the Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co2001

b:44.1
occ:0.50
CO A:CO2001 0.0 44.1 0.5
O A:HOH2274 1.9 35.8 1.0
O A:HOH2421 2.0 53.7 1.0
CO A:CO2001 2.4 20.4 0.5
O A:HOH2397 2.5 33.5 0.5
O A:HOH2380 2.5 31.0 1.0
OE1 A:GLU1873 3.9 24.1 1.0
O A:HOH2143 4.1 30.4 1.0
O A:HOH2122 4.1 24.1 1.0
OE2 A:GLU1873 4.2 21.8 1.0
O A:HOH2241 4.3 27.6 1.0
CD A:GLU1873 4.5 20.7 1.0
O A:ILE1882 4.6 24.3 1.0
O A:HOH2297 4.8 27.4 1.0
O A:PRO1880 4.9 38.0 1.0

Cobalt binding site 3 out of 8 in 4jka

Go back to Cobalt Binding Sites List in 4jka
Cobalt binding site 3 out of 8 in the Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co2002

b:26.1
occ:1.00
O A:HOH2414 1.5 31.6 1.0
NE2 A:HIS1966 2.2 19.7 1.0
O A:HOH2252 2.2 31.4 1.0
O A:HOH2378 2.2 25.0 1.0
NE2 A:HIS1965 2.2 25.5 1.0
OD1 A:ASP1922 2.3 24.0 1.0
CG A:ASP1922 3.0 20.9 1.0
OD2 A:ASP1922 3.1 31.1 1.0
CD2 A:HIS1966 3.1 18.7 1.0
CE1 A:HIS1966 3.2 21.5 1.0
CD2 A:HIS1965 3.2 24.4 1.0
CE1 A:HIS1965 3.2 31.1 1.0
O B:HOH2383 4.0 31.5 0.5
CG A:HIS1966 4.3 18.9 1.0
ND1 A:HIS1966 4.3 19.6 1.0
O B:HOH2176 4.3 23.4 1.0
ND1 A:HIS1965 4.3 27.3 1.0
CG A:HIS1965 4.4 23.5 1.0
CB A:ASP1922 4.4 17.8 1.0
O B:HOH2383 4.5 26.3 0.5
N A:ASP1922 4.6 13.5 1.0
O A:HOH2147 4.6 29.7 1.0
OE1 A:GLU1963 4.7 44.4 1.0
C A:ASP1921 4.8 13.3 1.0
CA A:ASP1922 4.8 14.0 1.0
O B:HOH2288 4.9 43.7 1.0

Cobalt binding site 4 out of 8 in 4jka

Go back to Cobalt Binding Sites List in 4jka
Cobalt binding site 4 out of 8 in the Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co2003

b:22.3
occ:0.40
O A:HOH2383 1.9 36.8 1.0
OE2 A:GLU1843 2.0 30.9 1.0
O A:HOH2395 2.1 37.7 1.0
O A:HOH2393 2.1 44.3 1.0
CD A:GLU1843 3.1 23.6 1.0
OE1 A:GLU1843 3.6 27.2 1.0
O A:HOH2385 3.9 43.4 1.0
CG A:GLU1843 4.4 17.9 1.0
NZ A:LYS1840 5.0 29.4 1.0

Cobalt binding site 5 out of 8 in 4jka

Go back to Cobalt Binding Sites List in 4jka
Cobalt binding site 5 out of 8 in the Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co2001

b:17.6
occ:1.00
OD1 B:ASP1781 2.1 15.3 1.0
O B:HOH2160 2.1 21.4 1.0
O B:HOH2414 2.1 23.2 1.0
O B:HOH2179 2.1 22.4 1.0
O B:HOH2156 2.1 20.9 1.0
O B:HOH2426 2.1 21.1 1.0
CG B:ASP1781 3.0 14.8 1.0
OD2 B:ASP1781 3.3 18.3 1.0
O B:ASP1782 4.0 19.0 1.0
O B:HOH2261 4.0 38.8 1.0
O B:HOH2239 4.1 41.9 1.0
O B:HOH2253 4.1 36.8 1.0
OE1 B:GLN1894 4.2 22.0 1.0
O B:HOH2233 4.3 27.6 0.8
CB B:ASP1781 4.4 13.5 1.0
OD1 B:ASP1782 4.5 18.5 1.0
O B:HOH2122 4.5 26.7 1.0
N B:ASP1782 4.5 12.9 1.0
O B:HOH2151 4.6 34.2 1.0
O B:HOH2234 4.7 15.2 0.2
OG1 B:THR1864 4.7 29.1 1.0
O B:HOH2144 4.8 25.2 1.0
CA B:ASP1781 4.8 12.7 1.0
CE B:MET1868 4.9 24.4 0.8
CD B:GLN1894 5.0 23.2 1.0

