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Mercury in PDB 5td8: Crystal Structure of An Extended Dwarf NDC80 Complex

Protein crystallography data

The structure of Crystal Structure of An Extended Dwarf NDC80 Complex, PDB code: 5td8 was solved by R.Valverde, J.Ingram, S.C.Harrison, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 113.41 / 7.53
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 226.825, 226.825, 237.270, 90.00, 90.00, 90.00
R / Rfree (%) 31.2 / 32.8

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of An Extended Dwarf NDC80 Complex (pdb code 5td8). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 6 binding sites of Mercury where determined in the Crystal Structure of An Extended Dwarf NDC80 Complex, PDB code: 5td8:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6;

Mercury binding site 1 out of 6 in 5td8

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Mercury binding site 1 out of 6 in the Crystal Structure of An Extended Dwarf NDC80 Complex


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 An Extended Dwarf NDC80 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg701

b:81.5
occ:0.85
HD11 A:LEU304 2.4 14.5 1.0
HG B:CYS140 2.4 14.5 1.0
HD13 A:LEU304 2.4 14.5 1.0
HH A:TYR282 2.5 14.5 1.0
OH A:TYR282 2.6 0.1 1.0
CZ A:TYR282 2.7 98.9 1.0
SG B:CYS140 2.8 78.2 1.0
CD1 A:LEU304 2.8 98.6 1.0
HE2 A:TYR282 2.9 14.5 1.0
CE2 A:TYR282 2.9 97.4 1.0
HD21 A:LEU304 3.1 14.5 1.0
HD22 A:LEU304 3.2 14.5 1.0
CD2 A:LEU304 3.5 0.1 1.0
HD12 A:LEU304 3.6 14.5 1.0
CE1 A:TYR282 3.6 99.2 1.0
CG A:LEU304 3.8 0.5 1.0
CD2 A:TYR282 3.9 96.3 1.0
HE1 A:TYR282 3.9 14.5 1.0
HB3 B:CYS140 4.1 14.5 1.0
CB B:CYS140 4.2 75.0 1.0
HG A:LEU304 4.3 14.5 1.0
HD2 A:TYR282 4.4 14.5 1.0
HD23 A:LEU304 4.4 14.5 1.0
CD1 A:TYR282 4.4 98.1 1.0
CG A:TYR282 4.5 96.6 1.0
HB2 A:LEU304 4.7 14.5 1.0
HB2 B:CYS140 4.8 14.5 1.0
CB A:LEU304 4.8 0.2 1.0
HA B:CYS140 5.0 14.5 1.0

Mercury binding site 2 out of 6 in 5td8

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Mercury binding site 2 out of 6 in the Crystal Structure of An Extended Dwarf NDC80 Complex


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 An Extended Dwarf NDC80 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg702

b:0.9
occ:0.71
HG B:SER64 2.0 14.5 1.0
HA A:CYS235 2.1 14.5 1.0
HA B:SER64 2.4 14.5 1.0
SG A:CYS235 2.4 0.5 1.0
O A:CYS235 2.6 0.7 1.0
CA A:CYS235 2.6 0.2 1.0
OG B:SER64 2.7 0.9 1.0
O B:SER64 2.8 0.3 1.0
CB A:CYS235 2.8 0.7 1.0
C A:CYS235 2.9 0.5 1.0
CA B:SER64 3.0 0.1 1.0
HB2 A:CYS235 3.0 14.5 1.0
CB B:SER64 3.1 0.0 1.0
HB2 B:SER64 3.2 14.5 1.0
C B:SER64 3.3 0.8 1.0
HG23 A:VAL239 3.4 14.5 1.0
HB3 A:CYS235 3.7 14.5 1.0
N A:CYS235 4.0 0.6 1.0
HB3 B:SER64 4.1 14.5 1.0
HB2 A:LYS238 4.1 14.5 1.0
N A:LEU236 4.1 0.5 1.0
CG2 A:VAL239 4.2 0.9 1.0
HG21 A:VAL239 4.3 14.5 1.0
N B:SER64 4.3 0.8 1.0
H A:CYS235 4.4 14.5 1.0
HD2 A:LYS238 4.5 14.5 1.0
O B:SER63 4.6 90.5 1.0
N B:ASN65 4.6 0.2 1.0
HG22 A:VAL239 4.6 14.5 1.0
H A:LEU236 4.6 14.5 1.0
HA A:LEU236 4.7 14.5 1.0
H A:VAL239 4.7 14.5 1.0
O A:MET234 4.7 0.2 1.0
C A:MET234 4.8 0.8 1.0
H B:SER64 4.9 14.5 1.0
C B:SER63 4.9 92.3 1.0
CA A:LEU236 5.0 0.7 1.0

Mercury binding site 3 out of 6 in 5td8

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Mercury binding site 3 out of 6 in the Crystal Structure of An Extended Dwarf NDC80 Complex


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 An Extended Dwarf NDC80 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg501

b:0.1
occ:1.00
HG13 B:VAL127 2.5 14.5 1.0
SG B:CYS23 2.7 44.9 1.0
HZ B:PHE52 2.9 14.5 1.0
HB3 B:ALA130 2.9 14.5 1.0
HG3 B:ARG131 3.0 14.5 1.0
CG1 B:VAL127 3.5 0.6 1.0
HB3 B:CYS23 3.5 14.5 1.0
HA B:VAL127 3.5 14.5 1.0
CZ B:PHE52 3.6 0.4 1.0
HG2 B:ARG131 3.7 14.5 1.0
HG B:CYS23 3.7 14.5 1.0
HE1 B:PHE52 3.7 14.5 1.0
HB1 B:ALA130 3.7 14.5 1.0
CB B:ALA130 3.7 0.5 1.0
CG B:ARG131 3.7 0.3 1.0
O B:VAL127 3.8 0.7 1.0
HG22 B:VAL127 3.8 14.5 1.0
CB B:CYS23 3.8 44.5 1.0
HG12 B:VAL127 3.8 14.5 1.0
HE B:ARG131 3.8 14.5 1.0
HG11 B:VAL127 4.0 14.5 1.0
H B:ARG131 4.0 14.5 1.0
CE1 B:PHE52 4.0 0.4 1.0
HA B:CYS23 4.1 14.5 1.0
CA B:VAL127 4.2 0.1 1.0
NE B:ARG131 4.2 0.9 1.0
CB B:VAL127 4.2 0.5 1.0
N B:ARG131 4.3 0.9 1.0
HB2 B:ALA130 4.3 14.5 1.0
C B:VAL127 4.3 0.9 1.0
CD B:ARG131 4.4 0.5 1.0
CG2 B:VAL127 4.5 0.8 1.0
HB2 B:CYS23 4.5 14.5 1.0
HD2 B:ARG131 4.5 14.5 1.0
CA B:CYS23 4.6 44.6 1.0
C B:ALA130 4.6 0.6 1.0
HA B:ARG131 4.7 14.5 1.0
CE2 B:PHE52 4.7 0.4 1.0
CA B:ALA130 4.7 0.4 1.0
HE2 B:PHE25 4.7 14.5 1.0
HE2 B:PHE52 4.8 14.5 1.0
HG21 B:VAL127 4.9 14.5 1.0
CB B:ARG131 4.9 0.2 1.0
CA B:ARG131 4.9 0.4 1.0
CZ B:ARG131 5.0 0.7 1.0
HH21 B:ARG131 5.0 14.5 1.0

Mercury binding site 4 out of 6 in 5td8

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Mercury binding site 4 out of 6 in the Crystal Structure of An Extended Dwarf NDC80 Complex


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 An Extended Dwarf NDC80 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg502

b:0.3
occ:0.83
HD11 B:ILE49 2.1 14.5 1.0
CD1 B:ILE49 2.9 97.1 1.0
HD12 B:ILE49 3.0 14.5 1.0
HE2 B:PHE98 3.0 14.5 1.0
SG B:CYS94 3.1 0.6 1.0
HD1 B:TYR45 3.1 14.5 1.0
HG13 B:ILE49 3.2 14.5 1.0
HB3 B:TYR45 3.2 14.5 1.0
CD2 B:PHE97 3.2 0.9 1.0
CB B:CYS94 3.4 0.7 1.0
CD1 B:TYR45 3.4 0.8 1.0
CG1 B:ILE49 3.5 96.7 1.0
CA B:CYS94 3.5 0.9 1.0
CE2 B:PHE97 3.6 0.5 1.0
CE2 B:PHE98 3.6 0.6 1.0
HD13 B:ILE49 3.7 14.5 1.0
CG B:TYR45 3.8 0.6 1.0
HG12 B:ILE49 3.8 14.5 1.0
CB B:TYR45 3.9 0.6 1.0
CG B:PHE97 4.0 0.3 1.0
HA B:TYR45 4.1 14.5 1.0
CE1 B:TYR45 4.2 0.8 1.0
HZ B:PHE98 4.2 14.5 1.0
CZ B:PHE98 4.2 1.0 1.0
HD21 B:LEU123 4.3 14.5 1.0
CD2 B:PHE98 4.3 0.8 1.0
HD2 B:PHE98 4.3 14.5 1.0
HE1 B:TYR45 4.4 14.5 1.0
CB B:PHE97 4.4 0.7 1.0
N B:CYS94 4.4 0.6 1.0
CA B:TYR45 4.4 0.6 1.0
O B:TYR45 4.6 0.5 1.0
HE1 B:PHE106 4.6 14.5 1.0
C B:CYS94 4.6 0.3 1.0
O B:CYS94 4.6 0.3 1.0
CZ B:PHE97 4.6 0.4 1.0
HB2 B:TYR45 4.7 14.5 1.0
CD2 B:TYR45 4.7 0.3 1.0
C B:TYR45 4.8 0.3 1.0
H B:ILE49 4.8 14.5 1.0
HB B:ILE48 4.9 14.5 1.0
CB B:ILE49 4.9 96.1 1.0
CD1 B:PHE97 4.9 0.2 1.0
CD2 B:LEU123 5.0 0.7 1.0

Mercury binding site 5 out of 6 in 5td8

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Mercury binding site 5 out of 6 in the Crystal Structure of An Extended Dwarf NDC80 Complex


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 An Extended Dwarf NDC80 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg301

b:68.2
occ:0.77
HB3 D:CYS169 1.9 14.5 1.0
HB2 D:LEU217 2.2 14.5 1.0
HD12 D:LEU217 2.3 14.5 1.0
HD2 D:PHE163 2.4 14.5 1.0
HD13 D:LEU217 2.5 14.5 1.0
CD1 D:LEU217 2.8 73.5 1.0
CB D:CYS169 2.8 64.8 1.0
CD2 D:PHE163 2.8 68.4 1.0
HB3 D:LEU217 2.8 14.5 1.0
HB2 D:PHE163 2.8 14.5 1.0
CB D:LEU217 2.8 73.5 1.0
HB2 D:CYS169 2.9 14.5 1.0
HA D:ARG214 3.0 14.5 1.0
CG D:PHE163 3.3 68.0 1.0
CG D:LEU217 3.4 73.5 1.0
HG D:CYS169 3.4 14.5 1.0
CB D:PHE163 3.5 67.5 1.0
CE2 D:PHE163 3.5 69.0 1.0
HD11 D:LEU217 3.6 14.5 1.0
SG D:CYS169 3.7 65.1 1.0
HE2 D:PHE163 3.7 14.5 1.0
HG D:LEU217 3.9 14.5 1.0
CA D:CYS169 3.9 64.5 1.0
HB3 D:PHE163 3.9 14.5 1.0
CA D:ARG214 4.0 67.2 1.0
C D:CYS169 4.0 64.5 1.0
HG D:LEU218 4.1 14.5 1.0
O D:ALA213 4.1 67.1 1.0
HG3 D:ARG214 4.1 14.5 1.0
CA D:LEU217 4.2 73.5 1.0
H D:LEU218 4.2 14.5 1.0
O D:ARG214 4.2 67.1 1.0
HA D:CYS169 4.2 14.5 1.0
H D:PHE163 4.3 14.5 1.0
CD1 D:PHE163 4.3 68.3 1.0
O D:CYS169 4.4 64.1 1.0
H D:LEU217 4.4 14.5 1.0
N D:TRP170 4.4 66.2 1.0
N D:LEU218 4.5 75.1 1.0
HD22 D:LEU217 4.5 14.5 1.0
CZ D:PHE163 4.5 69.3 1.0
C D:LEU217 4.5 73.5 1.0
HA D:TRP170 4.6 14.5 1.0
CD2 D:LEU217 4.6 73.5 1.0
C D:ARG214 4.6 67.2 1.0
H D:TRP170 4.6 14.5 1.0
N D:ARG214 4.7 67.2 1.0
C D:ALA213 4.7 67.2 1.0
CA D:PHE163 4.7 66.8 1.0
N D:LEU217 4.8 73.7 1.0
N D:PHE163 4.8 66.8 1.0
CB D:ARG214 4.8 67.2 1.0
CE1 D:PHE163 4.8 69.0 1.0
HB2 D:ARG214 4.8 14.5 1.0
HA D:LEU217 4.9 14.5 1.0
CG D:ARG214 4.9 67.2 1.0
HD23 D:LEU218 4.9 14.5 1.0
HD1 D:PHE163 4.9 14.5 1.0
CG D:LEU218 5.0 75.2 1.0
CA D:TRP170 5.0 66.5 1.0

Mercury binding site 6 out of 6 in 5td8

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Mercury binding site 6 out of 6 in the Crystal Structure of An Extended Dwarf NDC80 Complex


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 An Extended Dwarf NDC80 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg302

b:77.6
occ:0.68
HA D:MET175 2.3 14.5 1.0
O D:MET175 2.8 74.6 1.0
CA D:MET175 3.1 73.1 1.0
SD D:MET175 3.1 70.6 1.0
O D:ALA174 3.2 74.1 1.0
C D:MET175 3.3 74.5 1.0
HG3 D:MET175 3.5 14.5 1.0
CG D:MET175 3.7 72.2 1.0
CB D:MET175 4.0 72.8 1.0
C D:ALA174 4.1 74.5 1.0
N D:MET175 4.1 73.0 1.0
HB2 D:MET175 4.5 14.5 1.0
HG23 D:VAL173 4.6 14.5 1.0
N D:HIS176 4.6 82.2 1.0
HG2 D:MET175 4.6 14.5 1.0
HB3 D:MET175 4.7 14.5 1.0
HG21 D:VAL159 4.8 14.5 1.0
CE D:MET175 4.8 69.5 1.0
H D:MET175 4.9 14.5 1.0

Reference:

R.Valverde, J.Ingram, S.C.Harrison. Conserved Tetramer Junction in the Kinetochore NDC80 Complex. Cell Rep V. 17 1915 2016.
ISSN: ESSN 2211-1247
PubMed: 27851957
DOI: 10.1016/J.CELREP.2016.10.065
Page generated: Sun Dec 13 19:13:12 2020

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