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Mercury in PDB 3mqi: Human Early B-Cell Factor 1 (EBF1) Ipt/Tig Domain

Protein crystallography data

The structure of Human Early B-Cell Factor 1 (EBF1) Ipt/Tig Domain, PDB code: 3mqi was solved by M.I.Siponen, L.Lehtio, C.H.Arrowsmith, C.Bountra, R.Collins, A.M.Edwards, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, I.Johansson, T.Karlberg, T.Kotenyova, M.Moche, P.Nordlund, T.Nyman, C.Persson, H.Schueler, P.Schutz, L.Svensson, A.G.Thorsell, L.Tresaugues, S.Van Den Berg, E.Wahlberg, J.Weigelt, M.Welin, M.Wisniewska, H.Berglund, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.53 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 86.291, 57.073, 69.140, 90.00, 93.17, 90.00
R / Rfree (%) 23.3 / 27.3

Mercury Binding Sites:

The binding sites of Mercury atom in the Human Early B-Cell Factor 1 (EBF1) Ipt/Tig Domain (pdb code 3mqi). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 6 binding sites of Mercury where determined in the Human Early B-Cell Factor 1 (EBF1) Ipt/Tig Domain, PDB code: 3mqi:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6;

Mercury binding site 1 out of 6 in 3mqi

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Mercury binding site 1 out of 6 in the Human Early B-Cell Factor 1 (EBF1) Ipt/Tig Domain


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Human Early B-Cell Factor 1 (EBF1) Ipt/Tig Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg1

b:71.5
occ:1.00
HG A:EMC1 0.0 71.5 1.0
C1 A:EMC1 2.4 69.5 1.0
SG A:CYS335 2.5 36.9 1.0
C2 A:EMC1 3.3 69.9 1.0
O A:PHE334 3.3 31.9 1.0
CB A:CYS335 3.3 33.8 1.0
CA A:CYS335 3.6 33.9 1.0
C A:PHE334 3.9 32.0 1.0
N A:CYS335 4.1 32.9 1.0
CB A:GLN333 4.5 32.3 1.0
CG A:GLN333 4.6 34.2 1.0
CD A:GLN333 4.6 36.7 1.0
NE2 A:GLN333 4.8 36.4 1.0
O A:HOH73 4.8 33.6 1.0
O A:HOH94 4.9 36.6 1.0
N A:PHE334 5.0 31.4 1.0
C A:GLN333 5.0 31.5 1.0

Mercury binding site 2 out of 6 in 3mqi

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Mercury binding site 2 out of 6 in the Human Early B-Cell Factor 1 (EBF1) Ipt/Tig Domain


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Human Early B-Cell Factor 1 (EBF1) Ipt/Tig Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg2

b:63.7
occ:1.00
HG A:EMC2 0.0 63.7 1.0
SG A:CYS263 2.3 39.1 1.0
C1 A:EMC2 2.4 63.2 1.0
CB A:CYS263 3.1 30.9 1.0
C2 A:EMC2 3.3 62.6 1.0
OD2 A:ASP285 3.5 30.0 1.0
C A:CYS263 3.9 29.0 1.0
O A:CYS263 4.0 29.1 1.0
CA A:CYS263 4.0 30.7 1.0
O A:ILE264 4.1 26.2 1.0
C A:ILE264 4.2 26.3 1.0
CG A:ASP285 4.2 28.0 1.0
N A:ILE264 4.2 27.7 1.0
N A:LYS265 4.4 25.9 1.0
CB A:ASP285 4.5 26.9 1.0
N A:ASP285 4.6 25.9 1.0
CA A:LYS265 4.7 25.7 1.0
CA A:ILE264 4.8 26.3 1.0
CB A:LYS265 4.9 25.9 1.0

Mercury binding site 3 out of 6 in 3mqi

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Mercury binding site 3 out of 6 in the Human Early B-Cell Factor 1 (EBF1) Ipt/Tig Domain