Cobalt binding site 6 out of 8 in 4jka

Go back to Cobalt Binding Sites List in 4jka
Cobalt binding site 6 out of 8 in the Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co2002

b:28.2
occ:1.00
O B:HOH2218 1.5 29.2 1.0
O B:HOH2416 2.1 35.2 1.0
O B:HOH2366 2.2 27.9 1.0
NE2 B:HIS1966 2.2 21.1 1.0
OD1 B:ASP1922 2.2 25.4 1.0
NE2 B:HIS1965 2.3 27.8 1.0
CG B:ASP1922 2.9 22.9 1.0
OD2 B:ASP1922 3.1 32.9 1.0
CD2 B:HIS1966 3.1 21.3 1.0
CE1 B:HIS1965 3.2 29.8 1.0
CE1 B:HIS1966 3.2 22.8 1.0
CD2 B:HIS1965 3.3 27.6 1.0
O B:HOH2384 3.4 37.2 0.5
O A:HOH2367 4.3 46.0 1.0
CG B:HIS1966 4.3 19.6 1.0
CB B:ASP1922 4.3 18.5 1.0
ND1 B:HIS1966 4.3 21.0 1.0
ND1 B:HIS1965 4.4 32.6 1.0
O A:HOH2153 4.4 25.3 1.0
CG B:HIS1965 4.4 27.5 1.0
O A:HOH2236 4.4 25.0 0.5
O B:HOH2241 4.5 33.2 1.0
OE1 B:GLU1963 4.5 51.0 1.0
O A:HOH2291 4.5 52.9 1.0
O A:HOH2235 4.6 26.5 0.5
N B:ASP1922 4.6 14.7 1.0
C B:ASP1921 4.7 14.1 1.0
CA B:ASP1922 4.8 14.9 1.0

Cobalt binding site 7 out of 8 in 4jka

Go back to Cobalt Binding Sites List in 4jka
Cobalt binding site 7 out of 8 in the Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co2003

b:20.0
occ:0.50
CO B:CO2003 0.0 20.0 0.5
CO B:CO2003 1.6 34.9 0.5
OE2 B:GLU1856 1.7 19.1 0.4
O B:HOH2421 2.0 24.8 0.5
O B:HOH2362 2.1 29.0 1.0
O B:HOH2365 2.1 23.9 1.0
O B:HOH2421 2.2 24.8 0.5
O B:HOH2175 2.8 27.0 0.5
CD B:GLU1856 2.8 14.0 0.4
OE1 B:GLU1856 2.9 23.3 0.6
OE1 B:GLU1856 3.3 13.4 0.4
O A:HOH2386 3.5 47.6 1.0
CD B:GLU1856 3.8 25.2 0.6
OE1 A:GLU1856 3.8 23.1 1.0
O B:HOH2175 3.9 20.3 0.5
O B:HOH2342 3.9 21.5 0.4
OE2 B:GLU1856 3.9 27.7 0.6
O B:HOH2341 3.9 26.1 0.6
CG B:GLU1856 4.1 12.0 0.4
OE2 B:GLU1855 4.2 37.1 1.0
OE2 A:GLU1856 4.2 26.5 1.0
O B:GLU1855 4.4 18.8 1.0
CD A:GLU1856 4.4 24.8 1.0
O A:HOH2389 4.5 39.1 1.0
OE1 A:GLU1855 4.7 35.7 0.7
CD1 B:ILE1776 5.0 22.5 1.0

Cobalt binding site 8 out of 8 in 4jka

Go back to Cobalt Binding Sites List in 4jka
Cobalt binding site 8 out of 8 in the Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Open and Closed Forms of R1865A Human PRP8 Rnase H-Like Domain with Bound Co Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co2003

b:34.9
occ:0.50
CO B:CO2003 0.0 34.9 0.5
CO B:CO2003 1.6 20.0 0.5
O B:HOH2175 2.0 27.0 0.5
O A:HOH2386 2.3 47.6 1.0
OE2 B:GLU1856 2.4 19.1 0.4
OE1 A:GLU1856 2.4 23.1 1.0
O B:HOH2365 2.5 23.9 1.0
O B:HOH2421 2.6 24.8 0.5
O B:HOH2421 2.7 24.8 0.5
CD A:GLU1856 3.3 24.8 1.0
OE1 B:GLU1856 3.4 23.3 0.6
OE2 A:GLU1856 3.4 26.5 1.0
CD B:GLU1856 3.4 14.0 0.4
O B:HOH2175 3.7 20.3 0.5
O B:HOH2362 3.7 29.0 1.0
OE1 B:GLU1856 3.8 13.4 0.4
O A:HOH2389 4.1 39.1 1.0
OE2 B:GLU1856 4.1 27.7 0.6
CD B:GLU1856 4.2 25.2 0.6
OE1 A:GLU1855 4.2 35.7 0.7
O A:GLU1855 4.5 21.1 1.0
O B:HOH2342 4.6 21.5 0.4
CG A:GLU1856 4.6 21.7 1.0
CG B:GLU1856 4.7 12.0 0.4
O A:HOH2404 4.8 49.1 1.0
OE2 B:GLU1855 4.9 37.1 1.0
CA A:GLU1856 5.0 14.6 1.0

Reference:

M.J.Schellenberg, T.Wu, D.B.Ritchie, S.Fica, J.P.Staley, K.A.Atta, P.Lapointe, A.M.Macmillan. A Conformational Switch in PRP8 Mediates Metal Ion Coordination That Promotes Pre-Mrna Exon Ligation. Nat.Struct.Mol.Biol. V. 20 728 2013.
ISSN: ISSN 1545-9993
PubMed: 23686287
DOI: 10.1038/NSMB.2556
Page generated: Sun Dec 13 10:44:54 2020

Last articles

Zn in 7O75
Zn in 7O73
Zn in 7O4I
Zn in 7O72
Zn in 7O4J
Zn in 7NVR
Zn in 7NVY
Zn in 7NVZ
Zn in 7NW0
Zn in 7O4K
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy