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Mercury in PDB 4ac9: Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp

Protein crystallography data

The structure of Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp, PDB code: 4ac9 was solved by M.Leibundgut, C.Frick, M.Thanbichler, A.Boeck, N.Ban, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.975 / 3.03
Space group P 31 1 2
Cell size a, b, c (Å), α, β, γ (°) 146.920, 146.920, 297.480, 90.00, 90.00, 120.00
R / Rfree (%) 18.99 / 22.21

Other elements in 4ac9:

The structure of Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Mercury Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Mercury atom in the Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp (pdb code 4ac9). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 16 binding sites of Mercury where determined in the Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp, PDB code: 4ac9:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 16 in 4ac9

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Mercury binding site 1 out of 16 in the Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg264

b:0.8
occ:0.58
HG A:CMH264 0.0 0.8 0.6
CM A:CMH264 2.1 0.3 0.6
SG A:CMH264 2.4 0.4 1.0
N A:CMH264 2.9 0.7 1.0
CA A:CMH264 3.0 0.2 1.0
CB A:CMH264 3.2 0.5 1.0
C A:GLY263 3.2 0.4 1.0
CD A:PRO222 3.3 0.3 1.0
CZ A:TYR261 3.5 0.5 1.0
CE2 A:TYR261 3.7 0.5 1.0
O A:GLY263 3.7 0.6 1.0
CE1 A:TYR261 3.7 0.4 1.0
O A:LEU221 3.8 0.8 1.0
OH A:TYR261 3.9 0.2 1.0
CA A:GLY263 3.9 0.8 1.0
CD2 A:TYR261 4.0 1.0 1.0
N A:GLY263 4.1 0.8 1.0
CD1 A:TYR261 4.1 0.1 1.0
CG A:PRO222 4.1 0.2 1.0
O A:TYR261 4.2 0.2 1.0
CG A:TYR261 4.2 0.1 1.0
N A:PRO222 4.4 0.1 1.0
C A:CMH264 4.5 0.3 1.0
C A:LEU221 4.5 1.0 1.0
N A:TYR261 4.6 1.0 1.0
C A:TYR261 4.7 0.2 1.0

Mercury binding site 2 out of 16 in 4ac9

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Mercury binding site 2 out of 16 in the Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg338

b:0.9
occ:0.23
HG A:CMH338 0.0 0.9 0.2
CM A:CMH338 2.1 0.9 0.2
SG A:CMH338 2.3 0.7 1.0
CB A:CMH338 3.1 0.1 1.0
CG2 A:ILE333 3.3 0.5 1.0
O A:ASN336 3.6 0.7 1.0
CD1 A:ILE285 3.7 0.9 1.0
N A:CMH338 3.9 0.2 1.0
O A:GLU337 3.9 0.2 1.0
C A:GLU337 3.9 0.6 1.0
C A:ASN336 4.0 0.9 1.0
CA A:CMH338 4.0 0.6 1.0
O A:ILE283 4.1 0.1 1.0
CG1 A:ILE285 4.3 0.6 1.0
N A:GLU337 4.4 0.1 1.0
O A:GLY335 4.5 0.6 1.0
CA A:ASN336 4.6 0.5 1.0
CB A:ILE333 4.7 0.6 1.0
CA A:GLU337 4.7 0.3 1.0
O A:ILE333 4.8 0.1 1.0
CA A:ILE333 4.9 1.0 1.0

Mercury binding site 3 out of 16 in 4ac9

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Mercury binding site 3 out of 16 in the Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg340

b:0.3
occ:0.88
HG A:CMH340 0.0 0.3 0.9
CM A:CMH340 2.1 0.6 0.9
SG A:CMH340 2.4 0.0 1.0
CB A:CMH340 3.2 0.7 1.0
CD1 A:ILE283 3.5 0.9 1.0
CG A:PRO314 3.9 0.5 1.0
CB A:PRO314 3.9 0.1 1.0
OH A:TYR291 3.9 0.5 1.0
CA A:PRO314 4.1 0.9 1.0
CA A:CMH340 4.1 0.1 1.0
O A:CMH338 4.2 0.8 1.0
CB A:ILE283 4.4 0.0 1.0
CG1 A:ILE283 4.4 0.5 1.0
CG2 A:ILE283 4.5 0.6 1.0
N A:PRO314 4.5 0.4 1.0
CB A:CMH338 4.5 0.1 1.0
N A:CMH340 4.6 0.0 1.0
CD A:PRO314 4.7 0.3 1.0
CE1 A:TYR291 4.8 0.2 1.0
O A:TYR339 4.8 0.2 1.0
C A:CMH338 4.8 0.0 1.0
CZ A:TYR291 4.9 0.1 1.0
C A:TYR339 4.9 0.6 1.0
SG A:CMH338 5.0 0.7 1.0