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Human Early B-Cell Factor 1 (EBF1) Ipt/Tig Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg4

b:85.1
occ:1.00
HG B:EMC4 0.0 85.1 1.0
C1 B:EMC4 2.4 83.6 1.0
SG B:CYS263 2.7 33.9 1.0
C2 B:EMC4 3.2 83.4 1.0
CB B:CYS263 3.3 28.4 1.0
OD2 B:ASP285 3.5 27.3 1.0
O B:CYS263 3.9 26.5 1.0
C B:CYS263 3.9 27.2 1.0
O B:ILE264 4.2 26.2 1.0
CA B:CYS263 4.2 28.4 1.0
C B:ILE264 4.4 26.2 1.0
N B:ILE264 4.4 26.4 1.0
CG B:ASP285 4.4 24.6 1.0
CB B:ASP285 4.5 23.0 1.0
N B:LYS265 4.5 26.1 1.0
N B:ASP285 4.6 21.9 1.0
CA B:LYS265 4.8 25.8 1.0
CB B:LYS265 4.9 26.0 1.0
CA B:GLY284 5.0 20.2 1.0
N B:CYS263 5.0 28.8 1.0
CA B:ILE264 5.0 26.4 1.0

Mercury binding site 4 out of 6 in 3mqi

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Mercury binding site 4 out of 6 in the Human Early B-Cell Factor 1 (EBF1) Ipt/Tig Domain


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Human Early B-Cell Factor 1 (EBF1) Ipt/Tig Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg5

b:95.6
occ:1.00
HG B:EMC5 0.0 95.6 1.0
C1 B:EMC5 2.4 95.1 1.0
SG B:CYS335 2.8 44.9 1.0
CB B:CYS335 3.0 40.4 1.0
C2 B:EMC5 3.2 94.9 1.0
C B:CYS335 3.6 41.0 1.0
O B:CYS335 3.7 41.1 1.0
O B:GLY337 3.7 45.1 1.0
CA B:CYS335 3.7 40.1 1.0
N B:LYS336 4.2 42.4 1.0
N B:GLY337 4.7 44.7 1.0
C B:GLY337 4.8 45.0 1.0
CA B:LYS336 4.9 43.4 1.0
C B:LYS336 5.0 44.1 1.0

Mercury binding site 5 out of 6 in 3mqi

Go back to Mercury Binding Sites List in 3mqi
Mercury binding site 5 out of 6 in the Human Early B-Cell Factor 1 (EBF1) Ipt/Tig Domain


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Human Early B-Cell Factor 1 (EBF1) Ipt/Tig Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg3

b:0.2
occ:1.00
HG C:EMC3 0.0 0.2 1.0
SG C:CYS335 2.4 50.3 1.0
C1 C:EMC3 2.4 0.9 1.0
C2 C:EMC3 3.2 0.7 1.0
CB C:CYS335 3.3 45.5 1.0
CA C:CYS335 4.1 45.2 1.0
C C:CYS335 4.1 46.3 1.0
O C:CYS335 4.4 47.0 1.0
N C:LYS336 4.5 47.2 1.0
O C:GLY337 4.5 48.8 1.0

Mercury binding site 6 out of 6 in 3mqi

Go back to Mercury Binding Sites List in 3mqi
Mercury binding site 6 out of 6 in the Human Early B-Cell Factor 1 (EBF1) Ipt/Tig Domain


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Human Early B-Cell Factor 1 (EBF1) Ipt/Tig Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg6

b:0.7
occ:1.00
HG C:EMC6 0.0 0.7 1.0
C1 C:EMC6 2.4 99.8 1.0
SG C:CYS263 2.6 38.1 1.0
C2 C:EMC6 3.2 99.5 1.0
CB C:CYS263 3.5 32.5 1.0
O C:CYS263 3.9 30.8 1.0
OD2 C:ASP285 3.9 27.3 1.0
NZ C:LYS336 4.0 52.9 1.0
C C:CYS263 4.1 31.3 1.0
O C:ILE264 4.3 29.5 1.0
CA C:CYS263 4.4 32.6 1.0
C C:ILE264 4.5 29.2 1.0
N C:LYS265 4.6 28.4 1.0
CB C:ASP285 4.6 23.5 1.0
N C:ILE264 4.6 30.4 1.0
CG C:ASP285 4.7 25.5 1.0
N C:ASP285 4.8 22.3 1.0
CA C:LYS265 4.9 27.8 1.0
CB C:LYS265 5.0 27.9 1.0

Reference:

M.I.Siponen, M.Wisniewska, L.Lehtio, I.Johansson, L.Svensson, G.Raszewski, L.Nilsson, M.Sigvardsson, H.Berglund. Structural Determination of Functional Domains in Early B-Cell Factor (Ebf) Family of Transcription Factors Reveals Similarities to Rel Dna-Binding Proteins and A Novel Dimerization Motif. J.Biol.Chem. V. 285 25875 2010.
ISSN: ISSN 0021-9258
PubMed: 20592035
DOI: 10.1074/JBC.C110.150482
Page generated: Wed Oct 28 18:42:53 2020

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