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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

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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

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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

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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

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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

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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

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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

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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: Tue Jul 30 17:14:14 2024

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