Mercury binding site 4 out of 16 in 4ac9

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Mercury binding site 4 out of 16 in the Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg371

b:0.1
occ:0.35
HG A:CMH371 0.0 0.1 0.4
CM A:CMH371 2.1 0.6 0.4
SG A:CMH371 2.3 1.0 1.0
CB A:CMH371 3.1 0.4 1.0
CA A:CMH371 3.3 0.2 1.0
N A:CMH371 3.4 0.5 1.0
O A:ILE370 3.6 0.1 1.0
C A:ILE370 3.6 0.2 1.0
O A:ARG369 4.1 0.5 1.0
C A:ARG369 4.3 0.5 1.0
CB A:ARG360 4.3 0.4 1.0
N A:ILE370 4.4 0.3 1.0
CA A:ILE370 4.5 0.2 1.0
C A:CMH371 4.7 0.3 1.0
N A:ARG360 4.7 0.2 1.0
O A:LEU368 4.9 0.3 1.0

Mercury binding site 5 out of 16 in 4ac9

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Mercury binding site 5 out of 16 in the Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg264

b:84.4
occ:0.80
HG B:CMH264 0.0 84.4 0.8
CM B:CMH264 2.1 54.1 0.8
SG B:CMH264 2.4 71.0 1.0
N B:CMH264 2.9 49.5 1.0
CZ B:TYR261 3.1 0.6 1.0
CA B:CMH264 3.2 64.0 1.0
CE1 B:TYR261 3.2 0.3 1.0
C B:GLY263 3.2 95.6 1.0
CB B:CMH264 3.2 58.2 1.0
CE2 B:TYR261 3.3 0.7 1.0
CD1 B:TYR261 3.5 0.4 1.0
CD B:PRO222 3.5 85.7 1.0
CD2 B:TYR261 3.6 0.9 1.0
OH B:TYR261 3.7 0.1 1.0
CG B:TYR261 3.7 0.5 1.0
O B:GLY263 3.7 76.1 1.0
N B:GLY263 3.7 93.2 1.0
O B:TYR261 3.8 84.4 1.0
CG B:PRO222 3.8 84.6 1.0
CA B:GLY263 3.8 0.2 1.0
C B:TYR261 4.1 85.3 1.0
N B:TYR261 4.5 69.4 1.0
CA B:TYR261 4.6 72.4 1.0
CG1 B:ILE223 4.6 0.0 1.0
C B:ARG262 4.6 96.8 1.0
N B:PRO222 4.7 60.8 1.0
C B:CMH264 4.7 70.6 1.0
N B:ARG262 4.7 61.8 1.0
CB B:TYR261 4.7 70.0 1.0
O B:LEU221 4.8 95.0 1.0
CD1 B:ILE223 4.8 0.5 1.0

Mercury binding site 6 out of 16 in 4ac9

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Mercury binding site 6 out of 16 in the Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg338

b:0.5
occ:0.22
HG B:CMH338 0.0 0.5 0.2
CM B:CMH338 2.1 0.1 0.2
SG B:CMH338 2.3 0.2 1.0
O B:GLU337 3.1 0.2 1.0
C B:GLU337 3.1 0.9 1.0
CB B:CMH338 3.1 0.7 1.0
N B:CMH338 3.4 0.0 1.0
CG2 B:ILE285 3.5 0.4 1.0
CA B:CMH338 3.8 0.4 1.0
CA B:GLU337 3.8 0.8 1.0
O B:ILE283 4.1 0.7 1.0
N B:GLU337 4.4 0.8 1.0
CB B:ILE285 4.5 0.9 1.0
C B:CMH338 4.8 0.9 1.0
CD2 B:LEU329 4.9 0.3 1.0
O B:SER334 4.9 0.3 1.0
CM B:CMH340 4.9 0.7 0.9
N B:ILE285 4.9 0.5 1.0
C B:ASN336 4.9 0.3 1.0
O B:ASN336 4.9 0.3 1.0
CB B:SER334 4.9 0.1 1.0

Mercury binding site 7 out of 16 in 4ac9

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Mercury binding site 7 out of 16 in the Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg340

b:0.6
occ:0.85
HG B:CMH340 0.0 0.6 0.9
CM B:CMH340 2.1 0.7 0.9
SG B:CMH340 2.4 0.1 1.0
CB B:CMH340 3.2 0.0 1.0
CM B:CMH371 3.7 0.5 0.4
CE B:MET297 3.8 0.4 1.0
O B:TYR339 3.9 0.3 1.0
CB B:PRO314 4.0 0.9 1.0
CA B:CMH340 4.0 0.2 1.0
CG1 B:ILE283 4.0 0.8 1.0
CA B:PRO314 4.0 0.0 1.0
N B:PRO314 4.2 0.1 1.0
C B:TYR339 4.4 0.9 1.0
CD B:PRO314 4.5 0.6 1.0
CD1 B:ILE358 4.5 0.5 1.0
N B:CMH340 4.5 0.5 1.0
CB B:ILE283 4.5 0.3 1.0
CG2 B:ILE283 4.5 0.6 1.0
SG B:CMH338 4.6 0.2 1.0
C B:VAL313 4.7 0.9 1.0
CG B:PRO314 4.7 0.2 1.0
O B:VAL313 4.8 0.6 1.0
CZ B:PHE342 5.0 0.8 1.0

Mercury binding site 8 out of 16 in 4ac9

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Mercury binding site 8 out of 16 in the Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg371

b:0.8
occ:0.36
HG B:CMH371 0.0 0.8 0.4
CM B:CMH371 2.1 0.5 0.4
SG B:CMH371 2.3 0.0 1.0
CB B:CMH371 3.2 1.0 1.0
C B:CMH371 3.5 0.0 1.0
O B:CMH371 3.5 0.4 1.0
CD1 B:ILE358 3.7 0.5 1.0
N B:GLY372 3.9 0.5 1.0
CG2 B:ILE358 3.9 96.0 1.0
CA B:CMH371 3.9 0.5 1.0
CB B:ILE358 4.0 1.0 1.0
CD1 B:ILE285 4.1 0.5 1.0
CA B:GLY372 4.4 0.1 1.0
CE B:MET297 4.4 0.4 1.0
CG1 B:ILE358 4.5 0.7 1.0
CG1 B:ILE285 4.7 0.1 1.0
N B:CMH371 4.7 0.4 1.0
CM B:CMH340 4.9 0.7 0.9
NH1 B:ARG360 5.0 0.9 1.0

Mercury binding site 9 out of 16 in 4ac9

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Mercury binding site 9 out of 16 in the Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 9 of Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg264

b:0.9
occ:0.90
HG C:CMH264 0.0 0.9 0.9
CM C:CMH264 2.1 0.1 0.9
SG C:CMH264 2.4 92.4 1.0
N C:CMH264 2.9 72.1 1.0
CE1 C:TYR261 3.2 0.0 1.0
CA C:CMH264 3.2 51.8 1.0
CB C:CMH264 3.2 58.5 1.0
C C:GLY263 3.3 90.7 1.0
CZ C:TYR261 3.4 0.6 1.0
CD1 C:TYR261 3.4 0.4 1.0
CD C:PRO222 3.4 91.9 1.0
O C:TYR261 3.6 72.6 1.0
CE2 C:TYR261 3.7 1.0 1.0
CG C:TYR261 3.7 0.1 1.0
N C:GLY263 3.7 55.8 1.0
CA C:GLY263 3.8 0.5 1.0
CG C:PRO222 3.8 0.3 1.0
CD2 C:TYR261 3.9 0.7 1.0
OH C:TYR261 4.0 0.8 1.0
O C:GLY263 4.0 82.3 1.0
C C:TYR261 4.1 91.8 1.0
N C:TYR261 4.4 78.9 1.0
CA C:TYR261 4.6 91.5 1.0
C C:ARG262 4.6 0.8 1.0
O C:LEU221 4.6 75.2 1.0
N C:PRO222 4.6 77.1 1.0
CB C:TYR261 4.7 72.0 1.0
N C:ARG262 4.7 78.3 1.0
C C:CMH264 4.7 90.9 1.0

Mercury binding site 10 out of 16 in 4ac9

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Mercury binding site 10 out of 16 in the Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 10 of Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg338

b:0.8
occ:0.65
HG C:CMH338 0.0 0.8 0.7
CM C:CMH338 2.1 0.2 0.7
SG C:CMH338 2.4 0.6 1.0
O C:GLU337 3.0 0.1 1.0
CB C:CMH338 3.2 58.5 1.0
C C:GLU337 3.6 67.6 1.0
CA C:CMH338 3.6 83.7 1.0
N C:CMH338 3.9 77.2 1.0
CD1 C:LEU329 4.1 70.5 1.0
CB C:LYS316 4.3 79.7 1.0
N C:GLU337 4.4 82.4 1.0
CA C:GLU337 4.7 65.7 1.0
CB C:ASN336 4.9 69.4 1.0

Reference:

M.Leibundgut, C.Frick, M.Thanbichler, A.Bock, N.Ban. Selenocysteine Trna-Specific Elongation Factor Selb Is A Structural Chimaera of Elongation and Initiation Factors. Embo J. V. 24 11 2005.
ISSN: ISSN 0261-4189
PubMed: 15616587
DOI: 10.1038/SJ.EMBOJ.7600505
Page generated: Wed Oct 28 18:43:14 2020

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